|
| Status |
Public on Jul 02, 2014 |
| Title |
K562.DMSO.SCML2.PA |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
antibody: SCML2 (in-house) batch# Rb1199-1004
|
| Treatment protocol |
K562 cells were treated for 48 hours either with 160 nM PMA or 100 uM hemin or DMSO alone as a control
|
| Growth protocol |
K562 cells were grown in standard conditions (RPMI 10% FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Method for RNA: TRIzol. After polyA+ RNA isolation, libraries were prepared with the dUTP strand-specific protocol. After RT and second-strand synthesis, cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 ligase (Enzymatics). Fragments of 200±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after removal of the 2nd strand with heat-labile UDG (Roche).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: RIP-Seq
Trimmed (3') sequences to 35 nts
Mapped to hg19 using bowtie -v2 -m40
Duplicates were removed with samtools rmdup
Wig coverage was calculated separately on the minus and plus strand a custom script
Wigs were normalized to 10,000,000 sequenced reads using a custom script
Counts and RPKMs for lincRNAs was calculated using the R package DEGseq and the lincRNA catalog found at http://www.broadinstitute.org/genome_bio/human_lincrnas/
Genome_build: hg19
Supplementary_files_format_and_content: Normalized WIGs and TXT file (for RPKM table). In the wig files, the p and m in the names (e.g. 'p.wig' or 'm.wig') refer to the plus and minus strand respectively.
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE38274 |
RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells |
| GSE38275 |
ChIP-seq and RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells |
|
| Relations |
| SRA |
SRX149717 |
| BioSample |
SAMN00998612 |
