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,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
65782,SRR15626598,SRX11923661,SRS9937171,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP SC 5,GSM5538915,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP SC 5,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538915,GSM5538915: SP SC 5; Danio rerio; RNA Seq,GSM5538915,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538915,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_SC_5_1.fq.gz SP_SC_5_2.fq.gz,fastq fastq,15123413700.0,50411379.0,GSM5538915 r1,0:150 1:150,A:4455675867;C:2762093028;G:3064816838;T:4839518034;N:1309933,150,150,,,4455675867,2762093028,3064816838,4839518034,1309933,SRX11923661,SRS9937171,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.87431,0.86943,0.22595,0.2251,0.80282,0.80663,0.54345,0.53283,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65783,SRR15626597,SRX11923660,SRS9937170,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP SC 4,GSM5538914,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP SC 4,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538914,GSM5538914: SP SC 4; Danio rerio; RNA Seq,GSM5538914,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538914,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_SC_4_1.fq.gz SP_SC_4_2.fq.gz,fastq fastq,16743046500.0,55810155.0,GSM5538914 r1,0:150 1:150,A:4990111476;C:2997789090;G:3379928547;T:5374081112;N:1136275,150,150,,,4990111476,2997789090,3379928547,5374081112,1136275,SRX11923660,SRS9937170,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.78972,0.78594,0.27052,0.26874,0.85013,0.85342,0.57347,0.57843,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65784,SRR15626596,SRX11923659,SRS9937169,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP SC 3,GSM5538913,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP SC 3,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538913,GSM5538913: SP SC 3; Danio rerio; RNA Seq,GSM5538913,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538913,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_SC_3_1.fq.gz SP_SC_3_2.fq.gz,fastq fastq,18816263700.0,62720879.0,GSM5538913 r1,0:150 1:150,A:5718449534;C:3326587767;G:3765533138;T:6005600414;N:92847,150,150,,,5718449534,3326587767,3765533138,6005600414,92847,SRX11923659,SRS9937169,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.85756,0.85572,0.21036,0.20882,0.85222,0.85441,0.42132,0.6499,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65785,SRR15626595,SRX11923658,SRS9937168,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP SC 2,GSM5538912,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP SC 2,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538912,GSM5538912: SP SC 2; Danio rerio; RNA Seq,GSM5538912,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538912,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_SC_2_1.fq.gz SP_SC_2_2.fq.gz,fastq fastq,17380791000.0,57935970.0,GSM5538912 r1,0:150 1:150,A:5260639203;C:3099491904;G:3440470486;T:5579887776;N:301631,150,150,,,5260639203,3099491904,3440470486,5579887776,301631,SRX11923658,SRS9937168,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.75526,0.75779,0.22658,0.22782,0.86111,0.86237,0.59826,0.60551,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65786,SRR15626594,SRX11923657,SRS9937166,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP SC 1,GSM5538911,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP SC 1,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segments distal to the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538911,GSM5538911: SP SC 1; Danio rerio; RNA Seq,GSM5538911,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538911,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_SC_1_1.fq.gz SP_SC_1_2.fq.gz,fastq fastq,20361678900.0,67872263.0,GSM5538911 r1,0:150 1:150,A:6177247371;C:3549700804;G:3997102203;T:6637296058;N:332464,150,150,,,6177247371,3549700804,3997102203,6637296058,332464,SRX11923657,SRS9937166,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.80835,0.80708,0.24946,0.25241,0.84037,0.84303,0.5988,0.59871,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65787,SRR15626593,SRX11923656,SRS9937165,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP 6W 6,GSM5538910,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP 6W 6,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538910,GSM5538910: SP 6W 6; Danio rerio; RNA