|
| Status |
Public on Nov 25, 2015 |
| Title |
AB395 [Sample 53] |
| Sample type |
SRA |
| |
|
| Source name |
Cebpa control
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 Cebpa(flox/flox)
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 |
SAMN04279281 |
| SRA |
SRX1438870 |
