title: Blebbistatin 3

city: Seongnam

first: Jin Man

last: Kim

address: CHA BioComplex, Pangyoro 335

institute: CHA University

data_processing:
100nt paired-end sequencing by Illumina HiSeq4,000
The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer
Tophat v2.0.13 incorporating the Bowtie v2.2.3 algorithm were used to perform the alignment
Cufflinks v2.2.1 was used to assemble aligned reads into transcripts and to estimate their abundance
The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) from Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Embryo

extract_protocol:
Submandibular glands were collected and RNA was harvested using RNAeasy kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: Submandibular gland

tag: age


title: sham3

status: Public on Sep 25 2019

type: SRA

city: beijing

first: hui

middle: yun

last: du

state: beijing

address: 2 Anzhen Rd, Chaoyang District, Beijing

department: the Beijing Institute of Heart, Lung, and Blood Vessel Diseases

country: China

institute: Beijing Anzhen Hospital, Capital Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Multiplex Small RNA Library Prep Set for Illumina was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Heart

tag: group

value: sham

tag: strain


title: Treatment 1_hMeDIP-seq

city: nanning

first: xuefang

last: mei

address: 100, Daxue Road, Xixiangtang Area, Nanning, China

institute: College of Animal Science and Technology, Guangxi University

library_source: genomic

data_processing:
library strategy: hMeDIP-seq
Base calling were performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Bubalus genome (NCBI UMD_CASPUR_WB2) using HISAT2 software (V2.1.0).
hMeDIP enriched regions (peaks) with statistical significance were identified for each sample, using a q-value threshold of 10-5 by MACS v2.
hMeDIP enriched regions (peaks) were annotated by the nearest gene using the newest NCBI database.
Differentially hydromethylated regions (DhMRs) within promoter between two groups with statistically significant were identified by diffReps (Cut-off: log2FC=1.0, p-value=0.05).
Genome_build: NCBI UMD_CASPUR_WB2
Supplementary_files_format_and_content: The Ded format files contain genomic alignment result for the reads which passed Solexa CHASTITY quality filter (*_Bubalus_bubalis_UMD_CASPUR_WB2_hisat2_alignment.bed.gz, based on NCBI UMD_CASPUR_WB2).The xlsx format files contain all DNA methylation status of gene promoters and the gene body regions in all samples (*_peak_annotation.xlsx files).

molecule: genomic DNA

organism: Bubalus bubalis

source_name: treatment_dendritic cells

extract_protocol:
The genomic DNA of DCs were used for hMeDIP and library construction; it was isolated from each individual sample using a DNeasy Blood & Tissue Kit (Qiagen, USA). Quantification and quality assurance were evaluated using the NanoDrop 1000 (Agilent, USA).
To generate the library, the products of the hMeDIP, as well as the supernatant input DNA, were purified using Qiagen MinElute columns and eluted in 16 μL of elution buffer (Qiagen, USA). Fourteen cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns; then, a final size selection (~300-600 bp) was performed using AMPure XP beads. Quality control of the libraries was performed by the Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kitChip Kit (Agilent, USA). An aliquot of each library was diluted in EB to 5 ng/μL, and 1 μL was used in real-time PCR reactions to confirm enrichment of the hydroxymethylated region.

value: water buffalo

tag: source cell type

value: peripheral blood mononuclear cells

tag: cell type

value: PBMCs-derived dendritic cells

tag: treatment

value: Fasciola gigantica excretory/secretory products (FgESPs)

tag: medip antibody

value: a human monoclonal anti-5-hydroxymethylcytosine antibody (Diagenode, USA)


title: yccT mutant_H2O2 treated_rep2

city: Saint Paul

first: Sinisa

last: Vidovic

state: MN

address: 1971 Commonwealth Avenue

country: USA

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the S. enterica (P125109) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: S. enterica (P125109)
Supplementary_files_format_and_content: raw read counts

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Bacterial cells

growth_protocol: Each culture of the wild type and its yccT mutant was inoculated into 100 mL of freshly preapared LB broth followed incubation at 37 C with constant shaking 190 rpm.

extract_protocol: RNA was extracted using the RNAeasy Kit from Qiagen. All bacterial samples were re-suspended in RNAprotect bacterial agent (Qiagen, Valencia, CA, USA) and stored at -20°C until RNA extraction

treatment_protocol: The Salmonella cultures reaching their mid log growth phase (i.e., OD 600 nm 0.5) were treated with 3 uM of H2O2 followed by centrifugation and washing.

tag: genotype

value: Isogenic yccT mutant

value: H2O2 treatment


title: Control_input_DNA

source_name: control_dendritic cells


title: Blebbistatin 2

country: South Korea


title: Blebbistatin 1


title: Zar-KO-GV-Rep1

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the 1Cell-stage embryo sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: Zar1/2-null Mouse GV Oocyte

growth_protocol: Growing oocytes were collected from 13.5-day old female mice, GV stage oocytes were collected from 21-day old female mice 44 h after PMSG injection and MII stage oocytes were collected 16 h after hCG injection

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

treatment_protocol: No treatment

tag: stain

value: C57BL6/ICR hybrid strain


title: Control 3


title: yccT mutant_H2O2 treated_rep1


title: yccT mutant_untreated_rep2

value: No H2O2 treatment


title: Zar-KO-GV-Rep2


title: Control 2


title: Zar-WT-MII-Rep2

source_name: Mouse MII Oocyte


title: Control 3_hMeDIP-seq


title: yccT mutant_untreated_rep1


title: Zar-KO-Growing-Rep2

source_name: Zar1/2-null Mouse Growing Oocyte


title: yccT mutant_untreated_rep3


title: Zar-KO-Growing-Rep1


title: Control 1_hMeDIP-seq


title: Treatment input DNA

data_processing:
Base calling were performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Bubalus genome (NCBI UMD_CASPUR_WB2) using HISAT2 software (V2.1.0).
MeDIP enriched regions (peaks) with statistical significance were identified for each sample, using a q-value threshold of 10-5 by MACS v2.
MeDIP enriched regions (peaks) were annotated by the nearest gene using the newest NCBI database.
Differentially methylated regions (DMRs) within promoter between two groups with statistically significant were identified by diffReps (Cut-off: log2FC=1.0, p-value=0.05).
Genome_build: UMD_CASPUR_WB_2.0
Supplementary_files_format_and_content: The Ded format files contain genomic alignment result for the reads which passed Solexa CHASTITY quality filter (*_Bubalus_bubalis_UMD_CASPUR_WB2_hisat2_alignment.bed, based on NCBI UMD_CASPUR_WB2).The xlsx format files contain all DNA methylation status of gene promoters and the gene body regions in all samples (*_peak_annotation.xlsx files).

