{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"bulk\" and tissue_curation = \"Spinal Cord\"", "rows": [[62931, "SRR13447020", "SRX9860256", "SRS8040687", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 14 3 wpi sc 2", "GSM5023609", null, "source name:21 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:21 xxx post injury", "Z 14 3 wpi sc 2", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "21 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:21 xxx post injury", "GSM5023609", "GSM5023609: Z 14 3 wpi sc 2; Danio rerio; RNA Seq", "GSM5023609", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. 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Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:21 xxx post injury", "GSM5023608", "GSM5023608: Z 10 3 wpi sc 1; Danio rerio; RNA Seq", "GSM5023608", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. 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Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:10 xxx post injury", "GSM5023607", "GSM5023607: Z 13 10 dpi sc 2; Danio rerio; RNA Seq", "GSM5023607", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. 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Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:10 xxx post injury", "GSM5023606", "GSM5023606: Z 9 10 dpi sc 1; Danio rerio; RNA Seq", "GSM5023606", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023606", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_TAGGATG.fq.gz", "fastq", 1228530350.0, 24570607.0, "GSM5023606 r1", "0:50 1:0", "A:336797190;C:276687423;G:274112310;T:340700127;N:233300", 50, 0, null, null, 336797190, 276687423, 274112310, 340700127, 233300, "SRX9860253", "SRS8040684", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90494, null, 0.17991, null, 0.69789, null, 0.43663, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62935, "SRR13447016", "SRX9860252", "SRS8040683", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 12 5 dpi sc 2", "GSM5023605", null, "source name:5 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:5 xxx post injury", "Z 12 5 dpi sc 2", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "5 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:5 xxx post injury", "GSM5023605", "GSM5023605: Z 12 5 dpi sc 2; Danio rerio; RNA Seq", "GSM5023605", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. 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Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:5 xxx post injury", "GSM5023604", "GSM5023604: Z 8 5 dpi sc 1; Danio rerio; RNA Seq", "GSM5023604", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. 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TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023602", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_CCCGCTA.fq.gz", "fastq", 1274023900.0, 25480478.0, "GSM5023602 r1", "0:50 1:0", "A:330443270;C:305732881;G:301431401;T:336172878;N:243470", 50, 0, null, null, 330443270, 305732881, 301431401, 336172878, 243470, "SRX9860249", "SRS8040680", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.92713, null, 0.09501, null, 0.71776, null, 0.49328, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62939, "SRR13447012", "SRX9860248", "SRS8040679", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 3 gp rp rna 1", "GSM5023601", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 3 gp rp rna 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023601", "GSM5023601: Z 3 gp rp rna 1; Danio rerio; RNA Seq", "GSM5023601", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023601", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_ATAGGCT.fq.gz", "fastq", 1480993150.0, 29619863.0, "GSM5023601 r1", "0:50 1:0", "A:407241408;C:335585510;G:332782981;T:405104683;N:278568", 50, 0, null, null, 407241408, 335585510, 332782981, 405104683, 278568, "SRX9860248", "SRS8040679", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90012, null, 0.13909, null, 0.75684, null, 0.59867, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62940, "SRR13447011", "SRX9860247", "SRS8040678", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 18 gp rp 3", "GSM5023600", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 18 gp rp 3", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023600", "GSM5023600: Z 18 gp rp 3; Danio rerio; RNA Seq", "GSM5023600", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023600", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_AATGACT.fq.gz", "fastq", 1583531750.0, 31670635.0, "GSM5023600 r1", "0:50 1:0", "A:429031314;C:366679713;G:363462738;T:424058514;N:299471", 50, 0, null, null, 429031314, 366679713, 363462738, 424058514, 299471, "SRX9860247", "SRS8040678", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90969, null, 0.12671, null, 0.7458, null, 0.57895, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62941, "SRR13447010", "SRX9860246", "SRS8040677", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 15 gp rp 1", "GSM5023599", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 15 gp rp 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023599", "GSM5023599: Z 15 gp rp 1; Danio rerio; RNA Seq", "GSM5023599", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023599", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_TTCTTCG.fq.gz", "fastq", 1324698650.0, 26493973.0, "GSM5023599 r1", "0:50 1:0", "A:361437407;C:301526323;G:300125135;T:361356767;N:253018", 50, 0, null, null, 361437407, 301526323, 300125135, 361356767, 253018, "SRX9860246", "SRS8040677", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90938, null, 0.14229, null, 0.70869, null, 0.50563, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [65793, "SRR15626575", "SRX11923642", "SRS9937160", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 C5", "GSM5538904", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "W6 C5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "GSM5538904", "GSM5538904: W6 C5; Danio rerio; RNA Seq", "GSM5538904", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538904", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_C5_1.fq.gz