|
| Status |
Public on Oct 26, 2023 |
| Title |
anti-FLAG, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Human small intestinal organoids
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human small intestinal organoids
chip antibody: anti-FLAG (Thermo)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Organoids were briefly dissociated with TrypLE (Thermo Fisher), fixed with formaldehyde (final concentration: 1%) and quenched by Glycine (final concentration: 0.125M). Chromatin was extracted by two-step lysis protocol in the presence of protease inhibitors: leupeptin hemisulfate, pepstatin A and phenylmethylsulfonyl fluoride. Chromatin was further sheared by sonication using Bioruptor Pico (Diagenode) with 7 cycles of 30s “ON” and 30s “OFF”.
Sequencing libraries for ChIP-seq were constructed by using NEBNext Ultra II DNA Library Prep kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Read mapping to the human genome (hg38) was done with Bowtie2 (2.4.1) using parameters: -q -N 0 -L 22 -X 500 --no-unal.
Unmapped reads, low mapping quality reads (Q<30) were discarded.
Peak calling was performed by using MACS2’s callpeak function (2.2.6) with a cutoff of q<0.01
Assembly: hg38
Supplementary files format and content: bigWig (except for Input sample)
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Jeff DeMartino |
| Organization name |
Princess Maxima Center
|
| Street address |
Heidelberglaan 25
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CS |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE229583 |
Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation [CHIP-seq] |
| GSE229586 |
Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation. |
|
| Relations |
| SRA |
SRX19950646 |
| BioSample |
SAMN34164173 |
