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Status |
Public on Sep 08, 2015 |
Title |
K-562 BRD3.3235 |
Sample type |
SRA |
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Source name |
Cell line
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Organism |
Homo sapiens |
Characteristics |
shRNA: BRD3.3235 diagnosis: Leukemia
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Extracted molecule |
total RNA |
Extraction protocol |
Cells were harvested, flash frozen on dry ice, and RNA was extracted using RLT plus buffer (Qiagen) reagent. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Description |
Sample 85 processed_data file: BRD_KD_counts.tsv processed_data file: BRD_KD_RPKMs.tsv
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Data processing |
The paired-end and single-read fragments were trimmed on their 5' end (6 cycles PE100, 2 cycles SR50 NEB RNA sample prep protocol) Adaptors were removed using cutadapt v1.4.2 and reads with a length of less than 18bp in any read of the pair were discarded. (Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, Read2: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT) The trimmed and adaptor free reads were aligned against rDNA of the respective organism using bowtie2 v2.0.2 for paired-end and bowtie v0.12.5 for single-end reads. (100PE: bowtie2 (v2.0.2) --sensitive-local, 50SR: bowtie v0.12.5 -v 3 -k 1 --tryhard --chunkmbs 256) The rRNA cleaned paired-end reads were aligned against the transcriptome to estimate the fragment size and the standard deviation of the fragment size using bwa v0.6.2. ( -N 1 -n 1 -a 1000) The rRNA cleaned reads were aligned to the genome with the TopHat splice junction mapper for RNA-Seq reads using splice junction guidance of a GTF annotation file (mouse: mm10, RefSeq from UCSC, 2012/5/23, human: hg19, RefSeq 2012/11/30) (--segment-mismatches 1 --max-multihits 20 --library-type fr-firststrand --initial-read-mismatches 2, 100PE: --segment-length 25 --mate-inner-dist value from transcriptome alignment --mate-std-dev value from transcriptome alignment; SR50: --segment-length 24) The uniquely aligning reads were used for counting per gene with htseq-count v 0.6.1p with the overlap-resolution mode option set to 'union' using the processed RefSeq-annotated gene database (supplementary files refseq.hg19.2014_0110.imp.merged.uniq.exons.fulltable.gtf and refseq.mm10.2014_3006.imp.merged.uniq.exons.fulltable.gtf) genome build: hg19 / mm10 processed data files format and content: Tab-delimited text files containing raw counts and RPKMs for given samples
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Submission date |
Dec 02, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Philipp Rathert |
E-mail(s) |
philipp.rathert@ibtb.uni-stuttgart.de
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Organization name |
University Stuttgart
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Department |
Biochemistry
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Street address |
Allmandring 31
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City |
Stuttgart |
State/province |
Germany |
ZIP/Postal code |
70569 |
Country |
Germany |
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Platform ID |
GPL18460 |
Series (1) |
GSE63782 |
Transcriptional plasticity promotes primary and acquired resistance to BET bromodomain inhibition |
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Relations |
BioSample |
SAMN03248145 |
SRA |
SRX793257 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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