|
| Status |
Public on Nov 21, 2016 |
| Title |
EB CTL 4d |
| Sample type |
SRA |
| |
|
| Source name |
mES cells, control, 4d
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: CTL
cell type: embryonic stem cells
time point: 4d
|
| Growth protocol |
WT and Tet3 KO mESCs differentiating into neuroectoderm under SFEB culture (days 6 and 10). Control and Tet3-overexpressing mESCs in non-permissive neural differentiation conditions containing FBS (days 4 and 7).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For mES cell samples, total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
For mES cell samples, multiplexed libraries were constructed using SOLiD Total RNA-seq kit. Libraries were sequenced on the SOLiD 5500 platforms according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
Tet3 KO mouse ESCs were generated in-house. They were from mice (C57BL/6-background) bearing the Tet3 floxed alleles, followed by excision of the floxed exon by transient expression of Cre recombinase.
Processed data file: ES_Cell_RPKM.txt
|
| Data processing |
Bulk RNA-Seq data was mapped against the mouse mm9 reference genome using tophat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site. Sequencing read coverage per gene was counted using HTSeqcount (-m union -s yes -t exon -i gene_id, http://www-huber.embl.de/users/anders/HTSeq/).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: ES_Cell_RPKM.txt: Tab-delimited text file includes RPKM values for each sample.
|
| |
|
| Submission date |
Oct 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
ANJANA RAO |
| E-mail(s) |
arao@lji.org
|
| Organization name |
La Jolla Institute for Allergy and Immunology
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16790 |
| Series (2) |
| GSE89314 |
Tet-dependent transcriptional programs during mESC differentiation |
| GSE89316 |
Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling |
|
| Relations |
| BioSample |
SAMN05953619 |
| SRA |
SRX2310401 |
