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| Status |
Public on Oct 04, 2018 |
| Title |
Patients with antibody mediated rejection S5 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
cells: Whole blood cells
human origin: human
organ: blood
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| Growth protocol |
Kidney transplanted patients with stable graft function, antibody mediated rejection or t cell mediated rejection episodes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (tRNA) was isolated from blood cells contained in PAXgene Blood RNA Tubes with the PAXgene blood miRNA Kit (PreAnalytix, Qiagen, Hilden, Germany) according to the manufacturers instruction. Total RNA concentration and quality of each sample were determined with the NanoDrop ND-Lite (peqlab, Erlangen, Germany) and Qubit fluorometer (ThermoFisher Scientific, Darmstadt, Germany). Dependent on quantity and quality of RNA, six samples from patients with ABMR, six samples from patients with SGF and 4 samples from patients with TCMR were chosen for high-throughput sequencing.
The “TruSeq Stranded Total RNA library PrepKit with Ribo-Zero” kit (Illumina, San Diego, CA, USA) was used to prepare cDNA libraries for small RNA sequencing from a minimum of 100ng of total RNA isolated from the whole blood of patients with Tx according to manufacturer’s instruction. RNA quality was assessed on a bioanalyzer using the RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and only RNA with a RIN >8 was considered for further processing. After quality control (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany). The final cDNA libraries were quality checked (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany), quantified (Qubit dsDNA HS Assay Kit, Invitrogen, Darmstadt, Germany) and were paired-end (100 bp) sequenced on a HiSeq2500 Illumina Next Generation Sequencing Device (Illumina, San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ABMR
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| Data processing |
GRCh37/hg19 genome with TopHat2 in very sensitive settings for Bowtie2 and GENCODE annotation release 19 (GRCh37.p13)
Gene expression was quantified by HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.
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| Submission date |
Sep 28, 2018 |
| Last update date |
Oct 04, 2018 |
| Contact name |
Pawel Durek |
| E-mail(s) |
pawel.durek@drfz.de
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| Organization name |
Deutsches Rheuma-Forschungszentrum
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| Street address |
Charitéplatz 1
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| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE120649 |
The Regulation of IFN Type I Pathway Related Genes RSAD2 and ETV7 Specifically Indicate Antibody-Mediated Rejection After Kidney Transplantation |
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| Relations |
| BioSample |
SAMN10144250 |
| SRA |
SRX4776958 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3406959_s5.txt.gz |
216.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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