 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 11, 2023 |
| Title |
GP5d, TFAP2A, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
GP5d
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GP5d
cell type: Colon adenocarcinoma
chip antibody: abcam: ab52222
|
| Growth protocol |
GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GP5d cells were formaldehyde cross-linked and sonicated chromatin was immunoprecipitated by using Dynal-bead coupled antibodies. Immunoprecipitated DNA was purified and used to prepare ChIP-seq library for Illumina sequencing.
Immunoprecipitated DNA was end-repaired, dA tailed and adapter ligated. Adaptor ligated DNA was PCR enriched as described earlier (Sahu et al., Nat. Gen. 2022).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQC v.0.11.9 was used for quality control and determination of read lengths of raw data.
Raw reads were mapped with bowtie2 v.2.4.1 (bowtie2 --very-sensitive) to the reference genome.
Picard v.2.23.4 was used to remove duplicates (MarkDuplicates -REMOVE_DUPLICATES false -ASSUME_SORT_ORDER coordinate).
Samtools v.1.7 was used to filter reads with MAPQ smaller than 20 and remove marked duplicates (samtools view -F 1024 -b -q 20).
Peaks were called with MACS2 v.2.2.7.1 (macs2 callpeak -f BAMPE -g hs --keep-dup all).
Peaks overlapping with ENCODE blacklisted regions were removed from the narrowPeak and summit files with bedtools v.2.29.2 (bedtools subtract -A).
A RPKM normalized bigwig file was created with deepTools v.3.5.0 (bamCoverage --binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2913022398).
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak/narrowPeak (except for the IgG samples)
|
| |
|
| Submission date |
Dec 15, 2022 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Konsta Karttunen |
| Organization name |
University of Helsinki
|
| Street address |
Haartmaninkatu 8
|
| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE221046 |
Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (ChIP-Seq) |
| GSE221053 |
Transposable elements as lineage-specific enhancers in endodermal-lineage cancers |
|
| Relations |
| BioSample |
SAMN32250343 |
| SRA |
SRX18711630 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6841188_GP5D_TFAP2A_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM6841188_TFAP2A_GP5D_final.bw |
169.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
