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| Status |
Public on Jun 01, 2020 |
| Title |
MCF10Ca1a_wt_rep2 |
| Sample type |
SRA |
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| Source name |
Human breast epithelial cells, virally transformed
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Human breast epithelial cells
cell type: MCF10Ca1A
treatment: none
days post treatment: 0
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| Treatment protocol |
For EMT induction, MCF-10A cells were treated with 5 ng/ml TGF-β1 (Redsystems) for 8 days. MCF-10A cells were transduced with the lentviral vector pLVTHM shH2A.Z as previously described (Domaschenz, 2017). GFP-positive cells were sorted 2 days post-transduction and further cultured for 8 days before being processed.
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| Growth protocol |
MCF-10A and MCF-10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% Horse Serum, 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human EGF, 500 ng/mL Hydrocortisone and 100 ng/mL Cholera Toxin.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified using the RNeasy Mini Kit (Qiagen) and cDNA synthesized using the QuantiTect Reverse Transcription Kit (Qiagen). The knockdown of H2A.Z expression was analysed by qPCR on the 7900HT Fast Real-Time PCR system using SYBR Green I master mix (applied biosystems) and 0.15mM primers as previously described (Domaschenz, 2017). Relative expression values were normalized to pooled housekeeping genes Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), Beta-actin (B- actin), Ribsomal Protein S23 (RPS23) and Splicing Factor 3a Subunit 1 (SF3A1) (Maltseva et al., 2013).
Libraries were constructed according to the Illumina TruSeq stranded mRNA protocol with poly-A enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
MCF10ACa1A rep2
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| Data processing |
base calling was performed using the bcl2fq script
transcript abundance estimation was performed using kallisto (0.43.0)
transcript abundances were further analysed and normalised using sleuth
gene-level abundance estimates were generated by summing transcript abundances per gene
Genome_build: UCSC hg19
Supplementary_files_format_and_content: TSV format; target ID, target length, target effective length, estimated counts, transcripts per million (TPM)
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| Submission date |
Jul 15, 2019 |
| Last update date |
Jun 02, 2020 |
| Contact name |
LAUREN A COLE |
| E-mail(s) |
LC13G@MY.FSU.EDU
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| Phone |
8506458573
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| Organization name |
FLORIDA STATE UNIVERSITY
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| Street address |
319 STADIUM DR
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| City |
TALLAHASSEE |
| State/province |
Florida |
| ZIP/Postal code |
32304 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE134298 |
Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells (RNA-seq) |
| GSE134299 |
Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells |
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| Relations |
| BioSample |
SAMN12276476 |
| SRA |
SRX6445062 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3941615_MCF10Ca1a_wt_rep2.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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