NBDC Research ID: hum0115.v1
SUMMARY
Aims: Transcriptome analyses for transgene induced ES cell (TF-hESC) lines which carry open reading frame (ORF) of transcriptional factors (TFs).
Methods: RNA sequencing and Microarray assay
Participants/Materials: Transcriptome data of each transcriptional factor induced human embryonic stem cell (TF-hESC) lines which were derived from SEES3.
<RNA-seq data>
Each TF-hESC line was specifically induced in response to 437 transgenes (almost all of them were categorized as transcriptional factor: TF). Each line has biological replicate from two independent clones (some are missing replicates because of poor gene inductions). Each data was obtained from cell culture with or without TF induction, at 48-hour , or multiple time points. As total, 2300 samples were analyzed in parallel experiments (437 genes x [1 or 2 clones] x [2 or more culture conditions]).
<microarray data>
Each TF-hESC line was specifically induced in response to 116 transgenes (almost all of them were categorized as transcriptional factor: TF). As total, 448 samples were obtained from 48-hour culture with or without transgene induction (116 genes x [1 or 2 clones] x 2 culture conditions).
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000121 | Microarray | Controlled-access (Type I) | 2020/05/15 |
| DRA006296 | NGS (RNA-seq) | Unrestricted-access | 2020/05/15 |
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MOLECULAR DATA
| Participants/Materials |
TF-hESC lines: total 448 samples (116 genes x [1 or 2 clones] x 2 culture conditions) |
| Targets | Microarray |
| Target Loci for Capture Methods | - |
| Platform |
Chip: Agilent SurePrint G3 Human GE v2 8x60K Microarray (Design ID: 039494) Scanner: Agilent SureScan G4900DA |
| Library Source | mRNA extracted from TF-hESC cells under each condition |
| Cell Lines | https://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HES0008 |
| Reagents (Kit, Version) | Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) |
| Filtering Methods | - |
| Normalization of microarray | Raw intensity data are provided |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000132 |
| Total Data Volume | 14 GB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
TF-hESC lines: total 2300 samples (437 genes x [1 or 2 lines] x [2 or more culture conditions]) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | mRNA extracted from TF-hESC cells under each condition |
| Cell Lines | https://www2.brc.riken.jp/lab/cell/detail.cgi?cell_no=HES0008 |
| Library Construction (kit name) | SureSelect Strand Specific RNA Library Preparation Kit for Illumina (Agilent Technologies) |
| Fragmentation Methods | RNA Seq Fragmentation Mix and heat treatment (94℃) |
| Spot Type | Single-end : 2240 samples, Paired-end : 60 samples |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | Single-end : 50 bp, Paired-end : 202 or 302 bp |
| DDBJ Sequence Read Archive ID | DRA006296 |
| Total Data Volume | 2.48 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigators: Minoru S.H. Ko
Affiliation: Department of Systems Medicine, Mitsunada SakaguchiLaboratory, Keio University School of Medicine
Project / Group Name: JST CREST: Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics / Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks
URL: http://www.jst.go.jp/kisoken/crest/en/project/35/e35_04.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| CREST / Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics | Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks | JPMJCR12W4 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors | doi: 10.1016/j.celrep.2020.107655 | JGAD000132 DRA006296 |
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
