|
Status |
Public on Sep 16, 2016 |
Title |
mRNA-seq_hESC |
Sample type |
SRA |
|
|
Source name |
H9 hESC
|
Organism |
Homo sapiens |
Characteristics |
cell line: H9 chip antibody: N/A passage: 58-60 treatment: none
|
Growth protocol |
H9 ESCs were obtained from WiCell as per agreement 15-W0341. H9 ESCs were cultured on matrigel coated plates (corning #354277) in mTeSR 1 media (stemcell technologies # 05857), washed with DMEM/F12 (GE healthcare # SH3002302) and passaged with accutase (MP Biomedicals # 091000449) and ROCK Inhibitor Y-27632 (BD # 562822).
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA-seq: Trizol followed by 2 rounds of poly A selection. Libraries were prepared by Illumina's Tru-seq Library Preparation Kit v2. Paired-end sequencing was carried out on Hi-Seq_v4 (PE50 runs).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
mRNA hg19
|
Data processing |
Illumina CASAVA version 1.8.2 software was used to create the fastq files from the bcl files for ChIP-seq. bcl2fastq version 1.8.4 was used for RNA-seq. ChIP fastq files were filtered using the fastx filter tool to have 80% of the reads with a Qual score of >= 20. The remaining reads were collapsed using the collapser tool to eliminate all PCR duplicates. The resulting FASTA file was aligned to a custom hg18 annotation that includes the rDNA consensus repeat as an added chromosome called 'chr24_rDNA' using Bowtie2 under default conditions. The aligned SAM files were converted to BAM using samtools then to BED format using BEDTools. RNA-seq datsets were aligned to hg19 using Tophat2 using default conditions. Differential gene expression for mRNA-seq datasets was determined by running DEseq2 in R Statistical Environment. Processed tag counts across genes tested are in processed data file 'mRNA-seq_GeneCounts_AllSamples.xlsx'. Genome_build: mRNA-seq = hg19, ChIP-seq = hg18plusrDNA custom build Supplementary_files_format_and_content: bed + counts
|
|
|
Submission date |
Jan 06, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Jessica L Woolnough |
E-mail(s) |
jlmakofske@gmail.com
|
Organization name |
Brigham and Women's Hospital
|
Department |
Genetics
|
Street address |
77 Avenue Louis Pasteur
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE76586 |
The control of rRNA synthesis during the directed differentiation of human embryonic stem cells precedes heterochromatin formation. |
|
Relations |
BioSample |
SAMN04386702 |
SRA |
SRX1519708 |