W6_C5_2.fq.gz", "fastq fastq", 11548053600.0, 38493512.0, "GSM5538904 r1", "0:150 1:150", "A:3284639772;C:2417614008;G:2424125351;T:3421247186;N:427283", 150, 150, null, null, 3284639772, 2417614008, 2424125351, 3421247186, 427283, "SRX11923642", "SRS9937160", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92424, 0.91753, 0.09206, 0.08921, 0.73817, 0.75006, 0.48669, 0.46123, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65794, "SRR15626574", "SRX11923641", "SRS9937158", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 C3", "GSM5538903", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "W6 C3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "GSM5538903", "GSM5538903: W6 C3; Danio rerio; RNA Seq", "GSM5538903", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538903", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_C3_1.fq.gz W6_C3_2.fq.gz", "fastq fastq", 8675036411.0, 29294039.0, "GSM5538903 r1", null, "A:2490417531;C:1754549667;G:1762976045;T:2666940038;N:153130", null, null, null, null, 2490417531, 1754549667, 1762976045, 2666940038, 153130, "SRX11923641", "SRS9937158", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.77214, 0.76518, 0.16042, 0.15604, 0.72425, 0.74251, 0.47844, 0.47263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65795, "SRR15626573", "SRX11923640", "SRS9937159", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 C2", "GSM5538902", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "W6 C2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "GSM5538902", "GSM5538902: W6 C2; Danio rerio; RNA Seq", "GSM5538902", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538902", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_C2_1.fq.gz W6_C2_2.fq.gz", "fastq fastq", 10539241978.0, 35799607.0, "GSM5538902 r1", null, "A:2981919265;C:2108326349;G:2140188676;T:3307713377;N:1094311", null, null, null, null, 2981919265, 2108326349, 2140188676, 3307713377, 1094311, "SRX11923640", "SRS9937159", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.79298, 0.77869, 0.15756, 0.14594, 0.71504, 0.73527, 0.52219, 0.3777, 126, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65796, "SRR15626572", "SRX11923639", "SRS9937157", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 C1", "GSM5538901", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "W6 C1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:6 xxx post injury", "GSM5538901", "GSM5538901: W6 C1; Danio rerio; RNA Seq", "GSM5538901", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538901", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_C1_1.fq.gz W6_C1_2.fq.gz", "fastq fastq", 10943049099.0, 37073140.0, "GSM5538901 r1", null, "A:3130283377;C:2198486300;G:2220073292;T:3393075128;N:1131002", null, null, null, null, 3130283377, 2198486300, 2220073292, 3393075128, 1131002, "SRX11923639", "SRS9937157", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.80382, 0.80796, 0.16342, 0.16071, 0.72275, 0.73456, 0.49635, 0.49821, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65797, "SRR15626571", "SRX11923638", "SRS9937156", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 R5", "GSM5538900", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "W6 R5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "GSM5538900", "GSM5538900: W6 R5; Danio rerio; RNA Seq", "GSM5538900", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538900", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_R5_1.fq.gz W6_R5_2.fq.gz", "fastq fastq", 12204896100.0, 40682987.0, "GSM5538900 r1", "0:150 1:150", "A:3461249396;C:2529425680;G:2571904738;T:3640345896;N:1970390", 150, 150, null, null, 3461249396, 2529425680, 2571904738, 3640345896, 1970390, "SRX11923638", "SRS9937156", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91134, 0.91584, 0.10821, 0.10746, 0.73588, 0.75207, 0.52657, 0.48765, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65798, "SRR15626570", "SRX11923637", "SRS9937155", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 R4", "GSM5538899", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "W6 R4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "GSM5538899", "GSM5538899: W6 R4; Danio rerio; RNA Seq", "GSM5538899", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538899", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_R4_1.fq.gz W6_R4_2.fq.gz", "fastq fastq", 11563962300.0, 38546541.0, "GSM5538899 r1", "0:150 1:150", "A:3303789178;C:2399710240;G:2415791330;T:3443551642;N:1119910", 150, 150, null, null, 3303789178, 2399710240, 2415791330, 3443551642, 1119910, "SRX11923637", "SRS9937155", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91143, 0.90985, 0.11486, 0.11393, 0.73825, 0.74533, 0.54532, 0.52817, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65799, "SRR15626569", "SRX11923636", "SRS9937154", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 R3", "GSM5538898", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "W6 R3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "GSM5538898", "GSM5538898: W6 R3; Danio rerio; RNA Seq", "GSM5538898", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538898", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_R3_1.fq.gz W6_R3_2.fq.gz", "fastq fastq", 10585954542.0, 35816604.0, "GSM5538898 r1", null, "A:3037575766;C:2127628123;G:2139476709;T:3281099271;N:174673", null, null, null, null, 3037575766, 2127628123, 2139476709, 3281099271, 174673, "SRX11923636", "SRS9937154", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.85058, 0.85296, 0.1621, 0.15714, 0.71713, 0.73582, 0.52255, 0.50069, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65800, "SRR15626568", "SRX11923635", "SRS9937153", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 R2", "GSM5538897", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "W6 R2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "GSM5538897", "GSM5538897: W6 R2; Danio rerio; RNA Seq", "GSM5538897", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538897", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_R2_1.fq.gz W6_R2_2.fq.gz", "fastq fastq", 10669861075.0, 36260298.0, "GSM5538897 