|
| Status |
Public on Mar 03, 2022 |
| Title |
RNAseq_Jurkat_WT_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat T-ALL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat
genotype: WT
|
| Growth protocol |
Cells were maintained in suspension culture at a density between 0.3X10^6 and 1X10^6 in 90% GlutaMAX supplemented RPMI 1640, 10%FBS. Cells were split 1:2 to 1:4 every 2-4 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were harvested by centrifugation and RNA was extracted using the Qiagen RNeasy Mini Kit.
500 ng of RNA was used going into the KAPA stranded mRNA-seq library preparation kit used according to manufacturer's recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA sequencing
|
| Data processing |
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25 –interleaved --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --interleaved --overlap 20 --minimum-length --adapter "A[100]" --adapter "T[100]").
Reads were aligned to the human reference genome (hg19) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts).
Transcripts were assembled using stringtie (version 2.0.6; parameters: -e) with GENCODE annotation (release 19).
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts from STAR output: <gene ID> <counts for unstranded RNA-seq> <counts for the 1st read strand aligned with RNA> <counts for the 2nd read strand aligned with RNA>
Supplementary_files_format_and_content: Gene abundance from stringtie output: <Gene ID> <Gene Name> <Reference> <Strand> <Start> <End> <Coverage> <FPKM> <TPM>
|
| |
|
| Submission date |
Dec 30, 2020 |
| Last update date |
Mar 03, 2022 |
| Contact name |
Sara Hetzel |
| E-mail(s) |
hetzel@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Genome Regulation
|
| Lab |
Meissner Lab
|
| Street address |
Ihnestraße 63
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE164040 |
Acute lymphoblastic leukemia displays a distinct highly methylated genome |
|
| Relations |
| BioSample |
SAMN17185283 |
| SRA |
SRX9756763 |
