GSM2043606: villous_S9

Source name placental villous tissue
Organism Homo sapiens
Characteristics ercc spike-in pool: Mix_1
fetal sex: Female
gestational age (weeks): 41.43
tissue: placental villous tissue
Treatment protocol Placenta samples were collected and dissected post-delivery and incubated in RNAlater solution at 4 degrees celcius for 24 hours before being stored at -80 degrees celcius.
Extracted molecule total RNA
Extraction protocol RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with mix 1 or mix 2 of the 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts.
Ribosomal RNAs were depleted from samples using Ribo-Zero Gold. and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. Sequencing was performed on the Illumina Hi-Seq 2500 using a 100bp paired-end protocol at the Australian Cancer Genomics Facility in Adelaide.

Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500

Data processing Libraries were sequenced on the Illumina Hi-Seq 2500. Basecalls were performed with CASAVA version 1.8.
Sequence adapters were trimmed using AdapterRemoval with options --trimns, --minlength 20. Trimmed RNA-Seq reads were aligned to known UCSC hg19 genes and the hg19 genome using Bowtie 2 v2.1.0 and TopHat v2.0.9 with options --library-type=fr-firststrand --mate-inner-dist -20 --mate-std-dev 180. UCSC hg19 reference genome and transcriptome was obtained through Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Aligned RNA-Seq reads were summarised using the summarizeOverlaps algorithm with the UCSC known genes hg19 GTF file using the the options overlapMode=``Union'', ignoreStrand=FALSE, singleEnd=FALSE, fragments=TRUE to generate a table of unique read counts per gene for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: A count table of uniquely mapped read pairs overlapping genes.

样本名称 胎盘绒毛组织（placental villous tissue）
物种 智人（Homo sapiens）
样本特征 ERCC外参混合池：Mix_1
胎儿性别：女性
孕周：41.43周
组织类型：胎盘绒毛组织
样本处理流程 胎盘样本于分娩后采集并解剖，置于4℃ RNAlater溶液中静置24小时，随后转移至-80℃冻存。
提取分子 总RNA（total RNA）
提取流程 采用TRIzol试剂，按照厂商说明书从16份胎盘样本中提取总RNA。所有样本均掺入96种External RNA Controls Consortium（ERCC）ExFold RNA转录本的Mix 1或Mix 2外参。采用Ribo-Zero Gold试剂盒去除样本中的核糖体RNA，随后使用Illumina TruSeq Stranded Total RNA样本制备试剂盒构建测序文库。测序工作于澳大利亚阿德莱德的澳大利亚癌症基因组学平台完成，使用Illumina HiSeq 2500测序仪，采用100bp双端测序策略。

文库构建策略 RNA测序（RNA-Seq）
文库来源 转录组（transcriptomic）
文库选择方式 cDNA
测序仪器型号 Illumina HiSeq 2500

数据处理流程 测序文库在Illumina HiSeq 2500上完成测序，碱基识别使用CASAVA v1.8版本完成。使用AdapterRemoval工具修剪序列接头，参数设置为--trimns、--minlength 20。使用Bowtie 2 v2.1.0和TopHat v2.0.9工具，将修剪后的RNA测序读段比对至UCSC hg19已知基因及hg19参考基因组，比对参数为--library-type=fr-firststrand --mate-inner-dist -20 --mate-std-dev 180。UCSC hg19参考基因组及转录组数据从Illumina iGenomes平台获取（https://support.illumina.com/sequencing/sequencing_software/igenome.html）。使用summarizeOverlaps算法，结合UCSC hg19已知基因GTF文件，参数设置为overlapMode="Union"、ignoreStrand=FALSE、singleEnd=FALSE、fragments=TRUE，对比对后的RNA测序读段进行计数汇总，以生成每个样本的单基因唯一读段计数表。
基因组组装版本：hg19
补充文件格式及内容：覆盖基因的唯一比对读对计数表。