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| Status |
Public on Jun 23, 2020 |
| Title |
Hi-C_SCC1_diff_auxin_rep2 |
| Sample type |
SRA |
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| Source name |
SCC1-AID-mESC cell line
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| Organism |
Mus musculus |
| Characteristics |
cell type: SCC1_differentiation_auxin1D
genotype: SCC1 KO
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| Treatment protocol |
SCC1-AID-mESC cell line was generously provided by Dr. Robert Klose. mESCs were cultured in DMEM supplemented with 10 % Fetal Bovine Serum (FBS), MEM Non-Essential Amino Acids Solution (Gibco, Cat#. 111040050), GlutaMAX™ Supplement (Gibco, Cat # 35050061), 2-mercaptoethanol (Specialty media, Cat # ES-007-E), EmbryoMax 100X nucleosides (Millipore, Cat # ES-008-D), LIf (1000 U/ml, Millipore, Cat # ESG1107. For differentiation, ESCs were cultured in medium without LIF for 3 days. and treated without/with auxin (500 μM)(Nora et al., 2017) (Sigma, Cat # 6505-45-9) for 1 day. SCC1-AID differentiated cells were dissociated into single cells. Sorting was then conducted using FACS Jazz (BD Biosciences). Cells depleted of GFP fluorescence signals in auxin treatment group were collected as SCC1 KO groups, while the differentiated cells retaining relatively high GFP fluorescence signals without the auxin treatment were collected as SCC1 positive groups.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
EB_SCC1_auxin_rep12_allValidPairs.txt.gz
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| Data processing |
Basecalls performed using CASAVA version 1.8
For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size and 300Kb bin size wereused and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The gene rpkm txt file contains FPKM value for all samples. While the validpair txt file indicates the paired interaction reads for each sample.
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| Submission date |
Nov 06, 2019 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Ke Zhang |
| E-mail(s) |
zhangke16@mails.tsinghua.edu.cn
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| Organization name |
Tsinghua university
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| Department |
School of Life Sciences
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| Lab |
Wei Xie
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| Street address |
Haidian District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE139430 |
Analysis of genome architecture during SCNT reveals a role of cohesin in impeding minor ZGA |
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| Relations |
| BioSample |
SAMN13226775 |
| SRA |
SRX7107323 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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