 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 17, 2013 |
| Title |
Bcells_untreated_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
primary Bcells untreated
|
| Organism |
Mus musculus |
| Characteristics |
cell type: primary B cells
treatment: untreated
|
| Treatment protocol |
Cells were trypsinized and FACS-sorted to remove feeder and dead cells
|
| Growth protocol |
ESCs and iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen). MEF cultures were established by trypsin digestion of mouse embryos (embryonic day 13.5) and the resulting cells cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. CD19+ pro-B and pre-B cells were isolated from bone marrow using monoclonal antibodies to CD19 (1D3), obtained from BD Pharmingen, using MACS (Miltenyi Biotech). After isolation B cells were grown in RPMI medium supplemented with 10% FBS and IL-7. cell reprogramming experiments were conducted in gelatinized plates seeded with a feeder layer of the OP9 stromal cell line, using ESC medium supplemented with 2μg/ml of doxycycline and 15% FBS. For the reprogramming of B cells, IL-4 (10ng/ml), IL-7 (10ng/ml) and IL-15 (2ng/ml) were added to the medium.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA isolation was done with the miRNeasy Mini kit
Libraries was prepared with the Truseq stranded mRNA protocol, with an insert size of 200 to 400bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
Basecalls: performed with Illumina's CASAVA-1.8.2 software
Reads alignement: performed with STAR v2.3.0.1 (option: outFilterMismatchNmax 2, outFilterMultimapNmax 1)
Reads counting: performed with Htseq count (option: mode union, stranded, features exons, attribute gene_id) on Refseq mm9 annotation
Filtering: genes for which no reads were counted in both conditions were removed before normalisation
Normalization: performed with Deseq (option: method blind, sharingMode fit-only, fitType local)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated file. Col1=gene Name; Col2=normalized reads count
|
| |
|
| Submission date |
Nov 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruno Di Stefano |
| E-mail(s) |
distefanob@gmail.com
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Cellular Biology
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE52396 |
C/EBPα poises B cells for rapid reprogramming into iPS cells [RNA-Seq] |
| GSE52397 |
C/EBPα poises B cells for rapid reprogramming into iPS cells |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02402775 |
| SRA |
SRX377717 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1264669_RNAseq_Bcells_UT_Normalized.tsv.gz |
159.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
