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| Status |
Public on Jun 28, 2021 |
| Title |
IFIH1KO_P2_15 |
| Sample type |
SRA |
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| Source name |
library of 96 IFIH1-/- HSCs
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: IFIH1-/-
age: 8 weeks
tissue: bone marrow
cell type: hematopoietic stem cells (HSCs)
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| Treatment protocol |
No treatmenat was performed on the isolated HSCs.
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| Growth protocol |
Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow cells isolated from tibiae, femurs and hip bones and red cells were lysed. For cell sorting, samples where additionally enriched for hematopoietic progenitor cells by depleting the lineage positive fraction using the biotin-conjugated lineage cocktail with antibodies against CD3e, CD11b/Mac-1, CD45R/B220, Ly-6/Ly6C, and TER-119. The lineage negative fraction was then washed and resuspended in staining buffer at a concentration of 10x106 cells per ml, and were then stained with FITC or PE-conjugated lineage cocktail antibodies, CD117/c-kit, Sca-1, CD48, CD150, CD135/Flk2, CD34. We used CD150+CD48- LSK cells for the scRNA-seq experiments.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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).
Genome_build: 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.
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| Submission date |
Apr 11, 2019 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Sagar - |
| E-mail(s) |
sagar@uniklinik-freiburg.de
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| Organization name |
University Medical Center Freiburg
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| Department |
Department of Internal Medicine II
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| Lab |
Sagar
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| Street address |
Hugstetter Straße 55
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| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE129631 |
Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration |
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| Relations |
| BioSample |
SAMN11397385 |
| SRA |
SRX5667840 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3717661_IFIH1KO_P2_15.coutt.csv.gz |
255.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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