Seq,GSM5538910,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538910,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_6W_6_1.fq.gz SP_6W_6_2.fq.gz,fastq fastq,22472709600.0,74909032.0,GSM5538910 r1,0:150 1:150,A:6919488736;C:3623491665;G:4350778578;T:7578832909;N:117712,150,150,,,6919488736,3623491665,4350778578,7578832909,117712,SRX11923656,SRS9937165,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.81992,0.81637,0.29919,0.29843,0.83309,0.83707,0.62577,0.60938,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65788,SRR15626592,SRX11923655,SRS9937167,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP 6W 5,GSM5538909,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP 6W 5,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538909,GSM5538909: SP 6W 5; Danio rerio; RNA Seq,GSM5538909,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538909,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_6W_5_1.fq.gz SP_6W_5_2.fq.gz,fastq fastq,20583610500.0,68612035.0,GSM5538909 r1,0:150 1:150,A:6360709506;C:3307195715;G:4004718826;T:6910881382;N:105071,150,150,,,6360709506,3307195715,4004718826,6910881382,105071,SRX11923655,SRS9937167,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.80493,0.80492,0.3258,0.3244,0.82682,0.83002,0.58555,0.58892,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65789,SRR15626591,SRX11923654,SRS9937164,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP 6W 4,GSM5538908,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP 6W 4,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538908,GSM5538908: SP 6W 4; Danio rerio; RNA Seq,GSM5538908,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538908,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_6W_4_1.fq.gz SP_6W_4_2.fq.gz,fastq fastq,19724695800.0,65748986.0,GSM5538908 r1,0:150 1:150,A:6112379944;C:3229510802;G:3753824243;T:6628648367;N:332444,150,150,,,6112379944,3229510802,3753824243,6628648367,332444,SRX11923654,SRS9937164,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.76792,0.76848,0.22326,0.22438,0.8747,0.87732,0.68095,0.68566,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65790,SRR15626590,SRX11923653,SRS9937163,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP 6W 3,GSM5538907,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP 6W 3,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538907,GSM5538907: SP 6W 3; Danio rerio; RNA Seq,GSM5538907,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538907,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_6W_3_1.fq.gz SP_6W_3_2.fq.gz,fastq fastq,22917868200.0,76392894.0,GSM5538907 r1,0:150 1:150,A:6801610029;C:4223124283;G:4702480567;T:7190055774;N:597547,150,150,,,6801610029,4223124283,4702480567,7190055774,597547,SRX11923653,SRS9937163,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.57129,0.57016,0.16002,0.16225,0.91634,0.91729,0.59641,0.5943,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65791,SRR15626589,SRX11923652,SRS9937161,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP 6W 2,GSM5538906,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP 6W 2,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538906,GSM5538906: SP 6W 2; Danio rerio; RNA Seq,GSM5538906,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538906,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_6W_2_1.fq.gz SP_6W_2_2.fq.gz,fastq fastq,24852190200.0,82840634.0,GSM5538906 r1,0:150 1:150,A:7405379331;C:4430315593;G:5004669375;T:8011250066;N:575835,150,150,,,7405379331,4430315593,5004669375,8011250066,575835,SRX11923652,SRS9937161,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.62502,0.61952,0.13619,0.13651,0.90433,0.90569,0.6187,0.64354,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
65792,SRR15626588,SRX11923651,SRS9937162,SRP334274,PRJNA758087,Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury,GSE182869,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.,parent bioproject:PRJNA758278,pubmed:34876587,,SP 6W 1,GSM5538905,,source name:spinal cord|strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,SP 6W 1,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. HTSeq v0.9.1 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,,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:Tgtph2:GFP|tissue:spinal cord segment in the injury site|cell type:serot1rgic neuron|disease state:6 8 xxx post injury,GSM5538905,GSM5538905: SP 6W 1; Danio rerio; RNA Seq,GSM5538905,,1,Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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:GSM5538905,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP334274,,loader:fastq load.py,SP_6W_1_1.fq.gz SP_6W_1_2.fq.gz,fastq fastq,24620126100.0,82067087.0,GSM5538905 r1,0:150 1:150,A:7560561068;C:3977462807;G:4611993481;T:8469791572;N:317172,150,150,,,7560561068,3977462807,4611993481,8469791572,317172,SRX11923651,SRS9937162,SRA1284222,GEO,"Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.82479,0.8193,0.2795,0.27737,0.83011,0.83374,0.58026,0.57852,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2021-08-26,Undetermined,Undetermined,Spinal Cord,Nervous System
