|
Status |
Public on Feb 05, 2024 |
Title |
mESCs NELFb, 28 -- 30 mins HS at 42 with pre-treatment 30 mins of dTAG |
Sample type |
SRA |
|
|
Source name |
Mouse mESCs
|
Organism |
Mus musculus |
Characteristics |
assay: PRO-seq degron type: NELFb-dTAG dtag-13 treatment: 60min dTAG heat shock: yes replicate: 1 media used to grow the cells: serum lift (S/L)
|
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.
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|
|
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 |
GPL19057 |
Series (1) |
GSE223913 |
Pol II pausing is a milestone on the road to complex animals |
|
Relations |
BioSample |
SAMN32949447 |
SRA |
SRX19205941 |