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Sample GSM8187160 Query DataSets for GSM8187160
Status Public on Apr 30, 2024
Title in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXUDU96VW
Sample type SRA
 
Source name stem cell
Organism Homo sapiens
Characteristics tissue: stem cell
cell line: H1-hESC
cell type: stem cell derived cell line
genotype: pancreatic precursor cells - H1
treatment: Early pancreatic differentiation
Growth protocol All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM). DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PFG stage. description: Huang Lab hESC to PP differentiation protocol download:https://data.4dnucleome.org/protocols/017e237c-116e-49f0-8bae-8fd4c3deeaf2/@@download/attachment/Huang_lab_PP_diff_protocol.pdf
Extracted molecule genomic DNA
Extraction protocol description: Arima Hi-C Protocol v01 download: https://data.4dnucleome.org/protocols/1686012d-09fd-44e5-b01b-14789205a091/@@download/attachment/Arima_HiC_Kit_V01.pdf
KAPA HyperPrep kit (KAPA, KK8502)
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description lab: Danwei Huangfu, MSKCC award: 1U01DK128852-01 4DN accession: 4DNEXUDU96VW description: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXUDU96VW replicate_information: Biological replicate 2 ,Technical replicate 1 digestion_enzyme: Arima - A1, A2 digestion_time: 30.0 digestion_temperature: 37.0 crosslinking_method: 1% Formaldehyde crosslinking_time: 10.0 crosslinking_temperature: 23.0 ligation_time: 15.0 ligation_temperature: 23.0 ligation_volume: 0.082 biotin_removed: No biosample_quantity: 2000000.0 biosample_quantity_units: cells fragment_size_selection_method: SPRI beads fragment_size_range: 200-600 fragmentation_method: sonication donor sex: male donor life_stage: embryonic donor 4DN accession: 4DNIN3RG3ZKE description: Huang Lab hESC to PP differentiation download:https://data.4dnucleome.org/protocols/017e237c-116e-49f0-8bae-8fd4c3deeaf2@@download/attachment/Huang_lab_PP_diff_protocol.pdf
Data processing Hi-C Post-alignment Processing 0.2.6: https://data.4dnucleome.org/workflows/4DNWFT69RBY4/ This is a subworkflow of the Hi-C data processing pipeline. It takes a bam file as input and performs parsing, sorting, filtering and deduping. It produces two output files, a lossless, filter-annotated bam file and a filtered pairs (contact list) file. Detailed Steps are as follows: 1. Parsing and sorting bam file using pairsamtools software 2. Merging pairsam files using pairsamtools software 3. Marking duplicates to pairsam file using pairsamtools software 4. Filtering duplicate and invalid reads using pairsamtools software
Assembly: GRCh38
Supplementary files format and content: File type: contact list-replicate (pairs). Description: Pairs files are generated during analysis of genomic contact data and consist of a list of pairs of genomic loci, represented by chromosomal position.
Supplementary files format and content: PFG-stage .bed file containing called TADs
 
Submission date Apr 03, 2024
Last update date Apr 30, 2024
Contact name 4DN DCIC
E-mail(s) support@4dnucleome.org
Organization name 4D Nucleome - Data Coordination and Integration Center
Street address 10 Shattuck St
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL20301
Series (2)
GSE263174 CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant [Hi-C]
GSE267330 CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant
Relations
BioSample SAMN40744171
SRA SRX24151024

Supplementary file Size Download File type/resource
GSM8187160_4DNFINK7ALPW.pairs.gz 5.8 Gb (ftp)(http) PAIRS
SRA Run SelectorHelp
Raw data are available in SRA

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