71344,SRR21518655,SRX17521097,SRS15071653,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D8W 6,GSM6571299,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,D8W 6,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,GSM6571299,GSM6571299: D8W 6; Danio rerio; RNA Seq,GSM6571299 r1,GSM6571299,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D8W_6_1.fq.gz D8W_6_2.fq.gz,fastq fastq,23074195800.0,76913986.0,GSM6571299 r1,0:150 1:150,A:6989471908;C:3827149440;G:4489649569;T:7767681395;N:243488,150,150,,,6989471908,3827149440,4489649569,7767681395,243488,SRX17521097,SRS15071653,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.81011,0.80484,0.25365,0.25069,0.85669,0.86091,0.74292,0.73244,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71345,SRR21518656,SRX17521096,SRS15071652,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D8W 5,GSM6571298,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,D8W 5,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,GSM6571298,GSM6571298: D8W 5; Danio rerio; RNA Seq,GSM6571298 r1,GSM6571298,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D8W_5_1.fq.gz D8W_5_2.fq.gz,fastq fastq,18633190800.0,62110636.0,GSM6571298 r1,0:150 1:150,A:5623498658;C:3193233759;G:3663268093;T:6152718258;N:472032,150,150,,,5623498658,3193233759,3663268093,6152718258,472032,SRX17521096,SRS15071652,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.8566,0.85472,0.26238,0.26061,0.84875,0.85273,0.76538,0.76758,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71346,SRR21518657,SRX17521095,SRS15071651,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D8W 4,GSM6571297,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,D8W 4,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,GSM6571297,GSM6571297: D8W 4; Danio rerio; RNA Seq,GSM6571297 r1,GSM6571297,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D8W_4_1.fq.gz D8W_4_2.fq.gz,fastq fastq,19215064800.0,64050216.0,GSM6571297 r1,0:150 1:150,A:5704671476;C:3361605086;G:3869454140;T:6279125220;N:208878,150,150,,,5704671476,3361605086,3869454140,6279125220,208878,SRX17521095,SRS15071651,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.84346,0.84571,0.20336,0.20367,0.83609,0.8435,0.7068,0.70686,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71347,SRR21518658,SRX17521094,SRS15071650,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D8W 3,GSM6571296,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,D8W 3,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,GSM6571296,GSM6571296: D8W 3; Danio rerio; RNA Seq,GSM6571296 r1,GSM6571296,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D8W_3_1.fq.gz D8W_3_2.fq.gz,fastq fastq,16957395900.0,56524653.0,GSM6571296 r1,0:150 1:150,A:5009525932;C:3025736371;G:3483140337;T:5438695627;N:297633,150,150,,,5009525932,3025736371,3483140337,5438695627,297633,SRX17521094,SRS15071650,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.86527,0.86479,0.18805,0.19011,0.82962,0.83493,0.73182,0.71616,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71348,SRR21518659,SRX17521093,SRS15071649,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D8W 2,GSM6571295,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,D8W 2,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,GSM6571295,GSM6571295: D8W 2; Danio rerio; RNA Seq,GSM6571295 r1,GSM6571295,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D8W_2_1.fq.gz D8W_2_2.fq.gz,fastq fastq,19659164400.0,65530548.0,GSM6571295 r1,0:150 1:150,A:5762888910;C:3499173834;G:4061084152;T:6336002328;N:15176,150,150,,,5762888910,3499173834,4061084152,6336002328,15176,SRX17521093,SRS15071649,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.83786,0.84048,0.23272,0.23516,0.83735,0.84127,0.68532,0.66585,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71349,SRR21518660,SRX17521092,SRS15071648,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D8W 