r1", null, "A:3008779806;C:2132058614;G:2164237979;T:3363597660;N:1187016", null, null, null, null, 3008779806, 2132058614, 2164237979, 3363597660, 1187016, "SRX11923635", "SRS9937153", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.80233, 0.78844, 0.14557, 0.1354, 0.7179, 0.73914, 0.50279, 0.38358, 150, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65801, "SRR15626567", "SRX11923634", "SRS9937152", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W6 R1", "GSM5538896", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "W6 R1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:6 xxx post injury", "GSM5538896", "GSM5538896: W6 R1; Danio rerio; RNA Seq", "GSM5538896", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538896", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W6_R1_1.fq.gz W6_R1_2.fq.gz", "fastq fastq", 8919305763.0, 30118529.0, "GSM5538896 r1", null, "A:2544200186;C:1819461355;G:1834522593;T:2720239204;N:882425", null, null, null, null, 2544200186, 1819461355, 1834522593, 2720239204, 882425, "SRX11923634", "SRS9937152", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.81775, 0.81798, 0.17053, 0.16924, 0.7161, 0.72971, 0.50177, 0.49561, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65802, "SRR15626566", "SRX11923633", "SRS9937151", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 C5", "GSM5538895", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "W4 C5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "GSM5538895", "GSM5538895: W4 C5; Danio rerio; RNA Seq", "GSM5538895", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538895", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_C5_1.fq.gz W4_C5_2.fq.gz", "fastq fastq", 11543122500.0, 38477075.0, "GSM5538895 r1", "0:150 1:150", "A:3264584729;C:2405081333;G:2441204011;T:3430418662;N:1833765", 150, 150, null, null, 3264584729, 2405081333, 2441204011, 3430418662, 1833765, "SRX11923633", "SRS9937151", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91535, 0.91481, 0.10079, 0.09867, 0.73671, 0.75333, 0.497, 0.47606, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65803, "SRR15626565", "SRX11923632", "SRS9937150", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 C4", "GSM5538894", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "W4 C4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "GSM5538894", "GSM5538894: W4 C4; Danio rerio; RNA Seq", "GSM5538894", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_C4_1.fq.gz W4_C4_2.fq.gz", "fastq fastq", 12129480900.0, 40431603.0, "GSM5538894 r1", "0:150 1:150", "A:3451519288;C:2515952240;G:2531389661;T:3629453781;N:1165930", 150, 150, null, null, 3451519288, 2515952240, 2531389661, 3629453781, 1165930, "SRX11923632", "SRS9937150", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.90598, 0.90619, 0.11287, 0.10949, 0.74184, 0.75049, 0.52714, 0.51794, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65804, "SRR15626564", "SRX11923631", "SRS9937149", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 C3", "GSM5538893", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "W4 C3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "GSM5538893", "GSM5538893: W4 C3; Danio rerio; RNA Seq", "GSM5538893", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538893", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_C3_1.fq.gz W4_C3_2.fq.gz", "fastq fastq", 14082618084.0, 47123575.0, "GSM5538893 r1", null, "A:4015557919;C:3022962754;G:2997180467;T:4041325245;N:5591699", null, null, null, null, 4015557919, 3022962754, 2997180467, 4041325245, 5591699, "SRX11923631", "SRS9937149", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92908, 0.92957, 0.15754, 0.15803, 0.6929, 0.70116, 0.47235, 0.46006, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65805, "SRR15626563", "SRX11923630", "SRS9937148", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 C2", "GSM5538892", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "W4 C2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "GSM5538892", "GSM5538892: W4 C2; Danio rerio; RNA Seq", "GSM5538892", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_C2_1.fq.gz W4_C2_2.fq.gz", "fastq fastq", 9869014911.0, 33378223.0, "GSM5538892 r1", null, "A:2804174507;C:2004352577;G:2027844843;T:3031342717;N:1300267", null, null, null, null, 2804174507, 2004352577, 2027844843, 3031342717, 1300267, "SRX11923630", "SRS9937148", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.74408, 0.76084, 0.15302, 0.15477, 0.71871, 0.72863, 0.41139, 0.49828, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65806, "SRR15626562", "SRX11923629", "SRS9937147", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 C1", "GSM5538891", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "W4 C1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:4 xxx post injury", "GSM5538891", "GSM5538891: W4 C1; Danio rerio; RNA Seq", "GSM5538891", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538891", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_C1_1.fq.gz W4_C1_2.fq.gz", "fastq fastq", 10687932882.0, 36203087.0, "GSM5538891 r1", null, "A:3008283529;C:2182572792;G:2209894531;T:3285549998;N:1632032", null, null, null, null, 3008283529, 2182572792, 2209894531, 3285549998, 1632032, "SRX11923629", "SRS9937147", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.78654, 0.7865, 0.12675, 0.12286, 0.71973, 0.73154, 0.48571, 0.48208, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65807, "SRR15626561", "SRX11923628", "SRS9937146", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 R5", "GSM5538890", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "W4 R5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "GSM5538890", "GSM5538890: W4 R5; Danio rerio; RNA Seq", "GSM5538890", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538890", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_R5_1.fq.gz W4_R5_2.fq.gz", "fastq fastq", 10826625600.0, 36088752.0, "GSM5538890 r1", "0:150 1:150", "A:3070709719;C:2256203149;G:2290582547;T:3207400991;N:1729194", 150, 150, null, null, 3070709719, 2256203149, 2290582547, 3207400991, 