extract_protocol:
The genomic DNA of DCs were used for MeDIP and library construction; it was isolated from each individual sample using a DNeasy Blood & Tissue Kit (Qiagen, USA). Quantification and quality assurance were evaluated using the NanoDrop 1000 (Agilent, USA).
To generate the library, the products of the (h)MeDIP, as well as the supernatant input DNA, were purified using Qiagen MinElute columns and eluted in 16 μL of elution buffer (Qiagen, USA). Fourteen cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns; then, a final size selection (~300-600 bp) was performed using AMPure XP beads. Quality control of the libraries was performed by the Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kitChip Kit (Agilent, USA). An aliquot of each library was diluted in EB to 5 ng/μL, and 1 μL was used in real-time PCR reactions to confirm enrichment of the (hydroxy)methylated region.


title: Control 2_hMeDIP-seq


title: Control 1


title: Zar-WT-GV-Rep1

source_name: Mouse GV Oocyte


title: Zar-WT-GV-Rep2


title: rrc1_Light_3

city: Austin

first: Enamul

last: Huq

state: TX

address: 205 West 24th

department: IB

institute: University of Texas at Austin

description: rRNA depleted RNA lib

data_processing:
tophat2 to align the reads to the genome
Cufflink2 to calculate the differential gene expression
ASpli to calculate the splicing activities: https://bioconductor.org/packages/release/bioc/vignettes/ASpli/inst/doc/ASpli.pdf
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM to quantify the gene expression; PSI/PIR(percentages) to quantify the splicing activities
Supplementary_files_format_and_content: Supplemental_dataset1_DGE.xlsx: excel file including the gene differential expression analysis from cufflink2. Ⅰ. CR_D_DGE: differential gene expression analysis between Col-0 wild type and rrc1 mutant in the dark condition. Ⅱ. GO_CR_D_DGE: Go term enrichment analysis of  CR_D_DGE. Ⅲ. CR_L_DGE: differential gene expression analysis between Col-0 wild type and rrc1 mutant in the light condition. Ⅳ. GO_CR_L_DGE: Go term enrichment analysis of  CR_L_DGE. Ⅴ. R_DL_DGE: differential gene analysis between rrc1 dark and rrc1 light samples.VI. phenotypic_genes_D: The genes related to rrc1  phenotype in the gene list  CR_D_DGE. VII. phenotypic_genes_L: The genes related to rrc1  phenotype in the gene list  CR_L_DGE.
Supplementary_files_format_and_content: Supplemental_dataset2_AS.xlsx: excel file including the gene differential  splicing analysis using Aspli (Including the raw counts of the splicing junction reads and PSI(percentage of exon splicing in)/PIR(percentage of intron retention. More details are included in the documents of ASpli): Ⅰ. CR_D_AS: differential splicing analysis between Col-0 wild type and rrc1 dark sample. Ⅱ. GO_CR_D_AS.agri_go: go term enrichment analysis based on gene list in CR_D_AS. Ⅲ. CR_L_AS: differential splicing analysis between Col-0 wild type and rrc1 light sample. Ⅳ. GO_CR_L_AS.agri_go: go term enrichment analysis based on gene list in CR_L_AS. Ⅴ. R_DL_AS: differential splicing analysis between rrc1 dark and rrc1 light sample. Ⅵ. CR_D_AS_pathway：pathway enrichment analysis based on gene list in CR_D_AS. Ⅶ. CR_L_AS_pathway: pathway enrichment analysis based on gene list in CR_L_AS. Ⅷ. phenotypic_genes_D: genes related to the rrc1 phenotype in gene list in CR_D_AS. Ⅸ. phenotypic_genes_L: genes related to the rrc1 phenotype in gene list in CR_L_AS.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 1/2 MS media, grew under dark conditions for 4 days

extract_protocol:
Based on the commercial protocol of the RNA extraction kit (RNeasy Mini Kit (50) from QIAGEN)
based on the commercial protocol of NEB RNA library construction kit(NEBNext® Ultra™ DNA Library Prep Kit for Illumina)

treatment_protocol: 4 days dark grown seedling, irradiated with 7 μmolm-2s-1 red light for 3hrs

value: seedlings

tag: developmental stage

value: 4 days

tag: growth/treatment

value: Grown under dark conditions for 4 days, then irradiated with red light for 3hrs

tag: genotype/variation

tag: cultivar/background


title: Treatment 3_MeDIP-seq

value: a mouse monoclonal anti-5-methylcytosine antibody (Diagenode, USA)


title: Foxo3 RANKL

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TOPHAT
RPKM were calculated using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Bone Marrow Macrophages

growth_protocol: Bone marrow was flushed from femur and tibia and cultured with M-CSF for 3 days to get bone marrow macrophages.

extract_protocol:
RNA was harvested using RLT buffer from Rneasy RNA extraction kit. mRNA was purified by poly-A+ selection. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow macropahges were treated with RANKL for 2days.

value: Foxo3 KO

value: Bone Marrow Macrophages


title: Treatment 2_MeDIP-seq


title: WT RANKL

value: WT


title: Treatment 1_MeDIP-seq


title: Zar-WT-Growing-Rep2

source_name: Mouse Growing Oocyte


title: rrc1_Light_2

description: rRNA depleted RNA lib


title: Control input DNA


title: rrc1_Dark_3

description: rRNA depleted RNA lib

value: Grown under dark conditions for 4 days


title: Zar-WT-Growing-Rep1


title: G1.Wild_type_suspension1

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the Salmonella eneterica serovar Enteritidis str. P125109 as reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 (Taxonomy ID: 550537)
Supplementary_files_format_and_content: raw read count

growth_protocol: Planktonic cells were harvested during the mid log growth phase, while biofilm samples were harvested after a two-day growth period.