1,GSM6571294,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,D8W 1,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:8 weeks post spinal cord injury,GSM6571294,GSM6571294: D8W 1; Danio rerio; RNA Seq,GSM6571294 r1,GSM6571294,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D8W_1_1.fq.gz D8W_1_2.fq.gz,fastq fastq,20058508500.0,66861695.0,GSM6571294 r1,0:150 1:150,A:5906136798;C:3395273375;G:4258413193;T:6498464289;N:220845,150,150,,,5906136798,3395273375,4258413193,6498464289,220845,SRX17521092,SRS15071648,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.7974,0.81116,0.21656,0.21968,0.79287,0.80215,0.65113,0.6547,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71350,SRR21518661,SRX17521091,SRS15071647,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G8W 5,GSM6571293,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,G8W 5,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,GSM6571293,GSM6571293: G8W 5; Danio rerio; RNA Seq,GSM6571293 r1,GSM6571293,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G8W_5_1.fq.gz G8W_5_2.fq.gz,fastq fastq,22171398300.0,73904661.0,GSM6571293 r1,0:150 1:150,A:6542438393;C:3783436667;G:4476703495;T:7368512464;N:307281,150,150,,,6542438393,3783436667,4476703495,7368512464,307281,SRX17521091,SRS15071647,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.83396,0.82912,0.2318,0.23297,0.82714,0.83859,0.63506,0.41732,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71351,SRR21518662,SRX17521090,SRS15071646,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G8W 4,GSM6571292,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,G8W 4,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,GSM6571292,GSM6571292: G8W 4; Danio rerio; RNA Seq,GSM6571292 r1,GSM6571292,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G8W_4_1.fq.gz G8W_4_2.fq.gz,fastq fastq,18267788400.0,60892628.0,GSM6571292 r1,0:150 1:150,A:5463611469;C:3145201738;G:3640365993;T:6018256285;N:352915,150,150,,,5463611469,3145201738,3640365993,6018256285,352915,SRX17521090,SRS15071646,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.85801,0.84352,0.21702,0.21313,0.80633,0.81651,0.65914,0.65827,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71352,SRR21518663,SRX17521089,SRS15071645,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G8W 3,GSM6571291,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,G8W 3,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,GSM6571291,GSM6571291: G8W 3; Danio rerio; RNA Seq,GSM6571291 r1,GSM6571291,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G8W_3_1.fq.gz G8W_3_2.fq.gz,fastq fastq,15211018500.0,50703395.0,GSM6571291 r1,0:150 1:150,A:4500744393;C:2714882862;G:3099231886;T:4896086023;N:73336,150,150,,,4500744393,2714882862,3099231886,4896086023,73336,SRX17521089,SRS15071645,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.83681,0.83831,0.29306,0.29444,0.79176,0.79553,0.58355,0.58032,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71353,SRR21518664,SRX17521088,SRS15071644,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G8W 2,GSM6571290,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,G8W 2,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,GSM6571290,GSM6571290: G8W 2; Danio rerio; RNA Seq,GSM6571290 r1,GSM6571290,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G8W_2_1.fq.gz G8W_2_2.fq.gz,fastq fastq,17212627800.0,57375426.0,GSM6571290 r1,0:150 1:150,A:5152682984;C:3022128915;G:3452882594;T:5584505511;N:427796,150,150,,,5152682984,3022128915,3452882594,5584505511,427796,SRX17521088,SRS15071644,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.82626,0.82996,0.25153,0.2507,0.77289,0.77621,0.44519,0.58203,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71354,SRR21518665,SRX17521087,SRS15071643,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G8W 1,GSM6571289,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,G8W 1,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:8 weeks post spinal cord injury,GSM6571289,GSM6571289: G8W 1; Danio rerio; RNA Seq,GSM6571289 r1,GSM6571289,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G8W_1_1.fq.gz G8W_1_2.fq.gz,fastq fastq,9952163100.0,33173877.0,GSM6571289 r1,0:150 1:150,A:2928022189;C:1997447266;G:2105516271;T:2921136600;N:40774,150,150,,,2928022189,1997447266,2105516271,2921136600,40774,SRX17521087,SRS15071643,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.75404,0.75353,0.23994,0.24065,0.81726,0.81935,0.59225,0.60032,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Juvenile,Juvenile,Spinal Cord,Nervous System
