|
Status |
Public on Jul 13, 2016 |
Title |
AB398 (Sample 4) |
Sample type |
SRA |
|
|
Source name |
brain_E12.5
|
Organism |
Mus musculus |
Characteristics |
strain: CX3CR1-GFP+ C57BL/6J tissue: brain selection marker: CD45+CD11B+CX3CR1-GFP+ developmental stage: embryonic day 12.5
|
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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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|
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).
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|
|
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 |
SAMN04599703 |
SRA |
SRX1672756 |