|
| Status |
Public on Jan 15, 2019 |
| Title |
healthy individual-2 rep1 mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Skin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
passage: 5
rna type: polyA enriched mRNA-seq
|
| Growth protocol |
DMEM medium with 15% FBS serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA extracted with trizol and Direct-Zol kit from Zymo; ribosomal footprints isolated by fractionation of ribosomes using ultracentrifuge and then extracting footprints according to the protocol in the manuscript
mRNA-seq samples were prepared with TruSeq kit, Ribo-seq samples were prepared with custom protocol described in the manuscript
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
patient_vs_healthy_mRNAseq.csv
patient_vs_healthy_TE.csv
|
| Data processing |
analytical pipeline is available here: https://github.com/germaximus/OConnell_2018
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: "differential gene expression analysis" - contains output of DEseq2 package in R; "read count per gene" - contains count tables obtained from FeatureCount standalone software; "read coverage over transcripts" - sequencing read coverage of individual transripts.
|
| |
|
| Submission date |
Dec 10, 2018 |
| Last update date |
Jan 17, 2019 |
| Contact name |
Pankaj Agrawal |
| E-mail(s) |
pagrawal@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Street address |
300 Longwood ave
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE123564 |
Mammalian Hbs1L deficiency causes Pelota depletion and is associated with a unique phenotype |
|
| Relations |
| BioSample |
SAMN10574486 |
| SRA |
SRX5124097 |