71355,SRR21518666,SRX17521086,SRS15071642,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D3W 5,GSM6571288,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,D3W 5,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,GSM6571288,GSM6571288: D3W 5; Danio rerio; RNA Seq,GSM6571288 r1,GSM6571288,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D3W_5_1.fq.gz D3W_5_2.fq.gz,fastq fastq,21805797900.0,72685993.0,GSM6571288 r1,0:150 1:150,A:6534643663;C:3641045689;G:4308533806;T:7320661756;N:912986,150,150,,,6534643663,3641045689,4308533806,7320661756,912986,SRX17521086,SRS15071642,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.67175,0.667,0.196,0.19629,0.8761,0.88075,0.45229,0.68298,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71356,SRR21518667,SRX17521085,SRS15071641,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D3W 4,GSM6571287,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,D3W 4,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,GSM6571287,GSM6571287: D3W 4; Danio rerio; RNA Seq,GSM6571287 r1,GSM6571287,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D3W_4_1.fq.gz D3W_4_2.fq.gz,fastq fastq,16717299300.0,55724331.0,GSM6571287 r1,0:150 1:150,A:5025390550;C:2864680769;G:3245719757;T:5581424252;N:83972,150,150,,,5025390550,2864680769,3245719757,5581424252,83972,SRX17521085,SRS15071641,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.85363,0.84701,0.20854,0.20707,0.83108,0.83652,0.72258,0.72805,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71357,SRR21518668,SRX17521084,SRS15071640,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D3W 3,GSM6571286,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,D3W 3,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,GSM6571286,GSM6571286: D3W 3; Danio rerio; RNA Seq,GSM6571286 r1,GSM6571286,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D3W_3_1.fq.gz D3W_3_2.fq.gz,fastq fastq,20924629500.0,69748765.0,GSM6571286 r1,0:150 1:150,A:6065653962;C:3861200256;G:4352429986;T:6645186672;N:158624,150,150,,,6065653962,3861200256,4352429986,6645186672,158624,SRX17521084,SRS15071640,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.69652,0.69746,0.16932,0.16877,0.87722,0.88079,0.60821,0.62353,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71358,SRR21518669,SRX17521083,SRS15071639,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D3W 2,GSM6571285,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,D3W 2,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,GSM6571285,GSM6571285: D3W 2; Danio rerio; RNA Seq,GSM6571285 r1,GSM6571285,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D3W_2_1.fq.gz D3W_2_2.fq.gz,fastq fastq,17292138600.0,57640462.0,GSM6571285 r1,0:150 1:150,A:5112950597;C:3131593774;G:3471890080;T:5575578449;N:125700,150,150,,,5112950597,3131593774,3471890080,5575578449,125700,SRX17521083,SRS15071639,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.885,0.88321,0.21164,0.20863,0.79452,0.79884,0.65888,0.64527,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71359,SRR21518670,SRX17521082,SRS15071638,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,D3W 1,GSM6571284,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,D3W 1,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons with regrown axon|disease state:3 weeks post spinal cord injury,GSM6571284,GSM6571284: D3W 1; Danio rerio; RNA Seq,GSM6571284 r1,GSM6571284,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,D3W_1_1.fq.gz D3W_1_2.fq.gz,fastq fastq,25865223000.0,86217410.0,GSM6571284 r1,0:150 1:150,A:7663590336;C:4692982593;G:5239577239;T:8268318664;N:754168,150,150,,,7663590336,4692982593,5239577239,8268318664,754168,SRX17521082,SRS15071638,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.86075,0.85815,0.2275,0.22494,0.81203,0.81412,0.6136,0.60896,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71360,SRR21518671,SRX17521081,SRS15071637,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G3W 5,GSM6571283,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,G3W 5,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,GSM6571283,GSM6571283: G3W 5; Danio rerio; RNA Seq,GSM6571283 r1,GSM6571283,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G3W_5_1.fq.gz G3W_5_2.fq.gz,fastq fastq,19521420000.0,65071400.0,GSM6571283 r1,0:150 