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Sample GSM3320477 Query DataSets for GSM3320477
Status Public on Mar 13, 2020
Title control_3.coutt
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics genotype: wild type
Extracted molecule total RNA
Extraction protocol FACS sorting from Bone Marrow
CEL-seq2
single-cell RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing For single cell library preparation the CEL-Seq2 protocol (Hashimshony et al., 2016) was used with a nanoliter pipetting robot (mosquito® HTS, TTP Labtech) and the original volumes were reduced by 5-fold. 384-well plates (Corning, PCR-384-RGD-C) were prepared with 240 nl lysis buffer in every well. Lysis buffer consisted of the following reagents with final ratio in parentheses: 20 nl of 10 mM dNTP (1/12), 40 nl of 1:100000 ERCC mix 1 or 2 (2/12), 140 nl of water with 0.35% Triton® X-100 (7/12) and 40 nl of 25 ng/μl of 1 out of 192 uniquely barcoded polydT primers with UMI (2/12) (Table S4). Following the dispense of 240 nl of lysis buffer, 1.2 μl of hydrophobic encapsulation barrier (Vapor-Lock, Qiagen, 981611) were added to every well.
For transcript quantification we followed Herman et. al. (Herman et. al. 2018) pipeline. Briefly, paired end reads were aligned to the transcriptome by 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 and gene loci were merged to larger gene groups, if loci overlapped by >75%. This procedure resulted in 34,111 gene groups. 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: counts
 
Submission date Aug 06, 2018
Last update date Mar 13, 2020
Contact name Asifa Akhtar
E-mail(s) akhtarlab_data@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Chromatin Regulation
Lab Akhtar Lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL21493
Series (2)
GSE107154 Decoding the regulatory circuit by epigenetic regulator MOF in haematopoiesis
GSE118194 MOF directs erythroid fate during hematopoiesis via RUNX1-GFI1b feedforward control (scRNA-Seq)
Relations
BioSample SAMN09772366
SRA SRX4515268

Supplementary file Size Download File type/resource
GSM3320477_control_3.coutt.csv.gz 230.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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