extract_protocol: RNA was extracted using the RNAeasy Kit from Qiagen

treatment_protocol: Approximately 100 million colony-forming units of the wild-type and cpxR planktonic cells and biofilm were centrifuged at 1844 x g for 10 min. All bacterial samples were re-suspended in RNAprotect bacterial agent (Qiagen, Valencia, CA, USA) and stored at -20°C until RNA extraction

value: Wild type

tag: growth phase

value: Planktonic cells


title: H1.Wild_type_suspension2


title: Zar-WT-MII-Rep1


title: rrc1_Light_1

description: rRNA depleted RNA lib


title: Control 2_MeDIP-seq

value: water buffalo

value: peripheral blood mononuclear cells

value: PBMCs-derived dendritic cells


title: KO2

city: Beijing

first: Bingjie

last: Wang

address: Yiheyuan ROAD 5

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

source_name: Hiipocampus

extract_protocol:
Total RNA was isolated from freshly dissected tissue using the TRNzol Reagent kit (TIANGEN, DP405) according to the manufacturer instructions. NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hiipocampus

value: post natal day 90


title: Control 3_MeDIP-seq


title: KO3


title: rrc1_Dark_2

description: rRNA depleted RNA lib


title: rrc1_Dark_1

description: rRNA depleted RNA lib


title: KO1


title: Control 1_MeDIP-seq


title: WT2


title: E1.cpxR2biofilm

value: Isogenic cpxR mutant

value: Biofilm


title: D2.cpxR_suspension3


title: WT1


title: Liver416

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

description:
processed data file:
countsliver.csv
run0196_lane91_read*_indexD709-D504=RhLiver416-18

data_processing:
Alignment to the MMUL8.01 done with STAR
Read counts was done using FeatureCounts
Differential expression analysis was performed with DESEq2
Genome_build: MMUL8.01
Supplementary_files_format_and_content: counts

organism: Macaca mulatta

source_name: PO Betamethasone-phosphate_Liver

extract_protocol:
total RNA was extracted with Trizol per manufacturer's guidelines.
Afer polyA selection, paired-end RNA-sequencing with 75bp was done with a depth of 30M reads.

tag: gestational age

value: 132 days

tag: treatment route and drug

value: PO Betamethasone-phosphate

tag: dose

value: 0.15mg/kg x3 12h apart

tag: treatment to delivery interval

value: 5 days

value: Liver


title: WT3

tag: tissue

tag: age


title: D1.cpxR1biofilm


title: Ume6_E-ChRP_Pre-Induction_FLAG_rep2

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Data were normalized such that average value at a genomic position was 1.0
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

organism: Saccharomyces cerevisiae

growth_protocol: grown to mid-log; exponentially-growing W303 yeast cells

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, lysed by bead beating for 4 minutes, chromatin was sheared to ~300bp mean fragment length using Bioruptor high setting, ChIP was performed, crosslinks were reversed, protein was digested, RNA was degraded, DNA was recovered by Qiagen PCR Purification
Libraries were made with NuGEN Ovation Ultralow kit

tag: strain background

value: W303, Ume6-FLAG

tag: e-chrp added

tag: expression promoter

value: GAL (integrated at HO)

tag: chip antibody

value: FLAG

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat#

tag: chip antibody lot#


title: B2.cpxR_suspension1

tag: genotype

value: Planktonic cells


title: C1.Wild_type3biofilm

value: Wild type


title: Ume6_E-ChRP_Pre-Induction_FLAG_rep1


title: Ume6_E-ChRP_Pre-Induction_INPUT


title: Ume6_E-ChRP_Post-Induction_INPUT

tag: treatment

value: treated with 2% galactose 2hr


title: C2.cpxR_suspension2


title: F1.cpxR3biofilm


title: B1.Wild_type2biofilm


title: Ume6_E-ChRP_Post-Induction_FLAG_rep2


title: A2.Wild_type_suspension3


title: Tumor treated with SSZ+OXY 3

type: RNA

city: Shinjuku-ku

first: Yuji

last: Otsuki

state: Tokyo

address: 35 Shinanomachi

department: Institute for Advanced Medical Research

country: Japan

institute: Keio University

description: Tumor trreated with SSZ+OXY

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G system.

data_processing: The data were analyzed with Transcriptome Analysis Console version 4.0 (TAC 4.0) using Affymetrix default analysis settings.

label: biotin

organism: Homo sapiens

source_name: Subcutaneous tumor

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The mice were then injected i.p. with physiological saline, Sulfasalazine, Oxyfedrine, or both drugs

tag: injected mouse strain

value: BALB/C nu/nu

tag: injected mouse sex

value: male

tag: injected mouse health status

value: healthy

tag: injected human cell line

value: Subcutaneous tumor


title: Tumor treated with SSZ+OXY 1

description: Tumor trreated with SSZ+OXY


title: Tumor treated with OXY 3

description: Tumor trreated with OXY


title: asp1-10 rep3

city: Bunkyo-ku

first: Chie

last: Suzuki

department: School of Science, Department of Biological Sciences

institute: The University of Tokyo

description: asp1-10 inflorescence meristems

hyb_protocol: Hybridization, washing, and staining procedures were run on Fluidics Station 450 (Thermo Fisher Scientific) with GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: Normalization was performed by using the standard settings for GeneChip Gene 1.0 ST arrays on Expression Console Version 1.3 (Thermo Fisher Scientific).

organism: Oryza sativa

source_name: inflorescence meristems

label_protocol: The sense-strand DNA target was prepared by using a WT Expression Kit (Thermo Fisher Scientific) and a GeneChip WT Terminal Labeling and Controls Kit (Thermo Fisher Scientific) in accordance with the manufacturers’ instructions.

growth_protocol: Plants were grown in pots containing soil (outdoor) in Tokyo, Japan.

extract_protocol: Total RNA was extracted using TRIsure (BIOLINE).

treatment_protocol: The inflorescence meristems of each strain were dissected under microscope and frozen in liquid nitrogen for the subsequent RNA extraction.


