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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
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