|
| Status |
Public on Oct 30, 2017 |
| Title |
TruSeq4_IP_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Gfi1Cre/+;Rpl22HA/HA
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: neonatal pups P1
tissue: liver
antibody: HA
|
| Treatment protocol |
Untreated
|
| Growth protocol |
Mice were kept until P30
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell-type specific RNA from livers of P30 mice was obtained using the RiboTag protocol. Briefly, liver tissue expressing HA-tagged ribosomes in specific cells was homogenized followed by immunoprecipitation of the tagged ribosomes using an HA antibody. The RNA was extracted from the immunoprecipitated ribosomes to obtain cell-type specific enriched transcripts (IP samples). An aliquot of the homogenized tissue before immunoprecipitation was used for total RNA extraction (input samples).
Libraries were prepared from 0.25ng/4ng/70ng using NuGEN Ovation RNA-Seq system V2, TaKaRa SMARTer Stranded Total RNA-Seq Kit , TaKaRa SMART-Seq v4 Ultra Low Input RNA kit , Illumina TruSeq RNA Library Prep Kit v2 and NEBNext® Ultra™ Directional RNA Library Prep Kit, per manufacturer’s instructions, with minor modification for NuGEN prepared samples. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence. In order to maintain the best quality, all the reads were further trimmed to 60bp and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) and count per Million mapped reads(CPM) were calculated for each sample.
We evaluated the robustness of different kits for detecting enrichment (IP/input RNA > 1) or depletion (IP/input RNA < 1) of transcripts in the translatome (IP samples) compared to the transcriptome (input samples). Features with raw read counts ≥ 20 in input samples and with enrichment or depletion factor ≥ 2 were included as enriched (IP/Input ≥ 2) or depleted transcripts (Input/IP ≥ 2).
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Sep 25, 2017 |
| Last update date |
May 11, 2021 |
| Contact name |
yang song |
| E-mail(s) |
ysong@som.umaryland.edu
|
| Organization name |
University of Maryland in Baltimore
|
| Department |
Department: Institute for Genome Sciences
|
| Street address |
HSF-3, 3rd Floor; 670 W Baltimore St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE104213 |
A Comparative Analysis of Library Prep Approaches for Sequencing Low Input Translatome Samples |
|
| Relations |
| BioSample |
SAMN07693580 |
| SRA |
SRX3214325 |