title: Tumor treated with SSZ+OXY 2

description: Tumor trreated with SSZ+OXY


title: Ume6_E-ChRP_Post-Induction_FLAG_rep1


title: fon2-3 asp1-fe rep2

description: fon2-3 asp1-fe inflorescence meristems

value: fon2-3 asp1-fe


title: fon2-3 asp1-fe rep1

description: fon2-3 asp1-fe inflorescence meristems


title: Tumor treated with SSZ 2

description: Tumor trreated with SSZ


title: fon2-3 rep3

description: fon2-3 inflorescence meristems


title: Tumor treated with SSZ 3

description: Tumor trreated with SSZ


title: asp1-10 rep1

description: asp1-10 inflorescence meristems


title: Tumor treated with OXY 2

description: Tumor trreated with OXY


title: Ume6_E-ChRP_Catalytic_Null_INPUT

value: Chd1-Ume6 (D513N mutant)

value: GPD 2-micron


title: fon2-3 asp1-fe rep3

description: fon2-3 asp1-fe inflorescence meristems


title: Tumor treated with OXY 1

description: Tumor trreated with OXY


title: fon2-3 rep2

description: fon2-3 inflorescence meristems


title: A1.Wild_type1biofilm

tag: growth phase

value: Biofilm


title: TOX siRNA anti-H3K27ac antibody

city: Daejeon

first: Chang Gon

address: 291 Daehak-ro

institute: Korea Advanced Institute of Science and Technology

description:
TOX siRNA treated CD8+ T cell
Control siRNA specific peaks.txt

data_processing:
Alignment: Bowtie2 (for RNA-seq)
Assembly: EdgeR (for RNA-seq)
Additional processing: abundance measurement (for RNA-seq)
Mapping: BWA-mem (for ChIP-seq)
Filtering: reads with MAPQ < 10 were removed, PCR duplicates were removed by Picard
Additional processing: ChIP peaks were identified by MACS
Genome_build: hg38, mm9
Supplementary_files_format_and_content: Normal colon 1/2/3, MC38-OVA 1/2/3: raw read counts (.txt)  Control siRNA specific peaks: specific peaks in H3K27ac ChIP-seq in control siRNA-transfected CD8+ T cells

source_name: CD8+ T cells

extract_protocol: H3K27ac was purified with anti-H3K27ac antibody and RNA was extracted from cells using TRIZOL reagent.

tag: harvest time

value: Cells from Homo sapiens

value: TOX siRNA transfection


title: asp1-10 rep2

description: asp1-10 inflorescence meristems


title: fon2-3 rep1

description: fon2-3 inflorescence meristems


title: WT rep3

description: WT inflorescence meristems

value: WT


title: Tumor treated with SSZ 1

description: Tumor trreated with SSZ

tag: tissue


title: Ume6_E-ChRP_Catalytic_Null_FLAG_rep1

value: W303, Ume6-FLAG


title: plusDOX_G2_IL11RplusPLXDCplus

status: Public on Sep 24 2019

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: mRNA

data_processing:
Datasets were aligned to the mouse reference GRCm38/mm10 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic.
The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the mm10 refGene annotation file available at the UCSC Genome Browser.
Genome_build: mm10

source_name: lung

growth_protocol: MDA-MB-468 cells with DOX-inducible IL11 and FIGF were mixed with CFP-expressing cells (10%+10%+80% ratio, respectively), resuspended in 50% Matrigel and injected at 3 million per site into mammary fat pad of immunocompromised animals.

extract_protocol:
Lungs of tumor bearing animals were dissociated, stained for IL11RA and PLXDC and sorted into lysis buffer (Qiagen RNeasy kit). RNA extraction was performed according to the manufacturer's protocol.
cDNA libraries were constructed using Nextera XT DNA Sample preparation kit (Illumina) according to the manufacturer’s recommendations with minor modifications. Briefly, cDNA amplicons were fragmented and barcoded by tagmentation using Tn5 DNA transposase. Tagmented cDNA were amplified with a limited-cycle PCR program. During the PCR step, indices 1 and 2 were added to allow for cluster generation and multiplexed sequencing. The extension time was increased from 30s to 60s. The amplified cDNA libraries were purified and cleaned using 0.6x Agencourt AMPure XP (Beckman Coulter) and fresh ethanol, and eluted in TE buffer. The quality of sequencing libraries was assessed using a high-sensitivity DNA chip (Agilent). Finally, the libraries were sequenced deeply using the HiSeq2000 sequencer (Illumina).

treatment_protocol: 10 animals received DOX diet, starting from the first day post-inoculation. Control group was fed regular diet.

value: Dox

tag: cell sorting

value: IL11RA plus, PLXDC plus


title: Tumor treated with saline 3

description: control


title: plusDOX_G1_IL11Rminus

description: mRNA

value: IL11RA minus


title: plusDOX_G1_IL11RplusPLXDCplus

description: mRNA


title: TOX input


title: plusDOX_G2_IL11Rminus

description: mRNA


title: plusDOX_G1_IL11RplusPLXDCminus

description: mRNA

value: IL11RA plus, PLXDC minus


title: minusDOX_G2_IL11RplusPLXDCplus

description: mRNA

value: No Dox


title: WT rep1

description: WT inflorescence meristems


title: Ume6_E-ChRP_Catalytic_Null_FLAG_rep2

tag: strain background

value: FLAG

value: Sigma


title: minusDOX_G2_IL11Rminus

description: mRNA


title: minusDOX_G1_IL11RplusPLXDCminus

description: mRNA


title: Tumor treated with saline 1

description: control

value: BALB/C nu/nu

value: male

value: healthy


title: minusDOX_G1_IL11Rminus

description: mRNA


title: minusDOX_G2_IL11RplusPLXDCminus

description: mRNA


title: Tumor treated with saline 2

description: control

value: Subcutaneous tumor


title: WT rep2

description: WT inflorescence meristems


title: tumor_+DOX_2

description: Janiszewska_scRNASeq_gene_level_counts.txt

data_processing:
RNA-Seq: Basecalls were performed using CASAVA version 1.8.2
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics). Tumor sample fastq files were trimmed to 40 bases.
RNA-Seq: Datasets of tumor origin were aligned to the human reference GRCh37/hg19 genome and datasets of stroma origin were aligned to the mouse reference GRCm38/mm10 genome, both using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic. Samples were filtered to remove contamination (mouse contamination in tumor samples and human contamination in stroma samples). Reads uniquely mapped only to the target genome were kept, along with uniquely mapped reads that had significantly better alignment scores in the target genome compared to the contamination genome.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the hg19/mm10 refGene annotation file available at the UCSC Genome Browser.
RNA-Seq: For stroma samples, libraries were ran twice and reads for these duplicates were added together in the final gene-level counts file (Janiszewska_stroma-gene-level-counts.csv).
scRNA-seq: Samples were demultiplexed to FASTQ files using CellRanger v. 1.2. with cellranger mkfastq
scRNA-seq: FASTQ files were aligned and filtered using CellRanger v. 1.2. with cellranger count
scRNA-seq: Samples were aggregated into a single combined matrix and sequencing depth was normalized across runs, using CellRanger v. 1.2. with cellranger aggr
scRNA-seq: Data was filtered by selecting all genes expressed in at least 1 single cell, and all cells with at least 100 and at most 5,000 expressed genes, and with a maximum percent of mitochondrial DNA of 0.1 using the Seurat R package, v. 2.1.0. This amounted to keeping a total of 18,203 genes and 7,704 cells.
Genome_build: RNA-Seq and scRNA-Seq: hg19/mm10
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Supplementary_files_format_and_content: scRNA-seq: Tab-separated file of the UMI counts generated by 10x CellRanger and filtered with Seurat

