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Sample GSM1944941 Query DataSets for GSM1944941
Status Public on Nov 25, 2015
Title AB393 [Sample 51]
Sample type SRA
 
Source name Cebpa control
Organism Mus musculus
Characteristics strain: C57BL/6 Cebpa(flox/flox)Mx1-Cre
organ: bone marrow
selection marker: Lin- cKit+ Sca1-
treatment: poly(I:C)
Treatment protocol For samples 21-22, 25-26, 31-32, mice were injected three times with 300 µg poly(I:C) three weeks before bone marrow harvest
Growth protocol 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility (Samples 21-32 were 14 weeks old and housed at Biotech Research and Innovation Centre, Copenhagen)
Extracted molecule polyA RNA
Extraction protocol Each mouse was euthanized and bone marrow harvested by crushing of the femur, tibia and ilia. Cell suspensions were cKit enriched with MACS magnetic beads.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: single cell expression matrix include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: experimental_design.txt' associating each single cell with its amplification batch and index sorting readouts
 
Submission date Nov 19, 2015
Last update date May 15, 2019
Contact name Ido Amit
E-mail(s) ido.amit@weizmann.ac.il
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
 
Platform ID GPL19057
Series (2)
GSE72857 Transcriptional heterogeneity and lineage commitment in myeloid progenitors [single cell RNA-seq]
GSE72859 Transcriptional heterogeneity and lineage commitment in myeloid progenitors
Relations
BioSample SAMN04279279
SRA SRX1438868

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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