|
| Status |
Public on Dec 01, 2023 |
| Title |
Reanalysis of ChIP-Seq of GSE117155. |
| Sample organism |
Homo sapiens |
| Experiment type |
Third-party reanalysis
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
In this reanalysis, 20 GSM series were reanalyzed for ChIp-Seq data.
|
| |
|
| Overall design |
Reanalysis of the following ChIP-Seq samples in GSE117155:
BioProject accession: PRJNA481318
GEO Sample SRA Runs BioSample Title
========== ======== ========= =====
GSM3272322 SRR7525644 SAMN09665273 Pol II
GSM3272323 SRR7525645 SAMN09665272 Flag-LEDGF
GSM3272324 SRR7525646 SAMN09665271 Flag-HDGF2
GSM3272325 SRR7525647 SAMN09665270 H3K36me2
GSM3272326 SRR7525648 SAMN09665269 SPT16
GSM3272327 SRR7525649 SAMN09665268 H3K36me3_2
GSM3272328 SRR7525650 SAMN09665267 H3K27me3_2
GSM3272340 SRR7525662 SAMN09665253 MB_H3K27me3
GSM3272341 SRR7525663 SAMN09665314 MT_H3K27me3
GSM3272342 SRR7525664 SAMN09665313 MB_H3K36me2
GSM3272343 SRR7525665 SAMN09665310 MT_H3K36me2
GSM3272344 SRR7525666 SAMN09665309 MB_H3K36me3
GSM3272345 SRR7525667 SAMN09665308 MT_H3K36me3
GSM3272346 SRR7525668 SAMN09665307 MB_HDGF2
GSM3272347 SRR7525669 SAMN09665306 MT_HDGF2
GSM3272354 SRR7525676 SAMN09665299 MB_LEDGF
GSM3272355 SRR7525677 SAMN09665298 MT_LEDGF
GSM3272356 SRR7525678 SAMN09665297 MB_RNAPII
GSM3272357 SRR7525679 SAMN09665296 MT_RNAPII
GSM3272358 SRR7525680 SAMN09665295 MB_SPT16
*data processing step:
Raw files were downloaded from NCBI and were aligned against the UCSC hg19 human genome by bowtie with the parameter described by the original article (PMID: 31616795). Aligned files were converted to BAM with SAMtools version 1.3.1 and sorted with Picard tools. Differential peak calling was done with MACS2 version 2.1.1 with parameters --broad -g 2.7e9 --broad-cutoff 0.01 -f -B. The SRA file SRR7525652 was used as input for SRR7525645 and SRR7525646 whereas SRR7525651 was used as input for SRR7525644, SRR7525647, SRR7525648, SRR7525649, and SRR7525650. Further, file SRR7525674 was input for SRR7525662, SRR7525664, SRR7525666, SRR7525668, SRR7525678 and SRR7525680 whereas SRR7525675 was an input for SRR7525663, SRR7525665, SRR7525667, SRR7525669, SRR7525677 and SRR7525679.
wig and bed data. The SRR3538917_95P.txt contains coordinates of Speckles-associated domains or SPADs and was used in publications ( PMIDs:32665593 and 35203306).
|
| Web link |
https://pubmed.ncbi.nlm.nih.gov/35203306/
|
| |
|
| Contributor(s) |
Singh PK |
| Citation(s) |
35203306 |
| |
| Submission date |
Nov 26, 2023 |
| Last update date |
Apr 12, 2024 |
| Contact name |
Parmit Kumar Singh |
| E-mail(s) |
parmitcrassa@gmail.com
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Department of Cancer Immunology and Virology
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Relations |
| Reanalysis of |
GSM3272323 |
| Reanalysis of |
GSM3272324 |
| Reanalysis of |
GSM3272325 |
| Reanalysis of |
GSM3272327 |
| Reanalysis of |
GSM3272328 |
| Reanalysis of |
GSM3272322 |
| Reanalysis of |
GSM3272326 |
| Reanalysis of |
GSM3272340 |
| Reanalysis of |
GSM3272341 |
| Reanalysis of |
GSM3272342 |
| Reanalysis of |
GSM3272343 |
| Reanalysis of |
GSM3272344 |
| Reanalysis of |
GSM3272345 |
| Reanalysis of |
GSM3272346 |
| Reanalysis of |
GSM3272347 |
| Reanalysis of |
GSM3272354 |
| Reanalysis of |
GSM3272355 |
| Reanalysis of |
GSM3272356 |
| Reanalysis of |
GSM3272357 |
| Reanalysis of |
GSM3272358 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE248645_SRR7525644_51_polII_peaks.txt.gz |
443.8 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525645_52_LEDGF_293_peaks.txt.gz |
518.5 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525646_52_HDGF2_293T_peaks.txt.gz |
43.1 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525647_51_H3K26me2_peaks.txt.gz |
75.2 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525648_51_spt16_peaks.txt.gz |
1.5 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525649_51_H3K36me3a_peaks.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525650_51_H3K36me3c_peaks.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525662_74_MB_h3k27me3_peaks.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525663_75_MT_h3k27me3_peaks.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525664_74_MB_h3k36me2_peaks.txt.gz |
4.1 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525665_75_MT_h3k36me2_peaks.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525666_74_MB_h3k36me3_peaks.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525667_75_MT_h3k36me3_peaks.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525668_74_MB_HDGF2_peaks.txt.gz |
213.6 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525669_75_MT_hdgf2_peaks.txt.gz |
127.8 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525676_74_MB_LEDGF_peaks.txt.gz |
6.8 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525677_75_MT_LEDGF_peaks.txt.gz |
931 b |
(ftp)(http) |
TXT |
| GSE248645_SRR7525678_74_MB_polII_peaks.txt.gz |
377.9 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525679_75_MT_polII_peaks.txt.gz |
213.4 Kb |
(ftp)(http) |
TXT |
| GSE248645_SRR7525680_74_MB_SPT16_peaks.txt.gz |
3.5 Kb |
(ftp)(http) |
TXT |
| GSE248645_sample_to_processed_data_file_list.txt.gz |
680 b |
(ftp)(http) |
TXT |