source_name: +DOX

extract_protocol:
The mRNA selection and whole transcriptome amplification were performed as previously described with some modifications. A primer 5’-phosphorylated oligo-dT24 (pdT24) was used to select mRNA from total RNA. For denaturation and primer annealing, total RNA was mixed with dNTPs (25 mM) and pdT24, and put in a preheated 68°C PCR machine for 5 min and immediately placed on ice. Reverse transcription was performed with the addition of the First-Strand Buffer, DTT, RNase Inhibitor, and 10 U/μl Superscript Reverse Transcriptase III. The double-strand cDNA was generated by the addition of 30 μl mix containing 10x second100 strand buffer, dNTPs (25 mM), E.coli DNA ligase (10 U/μl), RNaseH, and DNA Polymerase (10U/μl), followed by 3 hr incubation at 16°C and 5 min at 70°C. The product was purified with the Genomic DNA Clean and Concentrator kit (Zymo). Then, DNA end-bluting, 5’-end phosphorylation, and ligation were performed with End-It DNA End-Repair Kit (Epicentre) and T4 DNA ligase (Epicentre). The product was directly amplified by adding the mixture of the Reaction Buffer and DNA polymerase from REPLI-g UltraFast Kit (Qiagen) in 15:1 ratio. The amplification reaction was carried at 30°C for 2 hr. The amplified product was purified using the same Genomic DNA Clean and Concentrator kit (Zymo). When eluted in 50 μl elution buffer, typically 5-10 μg of mRNA-derived cDNA amplicons were obtained. The amplicons were then evaluated for quantity, coverage, and purity by PCR using a set of primers for housekeeping genes (GAPDH, B2M), cDNA 5’ end (CREB5), and gDNA (10p).
cDNA libraries were constructed using Nextera XT DNA Sample preparation kit (Illumina) according to the manufacturer’s recommendations with minor modifications. Briefly, cDNA amplicons were fragmented and barcoded by tagmentation using Tn5 DNA transposase. Tagmented cDNA were amplified with a limited-cycle PCR program. During the PCR step, indices 1 and 2 were added to allow for cluster generation and multiplexed sequencing. The extension time was increased from 30s to 60s. The amplified cDNA libraries were purified and cleaned using 0.6x Agencourt AMPure XP (Beckman Coulter) and fresh ethanol, and eluted in TE buffer. The quality of sequencing libraries was assessed using a high-sensitivity DNA chip (Agilent). Finally, the libraries were sequenced deeply using the HiSeq2000 sequencer (Illumina). For the single cell RNA-Seq data, the cells were processed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).

