|
| Status |
Public on Jul 30, 2014 |
| Title |
Nanog-GFP SNEL#3 |
| Sample type |
SRA |
| |
|
| Source name |
Nanog-GFP SNEL
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed; 129Sv/Jae and C57/Bl6
cell type: Induced pluripotent stem cells
echotype: pluripotent
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bisulphite treatment and sequencing library preparation were performed as previously described (Lister et al., 2011). Briefly, genomic DNA from each iPSC and ESC was fragmented by sonication prior to ligation of methylated sequencing adaptors. Fragments were size-selected by gel electrophoresis and purification, treated with sodium-bisulphite and amplified with 4 cycles of PCR to generate libraries that were sequenced on the Illumina HiSeq platform.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NGFP_SNEL_3
|
| Data processing |
MethylC-seq data was processed as previously described (Lister et al., 2011, PMID: 21289626).
Genome_build: mm10
Supplementary_files_format_and_content: The processed data for the allc_<sample>_<chr>.tsv files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, total coverage, and methylation call. This is a tab delimited file.
|
| |
|
| Submission date |
Jul 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE59696 |
The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors |
|
| Relations |
| BioSample |
SAMN02944819 |
| SRA |
SRX665156 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1448292_allc_NGFP_SNEL_3_1.tsv.gz |
282.4 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_10.tsv.gz |
190.3 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_11.tsv.gz |
189.8 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_12.tsv.gz |
170.3 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_13.tsv.gz |
172.8 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_14.tsv.gz |
166.2 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_15.tsv.gz |
147.1 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_16.tsv.gz |
140.8 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_17.tsv.gz |
136.0 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_18.tsv.gz |
131.1 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_19.tsv.gz |
90.5 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_2.tsv.gz |
267.1 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_3.tsv.gz |
221.3 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_4.tsv.gz |
217.5 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_5.tsv.gz |
222.0 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_6.tsv.gz |
215.8 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_7.tsv.gz |
200.9 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_8.tsv.gz |
188.9 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_9.tsv.gz |
186.2 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_X.tsv.gz |
179.0 Mb |
(ftp)(http) |
TSV |
| GSM1448292_allc_NGFP_SNEL_3_Y.tsv.gz |
12.5 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
