|
| Status |
Public on Oct 31, 2019 |
| Title |
WTNoGlucose_PRO-seq_repB |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: mESC cells
treatment: Wild-type Glucose deprivation
sample type: nascent RNA
|
| Treatment protocol |
mESC cells were glucose deprived
PRO-seq: Biological replicates were generated using WT (3 replicates) mESC cells, SIRT6-KO (3 biological replicates) and Glucose deprivation (2 replicates).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nascent biotin-labeled RNA was isolated from permeabilized cells using Total RNA Purification kit (Norgen Biotek Corp.)
Custom library preparation
PROseq experiments: nascent biotin-labeled RNA was isolated from permeabilized cells using Total RNA Purification kit (Norgen Biotek Corp.).
PRO-seq experiments: custom Small RNA library preparation compatible with TruSeq Small RNA (Illumina), with 5% S2 cells spike-in RNAs.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
biotin labeled nascent RNA isolated from mESC permeabilized cells
small RNA-seq (hidrolysis fractionation)
mm9_mESC_PROseq_NG_N2_dedup_F.bw
mm9_mESC_PROseq_NG_N2_dedup_R.bw
|
| Data processing |
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
PRO-seq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt, for adapter using cutadapt 1.14, pairs containing reads trimmed shorter than 20 nt filtered
PRO-seq mapped to index composed of spike-in genome (dm3), successfully aligned pairs filtered, remaining mapped to reference (mm9) using bowtie 1.2.2 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 1.1.1 retaining uniquely mapped pairs only, allowing 2 mismatches
PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined
Genome_build: mm9 (PRO-seq), dm3 (PRO-seq)
Supplementary_files_format_and_content: PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment
|
| |
|
| Submission date |
May 03, 2019 |
| Last update date |
Oct 31, 2019 |
| Contact name |
Jean-Pierre Etchegaray |
| E-mail(s) |
[email protected]
|
| Phone |
9733530825
|
| Organization name |
Rutgers University
|
| Department |
Biological Sciences
|
| Street address |
225 University Ave
|
| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07102 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE130691 |
The histone deacetylase SIRT6 controls transcription elongation via promoter-proximal pausing (PRO-Seq) |
| GSE130692 |
The histone deacetylase SIRT6 restrains transcription elongation via promoter-proximal pausing |
|
| Relations |
| BioSample |
SAMN11569977 |
| SRA |
SRX5785883 |