tag: site

value: tumor

tag: cell type


title: tumor_+DOX_1


title: tumor_-DOX_2

source_name: -DOX


title: tumor_-DOX_1


title: lung_+DOX_2

value: lung


title: lung_+DOX_1


title: lung_naive_1

source_name: naïve


title: lung_-DOX_2


title: blood_+DOX_2

value: blood


title: lung_naive_2


title: plusDOX_G2_IL11RplusPLXDCminus

description: mRNA


title: blood_-DOX_2


title: blood_+DOX_1


title: minusDOX_G1_IL11RplusPLXDCplus

description: mRNA


title: blood_naive_2


title: Stroma_Fat-Pad_Control-1_2

description: Janiszewska_stroma-gene-level-counts.csv

source_name: stroma

tag: clonality

value: monoclonal

value: fat pad

value: control


title: Stroma_Lung_Thy1.1_7-1_2

value: metastasis


title: Stroma_Lung_Thy1.1_3-1_2


title: Stroma_Primary_Thy1.1_3-1_2

value: primary tumor


title: Stroma_Lung_Control-1_2


title: Stroma_Primary_Thy1.1_3-2_2


title: Stroma_Lung_Par_mch_11-2_2

value: parental


title: Stroma_Primary_Mix_1-1_2

value: polyclonal

value: mixed


title: Stroma_Lung_Mix_1-1_2


title: Stroma_Primary_Mix_1-4_2


title: Stroma_Primary_Mix_1-3_2


title: blood_naive_1


title: Stroma_Lung_Mix_1-5_2


title: Stroma_Primary_IL11_10-2_2


title: Stroma_Lung_IL11_10-2_2


title: Stroma_Lung_IL11_6-1_2


title: Stroma_Primary_FIGF_9-3_2

value: FIGF


title: Stroma_Lung_Mix_1-4_2


title: Stroma_Lung_IL11_10-1_2


title: Stroma_Primary_IL11_10-1_2


title: Stroma_Lung_IL11_6-2_2


title: Stroma_Lung_FIGF_9-3_2


title: lung_-DOX_1


title: blood_-DOX_1


title: Stroma_Primary_Par_mch_11-2_2


title: Stroma_Primary_FIGF_9-1_2


title: Stroma_Lung_Par_mch_11-3_2


title: Stroma_Lung_FIGF_5-3_2


title: Stroma_Lung_FIGF_5-4_2


title: Stroma_Lung_CFP_8-1_2

value: CFP


title: Stroma_Primary_CFP_4-4_2


title: Stroma_Lung_CFP_4-3_2


title: Stroma_Primary_CFP_4-3_2


title: Stroma_Lung_Thy1.1_7-1_1


title: Stroma_Fat-Pad_Control-1_1


title: Stroma_Lung_Thy1.1_3-1_1


title: Stroma_Primary_Mix_1-4_1


title: Stroma_Lung_Mix_1-5_1


title: Stroma_Lung_Par_mch_11-3_1


title: Stroma_Primary_Par_mch_11-2_1


title: Stroma_Primary_Thy1.1_3-1_1


title: Stroma_Primary_Thy1.1_3-2_1


title: Stroma_Lung_Par_mch_11-2_1


title: Stroma_Lung_Mix_1-4_1


title: Stroma_Lung_FIGF_9-1_2


title: Stroma_Primary_Mix_1-3_1


title: Stroma_Lung_Mix_1-1_1


title: Stroma_Primary_Mix_1-1_1


title: Stroma_Lung_IL11_6-2_1


title: Stroma_Lung_IL11_6-1_1


title: Stroma_Lung_IL11_10-2_1


title: Stroma_Primary_IL11_10-1_1


title: Stroma_Lung_IL11_10-1_1


title: Stroma_Lung_FIGF_9-3_1


title: Stroma_Primary_FIGF_9-3_1


title: Stroma_Primary_FIGF_9-1_1


title: Stroma_Lung_FIGF_9-1_1


title: Stroma_Lung_Control-1_1


title: Stroma_Lung_FIGF_5-4_1


title: Stroma_Primary_CFP_4-4_1


title: Stroma_Lung_CFP_8-1_1


title: Stroma_Lung_CFP_4-3_1


title: Stroma_Primary_CFP_4-3_1


title: Stroma_Primary_IL11_10-2_1


title: 201503670152_R01C01

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC array using standard Illumina protocol

scan_protocol: Arrays were imaged with BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Minfi preprocessIllumina (R package) was used to process samples (for background subtraction and colour correction).
Average Beta (after minfi::preprocessIllumina in R)
Unmethylated and methylated signal intensities

label: Cy5 and Cy364

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Isohelix DDK-50 kit and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

tag: age

tag: gender

value: M


title: 201503670152_R04C01

label: Cy5 and Cy366


title: 201503670127_R04C01

label: Cy5 and Cy361


title: 201503670152_R02C01

label: Cy5 and Cy365


title: 201503670115_R04C01

label: Cy5 and Cy357


title: 201503670127_R02C01

label: Cy5 and Cy360

value: F


title: 201503670127_R07C01

label: Cy5 and Cy363


title: 201503670152_R07C01

label: Cy5 and Cy368


title: 201503670115_R07C01

label: Cy5 and Cy359


title: 201503670152_R05C01

label: Cy5 and Cy367


title: 201503670044_R08C01

label: Cy5 and Cy355


title: 201503670044_R03C01

label: Cy5 and Cy353


title: 201503670044_R05C01

label: Cy5 and Cy354


title: 201496860173_R07C01

label: Cy5 and Cy352


title: 201496860173_R05C01

label: Cy5 and Cy351


title: Stroma_Lung_FIGF_5-3_1


title: Mut rep5

city: Kuopio

first: Riikka

middle: H

last: Hämäläinen

address: Neulaniementie 2

country: Finland

institute: university of eastern Finland

data_processing:
Basecalling by Illumina software
Paired sequences were further processed and analyzed with the SePIA transcriptomics analysis pipeline (doi:  10.1186/s13040-016-0099-z).
Pre-processed reads were aligned to the mouse genome (mmu38_Ensemblv69) using STAR (https://doi.org/10.1093/bioinformatics/bts635).
Gene and transcript level expression was quantified and normalized to fragments per kilobase per million (FPKM) with Cufflinks.
Genome_build: mmu38_Ensemblv69
Supplementary_files_format_and_content: Excel file includes FPKM values for all samples

source_name: cultured iPS cells

growth_protocol: Cells were grown on mitotically arrested feeder cells on basic mouse ES media suplemented with LIF. Prior to RNA extraction, the cells were passaged once on gelatin to remove feeder cells.

extract_protocol:
RNA was extracted from fresh cell cultures using Trizol reagent and purified through Qiagen RNeasy minicolumns.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: D257A homo


title: Mut rep3


title: Mut rep4


title: 201496860173_R03C01

label: Cy5 and Cy350


title: Mut rep1


title: 201496860173_R01C01

label: Cy5 and Cy349


title: 201496860171_R08C01

label: Cy5 and Cy348


title: 201503670127_R06C01

label: Cy5 and Cy362


title: wt rep2

value: wild type


title: 201503670115_R05C01

label: Cy5 and Cy358


title: wt rep1


title: 201496860171_R02C01

label: Cy5 and Cy345


title: 201496860171_R01C01

label: Cy5 and Cy344


title: 201503670115_R02C01

label: Cy5 and Cy356


title: 201496860148_R04C01

label: Cy5 and Cy341


title: 201496860148_R07C01

label: Cy5 and Cy343


title: Mut rep2


title: 201496860171_R06C01

label: Cy5 and Cy346


title: 201496860148_R06C01

label: Cy5 and Cy342


title: wt rep3


title: 201496860082_R06C01

label: Cy5 and Cy337


title: 201496860082_R07C01

label: Cy5 and Cy338


title: 201496860148_R03C01

label: Cy5 and Cy340


title: 201496860082_R04C01

label: Cy5 and Cy336


title: 201496860082_R03C01

label: Cy5 and Cy335


title: 201496860171_R07C01

label: Cy5 and Cy347


title: 201496860082_R01C01

label: Cy5 and Cy334


title: 201496860148_R02C01

label: Cy5 and Cy339


title: 201496710111_R06C01

label: Cy5 and Cy332


title: 201496710111_R05C01

label: Cy5 and Cy331


title: 201496710111_R03C01

label: Cy5 and Cy330


title: poly_shERa_rep1

type: other

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institute

description: BM67 shERα cells, polysome-associated RNA rep1

hyb_protocol: The resulting labeled samples were hybridized to the Mouse Gene 1.1 ST Array from Affymetrix according to the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Gene expression was normalized using Robust Multiarray Averaging and annotated with a custom probeset definition (mogene11st_Mm_ENTREZG version 19.0.0). R/Bioconductor was used for the analysis.

label: biotin

molecule: other

source_name: PTEN-deficient prostate cancer cell line (BM67) derived from the PB-Cre;PtenFlox/Flox mouse model of prostate cancer

label_protocol: Affymetrix kit for the Mouse Gene 1.1 ST Array using conditions recommended by the manufacturer.

