|
| Status |
Public on Jun 25, 2018 |
| Title |
Chromatin control |
| Sample type |
SRA |
| |
|
| Source name |
HeLa_Chromatin control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
genotype/variation: wild type (control)
treated with: none
molecule subtype: Chromatin RNA
|
| Treatment protocol |
HeLa cells were transfected with control Spt5 RNAi plasmids along with a plasmid direcing puromycin resistant gene. Transfected cells were selected with puromycin. 72 hours post transfection cell were trearted with TNFα for one hour.
|
| Growth protocol |
Hela cells were grown using standard growth conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were separated into cytosol and chromatin fractions which were then subjected to RNA extraction and DNAseI tretment
Cytosolic and chromatin associated RNA samples were depleted of ribosomal RNA using Ribozero gold rRNA depletion kit (Epicentre). RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina)without poly A capturing. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 4 samples on one lane. Paired-end 101 bp reads were sequenced on Illumina HiSeq 2500 rapid mode with cBot on HiSeq Rapid Flow Cell v1 HCS: 2.0.12.0.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Demultiplexing and base calling was done with CASAVA 1.8.2 (RTA 1.17.21.3).
Reads were aligned to the hg19 genome built using Tophat (v2.0.04) with an annotation file (refSeq from igenomes UCSC).
Raw gene read counts were calculated by HTSeq using refSeq gene annotations (igenomes).
Normalized gene counts were calculated with DESeq. Chromatin and cytosol samples were analysed separately.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing gene counts
|
| |
|
| Submission date |
Jun 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rivka Dikstein |
| E-mail(s) |
rivka.dikstein@weizmann.ac.il
|
| Organization name |
The Weizmann Institute of Science
|
| Street address |
2 Hertzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE70268 |
RNA-seq of cytosolic and chromatin-associated transcripts following TNFα and Spt5 KD |
|
| Relations |
| BioSample |
SAMN03794770 |
| SRA |
SRX1073581 |
