|
| Status |
Public on Jul 29, 2016 |
| Title |
Trisomic, T cells, Female, 13 Year old [T21_M13YR] |
| Sample type |
SRA |
| |
|
| Source name |
T cells
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Trisomic
batch: C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was prepared using the AllPrep Kit from Qiagen
Libraries were prepared using the Truseq Stranded Kit from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M13YR
|
| Data processing |
Basecalls performed using bcl2fastq_v1.8.4 with the following options (--mismatches 1 fastq-cluster-count 0 )
FASTQC v0.11.2 was used to determine sequence quality
fastqc-mcf was used to trim low quality bases, adapters and N content from 3’ end (<q10). Removed reads that were shorter than 30bp after trimming
Reads were mapped using Tophat2 (v2.0.13) with the following options (--b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand)
Reads with MAPQ > 10 were kept using Samtools (v0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Raw count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene --mode=intersection-nonempty)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts for each sample
|
| |
|
| Submission date |
Jul 18, 2016 |
| Last update date |
Dec 03, 2021 |
| Contact name |
Matthew D Galbraith |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Department of Pharmacology; Linda Crnic Institute for Down Syndrome
|
| Street address |
12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE79843 |
Trisomy 21 consistently activates the interferon response |
| GSE84531 |
RNAseq from disomic and trisomic T cells and monocytes |
|
| Relations |
| BioSample |
SAMN05415219 |
| SRA |
SRX1959672 |
