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| Status |
Public on Feb 23, 2021 |
| Title |
PROseq_4h_R3 |
| Sample type |
SRA |
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| Source name |
CTCF-AID-mCherry+TIR
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| Organism |
Mus musculus |
| Characteristics |
cell type: ES-derived erythroid progenitor cells
strain: C57BL/6
treatment: 4h auxin
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| Treatment protocol |
Auxin concentraton was 1mM. See Description column for Samples.
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| Growth protocol |
G1E-ER4 (Weiss et al., 1997) derived single-cell clones were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated for PRO-seq, followed by run-on reactions, nascent RNA isolation, and cDNA library preparaion as described in the paper: Mahat, D.B., Kwak, H., Booth, G.T., Jonkers, I.H., Danko, C.G., Patel, R.K., Waters, C.T., Munson, K., Core, L.J., Lis, J.T., 2016a. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 11, 1455–1476. doi:10.1038/nprot.2016.086
library srategy: PRO-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
4h auxin; replicate #3
2008
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| Data processing |
Seqtk (https://github.com/lh3/seqtk/blob/master/README.md) was run to trim the 6-base UMI.
Reads were mapped to both fly (dm6) and mouse (mm9) genomes, with only those mapped exclusively to one genome kept for downstream analysis.
Only primary alignments with mapq score at least 20 and without INDEL were reported and saved in bam files.
Duplicated reads with the same UMI and aligned to the same genomic loci were removed.
Bigwig files were generated and normalized using the sample size factor calculated by DEseq2.
Genome_build: mm9
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| Submission date |
May 12, 2020 |
| Last update date |
Feb 23, 2021 |
| Contact name |
Jing Luan |
| E-mail(s) |
jluan@pennmedicine.upenn.edu
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| Organization name |
University of Pennsylvania
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| Street address |
3615 Civic Center Blvd, ARC 315
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| City |
Philadelphia |
| ZIP/Postal code |
19103 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE150414 |
Distinct properties and functions of CTCF revealed by a rapidly inducible degron system [PRO-Seq] |
| GSE150418 |
Distinct properties and functions of CTCF revealed by a rapidly inducible degron system |
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| Relations |
| BioSample |
SAMN14906156 |
| SRA |
SRX8332821 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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