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| Status |
Public on Dec 01, 2021 |
| Title |
4dTGFB_4dwithdrawn_ATAC_Rep2 |
| Sample type |
SRA |
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| Source name |
MCF10A
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| Organism |
Homo sapiens |
| Characteristics |
protocol: ATAC-seq
culture conditions: 2D culture
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| Treatment protocol |
5 ng/mL TGFB in 4 mM HCL with 0.01% BSA
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| Growth protocol |
Cells were plated at 10,000 cells/mm2 and treated with TGFB. Cell density was maintained every other day and media was removed and replenished with TGFB
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were centrifuged and resuspended in 50 uL lysis buffer (10 mM Tris, 10 mM NaCl, 3 mM MgCl2, 0.01% IGEPAL) and centrifuged at 500g for 10 min at 4C.
Pellet was resuspended in transposase reaction mix (25 uL 2X TD buffer, 2.5 uL transposase, 22.5 uL H2O. Tagmented DNA was purified and amplified using Nextera DNA Sample Preparation Kit using the following PCR conditions: 98C for 30s, then thermocycling for 98C for 10s, 63C for 30s, and 72C for 1 min for 11 cycles followed by 72C for 5 min
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
4d +TGFB, 4d -TGFB MCF10A ATAC DNA
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| Data processing |
Adapter sequences were removed using cutadapt (Galaxy version 1.16.6)
Cropped to 30 bp with Trimmomatic (Galaxy version 0.36.6)
Aligned to hg19 using Bowtie2 (v2.3.4.2)
mtDNA, unmapped and random contigs, and ChrY reads excluded using samtools (v1.9)
Tag directories, peaks, and motif enrichment generated by HOMER (version 4.10.3)
Genome_build: hg19
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| Submission date |
Feb 24, 2020 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Joe Taube |
| E-mail(s) |
[email protected]
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| Phone |
2547102097
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| Organization name |
Baylor University
|
| Street address |
One Bear Place #97388
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| City |
Waco |
| State/province |
Texas |
| ZIP/Postal code |
76798-7388 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE145849 |
Phased gene expression and chromatin accessibility during progressive EMT and MET linked to dynamic CTCF engagement (ATAC-Seq) |
| GSE145851 |
Phased gene expression and chromatin accessibility during progressive EMT and MET linked to dynamic CTCF engagement |
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| Relations |
| BioSample |
SAMN14175746 |
| SRA |
SRX7795694 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4337703_4dTGFB_4dwithdrawn_ATAC_Rep2peaks.txt.gz |
6.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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