|
| Status |
Public on Dec 09, 2022 |
| Title |
FR105_P1_2 |
| Sample type |
SRA |
| |
|
| Source name |
whole kidney marrow (WKM)
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole kidney marrow (WKM)
age: 3 months
genotype/variation: FR105 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 |
SAMN27567789 |
| SRA |
SRX14845514 |