1:150,A:5820386498;C:3315686301;G:4078308509;T:6306924981;N:113711,150,150,,,5820386498,3315686301,4078308509,6306924981,113711,SRX17521081,SRS15071637,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.78769,0.7856,0.29623,0.29402,0.81085,0.82114,0.60933,0.60853,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71361,SRR21518672,SRX17521080,SRS15071636,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G3W 4,GSM6571282,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,G3W 4,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,GSM6571282,GSM6571282: G3W 4; Danio rerio; RNA Seq,GSM6571282 r1,GSM6571282,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G3W_4_1.fq.gz G3W_4_2.fq.gz,fastq fastq,21647934600.0,72159782.0,GSM6571282 r1,0:150 1:150,A:6490465443;C:3742052860;G:4344871492;T:7070158060;N:386745,150,150,,,6490465443,3742052860,4344871492,7070158060,386745,SRX17521080,SRS15071636,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.82718,0.83047,0.33407,0.33744,0.80312,0.81002,0.60443,0.58622,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71362,SRR21518673,SRX17521079,SRS15071635,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G3W 3,GSM6571281,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,G3W 3,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,GSM6571281,GSM6571281: G3W 3; Danio rerio; RNA Seq,GSM6571281 r1,GSM6571281,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G3W_3_1.fq.gz G3W_3_2.fq.gz,fastq fastq,25032046200.0,83440154.0,GSM6571281 r1,0:150 1:150,A:7589944903;C:4358061815;G:4905089496;T:8178211087;N:738899,150,150,,,7589944903,4358061815,4905089496,8178211087,738899,SRX17521079,SRS15071635,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.83482,0.83258,0.35619,0.35421,0.80036,0.80555,0.55701,0.56318,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71363,SRR21518674,SRX17521078,SRS15071634,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G3W 2,GSM6571280,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,G3W 2,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,GSM6571280,GSM6571280: G3W 2; Danio rerio; RNA Seq,GSM6571280 r1,GSM6571280,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G3W_2_1.fq.gz G3W_2_2.fq.gz,fastq fastq,25763705100.0,85879017.0,GSM6571280 r1,0:150 1:150,A:7797694134;C:4570702435;G:5051801444;T:8342741493;N:765594,150,150,,,7797694134,4570702435,5051801444,8342741493,765594,SRX17521078,SRS15071634,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.84886,0.84832,0.33366,0.33438,0.7947,0.79448,0.57924,0.58144,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71364,SRR21518675,SRX17521077,SRS15071633,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,G3W 1,GSM6571279,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,G3W 1,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:V2a interneurons without xxx axon|disease state:3 weeks post spinal cord injury,GSM6571279,GSM6571279: G3W 1; Danio rerio; RNA Seq,GSM6571279 r1,GSM6571279,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,G3W_1_1.fq.gz G3W_1_2.fq.gz,fastq fastq,24213689700.0,80712299.0,GSM6571279 r1,0:150 1:150,A:7283815011;C:4309684913;G:4783743695;T:7835730940;N:715141,150,150,,,7283815011,4309684913,4783743695,7835730940,715141,SRX17521077,SRS15071633,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.85001,0.8472,0.3304,0.33339,0.79442,0.80075,0.56694,0.56866,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Larval,Larval,Spinal Cord,Nervous System
71365,SRR21518676,SRX17521076,SRS15071632,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Dcon 5,GSM6571278,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,Dcon 5,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,GSM6571278,GSM6571278: Dcon 5; Danio rerio; RNA Seq,GSM6571278 r1,GSM6571278,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Dcon_5_1.fq.gz Dcon_5_2.fq.gz,fastq fastq,20197199700.0,67323999.0,GSM6571278 r1,0:150 1:150,A:5922004973;C:3620512485;G:4138056693;T:6516462073;N:163476,150,150,,,5922004973,3620512485,4138056693,6516462073,163476,SRX17521076,SRS15071632,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.86351,0.86525,0.19272,0.19286,0.81919,0.82509,0.62647,0.63232,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71366,SRR21518677,SRX17521075,SRS15071631,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Dcon 4,GSM6571277,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,Dcon 4,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,GSM6571277,GSM6571277: Dcon 4; Danio rerio; RNA Seq,GSM6571277 