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| Status |
Public on Oct 26, 2015 |
| Title |
HF-37231 |
| Sample type |
SRA |
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| Source name |
Colonic biopsy
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| Organism |
Homo sapiens |
| Characteristics |
disease state: UC
inventory sample name: HF-37231
tissue diagnosis: No Dx
remission at week 10: Non-remitter
prior anti.tnf: Naive
tnf ir: ND
tissue: colonic biopsy
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| Treatment protocol |
None
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| Growth protocol |
N/A
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNAlater® biopsies were homogenized using Tissuelyzer (Qiagen, Hilden, Germany) and ribonucleic acid (RNA) was isolated using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) according to manufacturer instructions.
Total RNA (RNA integrity number > 5; 250 ng) was put into the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and run in conjunction with Biomek liquid handling platforms (Beckman Coulter Life Sciences).
RNA libraries were evaluated using the Agilent 2200 TapeStation HighSensitivity D1K Tape and quantitative polymerase chain reaction (qPCR) with the KAPA Library Quantification Kit for Illumina sequencing.
2 nM of library (12 samples per lane) was loaded for cluster generation and sequenced on the Illumina HiSeq 2000 Sequencing System at 2 × 50 base pairs read length plus index read.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Patient ID: HF-37231; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963064
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| Data processing |
Reads that passed quality filters were determined, and fastq files were generated by Illumina CASAVA v1.8
50bp Illumina paired-end reads were aligned to build 37 of the NCBI human genome using Bioconductor package, HTSeqGenie version 3.10.1 (Pau and Reeder, 2014). The alignment was performed using GSNAP (Genomic Short-read Nucleotide Alignment Program) version ’2013-03-31’ (Wu and Nacu, 2010).
The Bioconductor package, DESeq2 (version 1.2.6) (Love et al., 2014), was used to normalize expression across samples and identify genes that were significantly differentially expressed using the default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values
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| Submission date |
Sep 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark McCreary |
| E-mail(s) |
[email protected]
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| Phone |
6502254332
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| Organization name |
Genentech
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| Department |
Bioinformatics
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| Street address |
1 DNA Way, MS 93
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| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE72819 |
Gene expression of baseline biopsies from etrolizumab-treated ulcerative colitis (UC) patients |
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| Relations |
| BioSample |
SAMN04041628 |
| SRA |
SRX1211317 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1872906_R1518_LIB12312_SAM9963064_L3_NXG16056.counts_gene_exonic.tab.gz |
351.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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