growth_protocol: cells were grown in RPMI-1640 (Gibco) and supplemented to a final concentration of 5% Fetal Bovine Serum (FBS, Sigma) and 100 IU/mL penicillin and 10 µg/mL streptomycin (P/S, Invitrogen) and kept in a humidified incubator at 37°C supplemented with 5% CO2.

extract_protocol: Polysome profiling was performed on four replicates of each condition as previously described (Gandin et al. J Vis Exp JoVE, 2014). Briefly, cytosolic lysates were loaded on a 5-50% sucrose gradient allowing for isolation of mRNAs associated with more than 3 ribosomes (hereafter referred to as polysome-associated mRNA) after ultracentrifugation. Total cytosolic RNA was isolated in parallel (Gandin et al. J Vis Exp JoVE, 2014).

treatment_protocol: Stable knockdown of ERα was achieved using the pGIPZ vector (Open Biosystems) containing a non-silencing control (shCtrl) or a mouse ERα shRNA (shERa)

tag: rna type

value: polysome-associated RNA

tag: shRNA

value: shERa


title: poly_shCtrl_rep3

description: BM67 control cells, polysome-associated RNA rep3

value: shCtrl


title: 201496710111_R02C01

label: Cy5 and Cy329


title: Lin- HSPC, Stag2 KO, XA2

city: New York

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
RNA-seq data was processed from raw fastq files to count matrices with SEQC (see https://github.com/ambrosejcarr/seqc.git)
SEQC provides cell (barcodes) by gene matrices as a standard format and first column (CLUSTER) represents Phenograph clustering of the data.
Genome_build: mm38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in gzipped csv format

molecule: polyA RNA

source_name: Lin- HSPC

extract_protocol: Sequencing librairies were prepared using 10X Chromium Single Cell 3' Solution V2

value: Lin- HSPC

tag: genotype

value: Stag2 KO


title: Lin- HSPC, Stag2 wt, XN3

value: Stag2 wt


title: Lin- HSPC, Stag2 KO, XA1


title: Lin- HSPC, Stag2 wt, XA3


title: Lin- HSPC, Stag2 KO, XA4


title: 201496710063_R08C01

label: Cy5 and Cy328


title: poly_shERa_rep4

description: BM67 shERα cells, polysome-associated RNA rep4. In initial publication, replicate identifier was labelled as: 2


title: poly_shCtrl_rep2

description: BM67 control cells, polysome-associated RNA rep2


title: poly_shCtrl_rep1

description: BM67 control cells, polysome-associated RNA rep1


title: cyto_shERa_rep4

description: BM67 shERα cells, cytosolic RNA rep4. In initial publication, replicate identifier was labelled as: 2.

value: cytosolic RNA


title: cyto_shERa_rep3

description: BM67 shERα cells, cytosolic RNA rep3


title: cyto_shCtrl_rep1

description: BM67 control cells, cytosolic RNA rep1


title: cyto_shERa_rep1

description: BM67 shERα cells, cytosolic RNA rep1


title: cyto_shCtrl_rep2

description: BM67 control cells, cytosolic RNA rep2


title: 201496710063_R05C01

label: Cy5 and Cy327


title: cyto_shCtrl_rep3

description: BM67 control cells, cytosolic RNA rep3


title: 201496710111_R08C01

label: Cy5 and Cy333


title: Lin- HSPC, Stag2 wt, XG3


title: 201496710063_R04C01

label: Cy5 and Cy326


title: WT.zygote.rep1

city: Shanghai

first: Mingyue

last: Guo

state: Shanghai

address: Siping

department: School of Life science and technology

institute: Tongji University

description: Gene Abundance

data_processing:
reads( >35bp) were then aligned to the mouse genome (mm9)  using STAR
all Refseq genes were quantified to FPKM using Stringtie
Deseq2 was used to perform differential analysis
Genome_build: mm9
Supplementary_files_format_and_content: fpkm files were quantified using Stringtie

source_name: Embryos

extract_protocol:
RNAs in embryos lysis with a polyadenylated tail were captured, reverse transcripted and preamplified following the protocol for Smart-seq2 sequence library generation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Wild type

