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| Status |
Public on Sep 06, 2019 |
| Title |
ES-HiC-Arima rep1 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell tye: V6.5
culture condition: cultured in 2i condition
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| Treatment protocol |
dox was added for reprogramming samples and TKO samples for the amount of time indicated
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| Growth protocol |
MEF were grown in low oxygen incubator with DMEM media, V6.5 were grown in KO-DMEM media in 2i conditions (TKO samples-with or without dox for 24 hrs) , MEF at different times of reprogramming were grown in the presence of dox and ascorbic acid
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were collected with trypsin and fixed with 1% formaldehyde
Hi-C libraries were prepared using the KAPA Hyper prep kit following Arima's manufacturer's instructions.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ES-HiC-Arima_TADs.bed
Hi-C
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| 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).
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| Submission date |
Apr 09, 2019 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Effie Apostolou |
| E-mail(s) |
efa2001@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Street address |
1161 York Avenue, Apt 8A
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN11388153 |
| SRA |
SRX5661651 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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