1729194, "SRX11923628", "SRS9937146", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92731, 0.92152, 0.09349, 0.09234, 0.74298, 0.75749, 0.51393, 0.5062, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65808, "SRR15626560", "SRX11923627", "SRS9937144", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 R4", "GSM5538889", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "W4 R4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "GSM5538889", "GSM5538889: W4 R4; Danio rerio; RNA Seq", "GSM5538889", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538889", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_R4_1.fq.gz W4_R4_2.fq.gz", "fastq fastq", 12376562700.0, 41255209.0, "GSM5538889 r1", "0:150 1:150", "A:3541278294;C:2530972782;G:2556584213;T:3745659123;N:2068288", 150, 150, null, null, 3541278294, 2530972782, 2556584213, 3745659123, 2068288, "SRX11923627", "SRS9937144", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.89512, 0.89467, 0.10934, 0.10598, 0.7501, 0.76045, 0.55625, 0.53279, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65809, "SRR15626559", "SRX11923626", "SRS9937145", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 R3", "GSM5538888", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "W4 R3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "GSM5538888", "GSM5538888: W4 R3; Danio rerio; RNA Seq", "GSM5538888", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538888", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_R3_1.fq.gz W4_R3_2.fq.gz", "fastq fastq", 12994033001.0, 43618576.0, "GSM5538888 r1", null, "A:3734612575;C:2723842641;G:2695083832;T:3835271719;N:5222234", null, null, null, null, 3734612575, 2723842641, 2695083832, 3835271719, 5222234, "SRX11923626", "SRS9937145", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92675, 0.92704, 0.17531, 0.17471, 0.71407, 0.72421, 0.49948, 0.49784, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65810, "SRR15626558", "SRX11923625", "SRS9937143", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 R2", "GSM5538887", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "W4 R2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "GSM5538887", "GSM5538887: W4 R2; Danio rerio; RNA Seq", "GSM5538887", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_R2_1.fq.gz W4_R2_2.fq.gz", "fastq fastq", 9939535918.0, 33661519.0, "GSM5538887 r1", null, "A:2798350929;C:2035721017;G:2056764740;T:3047330104;N:1369128", null, null, null, null, 2798350929, 2035721017, 2056764740, 3047330104, 1369128, "SRX11923625", "SRS9937143", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.83192, 0.82813, 0.14852, 0.14323, 0.70822, 0.7247, 0.5042, 0.39639, 150, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65811, "SRR15626557", "SRX11923624", "SRS9937142", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W4 R1", "GSM5538886", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "W4 R1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:4 xxx post injury", "GSM5538886", "GSM5538886: W4 R1; Danio rerio; RNA Seq", "GSM5538886", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538886", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W4_R1_1.fq.gz W4_R1_2.fq.gz", "fastq fastq", 11296616614.0, 38212724.0, "GSM5538886 r1", null, "A:3243016820;C:2270852137;G:2299184572;T:3481964410;N:1598675", null, null, null, null, 3243016820, 2270852137, 2299184572, 3481964410, 1598675, "SRX11923624", "SRS9937142", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.82944, 0.83777, 0.17869, 0.17723, 0.71887, 0.72855, 0.55802, 0.54964, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65812, "SRR15626556", "SRX11923623", "SRS9937141", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 C5", "GSM5538885", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "W2 C5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "GSM5538885", "GSM5538885: W2 C5; Danio rerio; RNA Seq", "GSM5538885", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538885", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_C5_1.fq.gz W2_C5_2.fq.gz", "fastq fastq", 12070135500.0, 40233785.0, "GSM5538885 r1", "0:150 1:150", "A:3401996219;C:2534578869;G:2548303668;T:3583247357;N:2009387", 150, 150, null, null, 3401996219, 2534578869, 2548303668, 3583247357, 2009387, "SRX11923623", "SRS9937141", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.9072, 0.90232, 0.11716, 0.11618, 0.72636, 0.73685, 0.5018, 0.49535, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65813, "SRR15626555", "SRX11923622", "SRS9937139", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 C4", "GSM5538884", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "W2 C4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "GSM5538884", "GSM5538884: W2 C4; Danio rerio; RNA Seq", "GSM5538884", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538884", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_C4_1.fq.gz W2_C4_2.fq.gz", "fastq fastq", 10594271400.0, 35314238.0, "GSM5538884 r1", "0:150 1:150", "A:2987614251;C:2191740653;G:2212201491;T:3200908482;N:1806523", 150, 150, null, null, 2987614251, 2191740653, 2212201491, 3200908482, 1806523, "SRX11923622", "SRS9937139", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91565, 0.91107, 0.10017, 0.09553, 0.74253, 0.7543, 0.57884, 0.57058, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65814, "SRR15626554", "SRX11923621", "SRS9937140", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 C3", "GSM5538883", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "W2 C3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "GSM5538883", "GSM5538883: W2 C3; Danio rerio; RNA Seq", "GSM5538883", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538883", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_C3_1.fq.gz W2_C3_2.fq.gz", "fastq fastq", 13355624941.0, 44841516.0, "GSM5538883 r1", null, "A:3801123201;C:2832441023;G:2806117424;T:3910715830;N:5227463", null, null, null, null, 3801123201, 2832441023, 2806117424, 3910715830, 5227463, "SRX11923621", "SRS9937140", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.93011, 0.93014, 0.14881, 0.1487, 0.70934, 