|
| Status |
Public on May 31, 2024 |
| Title |
Long noncoding RNA GATA2AS regulates human erythroid differentiation by controlling erythroid transcription factors binding and regulatory landscape |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To study how GATA2AS regulates erythroid differentiation, GATA2AS ChIRP-seq, RNA-seq, LRF and KLF1 ChIP-seq, H3K27ac ChIP-seq and ATAC-seq were performed.
|
| |
|
| Overall design |
GATA2AS ChIRP-seq was performed in wild type Hudep2 cells. RNA-seq were performed in KO control and GATA2AS KO Hudep2 cells on day 0/4/7/9 during differentiation and in KD control and GATA2AS KD CD34 cells on day 6/10/14 during differentiation. LRF and KLF1 ChIP-seq were performed in KO control and GATA2AS KO Hudep2 cells to investigate how GATA2AS affects LRF and KLF1 binding. H3K27ac ChIP-seq and ATAC-seq were performed in KO control and GATA2AS KO Hudep2 cells to study how GATA2AS affects regulatory landscape.
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| |
|
| Contributor(s) |
Liu G, Dean A |
| Citation(s) |
38447046 |
| |
| Submission date |
Sep 20, 2022 |
| Last update date |
May 31, 2024 |
| Contact name |
Ann Dean |
| Organization name |
NIH
|
| Department |
NIDDK
|
| Lab |
LCDB
|
| Street address |
50 South Drive, Bldg 50
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
|
| Samples (57)
|
|
| Relations |
| BioProject |
PRJNA882432 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE213779_GATA2AS_ChIRP_peak_e2k.bed.gz |
62.3 Kb |
(ftp)(http) |
BED |
| GSE213779_d0_ko_DESeq_results.csv.gz |
92.5 Kb |
(ftp)(http) |
CSV |
| GSE213779_d4_ko_DESeq_results.csv.gz |
157.3 Kb |
(ftp)(http) |
CSV |
| GSE213779_d7_ko_DESeq_results.csv.gz |
148.8 Kb |
(ftp)(http) |
CSV |
| GSE213779_d9_ko_DESeq_results.csv.gz |
332.7 Kb |
(ftp)(http) |
CSV |
| GSE213779_featureCounts_combinedL1L2_days6.10.14_CD34.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE213779_ko_ATAC_diffbind_fdr0.05.bed.gz |
41.6 Kb |
(ftp)(http) |
BED |
| GSE213779_ko_H3K27ac_diffbind_fdr0.05.bed.gz |
17.2 Kb |
(ftp)(http) |
BED |
| GSE213779_ko_klf1_diffbind_fdr0.05.bed.gz |
9.7 Kb |
(ftp)(http) |
BED |
| GSE213779_ko_lrf_diffbind_fdr0.05.bed.gz |
18.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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