 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 20, 2016 |
| Title |
TBP_EB8KO |
| Sample type |
SRA |
| |
|
| Source name |
TAF4-/- EB8
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryoid bodies (EB)
genotype/variation: TAF4-/-
chip antibody: TBP (ab28175, Abcam)
|
| Treatment protocol |
Cells were differentiated by RA into neurons as described (Bibel et al 2007).
|
| Growth protocol |
ES cells were cultured on inactivated MEF feeders under standard conditions (DMEM 4.5g/l glucose/Glutamax supplemented with 15% heat inactivated FCS, LIF, nonessential amino acids and β-mercaptoethanol).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 8pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software was used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Igor Martianov |
| E-mail(s) |
martiano@igbmc.fr
|
| Phone |
0033388653440
|
| Organization name |
IGBMC
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch |
| ZIP/Postal code |
67400 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE70661 |
Taf4 is required for preinitiation complex formation at genes associated with neuronal differentiation |
|
| Relations |
| BioSample |
SAMN03852554 |
| SRA |
SRX1089851 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1816107_TBP-EB8KO.wig.gz |
153.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
