|
| Status |
Public on Jun 25, 2020 |
| Title |
Tsix +/- day 0 (replicate 1) |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tsix +/-
developmental stage: undifferentiated ES cells
Sex: female
strain: C57BL/6J x CAST/EiJ hybrid
|
| Treatment protocol |
Nuclei were isolated, permeabilized for nuclear run-on. Nascent transcripts were labeled with Biotin-11-ATP, Biotin-11-CTP, Biotin-11-GTP, Biotin-11-UTP
|
| Growth protocol |
Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium or differentiated accordingly
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol extraction,biotin-labeled RNA was enriched using strepatividing pulldown
Library preparation is combined to PROseq experiment (three individual streptavidin enrichment steps) and was performed as described in (Kwak et al. 2013 and Mahat et al. 2016); Strand-specific RNA sequencing, multiplexed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ES-d0_Rep1
|
| Data processing |
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using bowtie2 and novoalign
allele specific reads were called by custom script (Pinter et al., 2012)
Metagene analysis was done by deeptools2 (Ramirez et al., 2016) and custom python scripts
Strand-specific PRO-seq coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million with deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (fwd:watson, rev:crick strand) and RPKM normalized
|
| |
|
| Submission date |
Dec 21, 2018 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Eric Aeby |
| E-mail(s) |
aeby@molbio.mgh.harvard.edu
|
| Organization name |
Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School
|
| Department |
Department of Molecular Biology and Department of Genetics
|
| Lab |
Lee Lab
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE118943 |
DCP1A knockout: transcriptome-wide characterization |
| GSE124289 |
Genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) during female mouse ES differentiation |
|
| Relations |
| BioSample |
SAMN10637964 |
| SRA |
SRX5174621 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3528170_ERa7-1_ES-d0_Rep1.b2def.fwd.RPKM.bw |
41.5 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7-1_ES-d0_Rep1.b2def.rev.RPKM.bw |
40.9 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7_1_ES-d0_Rep1_cas.fwd.RPKM.bw |
2.7 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7_1_ES-d0_Rep1_cas.rev.RPKM.bw |
2.7 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7_1_ES-d0_Rep1_mus.fwd.RPKM.bw |
9.3 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7_1_ES-d0_Rep1_mus.rev.RPKM.bw |
9.2 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7_1_comp.fwd.RPKM.bw |
23.6 Mb |
(ftp)(http) |
BW |
| GSM3528170_ERa7_1_comp.rev.RPKM.bw |
23.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
