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| Status |
Public on Jan 11, 2024 |
| Title |
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [Multiome-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed simultaneous gene expression profiling and chromatin analysis at single cell level using data obtained from Multiome-seq at various time points.
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| Overall design |
Multiome-seq at various time points
Please note that processed data generated from both RNA and ATAC is linked to the corresponding *Multiome-seq, RNA sample records.
barhash.csv.gz
filteredinbarcodes.csv.gz
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| Web link |
https://www.cell.com/cell-stem-cell/abstract/S1934-5909(24)00142-5?rss=yes
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| Contributor(s) |
Singh PN, Shivdasani RA |
| Citation(s) |
38733993 |
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| Submission date |
Jul 26, 2023 |
| Last update date |
Aug 22, 2024 |
| Contact name |
Ramesh A Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
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| Phone |
(617) 632-5746
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| Organization name |
DFCI
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| Department |
Medical Oncology
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| Lab |
Shivdasani lab
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| Street address |
SM1052, Smith10, 450 Brookline Ave
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| City |
Brookline |
| State/province |
Massachusetts |
| ZIP/Postal code |
02445 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (28)
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| GSM7661371 |
Line#2, D1, tam-inducible, Multiome-seq, RNA |
| GSM7661372 |
Line#2, D3, tam-inducible, Multiome-seq, RNA |
| GSM7661373 |
Line#2, D5, tam-inducible, Multiome-seq, RNA |
| GSM7661374 |
Line#2, D6, tam-inducible, Multiome-seq, RNA |
| GSM7661375 |
Line#2, D1, tam-inducible, Multiome-seq, ATAC |
| GSM7661376 |
Line#2, D3, tam-inducible, Multiome-seq, ATAC |
| GSM7661377 |
Line#2, D5, tam-inducible, Multiome-seq, ATAC |
| GSM7661378 |
Line#2, D6, tam-inducible, Multiome-seq, ATAC |
| GSM7661379 |
Line#2, D3 scrambled, tam-inducible, Multiome-seq, RNA, rep1 |
| GSM7661380 |
Line#2, D3 scrambled, tam-inducible, Multiome-seq, RNA, rep2 |
| GSM7661381 |
Line#2, D6 scrambled, tam-inducible, Multiome-seq, RNA, rep1 |
| GSM7661382 |
Line#2, D6 scrambled, tam-inducible, Multiome-seq, RNA, rep2 |
| GSM7661383 |
Line#2, D3 scrambled, tam-inducible, Multiome-seq, ATAC, rep1 |
| GSM7661384 |
Line#2, D3 scrambled, tam-inducible, Multiome-seq, ATAC, rep2 |
| GSM7661385 |
Line#2, D6 scrambled, tam-inducible, Multiome-seq, ATAC, rep1 |
| GSM7661386 |
Line#2, D6 scrambled, tam-inducible, Multiome-seq, ATAC, rep2 |
| GSM7661387 |
Line#2, D3 ASCL1-KO, tam-inducible, Multiome-seq, RNA |
| GSM7661388 |
Line#2, D6 ASCL1-KO, tam-inducible, Multiome-seq, RNA |
| GSM7661389 |
Line#2, D3 ASCL1-KO, tam-inducible, Multiome-seq, ATAC |
| GSM7661390 |
Line#2, D6 ASCL1-KO, tam-inducible, Multiome-seq, ATAC |
| GSM7661391 |
Line#2, D6 NEUROD1-DBD-KO, tam-inducible, Multiome-seq, RNA |
| GSM7661392 |
Line#2, D6 NEUROD1-DBD-KO, tam-inducible, Multiome-seq, ATAC |
| GSM7661393 |
Line#2, D6 NEUROD1-TAD-KO, tam-inducible, Multiome-seq, RNA |
| GSM7661394 |
Line#2, D6 NEUROD1-TAD-KO, tam-inducible, Multiome-seq, ATAC |
| GSM7661395 |
Line#2, D3 HES6-KO, tam-inducible, Multiome-seq, RNA |
| GSM7661396 |
Line#2, D6 HES6-KO, tam-inducible, Multiome-seq, RNA |
| GSM7661397 |
Line#2, D3 HES6-KO, tam-inducible, Multiome-seq, ATAC |
| GSM7661398 |
Line#2, D6 HES6-KO, tam-inducible, Multiome-seq, ATAC |
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| This SubSeries is part of SuperSeries: |
| GSE238276 |
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation |
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| Relations |
| BioProject |
PRJNA998715 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE238275_RAW.tar |
18.9 Gb |
(http)(custom) |
TAR (of BED, MTX, TBI, TSV) |
| GSE238275_barcodes.tsv.gz |
25.6 Kb |
(ftp)(http) |
TSV |
| GSE238275_features.tsv.gz |
2.6 Mb |
(ftp)(http) |
TSV |
| GSE238275_matrix.mtx.gz |
85.2 Mb |
(ftp)(http) |
MTX |
| GSE238275_snMultiome_celltype_annotation.txt.gz |
92.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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