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Sample GSM3754936 Query DataSets for GSM3754936
Status Public on May 31, 2021
Title H3K4me1_E24R1
Sample type SRA
Source name H9 cells
Organism Homo sapiens
Characteristics type: embryonic stem cells
treatment: Mesendoderm 24h
biological replicate: Replicate 1
Treatment protocol H9 cells were synchronized in their cell cycle by incubating them with nocodazole (100 ng/ml) for 16h. Then, nocodazole was withdrawn and cells induced to differentiated into mesendoderm for 24h (In CDM-PVA medium supplemented with Insulin (7ug/ml), Activin A (100 ng/ml), BMP (10 ng/ml), LY294002 (10 mM ), and CHIR99021 (3 mM). To block cells in their S phase during differentiation, we added Hydroxyurea (200 mM) at the start of the differentiation. To block the cells in their G2/M phases during differentiation, we added nocodazole 8h after the induction of the differentiation. In this way, we made sure that the cells were able to re-initiate the cell cycle and get blocked in the following G2/M phase. After 24h of differentiation, cells were collected and processed for ChIP-seq library preparation.
Growth protocol H9 cells were grown in E8 medium containing penicillin (50 units/ml) and streptomycin (100 mg/ml)mycin, on plates coated with Vitronectin-XF (Stem Cells Technologies). Cells were incubated at 37ºC in atmosphere of 5% CO2
Extracted molecule genomic DNA
Extraction protocol Lysates were sonicated and histone-DNA complexes were pull-down with antibody.
Libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina; Ref N: E7645S
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
Description Mesendoder 24h
Data processing Base calling was done using illumina package RTA v2.7.7, and instrument control package called HCS v3.4.0.38.
Adaptors were clipped before alignment and then re-inserted
Alignment files were converted into BAM files.
Genome_build: GRCh38_genecode
Supplementary_files_format_and_content: All bigWig files were generated using the function bamCompare from the Deeptools software for Histone marks vs Input, with a bin size = 10, normalized using RPKM method, and an effective genome size of 2913022398 
Submission date May 07, 2019
Last update date May 31, 2021
Contact name Rodrigo Andres Grandy
Organization name University of Cambridge
Department Surgery
Lab Vallier Lab
Street address Cambridge Stem Cell Institute/ Anne McLaren Laboratory West Forvie Building, Robinson Way
City Cambridge
ZIP/Postal code CB2 0SZ
Country United Kingdom
Platform ID GPL20301
Series (2)
GSE130826 Effect of Cell Division on Cell Differentiation (ChIP-Seq HUvsNoc)
GSE130830 Effect of Cell Division on Cell Differentiation
BioSample SAMN11587021
SRA SRX5802410

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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