|
| Status |
Public on Mar 26, 2013 |
| Title |
HeLaS3.siCtrl.R |
| Sample type |
SRA |
| |
|
| Source name |
HeLa S3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa S3
treatment: siRNA control
internal reference: 120123_lane7_VLB1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with TRIzol, depleted of polyA+ transcripts with oligo-dT beads, and depleted of rRNA with the Ribominus kit
libraries were prepared with the dUTP strand-specific protocol. After RT and second-strand synthesis, cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 ligase (Enzymatics). Fragments of 200±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after removal of the 2nd strand with heat-labile UDG (Roche).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
depleted of polyA+ and rRNA
|
| Data processing |
Trimmed sequences in 3' to 36 nts
mapped to hg19 with BOWTIE -m40 -v2
assigned counts to gene models in ENS65 with DEGseq
Genome_build: hg19 (HeLaS3) or mm9 (germ cells)
Supplementary_files_format_and_content: RPKM and count table for ENS65
|
| |
|
| Submission date |
Mar 22, 2013 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE45442 |
SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors [RNA-Seq] |
| GSE45489 |
SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors |
|
| Relations |
| SRA |
SRX254634 |
| BioSample |
SAMN01986103 |
