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Sample GSM2877935

Query DataSets for GSM2877935

Status

Public on Nov 20, 2018

Title

Antral_follicle_C8C2G

Sample type

SRA

Source name

Granulosa cells from antral follicle

Organism

Homo sapiens

Characteristics

tissue: Ovary
developmental stage: Antral

Extracted molecule

total RNA

Extraction protocol

Each oocyte and 10 randomly selected granulosa cells were transferred into lysis buffer using a mouth pipette. The reverse transcription reaction was performed on the whole-cell lysate and terminal deoxynucleotidyl transferase was used to add a poly A tail to the 3′ end of the first-strand cDNAs, and then 20 cycles of PCR were performed to amplify the single-cell cDNA
RNA libraries were prepared according to instructions of Kappa Hyper Prep Kit (Kappa Biosystems).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

C8C2G

Data processing

Illumina bcl2fastq version 2.19 were used to the basecalling.
Sequenced reads with 10% low quality bases, adapters and artificial sequences (including UP1, UP2, polyA sequences) introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the UCSC human hg19 reference using Tophat2 (v2.1.0) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs

Submission date

Dec 06, 2017

Last update date

Apr 03, 2020

Contact name

Zhiqiang Yan

E-mail(s)

zqyan@pku.edu.cn

Organization name

Peking University

Street address

No.5 Yiheyuan Road Haidian District