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Sample GSM6384040

Query DataSets for GSM6384040

Status

Public on Jul 26, 2022

Title

40280_input_R1_May2021 (Control for ChIP)

Sample type

SRA

Source name

PT Rep 2 (40280 line)

Organism

Pan troglodytes

Characteristics

cell type: Hippocampal_Intermediate_Progenitors_Day5
antibodies: N/A

Extracted molecule

genomic DNA

Extraction protocol

Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NovaSeq6000, producing 100x100 PE reads or the NextSeq500 producing 80x80 PE reads

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NovaSeq 6000

Data processing

ChIP-seq and ATAC-seq data were aligned to hg19 or panTro5 as appropriate using BWA-mem
RNA-seq data were analyzed with kallisto using hg19 or panTro5 as appropriate
scRNAseq data were mapped with cellranger using hg19 or panTro5 as appropriate, then analyzed in the R Package Seurat
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Assembly: hg19 for Homo sapiens samples and panTro5 for Pan troglodytes samples.
Supplementary files format and content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq, matrix + features + barcode files for scRNAseq

Submission date

Jul 25, 2022

Last update date

Aug 05, 2022

Contact name

Marco Trizzino

E-mail(s)

m.trizzino@imperial.ac.uk

Phone

07521215018

Organization name

Imperial College London