0.72023, 0.50145, 0.49419, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65815, "SRR15626553", "SRX11923620", "SRS9937138", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 C2", "GSM5538882", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "W2 C2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "GSM5538882", "GSM5538882: W2 C2; Danio rerio; RNA Seq", "GSM5538882", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538882", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_C2_1.fq.gz W2_C2_2.fq.gz", "fastq fastq", 9734471313.0, 32968420.0, "GSM5538882 r1", null, "A:2724735296;C:2009064775;G:2033048131;T:2966320646;N:1302465", null, null, null, null, 2724735296, 2009064775, 2033048131, 2966320646, 1302465, "SRX11923620", "SRS9937138", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.7713, 0.78947, 0.11743, 0.11671, 0.71741, 0.72736, 0.49335, 0.4863, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65816, "SRR15626552", "SRX11923619", "SRS9937137", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 C1", "GSM5538881", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "W2 C1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:2 xxx post injury", "GSM5538881", "GSM5538881: W2 C1; Danio rerio; RNA Seq", "GSM5538881", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538881", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_C1_1.fq.gz W2_C1_2.fq.gz", "fastq fastq", 9082436552.0, 30805602.0, "GSM5538881 r1", null, "A:2559732121;C:1843621019;G:1872765497;T:2804939348;N:1378567", null, null, null, null, 2559732121, 1843621019, 1872765497, 2804939348, 1378567, "SRX11923619", "SRS9937137", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.76943, 0.78719, 0.13099, 0.13069, 0.7259, 0.73679, 0.51491, 0.39397, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65817, "SRR15626551", "SRX11923618", "SRS9937136", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 R5", "GSM5538880", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "W2 R5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "GSM5538880", "GSM5538880: W2 R5; Danio rerio; RNA Seq", "GSM5538880", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538880", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_R5_1.fq.gz W2_R5_2.fq.gz", "fastq fastq", 13733467500.0, 45778225.0, "GSM5538880 r1", "0:150 1:150", "A:3893031167;C:2866552637;G:2882457798;T:4090098547;N:1327351", 150, 150, null, null, 3893031167, 2866552637, 2882457798, 4090098547, 1327351, "SRX11923618", "SRS9937136", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92215, 0.91781, 0.10294, 0.10091, 0.73434, 0.74164, 0.50738, 0.50448, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65818, "SRR15626550", "SRX11923617", "SRS9937135", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 R4", "GSM5538879", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "W2 R4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "GSM5538879", "GSM5538879: W2 R4; Danio rerio; RNA Seq", "GSM5538879", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538879", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_R4_1.fq.gz W2_R4_2.fq.gz", "fastq fastq", 11955951600.0, 39853172.0, "GSM5538879 r1", "0:150 1:150", "A:3384460570;C:2474116532;G:2513217291;T:3582811941;N:1345266", 150, 150, null, null, 3384460570, 2474116532, 2513217291, 3582811941, 1345266, "SRX11923617", "SRS9937135", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.9114, 0.90987, 0.09871, 0.09717, 0.73675, 0.75148, 0.50932, 0.50986, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65819, "SRR15626549", "SRX11923616", "SRS9937134", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 R3", "GSM5538878", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "W2 R3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "GSM5538878", "GSM5538878: W2 R3; Danio rerio; RNA Seq", "GSM5538878", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538878", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_R3_1.fq.gz W2_R3_2.fq.gz", "fastq fastq", 11388586527.0, 38223361.0, "GSM5538878 r1", null, "A:3239034105;C:2424523990;G:2400765702;T:3319676527;N:4586203", null, null, null, null, 3239034105, 2424523990, 2400765702, 3319676527, 4586203, "SRX11923616", "SRS9937134", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.93006, 0.93152, 0.13219, 0.1324, 0.71202, 0.72316, 0.46964, 0.46882, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65820, "SRR15626548", "SRX11923615", "SRS9937132", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 R2", "GSM5538877", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "W2 R2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "GSM5538877", "GSM5538877: W2 R2; Danio rerio; RNA Seq", "GSM5538877", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538877", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_R2_1.fq.gz W2_R2_2.fq.gz", "fastq fastq", 10857439998.0, 36629327.0, "GSM5538877 r1", null, "A:3065308254;C:2244107418;G:2279781972;T:3267100338;N:1142016", null, null, null, null, 3065308254, 2244107418, 2279781972, 3267100338, 1142016, "SRX11923615", "SRS9937132", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.81356, 0.80696, 0.11265, 0.11068, 0.72184, 0.73456, 0.48354, 0.47728, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65821, "SRR15626547", "SRX11923614", "SRS9937133", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W2 R1", "GSM5538876", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "W2 R1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:2 xxx post injury", "GSM5538876", "GSM5538876: W2 R1; Danio rerio; RNA Seq", "GSM5538876", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538876", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W2_R1_1.fq.gz W2_R1_2.fq.gz", "fastq fastq", 11341017399.0, 38401504.0, "GSM5538876 r1", null, "A:3207542121;C:2323545802;G:2348890309;T:3459431647;N:1607520", null, null, null, null, 3207542121, 2323545802, 2348890309, 3459431647, 1607520, "SRX11923614", "SRS9937133", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.83184, 0.84917, 0.10758, 0.10732, 0.73699, 0.7445, 0.54011, 0.53193, 150, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65822, "SRR15626546", "SRX11923613", "SRS9937131", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 C5", "GSM5538875", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "W1 C5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "GSM5538875", "GSM5538875: W1 C5; Danio rerio; RNA Seq", "GSM5538875", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_C5_1.fq.gz W1_C5_2.fq.gz", "fastq fastq", 11249022600.0, 37496742.0, "GSM5538875 r1", "0:150 1:150", "A:3152341668;C:2390909295;G:2404570914;T:3300128090;N:1072633", 150, 150, null, null, 3152341668, 2390909295, 2404570914, 3300128090, 1072633, "SRX11923613", "SRS9937131", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92641, 0.92074, 0.09283, 0.09209, 0.73105, 0.7388, 0.52978, 0.514, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65823, "SRR15626545", "SRX11923612", "SRS9937130", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 C4", "GSM5538874", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "W1 C4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "GSM5538874", "GSM5538874: W1 C4; Danio rerio; RNA Seq", "GSM5538874", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_C4_1.fq.gz W1_C4_2.fq.gz", "fastq fastq", 12941095500.0, 43136985.0, "GSM5538874 r1", "0:150 1:150", "A:3634175324;C:2714886172;G:2737085820;T:3852831271;N:2116913", 150, 150, null, null, 3634175324, 2714886172, 2737085820, 3852831271, 2116913, "SRX11923612", "SRS9937130", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91641, 0.91602, 0.10958, 0.10925, 0.72955, 0.73959, 0.53161, 0.51852, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65824, "SRR15626544", "SRX11923611", "SRS9937129", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 C3", "GSM5538873", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "W1 C3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "GSM5538873", "GSM5538873: W1 C3; Danio rerio; RNA Seq", "GSM5538873", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538873", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_C3_1.fq.gz W1_C3_2.fq.gz", "fastq fastq", 13936313921.0, 46809823.0, "GSM5538873 r1", null, "A:3961118753;C:2959742143;G:2931217720;T:4078708920;N:5526385", null, null, null, null, 3961118753, 2959742143, 2931217720, 4078708920, 5526385, "SRX11923611", "SRS9937129", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92907, 0.92635, 0.13776, 0.13693, 0.71007, 0.7219, 0.50164, 0.503, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65825, "SRR15626543", "SRX11923610", "SRS9937128", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 C2", "GSM5538872", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "W1 C2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "GSM5538872", "GSM5538872: W1 C2; Danio rerio; RNA Seq", "GSM5538872", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538872", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_C2_1.fq.gz W1_C2_2.fq.gz", "fastq fastq", 10863959491.0, 36713522.0, "GSM5538872 r1", null, "A:3045882932;C:2255239365;G:2294328860;T:3267345863;N:1162471", null, null, null, null, 3045882932, 2255239365, 2294328860, 3267345863, 1162471, "SRX11923610", "SRS9937128", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.74749, 0.74175, 0.11328, 0.11041, 0.71701, 0.72772, 0.50737, 0.50743, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65826, "SRR15626542", "SRX11923609", "SRS9937127", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 C1", "GSM5538871", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "W1 C1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:1 xxx post injury", "GSM5538871", "GSM5538871: W1 C1; Danio rerio; RNA Seq", "GSM5538871", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_C1_1.fq.gz W1_C1_2.fq.gz", "fastq fastq", 9041395405.0, 30629306.0, "GSM5538871 r1", null, "A:2497325427;C:1907249915;G:1926778789;T:2708703938;N:1337336", null, null, null, null, 2497325427, 1907249915, 1926778789, 2708703938, 1337336, "SRX11923609", "SRS9937127", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.84841, 0.85222, 0.12779, 0.12199, 0.7097, 0.72372, 0.52363, 0.51259, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65827, "SRR15626541", "SRX11923608", "SRS9937126", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 R5", "GSM5538870", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "W1 R5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "GSM5538870", "GSM5538870: W1 R5; Danio rerio; RNA Seq", "GSM5538870", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_R5_1.fq.gz W1_R5_2.fq.gz", "fastq fastq", 12916604400.0, 43055348.0, "GSM5538870 r1", "0:150 1:150", "A:3648889898;C:2717488564;G:2731231996;T:3817740667;N:1253275", 150, 150, null, null, 3648889898, 2717488564, 2731231996, 3817740667, 1253275, "SRX11923608", "SRS9937126", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92069, 0.9168, 0.08589, 0.08501, 0.73981, 0.74582, 0.5354, 0.52462, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65828, "SRR15626540", "SRX11923607", "SRS9937125", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 R4", "GSM5538869", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "W1 R4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "GSM5538869", "GSM5538869: W1 R4; Danio rerio; RNA Seq", "GSM5538869", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_R4_1.fq.gz W1_R4_2.fq.gz", "fastq fastq", 11607402900.0, 38691343.0, "GSM5538869 r1", "0:150 1:150", "A:3285548269;C:2400691541;G:2419353169;T:3499826563;N:1983358", 150, 150, null, null, 3285548269, 2400691541, 2419353169, 3499826563, 1983358, "SRX11923607", "SRS9937125", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.90628, 0.90638, 0.10284, 0.10084, 0.74119, 0.7516, 0.56967, 0.55805, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65829, "SRR15626539", "SRX11923606", "SRS9937124", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 R3", "GSM5538868", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "W1 R3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "GSM5538868", "GSM5538868: W1 R3; Danio rerio; RNA Seq", "GSM5538868", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_R3_1.fq.gz