 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 01, 2018 |
| Title |
PTL_6_Pax_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Preterm Delivery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood RNA was isolated from PAXgene tubes using microRNA isolation kit (Qiagen) using TRIsol LS (Invitrogen) following manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol.400 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94oC and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98oC for 10 seconds, followed by 15 cycles of 98oC for 10 seconds, 60oC for 30 seconds and 72oC for 30 seconds, and finally an extension step for 5 minutes at 72oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).
Libraries were pooled in equimolar quantities and paired-end sequenced on a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 126-bases in length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ProcessedWBFORGEO.txt
|
| Data processing |
Basecalls were performed using bcl2fastq2 v2.17.
Transcript abundances were calculated using the pseudo aligment method Kallisto, without bias, bootstrapping 100 permutations over 16 cores
Transcripts were filtered so that low expressing samples (mean read count <20), or mostly unexpressed (>50% of samples NA) transcripts were removed prior to preprocessing
Relative transcript abundances were calculated using the trimmed mean of M method, implimented within EdgeR, as described by M Robinson, A Oshlack, Genome Biology 2010
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files contain count values generated from Kallisto for each sample
|
| |
|
| Submission date |
Mar 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
alison g paquette |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Systems Biology
|
| Lab |
Price
|
| Street address |
401 Terry Avenue N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE96083 |
Genome Scale Analysis of miRNA and mRNA regulation during preterm labor [whole blood] |
| GSE96097 |
Genome Scale Analysis of miRNA and mRNA regulation during preterm labor |
|
| Relations |
| BioSample |
SAMN06562435 |
| SRA |
SRX2633991 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
