|
| Status |
Public on Feb 02, 2018 |
| Title |
sRNA_E14_IP_Ago1 |
| Sample type |
SRA |
| |
|
| Source name |
IP Ago1 in E14 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: E14 cells 129/Ola background
tissue: Blastocyst mouse ES cells
treatment: Formaldehyde crosslink IP
genotype: Wild Type
|
| Treatment protocol |
Cells were crosslinked with formaldehyde and AGO1/2 IP was performed.
|
| Growth protocol |
mESC were cultured in DMEM, 15% serum, 100 U/mL LIF, 01. mM Beta-mercaptoethanol, 1% Pen/Strep on gelatine coated plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries and 20-100 ng for the IP libraries.
Small RNA libraries were prepared for sequencing using standard Illumina protocols by the Fasteris company (Switzerland).
small RNA-Seq
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Single stranded TrueSeq illumina small RNA library Protocol
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 and mature miRNAs (miRbase r21) using Bowtie allowing up to 2 mismatches, multiple mappers were randomly matched to single position
reads counts from bowtie alignement were parsed against mature miRNA index (miRbase r21)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count
|
| |
|
| Submission date |
Apr 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Constance Ciaudo |
| E-mail(s) |
cciaudo@ethz.ch, ciaudobeyer@gmail.com
|
| Phone |
+41 44 633 08 58
|
| Organization name |
ETH
|
| Department |
D-BIOL
|
| Lab |
Chair of RNAi and Genome Integrity
|
| Street address |
Otto-Stern-Weg 7
|
| City |
Zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE80211 |
Small RNA profiling of WT E14, Ago2_KO and Ago1_KO mouse embryonic stem cells before and after XEN conversion and small RNA profiling after Immunoprecipitation of AGO1&2 proteins in WT E14, Ago1_KO and Ago2_KO mESCs. |
| GSE80454 |
Roles of Argonaute protein in mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN04687762 |
| SRA |
SRX1700573 |
