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Sample GSM6043270 Query DataSets for GSM6043270
Status Public on Dec 09, 2022
Title IT325_P2_1
Sample type SRA
 
Source name whole kidney marrow (WKM)
Organism Danio rerio
Characteristics tissue: whole kidney marrow (WKM)
age: 3 months
genotype/variation: IT325 Mutant WKM cells
Treatment protocol No Treatment was performed.
Growth protocol Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.
Extracted molecule total RNA
Extraction protocol Three months old wild-type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral, midline incision was made and kidney were dissected and placed into ice-cold 0.9× PBS containing 5% FCS. Single-cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40-μm nylon mesh filter with a plunger from a 1-ml syringe.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Assembly: ENCODE VM9
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
 
Submission date Apr 13, 2022
Last update date Dec 09, 2022
Contact name Sagar -
E-mail(s) sagar@uniklinik-freiburg.de
Organization name University Medical Center Freiburg
Department Department of Internal Medicine II
Lab Sagar
Street address Hugstetter Straße 55
City Freiburg
ZIP/Postal code 79106
Country Germany
 
Platform ID GPL18413
Series (1)
GSE200756 Stage- and cell type-specific requirements of ikzf1 during haematopoietic differentiation in zebrafish
Relations
BioSample SAMN27567778
SRA SRX14845525

Supplementary file Size Download File type/resource
GSM6043270_IT325_P2_1.coutt.csv.gz 295.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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