|
Status |
Public on Jul 29, 2016 |
Title |
Disomic, T cells, Female, 29 Year old [D21_F29YR] |
Sample type |
SRA |
|
|
Source name |
T cells
|
Organism |
Homo sapiens |
Characteristics |
condition: Disomic 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 D21_F29YR
|
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
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|
|
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 |
Pharmacology & Linda Crnic Institute for Down Syndrome
|
Street address |
RC1-N, Mail Stop 8303, Rm. P18-6114 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 |
SAMN05415215 |
SRA |
SRX1959668 |