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Sample GSM3840054

Query DataSets for GSM3840054

Status

Public on Aug 09, 2019

Title

CTCL992.POST.H3AC.CD4P_CD7N

Sample type

SRA

Source name

Peripheral blood

Organism

Homo sapiens

Characteristics

cell markers: CD4+, CD7-
disease: Mycosis fungoides
hdaci group: Sensitive
treatment: N/A
chip antibody: H3ac (EMD Millipore, 06-599)

Treatment protocol

N/A

Growth protocol

N/A

Extracted molecule

genomic DNA

Extraction protocol

0.05-0.5x106 cells were snap-frozen on dry ice for 15 minutes after 3 washes with PBS. Chromatin was prepared and ultra-low-input ChIP performed according to Brind'Amour et al., 2015 (Nature Communications).
ChIP DNA was end-repaired, A-tailed, and ligated to Illumina PE adapters. Ligated fragments were PCR amplified using Illumina indexed primers for 12 cycles. DNA was purified using Ampure XP DNA purification beads between each step. Full methodology is available in Brind'Amour et al., 2015 (Nature Communications).

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 3000

Data processing

Base-calling was performed with bcl2fastq (v2.2.0). Adaptors were trimmed and RNA-seq reads were aligned to hg19 using UCSC knownGene annotations with STAR using default settings (v2.5.3a).
Read quantification was performed with Salmon (v0.11.0) with the parameters –fldMean 50 –fldSD 1 –seqBias and UCSC knownGene annotations.
Genes with fewer than 100 total counts were removed, and normalized abundance measurements were determined with DESeq2 (v1.20.0).
ChIP-seq reads were aligned to hg19 with bowtie2 (v2.2.5). Reads in ENCODE blacklist regions were removed with samtools (v1.3).
Peaks were called with MACS2 (v2.1.0.20150420) using parameters –q 0.01 –m 10 50 --nomodel --shiftsize=150 and input controls.
The consensus peak set, normalized peak signal, and differential peak binding were determined with diffBind (v2.8.0). chipSeeker (v1.16.1) was used to annotate peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized gene-level abundance counts derived from DESeq2 are provided for each in RNAseq.NormalizedAbundance.txt. Normalized signal across consensus peak sets derived from DiffBind for both H3K9/14ac and H3K27ac are available in Resistant-v-Sensitive.H3AC.ConsensusPeaks.txt, Resistant-v-Sensitive.H3K27AC.ConsensusPeaks.txt, Romidepsin-v-Untreated.H3AC.ConsensusPeaks.txt, and Romidepsin-v-Untreated.H3K27AC.ConsensusPeaks.txt. Each row is a feature (gene or peak) and each column contains the normalized values for a given sample.

Submission date

May 31, 2019

Last update date

Aug 09, 2019

Contact name

Jared Andrews

E-mail(s)

jared.andrews@stjude.org

Organization name

St. Jude Children's Research Hospital

Department

Developmental Neurobiology