|
| Status |
Public on Aug 09, 2019 |
| Title |
Vol2.CD4P.Romi.RNA |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell markers: CD4+
disease: N/A
hdaci group: N/A
treatment: 2.5 nM romidepsin
chip antibody: N/A
|
| Treatment protocol |
Cells were immediately placed into culture after collection and sorting. Cells were treated with 2.5 nM romidepsin for 4 hours before transfer to fresh media. Cells were collected for RNA isolation and sequencing after 24 hours in culture.
|
| Growth protocol |
Cells were cultured in IMDM supplemented with 20% FBS and 1% penicillin/streptomycin in a 37°C incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 0.5-2x106 cells stored in TRIzol reagent following manufacturer's instruction.
cDNA from total RNA was synthesized with a Clontech SMARTer low input RNA kit. An Illumina TruSeq preparation kit was used for library constructon per manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE132053 |
Epigenetic Pathways of HDAC Inhibitor Resistance in Cutaneous T Cell Lymphoma |
|
| Relations |
| BioSample |
SAMN11917886 |
| SRA |
SRX5944532 |
