|
| Status |
Public on Feb 09, 2013 |
| Title |
KO_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hemangioblast equivalent cells
|
| Organism |
Mus musculus |
| Characteristics |
cell-type: Ldb1-/- from Flk1+ cells
genotype: Ldb1-/-
|
| Growth protocol |
Ldb1+/+ and Ldb1-/- ES cells were grown in suspension at 10.000 cells/ml on nonadherent dishes in IMDM medium (without Leukemia Inhibitory Factor (LIF)) with 15% FCS, 1% P/S, 1% L-glutamine (Gibco, Cat.25030-08), 0.05μg/ml transferrin (Roche, Cat.652-202), 0.05μg/ml ascorbic acid (Sigma, Cat.A-4544), 3μl/ml monothioglycerol (Sigma, Cat.M-6145) for day 4 EBs and 1.8μl/ml for day 6 and day 8 EBs. 5% protein free hybridoma medium II (Gibco, Cat.12040-077) was added for day 6 and day 8 EBs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq library was prepared according to the Illumina protocol (www.illumina.com).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
36 bp raw reads were mapped against NCBI build 37.1 of the mouse genome with ELAND (Illumina).
Uniquely mapped reads were extended to 200 bp and then transformed into the genome-wide reads density (coverage) with the ShortRead Bioconductor package. The coverage from ChIP and IgG control was visualized on a mirror of the UCSC genome browser.
MACS, CCAT, and in-house developed software (unpublished) were used to detect Ldb1 binding peaks.
Identified binding peaks from all software were combined to get the consensus regions. Negative binomial distribution was performed to assign p-value to each consensus region.
Raw reads were mapped with Bowtie10 to mouse NCBI m37 Ensembl transcripts. Count number of reads for each transcript and reads per kb of a transcript per million mapped reads (RPKMs) were calculated and assigned to each transcript.
The longest transcript was chosen as a representative gene for downstream analysis and the highest expression level from alternative transcripts was assigned to the representative gene.
Read counts per representative genes were subjected to DESeq Bioconductor package11 for statistical testing of differentially expressed genes and p-values were adjusted with Benjamini and Hochberg (BH).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited identified number of read counts per Ensembl transcript for each sample (count table generated for DESeq pipeline)
|
| |
|
| Submission date |
Dec 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Supat Thongjuea |
| E-mail(s) |
supat.thongjuea@ndcls.ox.ac.uk
|
| Organization name |
The Weatherall Institute of Molecular Medicine
|
| Department |
MRC Molecular Haematology Unit
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE43041 |
The role of Ldb1 in hemangioblast development: genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis (sequencing) |
| GSE43044 |
The role of Ldb1 in hemangioblast development: genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis |
|
| Relations |
| SRA |
SRX212088 |
| BioSample |
SAMN01832244 |
