|
| Status |
Public on Nov 14, 2022 |
| Title |
GM18486 |
| Sample type |
SRA |
| |
|
| Source name |
B-Lymphocyte
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: untreated
ethnicity: YRI
cell line: GM18486
genotype: wildtype
seq_run_id: 10
pool_id: 55
cage_run: 10
e-gel: No
|
| Treatment protocol |
Samples were untreated.
|
| Growth protocol |
Epstein-Barr virus immortalized LCLs were obtained from the NIGMS Human Genetic Cell Repository at Coriell Institute for Medical Research. Cells were incubated at 37°C at 5% carbon dioxide in the Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of non-inactivated fetal bovine serum and antibiotics. Cell cultures were split every few days for maintenance. As these cell lines were freshly purchased, mycoplasma contamination screening was not undertaken.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol, and gDNA was eliminated by treatment with the RNase-Free DNase Set (Qiagen).
CAGE libraries were prepared as described in (Takahashi et al, 2012, PMID: 22362160) with an input of 1.5mg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were trimmed to remove linker sequences, filtered for minimum sequence quality of Q30 in 50%, and rRNA reads matching U13369.1 were removed using rRNAdust (version 1.06 (FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al. 2014))
Mapping to the human reference genome (hg38) was performed using BWA (version 0.7.15-r1140) allowing for max two mismatches per read. To limit mapping biases, reads were re-mapped using the WASP pipeline (van de Geijn et al. 2015) and BWA using the same parameters, taking into account biallelic SNVs (Lowy-Gallego et al. 2019). Reads with a mapping quality of at least 20 were retained for further analyses.
CAGE-defined transcription start sites (CTSSs) were identified from 5’ ends of CAGE read using CAGEfightR (version 1.10 (Thodberg et al. 2019))
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files of CAGE transcriptions start sites (CTSSs) with the score column containing the raw counts
|
| |
|
| Submission date |
Nov 04, 2021 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Robin Andersson |
| E-mail(s) |
robin@binf.ku.dk
|
| Organization name |
University of Copenhagen
|
| Department |
Biology
|
| Lab |
Andersson Lab
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE188130 |
Promoter sequence and architecture determine expression variability and confer robustness to genetic variants [immortalized lymphoblastoid cell lines] |
| GSE188131 |
Promoter sequence and architecture determine expression variability and confer robustness to genetic variants |
|
| Relations |
| BioSample |
SAMN22883005 |
| SRA |
SRX12970462 |