r1,GSM6571277,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Dcon_4_1.fq.gz Dcon_4_2.fq.gz,fastq fastq,22521319800.0,75071066.0,GSM6571277 r1,0:150 1:150,A:6684333956;C:4124475103;G:4550073380;T:7162006741;N:430620,150,150,,,6684333956,4124475103,4550073380,7162006741,430620,SRX17521075,SRS15071631,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.82476,0.82206,0.19781,0.19628,0.84104,0.84102,0.59314,0.60438,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71367,SRR21518678,SRX17521074,SRS15071630,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Dcon 3,GSM6571276,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,Dcon 3,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,GSM6571276,GSM6571276: Dcon 3; Danio rerio; RNA Seq,GSM6571276 r1,GSM6571276,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Dcon_3_1.fq.gz Dcon_3_2.fq.gz,fastq fastq,16765029000.0,55883430.0,GSM6571276 r1,0:150 1:150,A:4921481179;C:3099956110;G:3454683240;T:5288567628;N:340843,150,150,,,4921481179,3099956110,3454683240,5288567628,340843,SRX17521074,SRS15071630,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.87476,0.87529,0.19624,0.19794,0.81501,0.81655,0.60587,0.61167,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71368,SRR21518679,SRX17521073,SRS15071629,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Dcon 2,GSM6571275,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,Dcon 2,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,GSM6571275,GSM6571275: Dcon 2; Danio rerio; RNA Seq,GSM6571275 r1,GSM6571275,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Dcon_2_1.fq.gz Dcon_2_2.fq.gz,fastq fastq,18265782600.0,60885942.0,GSM6571275 r1,0:150 1:150,A:5350864835;C:3372151520;G:3777524042;T:5764900851;N:341352,150,150,,,5350864835,3372151520,3777524042,5764900851,341352,SRX17521073,SRS15071629,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.87272,0.86999,0.16983,0.17002,0.81633,0.81884,0.62413,0.61558,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71369,SRR21518680,SRX17521072,SRS15071628,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Dcon 1,GSM6571274,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,Dcon 1,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:retrogradely labeled V2a interneurons|disease state:uninjured,GSM6571274,GSM6571274: Dcon 1; Danio rerio; RNA Seq,GSM6571274 r1,GSM6571274,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Dcon_1_1.fq.gz Dcon_1_2.fq.gz,fastq fastq,23990335200.0,79967784.0,GSM6571274 r1,0:150 1:150,A:7105219301;C:4460741137;G:4888132155;T:7535524207;N:718400,150,150,,,7105219301,4460741137,4888132155,7535524207,718400,SRX17521072,SRS15071628,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.82243,0.82087,0.22622,0.22456,0.83587,0.83727,0.59612,0.59013,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71370,SRR21518681,SRX17521071,SRS15071627,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Gcon 6,GSM6571273,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,Gcon 6,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,GSM6571273,GSM6571273: Gcon 6; Danio rerio; RNA Seq,GSM6571273 r1,GSM6571273,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Gcon_6_1.fq.gz Gcon_6_2.fq.gz,fastq fastq,19206946200.0,64023154.0,GSM6571273 r1,0:150 1:150,A:5607359181;C:3628578022;G:3973548345;T:5997114011;N:346641,150,150,,,5607359181,3628578022,3973548345,5997114011,346641,SRX17521071,SRS15071627,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.86625,0.86509,0.21447,0.21384,0.7904,0.79214,0.54986,0.54595,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71371,SRR21518682,SRX17521070,SRS15071626,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Gcon 5,GSM6571272,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,Gcon 5,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,GSM6571272,GSM6571272: Gcon 5; Danio rerio; RNA Seq,GSM6571272 r1,GSM6571272,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Gcon_5_1.fq.gz Gcon_5_2.fq.gz,fastq fastq,23997814200.0,79992714.0,GSM6571272 r1,0:150 1:150,A:7064554458;C:4411941927;G:4941700646;T:7579149915;N:467254,150,150,,,7064554458,4411941927,4941700646,7579149915,467254,SRX17521070,SRS15071626,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.85378,0.85202,0.25333,0.25316,0.79166,0.7946,0.53581,0.53411,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71372,SRR21518683,SRX17521069,SRS15071625,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Gcon 4,GSM6571271,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,Gcon 