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Sample GSM7697951

Query DataSets for GSM7697951

Status

Public on Aug 09, 2023

Title

ATAC-seq ES replicate 1

Sample type

SRA

Source name

embryo

Organism

Homo sapiens

Characteristics

tissue: embryo
cell line: WA09
cell type: embryonic stem cell
genotype: ES wild type
treatment: none

Treatment protocol

Cells were defferentiated into Definitive Endoderm by treatment with 10 µM Y27632 on day 0, and their media was replaced on day 1 with DE induction Media A (Gibco Cat# A3062601), and on day 2 with DE induction Media B (Gibco Cat# A3062601). On day 3, cells were harvested for ChAR-seq.

Growth protocol

Human H9 ES cells were grown on matrigel in mTeSR1 medium in 5%C02 at 37°C

Extracted molecule

other

Extraction protocol

Cell extraction is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.
Library preparation is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.

Library strategy

ATAC-seq

Library source

other

Library selection

other

Instrument model

Illumina HiSeq 4000

Description

ES-ATAC.bw

Data processing

Demultiplexed fastq files from the ChAR-seq data were processed using a custom Snakemake pipeline (https://github.com/straightlab/charseq-pipelines), outputting pairs files containing the RNA and DNA coordinates of each RNA(cDNA)-DNA chimeric read and relevant annotations for each RNA-DNA contact.
RNA-seq data was processed using a Snakemake pipeline mirroring the ChAR-seq pipeline, but all of the operations related to the DNA-side of the reads were skipped. In brief, demultiplexed fastq files were deduplicated, sequencing adapters were removed, paired mates were merged as described for ChAR-seq reads. Reads that aligned to a rRNA sequence by Bowtie2 were filtered out using Picard. Reads were aligned to hg38 using STAR and were annotated with tagtools using the Gencode V29 gene models. Reads with low mapping scores (STAR Q < 255), reads which could not be attributed to a single known gene or a single locus, and reads that overlapped with a locus on the ENCODE black were discarded.
For ATAC-seq data Illumina Nextera Adapters were removed using a custom Python script. Reads were aligned to the hg38 using Bowtie2. Duplicates were removed with Picard. Mitochondrial reads or reads with Bowtie2 MAPQ score < 30 were removed using SAMtools. All replicates were similar, so their alignment files were merged to increase library complexity (>100 million mapped reads per cell type) and produce a single bigwig file per cell type used to display the ATAC-seq tracks, and a single bam file to determine ATAC-seq peaks. ATAC-seq peaks were identified in each cell line using HMMRATAC v1.2.10.
Assembly: hg38
Supplementary files format and content: bed

Submission date

Aug 09, 2023

Last update date

Aug 13, 2023

Contact name

Aaron F Straight

E-mail(s)

astraigh@stanford.edu

Organization name

Stanford University

Department

Biochemistry