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| Status |
Public on Mar 13, 2020 |
| Title |
het_HSC2 |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Haematopoetic progenitor cells
genotype: Mof -/+
illumina index: TGACCA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow progenitor cells were srted, flash frozen on liquid nitrogen, and RNA was harvested using Cel-Seq2 protocol. Cel-Seq2 was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Cel-seq2 protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Paired end reads were aligned to the transcriptome by bwa (version 0.6.2-r126)
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)
The right mate of each read pair was mapped to the ensemble of all gene groups and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left mate contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch and adjacent gene sequence. The left read was not used for quantification. For each cell barcode and gene locus, the number of UMIs was aggregated and, based on binomial statistics, converted into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include transcript count values for each Sample
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| Submission date |
Nov 20, 2017 |
| Last update date |
Mar 13, 2020 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
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| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Department |
Chromatin Regulation
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| Lab |
Akhtar Lab
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| Street address |
Stuebeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE107153 |
Single-cell RNA from Haematopoetic progenitor cells |
| GSE107154 |
Decoding the regulatory circuit by epigenetic regulator MOF in haematopoiesis |
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| Relations |
| BioSample |
SAMN08045436 |
| SRA |
SRX3409020 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2861748_het_HSC2.coutt.txt.gz |
267.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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