W1_R3_2.fq.gz", "fastq fastq", 12284640305.0, 41269517.0, "GSM5538868 r1", null, "A:3508836269;C:2584576349;G:2559159651;T:3627220752;N:4847284", null, null, null, null, 3508836269, 2584576349, 2559159651, 3627220752, 4847284, "SRX11923606", "SRS9937124", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92661, 0.92684, 0.16459, 0.16558, 0.70934, 0.72285, 0.51041, 0.50635, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65830, "SRR15626538", "SRX11923605", "SRS9937123", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 R2", "GSM5538867", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "W1 R2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "GSM5538867", "GSM5538867: W1 R2; Danio rerio; RNA Seq", "GSM5538867", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_R2_1.fq.gz W1_R2_2.fq.gz", "fastq fastq", 9613189318.0, 32414297.0, "GSM5538867 r1", null, "A:2694360914;C:2005932920;G:2043314603;T:2868647636;N:933245", null, null, null, null, 2694360914, 2005932920, 2043314603, 2868647636, 933245, "SRX11923605", "SRS9937123", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.76619, 0.73756, 0.12558, 0.12014, 0.71147, 0.72839, 0.49309, 0.49039, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65831, "SRR15626537", "SRX11923604", "SRS9937121", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "W1 R1", "GSM5538866", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "W1 R1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:1 xxx post injury", "GSM5538866", "GSM5538866: W1 R1; Danio rerio; RNA Seq", "GSM5538866", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "W1_R1_1.fq.gz W1_R1_2.fq.gz", "fastq fastq", 7386883792.0, 38487420.0, "GSM5538866 r1", null, "A:2066234577;C:1588682954;G:1585227765;T:2145801527;N:936969", null, null, null, null, 2066234577, 1588682954, 1585227765, 2145801527, 936969, "SRX11923604", "SRS9937121", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.8001, 0.79574, 0.12188, 0.11493, 0.82319, 0.83173, 0.50624, 0.50244, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65832, "SRR15626536", "SRX11923603", "SRS9937122", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C C5", "GSM5538865", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "C C5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "GSM5538865", "GSM5538865: C C5; Danio rerio; RNA Seq", "GSM5538865", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_C5_1.fq.gz C_C5_2.fq.gz", "fastq fastq", 10481010900.0, 34936703.0, "GSM5538865 r1", "0:150 1:150", "A:3033441666;C:2163397542;G:2160648918;T:3122508289;N:1014485", 150, 150, null, null, 3033441666, 2163397542, 2160648918, 3122508289, 1014485, "SRX11923603", "SRS9937122", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.92492, 0.92322, 0.09913, 0.09708, 0.75584, 0.76278, 0.41494, 0.39986, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65833, "SRR15626535", "SRX11923602", "SRS9937120", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C C4", "GSM5538864", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "C C4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "GSM5538864", "GSM5538864: C C4; Danio rerio; RNA Seq", "GSM5538864", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538864", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_C4_1.fq.gz C_C4_2.fq.gz", "fastq fastq", 13743878400.0, 45812928.0, "GSM5538864 r1", "0:150 1:150", "A:3950812518;C:2815585550;G:2826024540;T:4149189277;N:2266515", 150, 150, null, null, 3950812518, 2815585550, 2826024540, 4149189277, 2266515, "SRX11923602", "SRS9937120", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91264, 0.90781, 0.10415, 0.10052, 0.75623, 0.76414, 0.46029, 0.44137, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65834, "SRR15626534", "SRX11923601", "SRS9937119", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C C3", "GSM5538863", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "C C3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "GSM5538863", "GSM5538863: C C3; Danio rerio; RNA Seq", "GSM5538863", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538863", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_C3_1.fq.gz C_C3_2.fq.gz", "fastq fastq", 10004690274.0, 33763075.0, "GSM5538863 r1", null, "A:2912837817;C:2012257307;G:2009657924;T:3069767818;N:169408", null, null, null, null, 2912837817, 2012257307, 2009657924, 3069767818, 169408, "SRX11923601", "SRS9937119", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.78488, 0.77428, 0.16138, 0.15293, 0.7346, 0.75434, 0.47034, 0.45043, 130, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65835, "SRR15626533", "SRX11923600", "SRS9937118", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C C2", "GSM5538862", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "C C2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "GSM5538862", "GSM5538862: C C2; Danio rerio; RNA Seq", "GSM5538862", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538862", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_C2_1.fq.gz C_C2_2.fq.gz", "fastq fastq", 12342833153.0, 41656373.0, "GSM5538862 r1", null, "A:3479483357;C:2557023755;G:2575718106;T:3729085258;N:1522677", null, null, null, null, 3479483357, 2557023755, 2575718106, 3729085258, 1522677, "SRX11923600", "SRS9937118", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.81303, 0.8134, 0.10478, 0.10146, 0.74148, 0.75239, 0.44031, 0.4289, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65836, "SRR15626532", "SRX11923599", "SRS9937117", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C C1", "GSM5538861", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "C C1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment caudal to the injury site|disease state:uninjured", "GSM5538861", "GSM5538861: C C1; Danio rerio; RNA Seq", "GSM5538861", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538861", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_C1_1.fq.gz C_C1_2.fq.gz", "fastq fastq", 10829115925.0, 36675945.0, "GSM5538861 r1", null, "A:3087677087;C:2185500105;G:2207404987;T:3346933841;N:1599905", null, null, null, null, 3087677087, 