-
EXPR
P05
Project ID
OEP003206
Project NameSingle cell profiles of ICC with GOLP treatment
Experiment TypeTranscriptomic single cell
OEX019191
-
EXPR
P04
Project ID
OEP003206
Project NameSingle cell profiles of ICC with GOLP treatment
Experiment TypeTranscriptomic single cell
OEX019190
-
EXPR
P03
Project ID
OEP003206
Project NameSingle cell profiles of ICC with GOLP treatment
Experiment TypeTranscriptomic single cell
OEX019189
-
EXPR
P02
Project ID
OEP003206
Project NameSingle cell profiles of ICC with GOLP treatment
Experiment TypeTranscriptomic single cell
OEX019188
-
EXPR
P01
Project ID
OEP003206
Project NameSingle cell profiles of ICC with GOLP treatment
Experiment TypeTranscriptomic single cell
OEX019187
-
EXPR
Metagenomic
Project ID
OEP001920
Project Namemangrove_project
Experiment TypeMetagenomic
OEX012906
-
EXPR
test step by step single
Project ID
OEP000774
Project Nametest step by step project
Experiment TypeSynthetic
ProtocolProcessing methods used in the experiment (experiment design), for example: CD4+ T-cells were isolated from the C57BL/6 mice spleen by sorting after negative magnetic selection. Naive CD4+ T cells were characterized as CD4+CD25?CD44loCD62LhiCD127hi and effector memory (Tem) as CD4+CD25?CD44hiCD62LloCD127int-hi. Naive and Tem CD4+T-cells were activated by plate bound anti-CD3 (1μg/ml; clone 145-2C11, MAB484-500, R&D Systems) and soluble anti-CD28 (5μg/ml; clone 37.51, 16-0281-86, eBioscience) with IL-6 (20ng/ml, 406-ML-025/CF, R&D Systems) for 1 hour. After treatment, CD4+ T-cells were cross-linked, lysed and sonicated to obtain sheared DNA. Incubation with anti-STAT1 (sc-592, Santa Cruz Biotechnology) or anti-STAT3 (sc-482, Santa Cruz Biotechnology) antibodies was performed over-night after immunoprecipitation using ProteinG/A magnetic beads. DNA isolation for the immunoprecipitated samples and the corresponding input was execute following the Phenol/Chloroform/Isoamyl alcohol 25:24:1 protocol. DNA was precipitated adding 10ugr of Glycogen and 0.3M Sodium acetate in 70% ethanol. ChIP-seq libraries for STAT1 and STAT3 were performed following the Ion ChIP-Seq Library Preparation on the Ion Proton TM System (# 4473623) according to manufacturer's instructions. DNA fragments obtained from the DNA extraction were first end-repaired and after ligate the adaptors compatible to Ion Proton System, libraries were amplified and size-selected in order to sequence the inserts approximately between 100-250bp.
OEX002246
-
EXPR
OEX_weifen_2208091019
Project ID
OEP003561
Project NameEpigenetic regulation of human-specific gene expression in prefrontal cortex
Experiment TypeGenomic
Protocol0.15 g of PFC tissue was grinded into powder on dry ice and cross-linked in 1% formaldehyde for 10 min at room temperature. Then, the reaction was quenched by adding glycine, and the tissue was further homogenized in a glass douncer. Cell pellets were lysed successively in Farnham Lysis buffer (5mM PIPES pH 8.0, 85mM KCl, 0.5% NP-40) and Lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH8.0) on ice. Nuclei were sonicated for 5 seconds at 15% power of Misonix Q700 for 90 times with 10 seconds refractory period. The supernatant was diluted in Dilution buffer (1.1% Triton X-100, 0.25% sodium deoxycholate, 1.2mM EDTA, 167mM NaCl, 16.7mM Tris-HCl, pH8.0) and transferred to the Protein A/G magnetic beads which were pre-incubated with H3K4me3 (Millipore, 07-473) or H3K27ac (Active Motif, 39133) antibody in PBS with 0.5% BSA at 4 °C for at least 4 h, and rotated overnight at 4 °C. Beads were then washed sequentially with Low salt wash buffer (0.1% SDS, 1% Triton X-100, 0.25% sodium deoxycholate, 1mM EDTA, 150mM NaCl, 50mM Tris-HCl, pH8.0), High salt wash buffer (0.1% SDS, 1% Triton X-100, 0.25% sodium deoxycholate, 1mM EDTA, 500mM NaCl, 50mM Tris-HCl, pH8.0), LiCl wash buffer (500mM LiCl, 1% NP-40, 1% sodium deoxycholate, 100mM Tris-HCl, pH8.0), TE buffer, and eluted with Elution buffer (1% SDS, 0.1M NaHCO3) at 65°C. After adding NaCl to final 200mM, chromatin in the supernatant was reverse crosslinked overnight at 65 °C, and then treated with RNase A (final concentration of 0.1 μg/μl) for 0.5 h at 37 °C and proteinase K (final concentration of 0.4 μg/μl) for 1 h at 55 °C. DNA was extracted with QIAquick MinElute PCR Purification Kit (Qiagen, 28104). Genomic DNA without the immunoprecipitation was used as an input control. Sequencing library was prepared by using Illumina Truseq ChIP Sample Prep Kit (Illumina, USA). The pooled libraries were sequenced on Illumina HiSeq 2000 platform using the 100-bp singled-ended sequencing protocol.
OEX020247
-
EXPR
OEX_weifen_2208091005
Project ID
OEP003561
Project NameEpigenetic regulation of human-specific gene expression in prefrontal cortex
Experiment TypeTranscriptomic
ProtocolTotal RNA was isolated using TRIzol (Invitrogen, USA) according to the manufacturer's instructions. The RNA quality was assessed with Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number (RIN) values greater than 7.5 were selected. 1 μg total RNA from PFC sample was used to construct the sequencing library following the TruSeq Stranded mRNA Sample Prep (Illumina, USA) protocol. The libraries were pooled and sequenced on Illumina HiSeq 4000 platform with the 150-bp singled-ended mode.
OEX020246
-
EXPR
OEP002901_RSA_scRNAseq
Project ID
OEP002901
Project NameThe recurrent spontaneous abortion (RSA) patients' abnormal decidual microenvironment
Experiment TypeTranscriptomic single cell
ProtocolOn arrival, freshly human decidual tissues were transferred rapidly to a 10-cm dish and washed twice with 1x cold PBS(Gibco). Each tissue was trimmed into 1-mm3 pieces and digested for 45 min each at 37℃ with medium containing 1 mg/mL collagenase IV (Gibcol, 17104019) and 1 U/mL dispase II (Gibcol, 17105041). The cell suspensions were filtered through a 40-μm cell-strainer nylon mesh(BD) and were collected by centrifuging at 700 × g for 10 min. Dissociated cells were washed with MACS buffer (PBS containing 1% FBS, 0.5% EDTA, and 0.05% gentamycin).
OEX014794