|
| Status |
Public on Jan 12, 2022 |
| Title |
ATAC-seq analysis of Etv2 induced MEF reprogramming and EB differentiation. |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
ATAC-seq analysis of Etv2 induced ES/EB, MEFs,Brg1 KO EBs and Brg1 KD MEFs.
Methods: EBs were collected at different time points and disaggregated in 0.25% trypsin at 37C for 3 min incubation with gentle agitation followed by inactivation with culture medium containing 10% FBS. Cells were collected by centrifugation at 500g for 5 minutes, washed once with ice-cold PBS. iHA-Etv2 MEFs were harvested from the culture dishes at different time points by treating the cells with 0.25% trypsin at 37C for 4 min incubation followed by neutralizing and collecting the cells with culture medium containing 10% FBS. ATAC reaction was performed with 50,000 cells as previously described18 using the Tn5 transposase (Illumina) and libraries were created at the University of Minnesota Genome Center. Libraries were then sequenced on a NextSeq Illumina platform (2x50 bp) aiming for 25 million reads per sample.
|
| |
|
| Overall design |
ATAC-seq of undifferentiated MEF, 1 day, 2 days and 7 days post Etv2 induction MEFs; ATAC-seq of 3h and 12h post Etv2 induction in EBs; ATAC-seq of undifferentiated Brg1 KD MEFs, 1 day, 2 days and 7 days post Etv2 inducdtion in Brg1 KD MEFs and Brg1 KO EBs 4 days post Etv2 induction
|
| |
|
| Contributor(s) |
Gong W, Dsouza N |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 10, 2021 |
| Last update date |
Jan 14, 2022 |
| Contact name |
Daniel Garry |
| E-mail(s) |
garry@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Lillehei Heart Institute
|
| Street address |
2231 6th Street SE, 4th Floor
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (34)
|
|
| This SubSeries is part of SuperSeries: |
|
| Relations |
| BioProject |
PRJNA713313 |
| SRA |
SRP310105 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168636_EB_Dox_D25_Flk1pos_summits.bed.gz |
833.4 Kb |
(ftp)(http) |
BED |
| GSE168636_EB_Dox_D25_Flk1pos_treat_pileup.bw |
213.8 Mb |
(ftp)(http) |
BW |
| GSE168636_EB_Dox_D25_summits.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE168636_EB_Dox_D25_treat_pileup.bw |
375.5 Mb |
(ftp)(http) |
BW |
| GSE168636_EB_NoDox_D25_summits.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE168636_EB_NoDox_D25_treat_pileup.bw |
381.7 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_D0_summits.bed.gz |
519.4 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_D0_treat_pileup.bw |
273.2 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_Dox_D1_summits.bed.gz |
379.4 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_Dox_D1_treat_pileup.bw |
283.3 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_Dox_D2_summits.bed.gz |
530.9 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_Dox_D2_treat_pileup.bw |
289.8 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_Dox_D7_summits.bed.gz |
182.6 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_Dox_D7_treat_pileup.bw |
356.2 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_NoDox_D1_summits.bed.gz |
504.2 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_NoDox_D1_treat_pileup.bw |
248.3 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_NoDox_D2_summits.bed.gz |
622.0 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_NoDox_D2_treat_pileup.bw |
317.3 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Brg1_KD_NoDox_D7_summits.bed.gz |
151.8 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Brg1_KD_NoDox_D7_treat_pileup.bw |
363.7 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Dox_D1_summits.bed.gz |
708.5 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Dox_D1_treat_pileup.bw |
397.0 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Dox_D2_summits.bed.gz |
368.0 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Dox_D2_treat_pileup.bw |
371.6 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Dox_D7_Flk1pos_summits.bed.gz |
411.5 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Dox_D7_Flk1pos_treat_pileup.bw |
319.7 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_Dox_D7_summits.bed.gz |
250.0 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_Dox_D7_treat_pileup.bw |
386.4 Mb |
(ftp)(http) |
BW |
| GSE168636_MEF_NoDox_summits.bed.gz |
878.6 Kb |
(ftp)(http) |
BED |
| GSE168636_MEF_NoDox_treat_pileup.bw |
335.3 Mb |
(ftp)(http) |
BW |
| GSE168636_RAW.tar |
294.5 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...