2185500105, 2207404987, 3346933841, 1599905, "SRX11923599", "SRS9937117", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.86, 0.86399, 0.19457, 0.18642, 0.72616, 0.74093, 0.54866, 0.52664, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65837, "SRR15626531", "SRX11923598", "SRS9937116", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C R5", "GSM5538860", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "C R5", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "GSM5538860", "GSM5538860: C R5; Danio rerio; RNA Seq", "GSM5538860", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538860", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_R5_1.fq.gz C_R5_2.fq.gz", "fastq fastq", 13680284700.0, 45600949.0, "GSM5538860 r1", "0:150 1:150", "A:3941966047;C:2822961394;G:2831655507;T:4082375276;N:1326476", 150, 150, null, null, 3941966047, 2822961394, 2831655507, 4082375276, 1326476, "SRX11923598", "SRS9937116", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.9179, 0.91819, 0.08491, 0.08411, 0.76114, 0.76635, 0.45434, 0.44742, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65838, "SRR15626530", "SRX11923597", "SRS9937115", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C R4", "GSM5538859", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "C R4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "GSM5538859", "GSM5538859: C R4; Danio rerio; RNA Seq", "GSM5538859", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538859", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_R4_1.fq.gz C_R4_2.fq.gz", "fastq fastq", 13264501200.0, 44215004.0, "GSM5538859 r1", "0:150 1:150", "A:3823575952;C:2700864933;G:2712149070;T:4025644258;N:2266987", 150, 150, null, null, 3823575952, 2700864933, 2712149070, 4025644258, 2266987, "SRX11923597", "SRS9937115", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.91094, 0.90944, 0.09845, 0.09521, 0.76708, 0.77833, 0.47031, 0.43887, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65839, "SRR15626529", "SRX11923596", "SRS9937114", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C R3", "GSM5538858", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "C R3", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "GSM5538858", "GSM5538858: C R3; Danio rerio; RNA Seq", "GSM5538858", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538858", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_R3_1.fq.gz C_R3_2.fq.gz", "fastq fastq", 9668631408.0, 32685030.0, "GSM5538858 r1", null, "A:2796307940;C:1932208926;G:1949362622;T:2989642567;N:1109353", null, null, null, null, 2796307940, 1932208926, 1949362622, 2989642567, 1109353, "SRX11923596", "SRS9937114", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.80284, 0.80264, 0.12886, 0.12432, 0.75004, 0.76459, 0.47533, 0.47134, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65840, "SRR15626528", "SRX11923595", "SRS9937113", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C R2", "GSM5538857", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "C R2", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "GSM5538857", "GSM5538857: C R2; Danio rerio; RNA Seq", "GSM5538857", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538857", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_R2_1.fq.gz C_R2_2.fq.gz", "fastq fastq", 10753988922.0, 36365849.0, "GSM5538857 r1", null, "A:3015355138;C:2226805198;G:2242553671;T:3268192192;N:1082723", null, null, null, null, 3015355138, 2226805198, 2242553671, 3268192192, 1082723, "SRX11923595", "SRS9937113", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.83457, 0.83375, 0.1117, 0.10762, 0.74188, 0.75394, 0.44111, 0.34925, 126, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"], [65841, "SRR15626527", "SRX11923594", "SRS9937112", "SRP334272", "PRJNA758088", "Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury", "GSE182868", "Transcriptome Analysis", "The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.", "parent bioproject:PRJNA758278", "pubmed:34876587", null, "C R1", "GSM5538856", null, "source name:spinal cord|strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "C R1", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.", "spinal cord", null, "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:5 spinal segment rostral to the injury site|disease state:uninjured", "GSM5538856", "GSM5538856: C R1; Danio rerio; RNA Seq", "GSM5538856", null, "1", "Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5538856", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP334272", null, "loader:fastq load.py", "C_R1_1.fq.gz C_R1_2.fq.gz", "fastq fastq", 13403792132.0, 45426617.0, "GSM5538856 r1", null, "A:3857313379;C:2689731077;G:2652919866;T:4201982088;N:1845722", null, null, null, null, 3857313379, 2689731077, 2652919866, 4201982088, 1845722, "SRX11923594", "SRS9937112", "SRA1284220", "GEO", "Neuroscience, School of Medcine, Tongji University, 42508444-9", 2, 0.85629, 0.86608, 0.19336, 0.18757, 0.74213, 0.75732, 0.57712, 0.56646, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "China", "2021-08-26", "Undetermined", "Adult", "Spinal Cord", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 60, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", 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[experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, 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"selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 60, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord", "results": [{"value": "Adult", "label": "Adult", "count": 60, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord&devstage_curation=Undetermined", "selected": false}, {"value": "Adult", "label": "Adult", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord&devstage_curation=Adult", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=bulk&tissue_curation=Spinal+Cord", "results": [{"value": "Nervous System", "label": 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"toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spinal+Cord", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 94.33344200078864}