|
| Status |
Public on Feb 04, 2025 |
| Title |
Sibling_T21_V_3 |
| Sample type |
SRA |
| |
|
| Source name |
EBV immortalized suspension cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: EBV immortalized suspension cells
cell line: Sibling T21 (TIC001678)
cell type: Lymphoblastoid cell line
genotype: Trisomy 21
treatment: 0.1% DMSO
|
| Treatment protocol |
Cells were split and plated on T75 flasks, allowed to recover for 24 hours, then media containing either vehicle (final concentration 0.01% DMSO) or Cortistatin A (100 nM) was added to each flask
|
| Growth protocol |
Lymphoblastoid suspension cells were grown in RPMI medium supplemented with 20% fetal bovine serum, pennicilin/strep, and L-glutamine, in 37C incubators with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4.5 hours after vehicle or CA treatment, cells were collected, spun down, washed once in PBS, then resuspended in TRIzol reagent (Invitrogen, 15596026) and snap frozen. After all 3 biological replicates were collected, cell lysates in TRIzol were thawed and total RNA was extracted according to the manufacturer's protocol. RNA concentration was measured by Qubit and quality was verified using a TapeStation
Libraries prepped using 200 ng total RNA spiked with ERCC spike-in mix (Invitrogen #4456740) and the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research). Paired-end sequencing reads of 150 nucleotides were generated on a NovaSeq X.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cells treated with vehicle for 24 hours
T21_counts_combined.txt
sva_corrected_counts_SiblingT21_24h.csv
|
| Data processing |
Read trimming using bbduk (options: ktrim=r qtrim=r1, trimq=10, k=23 mink=11 hdist=1 maq=10 minlen=25 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA)
Reads were mapped to hg38 using hisat2
Reads over hg38 refseq gene annotations and ERCC "genome" were counted using featurecounts and then RPKM normalized. Highest average RPKM isoform (across replicates and treatments) was retained in cases where multiple isoform annotations existed
Tdfs were generated from trimmed BAM files using igvtools
SVA correction (Leek et al. Bionformatics 2012) was used to correct for batch effects in gene count data
Assembly: hg38
Supplementary files format and content: TDF files for gene count visualization were generated using igvtools
Supplementary files format and content: featurecounts output file containing both human (hg38) and ERCC gene counts
Supplementary files format and content: .csv files containing gene counts that have been corrected using SVA
|
| |
|
| Submission date |
Apr 04, 2024 |
| Last update date |
Feb 04, 2025 |
| Contact name |
Meaghan Courvan |
| E-mail(s) |
meaghancourvan@gmail.com, Meaghan.courvan@colorado.edu
|
| Organization name |
University of Colorado, Boulder
|
| Department |
Biofrontiers
|
| Street address |
596 UCB
|
| City |
Boulder |
| State/province |
CO |
| ZIP/Postal code |
80309 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE263239 |
Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome III |
|
| Relations |
| BioSample |
SAMN40753089 |
| SRA |
SRX24159609 |
