|
| Status |
Public on Feb 05, 2024 |
| Title |
Escherichia_coli_c1 |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli
|
| Organism |
Escherichia coli |
| Characteristics |
assay: PRO-seq
degron type: none
dtag-13 treatment: untreated
heat shock: no
replicate: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, run-on, and library preparation were executed according to “Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protoc. 11, 1455–1476 (2016).” (PMID: 27442863).
Library prep was performed using Illumina custom adapters: Reverse 3' RNA adapter (/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT) and Reverse 5' RNA Adapter (5'-CCUUGGCACCCGAGAAUUCCA-3').
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ data was aligned and processed using the proseq2.0 pipeline developed by Danko lab (https://github.com/Danko-Lab/proseq2.0).
The mESC data was competitively aligned to a merged genome assembly of mm10 and dm3. Merging the two genome builds was performed using fastq merge.
|
| |
|
| Submission date |
Jan 28, 2023 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Alexandra Georgiana Chivu |
| E-mail(s) |
agc94@cornell.edu
|
| Phone |
6072624972
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Danko and Lis labs
|
| Street address |
215 Tower Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE223913 |
Pol II pausing is a milestone on the road to complex animals |
|
| Relations |
| BioSample |
SAMN32949478 |
| SRA |
SRX19205905 |
