|
| Status |
Public on Oct 20, 2013 |
| Title |
Gro-Seq IMR90+TNF-α |
| Sample type |
SRA |
| |
|
| Source name |
fetal lung fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: TNF-α (10ng/mL) 1hr
experiment: GRO-seq
antibody: no
restriction enzyme: no
|
| Treatment protocol |
Untreated or IMR90 cells treated with TNF-α (R&D Systems, 10 ng/mL, 1 hr) or flavopiridol (Sigma, 1 μM for 1 hr for ChIP-seq experiments, and 1 μM for 2 hr for Hi-C experiments) were used.
|
| Growth protocol |
IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).). ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
groseq.IMR90_TNF.fwd.wig is for forward strand reads; and groseq.IMR90_TNF.rev.wig.gz is for reverse strand reads
|
| Data processing |
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
Genome_build: NCBI36
Supplementary_files_format_and_content: Mapped non-redundant reads for GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.
|
| |
|
| Submission date |
Dec 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Fulai Jin |
| E-mail(s) |
fxj45@case.edu
|
| Phone |
2163681811
|
| Organization name |
Case Western Reserve University
|
| Lab |
Fulai Jin
|
| Street address |
10900 Euclid Avenue
|
| City |
Cleveland |
| State/province |
OH - OHIO |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE43070 |
Genome-wide Analysis of Chromatin Interactions in Human Cells |
|
| Relations |
| SRA |
SRX212179 |
| BioSample |
SAMN01832317 |
