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Sample GSM2861752 Query DataSets for GSM2861752
Status Public on Mar 13, 2020
Title Lib_16_plate2_mof
Sample type SRA
 
Source name Bone Marrow
Organism Mus musculus
Characteristics tissue: Haematopoetic progenitor cells
genotype: Mof -/+
illumina index: ACTTGA
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Nov 20, 2017
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 GPL17021
Series (2)
GSE107153 Single-cell RNA from Haematopoetic progenitor cells
GSE107154 Decoding the regulatory circuit by epigenetic regulator MOF in haematopoiesis
Relations
BioSample SAMN08045432
SRA SRX3409024

Supplementary file Size Download File type/resource
GSM2861752_Lib16_plate2_mof.coutt.txt.gz 426.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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