4,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,GSM6571271,GSM6571271: Gcon 4; Danio rerio; RNA Seq,GSM6571271 r1,GSM6571271,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Gcon_4_1.fq.gz Gcon_4_2.fq.gz,fastq fastq,16100046000.0,53666820.0,GSM6571271 r1,0:150 1:150,A:4804113446;C:2861812622;G:3293136768;T:5140555256;N:427908,150,150,,,4804113446,2861812622,3293136768,5140555256,427908,SRX17521069,SRS15071625,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.7771,0.78275,0.30988,0.31288,0.79127,0.79454,0.59189,0.59182,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71373,SRR21518684,SRX17521068,SRS15071624,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Gcon 3,GSM6571270,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,Gcon 3,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,GSM6571270,GSM6571270: Gcon 3; Danio rerio; RNA Seq,GSM6571270 r1,GSM6571270,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Gcon_3_1.fq.gz Gcon_3_2.fq.gz,fastq fastq,18192741600.0,60642472.0,GSM6571270 r1,0:150 1:150,A:5315928341;C:3223817327;G:3900631135;T:5751919941;N:444856,150,150,,,5315928341,3223817327,3900631135,5751919941,444856,SRX17521068,SRS15071624,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.69985,0.71093,0.25385,0.25634,0.83291,0.83676,0.59191,0.58973,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71374,SRR21518685,SRX17521067,SRS15071623,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Gcon 2,GSM6571269,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,Gcon 2,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,GSM6571269,GSM6571269: Gcon 2; Danio rerio; RNA Seq,GSM6571269 r1,GSM6571269,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Gcon_2_1.fq.gz Gcon_2_2.fq.gz,fastq fastq,24566788200.0,81889294.0,GSM6571269 r1,0:150 1:150,A:7369409859;C:4411997495;G:4925325152;T:7859338650;N:717044,150,150,,,7369409859,4411997495,4925325152,7859338650,717044,SRX17521067,SRS15071623,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.84033,0.83745,0.30938,0.31035,0.80154,0.80677,0.55263,0.55114,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System
71375,SRR21518686,SRX17521066,SRS15071622,SRP396553,PRJNA879067,Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion post spinal cord injury,GSE213081,Transcriptome Analysis,The goals of this study is to compare transcriptome profiles RNA seq of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 42 370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without xxx axon in the spinal segments rostral to the lesion post spinal cord injury. Overall design: For purification of V2a interneurons with regrown axon  the fluorescent tracer Rhodamine Dextran RD was retrogradely applied to TgChx10:GFP fish at three or eight xxx post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3  or 8 wpi  and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD  cells were FAC sorted and subjected to RNA sequencing. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's instructions.,,,,Gcon 1,GSM6571268,,source name:spinal cord|strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,Gcon 1,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. HTSeq v0.9.1 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. Assembly: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.,spinal cord,,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,strain:TgChx10:GFP|tissue:spinal cord segments 1 to 7|cell type:non labeled V2a interneurons|disease state:uninjured,GSM6571268,GSM6571268: Gcon 1; Danio rerio; RNA Seq,GSM6571268 r1,GSM6571268,1,Spinal cord tissue were dissected out. V2a interneurons were isolated from TgChx10:GFP line by FAC sorting  flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® 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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP396553,,loader:fastq load.py|options:  doNotUseSharq,Gcon_1_1.fq.gz Gcon_1_2.fq.gz,fastq fastq,25366283100.0,84554277.0,GSM6571268 r1,0:150 1:150,A:7520309654;C:4649249325;G:5190507702;T:8005455375;N:761044,150,150,,,7520309654,4649249325,5190507702,8005455375,761044,SRX17521066,SRS15071622,SRA1499985,"Neuroscience, School of Medcine, Tongji University, 42508444-9","Neuroscience, School of Medcine, Tongji University, 42508444-9",2,0.76469,0.76407,0.26314,0.26213,0.83268,0.83416,0.5388,0.54301,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,China,2022-09-10,Undetermined,Undetermined,Spinal Cord,Nervous System