|
| Status |
Public on Sep 16, 2016 |
| Title |
ChIP-seq_IgG_hESC |
| Sample type |
SRA |
| |
|
| Source name |
H9 hESC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
chip antibody: Mouse IgG (Millipore #12-371)
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 |
genomic DNA |
| Extraction protocol |
Formaldehyde cross-linked nuclei were sonicated and IgG was purified using indicated antibody and protein A beads. Immunopurified DNA was reverse-cross-linked, phenol:chloroform extracted and ethanol precipitated.
Library was constructed using Illuina Tru-seq branched adapters and subjected to 25 PCR cycles
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP'd DNA
hg18plusrDNA custom
|
| 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 |
GPL11154 |
| Series (1) |
| GSE76586 |
The control of rRNA synthesis during the directed differentiation of human embryonic stem cells precedes heterochromatin formation. |
|
| Relations |
| BioSample |
SAMN04386700 |
| SRA |
SRX1519706 |
