|
| Status |
Public on Jan 01, 2014 |
| Title |
Runx1_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
DP thymocytes, Runx1 ChIP
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: thymus
cell type: CD4+ CD8+ double-positive thymocytes
chip antibody: anti-Runx1
|
| Growth protocol |
DP cells are directly sorted from mice thymus with Automacs (Miltenyi).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following standard ChIP-seq protocols. Chromatin from 1 x 10^7 cells was used for the ChIP-seq experiment. Antibodies against Runx1 (Abcam, ab23980, lot #GR66230-1) were used at 10µg/1x10^7 cells. After reverse cross-linking and purification with the Qiagen PCR purification kit.
The ChIP-seq libraries have been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066), using 15 PCR cycles. The quality of the libraries has been checked with the Bioanalyser DNA High sensitivity and by Q-PCR. The sequencing was performed with the AB SOLiD 4 System and SOLiD 5500xl sequencer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. For SOLiD 5500xl, basecalls were performed using 5500 Series Genetic Analyzers Instrument Control Software v1.2.
ChIP-seq reads were aligned to the Mus musculus genome (assembly NCBI 37/mm9) with BFast 0.7.0, and only reads with a unique best scoring alignment are retained.
Clonal artifacts were filtered out retaining the longer reads.
Peak calling was performed by using the Hypergeometric Optimization of Motif EnRichment (HOMER) tool (v4.1) with default settings (FDR: 0.001; local and input fold enrichment: 4.0).
Genome_build: MGSCv37
Supplementary_files_format_and_content: wig files were generated after reads elongation and normalization of the signal for 10 million reads; bed files contain HOMER scores.
|
| |
|
| Submission date |
Mar 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Aurelie Bergon |
| E-mail(s) |
aurelie.bergon@inserm.fr
|
| Phone |
+33(0) 491 828 724
|
| Organization name |
TAGC INSERM U1090
|
| Street address |
parc scientifique de Luminy, case 928
|
| City |
MARSEILLE CEDEX 09 |
| ZIP/Postal code |
13 288 |
| Country |
France |
| |
|
| Platform ID |
GPL15907 |
| Series (2) |
| GSE44578 |
Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals |
| GSE45014 |
Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (ChIP-Seq 2) |
|
| Relations |
| SRA |
SRX247731 |
| BioSample |
SAMN01942203 |
