|
| Status |
Public on Jul 13, 2016 |
| Title |
AB436 (Sample 9) |
| 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 |
SAMN04599707 |
| SRA |
SRX1672761 |
