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| Status |
Public on Feb 20, 2021 |
| Title |
RNAtagTest5_pool2 |
| Sample type |
SRA |
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| Source name |
fibroblast
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| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblast
cell line: GM00942
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| Treatment protocol |
In 96-well plates on Day 0 in 250µL media we added 0.7µL of drug stock in DMSO (See Table S1 of citation) or of DMSO (for control cultures), keeping total DMSO concentration of perturbation culture medium below 0.3% for all conditions.
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| Growth protocol |
Cardiac myocytes were obtained by differentiating human induced pluripotent stem cells to iPS-GM942-SeV3-CMs ("iPSC-CMs"), as previously described (Laflamme et al., 2007; Palpant et al., 2015; Shanmughapriya et al., 2018; Zhu et al., 2010, 2011). GM00942 (Coriell) human dermal fibroblasts were expanded per manufacturer's instructions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNaqueous-96 kits (Ambion) on day 4 after first drug treatment
RNAtag-seq (Shishkin et al., 2015) as previously described (includes rRNA depletion by Illumina RiboZero). Libraries sequenced 20:8:0:55 on a NextSeq550, with the RNAtag in R1 reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Base-calling performed by Illumina Basespace
Read filtering performed by Trimmomatic v0.32 with parameters MINLEN:11
Demultiplexing of samples from 32-sample pooled libraried performed by PyRNAtagSeq changeset 6ffd465 (Wallace, 2017, github)
Alignment to hg19 performed by STAR v2.5.2a using only the 55-nt R2 reads in single-end mode (excluding the RNAtag read on R1)
Gene counts quantified by HTSeq v0.6.1 with settings --mode=union \ --stranded=no \ --type=exon \ --order=name Genome_build: hg19
Supplementary_files_format_and_content: mapped counts is a csv containing the matrix of mapped counts for each ENSEMBL gene ID called by HTSeq in each of 576 samples. Top row = header. First column = ENSEMBL gene ID
Supplementary_files_format_and_content: colData for mapped counts is a tab-delimited text file containing a mapping between the sample IDs in the header of mapped counts and descriptions of the treatment conditions and quality controls for each sample
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| Submission date |
Feb 19, 2021 |
| Last update date |
Feb 21, 2021 |
| Contact name |
Ian A Mellis |
| E-mail(s) |
[email protected]
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| Organization name |
Columbia University
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| Street address |
622 W 168th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE167128 |
Perturbation panel profiling of human iPSC-derived cardiac myocytes and primary dermal fibroblasts |
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| Relations |
| BioSample |
SAMN18006427 |
| SRA |
SRX10135064 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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