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Sample GSM2104308 Query DataSets for GSM2104308
Status Public on Jul 13, 2016
Title AB440 (Sample 13)
Sample type SRA
 
Source name brain_E18
Organism Mus musculus
Characteristics strain: CX3CR1-GFP+ C57BL/6J
tissue: brain
selection marker: CD45intCD11BintCX3CR1-GFP+
developmental stage: embryonic day 18.5
Treatment protocol no treatment
Growth protocol Mice housed at the Weizmann Institute animal facility
Extracted molecule polyA RNA
Extraction protocol Each mouse was euthanized and brain or Yolk sac was extracted for proccessing
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
 
Description Raw data files were processed as single-end files since the read2 (mate) files contained only cell and molecule barcodes. This information is appended to the fastq entry header.
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: umitab.txt.gz is a single cell expression matrix reporting include mRNA molecule count values for each Sample. In experimental_design.txt, please each row represents a single cell. experimental_design.txt associates each single cell with its amplification batch and index sorting readouts. experimental_design.txt shows the correspondence of each single cell (WXXXX) in umitab.txt with its sample (ABXXXX).
 
Submission date Apr 01, 2016
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)
GSE79818 Microglia development follows a stepwise program to regulate brain homeostasis - Single Cell RNA-seq
GSE79819 Microglia development follows a stepwise program to regulate brain homeostasis
Relations
BioSample SAMN04599696
SRA SRX1672765

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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