 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 06, 2019 |
| Title |
MEF-H3K27ac rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Reprogrammable mouse embryonic fibroblasts (MEFs) prepared from rtTA3-OKSM embryos (embryonic day-E13.5) that were heterozygous for the Oct4-GFP reporter, OKSM cassette and rtTA3.
culture condition: collected at passage 3
antibody: H3K27Ac
|
| Growth protocol |
MEF were grown in low oxygen incubator with DMEM media, V6.5 were grown in KO-DMEM media and 2i conditions (for HiChIP and ChIP-seq), MEF at different times of reprogramming were grown in the presence of dox and ascorbic acid
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were collected with trypsin and fixed with 1% formaldehyde
Libraries were constructed according to the HiChIP protocol and sequenced on Illumina HiSeq2500.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MEF-H3K27ac_high-confidence_interactions.tsv
HiChIP
|
| Data processing |
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the mm10 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<10 kb)
Matrix generation: HicBench. For each replicate and each chromosome, a matrix with binned interactions (bin-size 10kb) was generated.
Normalization: custom script. Each loop with > 1 read across all replicates of the same condition was kept. We applied normalization by sequencing depth per replicate to raw read-counts (both Hi-C and HiChIP; leading to counts-per-million; CPM). Hi-C data only was additionally distance-normalized as recently described (Gong et al., 2018)
High-confidence interactions: custom script. We have applied an approach similar to mango, which employs a binomial test per diagnoal in the normalized counts-matrix. To define significant HiChIP loops, we have filtered all interactions for CPM>3 in all available replicates and p<0.1. For significant Hi-C loops, we have filtered more stringently using CPM>15 in all replicates and p<0.01.
Topologically associated domains (TADs): We called TADs from normalized corrected Hi-C matrices in PSCs processed at 10kb resolution using a recently published software (Ramirez et al., Nat Comm, 2018) with the use of the following parameters: --minDepth 120000 --maxDepth 420000 --thresholdComparison 0.001 --delta 0.01 --correctForMultipleTesting fdr
genome build: mm10
processed data files format and content: custom tsv: left anchor coordinates; right anchor coordiantes; raw read-counts per replicate; normalized read-counts (CPM) for all replicates; distance-normalized read-counts as described before (Gong et al., 2018).
|
| |
|
| Submission date |
Apr 18, 2018 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Effie Apostolou |
| E-mail(s) |
efa2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1161 York Avenue, Apt 8A
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE113339 |
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [HiChIP and HiC] |
| GSE113431 |
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency |
|
| Relations |
| BioSample |
SAMN08949614 |
| SRA |
SRX3962648 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
