|
| Status |
Public on Aug 29, 2018 |
| Title |
Genome-wide DNA accessibility maps and differential gene expression using ChIP-seq, ATAC-seq and RNA-seq for the human secondary fibroblast cell line hiF-T and whole worms with and without knockdown of FACT complex |
| Organisms |
Caenorhabditis elegans; Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
To assess the mechanisms by which FACT depletion leads to increased sensitivity of cells to be reprogrammed, we measured the chromatin accessibility landscape using ATAC-seq following mock treatment, SSRP1 knockdown, or SUPT16H knockdown in human fibroblasts and mock, hmg-3 or hmg-4 knockdown in whole worms, and differential gene expression in hmg-3 knockout mutants or following mock, hmg-4, or spt-16 knockdown by RNAseq.
|
| |
|
| Overall design |
Examination of two FACT complex components in human cells and worms with ChIP-seq, ATAC-seq and RNA-seq
|
| |
|
| Contributor(s) |
Lacadie S, Kolundzic E, Tursun B |
| Citation(s) |
30078731 |
| Submission date |
May 10, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Scott Allen Lacadie |
| E-mail(s) |
scott.lacadie@mdc-berlin.de
|
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Department |
Berlin Institute for Medical Systems Biology
|
| Lab |
Ohler
|
| Street address |
Robert-Rössle-Str. 10
|
| City |
Berlin-Buch |
| ZIP/Postal code |
13092 |
| Country |
Germany |
| |
|
| Platforms (5)
|
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL22765 |
Illumina HiSeq 4000 (Caenorhabditis elegans) |
|
| Samples (58)
|
|
| Relations |
| BioProject |
PRJNA386158 |
| SRA |
SRP106869 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98758_RAW.tar |
22.8 Mb |
(http)(custom) |
TAR (of BW, TXT) |
| GSE98758_gAtac_rluc.bw |
109.4 Mb |
(ftp)(http) |
BW |
| GSE98758_hmg3RNAcounts.tsv.gz |
763.9 Kb |
(ftp)(http) |
TSV |
| GSE98758_hmg3_totalCounts.txt.gz |
380.3 Kb |
(ftp)(http) |
TXT |
| GSE98758_hmg3haChIP.bw |
36.0 Mb |
(ftp)(http) |
BW |
| GSE98758_hmg4RNAcounts.tsv.gz |
771.1 Kb |
(ftp)(http) |
TSV |
| GSE98758_hmg4Spt16_totalCounts.txt.gz |
412.8 Kb |
(ftp)(http) |
TXT |
| GSE98758_hotFiltered_hmg3WholeCat_steric38.bed.bigWig |
243.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE98758_hotFiltered_hmg4SomaRepCat_steric38.bed.bigWig |
329.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE98758_hotFiltered_rlucSomaRepCat_steric38.bed.bigWig |
316.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE98758_hotFiltered_rlucWholeCat_steric38.bed.bigWig |
220.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE98758_hotFiltered_spt16SomaRepCat_steric38.bed.bigWig |
288.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE98758_humanPromoterChIPcounts.txt.gz |
551.9 Kb |
(ftp)(http) |
TXT |
| GSE98758_human_filteredPeaksCountsWithPeaks.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE98758_mockTotal.fwd.bw |
86.6 Mb |
(ftp)(http) |
BW |
| GSE98758_mockTotal.rev.bw |
83.4 Mb |
(ftp)(http) |
BW |
| GSE98758_sorted_reIded_mockCatRep1and3_true5end.bed_steric38.bed.bam.bam.bigWig |
1.4 Gb |
(ftp)(http) |
BIGWIG |
| GSE98758_sorted_ssrp1CatRep1and3_true5end.bed_steric38.bed.bam.bam.bigWig |
1.1 Gb |
(ftp)(http) |
BIGWIG |
| GSE98758_sorted_supt16hCatRep1and3_true5end.bed_steric38.bed.bam.bam.bigWig |
1.4 Gb |
(ftp)(http) |
BIGWIG |
| GSE98758_spt16RNAcounts.tsv.gz |
778.0 Kb |
(ftp)(http) |
TSV |
| GSE98758_ssrp1ChIP.bw |
632.9 Mb |
(ftp)(http) |
BW |
| GSE98758_ssrp1Total.fwd.bw |
105.5 Mb |
(ftp)(http) |
BW |
| GSE98758_ssrp1Total.rev.bw |
101.9 Mb |
(ftp)(http) |
BW |
| GSE98758_supt16hChIP.bw |
676.9 Mb |
(ftp)(http) |
BW |
| GSE98758_supt16hTotal.fwd.bw |
112.7 Mb |
(ftp)(http) |
BW |
| GSE98758_supt16hTotal.rev.bw |
108.0 Mb |
(ftp)(http) |
BW |
| GSE98758_wormPromoterChIPcounts.txt.gz |
407.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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