|
| Status |
Public on Nov 02, 2015 |
| Title |
DMSO5_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Erythroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: vehicle control
cell type: Erythroblasts
|
| Treatment protocol |
RNA-Seq analysis was performed in primary adult human erythroid cells at day 11 of erythroid differentiation and after 7 days of treatment with 0.25 μM UNC0638 or the vehicle control
|
| Growth protocol |
Primary human CD34+ hematopoietic stem and progenitor cells were differentiated in vitro towards the erythroid lineage using a 3-phase culture method, as described by Giarranata MC et al., Blood 2011
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the PrepEase RNA Spin Kit (USB Corporation) according to the manufacturer’s protocol.
The cDNA library was prepared from 50-100 ng of total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Biological replicate 2
|
| Data processing |
RNA-seq reads were mapped against human genome build hg19, downloaded from the UCSC genome browser, using TopHat version 2.0.13. Coding transcripts from GENCODE Release 12 (http://www.gencodegenes.org/) were provided in GTF format using the following options: “tophat -p 8 -G gencode.v12.annotation.gtf --no-novel-juncs Homo_sapiens_assembly19.”
Unambiguously mapped reads were counted at a gene-level using the HTSeq package version 0.6.1p1 in union mode with the following options: “htseq-count -s no -a 10 <alignment_file> gencode.v12.annotation.gtf.”
Filtering was applied to remove genes in which greater than half the samples had less than one count per million using the cpm() function in edgeR.
Counts were normalized using TMM normalization in edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: TMM normalized counts with samples as columns and gene-level features as rows.
|
| |
|
| Submission date |
Jul 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
John Krill-Burger |
| E-mail(s) |
jkrillbu@gmail.com
|
| Organization name |
Broad Institute
|
| Department |
Cancer Program
|
| Lab |
Golub
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE71421 |
EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression [RNA-seq] |
| GSE71422 |
EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression |
|
| Relations |
| BioSample |
SAMN03940479 |
| SRA |
SRX1122170 |