tag: developmental stage

value: zygote


title: WT.zygote.rep3

description: Gene Abundance


title: WT.mid2.rep4

description: Gene Abundance


title: 201496710063_R02C01

label: Cy5 and Cy325


title: WT.zygote.rep2

description: Gene Abundance


title: 201496710063_R01C01

label: Cy5 and Cy324


title: WT.mid2.rep3

description: Gene Abundance


title: WT.mid2.rep2

description: Gene Abundance


title: poly_shERa_rep3

description: BM67 shERα cells, polysome-associated RNA rep3


title: WT.mid2.rep1

description: Gene Abundance


title: 201496710035_R07C01

label: Cy5 and Cy322


title: 201496710035_R03C01

label: Cy5 and Cy320


title: 201496710035_R02C01

label: Cy5 and Cy319


title: 201496860008_R08C01

label: Cy5 and Cy318


title: 201496710035_R05C01

label: Cy5 and Cy321


title: WT.late2.rep4

description: Gene Abundance


title: WT.late2.rep3

description: Gene Abundance


title: WT.late2.rep1

description: Gene Abundance


title: 201496860008_R02C01

label: Cy5 and Cy316


title: WT.late2.rep5

description: Gene Abundance


title: WT.early2.rep5

description: Gene Abundance


title: 201496860008_R06C01

label: Cy5 and Cy317


title: 201496860007_R07C01

label: Cy5 and Cy314


title: WT.early2.rep6

description: Gene Abundance


title: WT.early2.rep4

description: Gene Abundance


title: WT.early2.rep3

description: Gene Abundance


title: 201496860007_R06C01

label: Cy5 and Cy313


title: 201496860007_R03C01

label: Cy5 and Cy312


title: WT.early2.rep2

description: Gene Abundance


title: 201496860007_R02C01

label: Cy5 and Cy311


title: WT.early2.rep1

description: Gene Abundance


title: OE.zygote.rep7

description: Gene Abundance

value: Dux overexpression


title: 201496710035_R08C01

label: Cy5 and Cy323


title: OE.zygote.rep8

description: Gene Abundance


title: 201496850073_R03C01

label: Cy5 and Cy308


title: 201496850073_R02C01

label: Cy5 and Cy307


title: WT.late2.rep2

description: Gene Abundance


title: OE.zygote.rep3

description: Gene Abundance


title: 201496860007_R08C01

label: Cy5 and Cy315


title: 201496850007_R04C01

label: Cy5 and Cy304


title: 201496850073_R01C01

label: Cy5 and Cy306


title: OE.zygote.rep4

description: Gene Abundance


title: OE.zygote.rep2

description: Gene Abundance


title: 201496850007_R03C01

label: Cy5 and Cy303


title: 201496850007_R07C01

label: Cy5 and Cy305


title: OE.zygote.rep1

description: Gene Abundance


title: OE.Late4cell.rep9

description: Gene Abundance


title: 201496850007_R01C01

label: Cy5 and Cy301


title: 201496710096_R08C01

label: Cy5 and Cy300


title: OE.Late4cell.rep7

description: Gene Abundance


title: OE.Late4cell.rep8

description: Gene Abundance


title: OE.Late4cell.rep6

description: Gene Abundance


title: 201496710096_R07C01

label: Cy5 and Cy299


title: 201496850073_R06C01

label: Cy5 and Cy309


title: OE.Late4cell.rep5

description: Gene Abundance


title: 201496710096_R06C01

label: Cy5 and Cy298


title: 201496850073_R08C01

label: Cy5 and Cy310


title: OE.zygote.rep6

description: Gene Abundance


title: OE.Late4cell.rep4

description: Gene Abundance


title: 201496710096_R05C01

label: Cy5 and Cy297


title: OE.zygote.rep5

description: Gene Abundance


title: 201496710096_R04C01

label: Cy5 and Cy296


title: OE.Late4cell.rep3

description: Gene Abundance


title: 201496710094_R07C01

label: Cy5 and Cy295


title: OE.Late4cell.rep2

description: Gene Abundance


title: OE.Late4cell.rep13

description: Gene Abundance


title: 201496710094_R04C01

label: Cy5 and Cy294


title: OE.Late4cell.rep12

description: Gene Abundance


title: 201496850007_R02C01

label: Cy5 and Cy302


title: 201496710094_R03C01

label: Cy5 and Cy293


title: 201496710094_R02C01

label: Cy5 and Cy292


title: OE.Late4cell.rep10

description: Gene Abundance


title: 201496710077_R08C01

label: Cy5 and Cy290


title: 201496710094_R01C01

label: Cy5 and Cy291


title: OE.Late4cell.rep11

description: Gene Abundance


title: OE.Late4cell.rep1

description: Gene Abundance


title: 201496710077_R07C01

label: Cy5 and Cy289


title: 201496710077_R05C01

label: Cy5 and Cy288


title: OE.4cellEarly.rep8

description: Gene Abundance


title: OE.4cellEarly.rep9

description: Gene Abundance


title: 201496710077_R03C01

label: Cy5 and Cy287


title: OE.4cellEarly.rep7

description: Gene Abundance


title: OE.4cellEarly.rep6

description: Gene Abundance


title: 201496710073_R07C01

label: Cy5 and Cy285


title: OE.4cellEarly.rep4

description: Gene Abundance


title: OE.4cellEarly.rep5

description: Gene Abundance


title: 201496710077_R01C01

label: Cy5 and Cy286


title: OE.4cellEarly.rep3

description: Gene Abundance


title: 201496710073_R04C01

label: Cy5 and Cy283


title: 201496710073_R05C01

label: Cy5 and Cy284


title: 201496710061_R08C01

label: Cy5 and Cy280


title: 201496710073_R01C01

label: Cy5 and Cy281


title: OE.4cellEarly.rep1

description: Gene Abundance


title: OE.4cellEarly.rep2

description: Gene Abundance


title: KO.zygote.rep3

description: Gene Abundance

value: Dux knockout


title: KO.zygote.rep1

description: Gene Abundance


title: KO.zygote.rep2

description: Gene Abundance


title: 201496710061_R03C01

label: Cy5 and Cy276


title: 201496710061_R07C01

label: Cy5 and Cy279


title: KO.mid2.rep3

description: Gene Abundance


title: KO.mid2.rep4

description: Gene Abundance


title: OE.4cellEarly.rep10

description: Gene Abundance


title: 201496710061_R04C01

label: Cy5 and Cy277


title: KO.mid2.rep2

description: Gene Abundance


title: 201496710044_R08C01

label: Cy5 and Cy275


title: 201496710044_R06C01

label: Cy5 and Cy273


title: 201496710061_R06C01

label: Cy5 and Cy278


title: KO.mid2.rep1

description: Gene Abundance


title: 201496710044_R04C01

label: Cy5 and Cy272


title: KO.late2.rep5

description: Gene Abundance


title: KO.late2.rep4

description: Gene Abundance


title: KO.late2.rep3

description: Gene Abundance


title: 201496710038_R08C01

label: Cy5 and Cy270


title: 201496710044_R02C01

label: Cy5 and Cy271


title: 201496710073_R02C01

label: Cy5 and Cy282


title: KO.late2.rep2

description: Gene Abundance


title: 201496710038_R07C01

label: Cy5 and Cy269


title: 201496710038_R05C01

label: Cy5 and Cy268


title: KO.late2.rep1

description: Gene Abundance


title: 201496710038_R03C01

label: Cy5 and Cy267


title: KO.early2.rep4

description: Gene Abundance


title: KO.early2.rep2

description: Gene Abundance


title: 201496710038_R01C01

label: Cy5 and Cy266


title: KO.early2.rep3

description: Gene Abundance


title: 201503670136_R08C01

label: Cy5 and Cy265


title: 201496710044_R07C01

label: Cy5 and Cy274


title: 201503670136_R02C01

label: Cy5 and Cy262


title: 201503670136_R05C01

label: Cy5 and Cy263


title: KO.early2.rep1

description: Gene Abundance


title: Ctrl.zygote.rep7

description: Gene Abundance

value: Control


title: Ctrl.zygote.rep6

description: Gene Abundance


title: 201503670136_R01C01

label: Cy5 and Cy261


title: 201503670049_R01C01

label: Cy5 and Cy258


title: Ctrl.zygote.rep8

description: Gene Abundance


title: 201503670049_R02C01

label: Cy5 and Cy259


title: Ctrl.zygote.rep3

description: Gene Abundance


title: Ctrl.zygote.rep4

description: Gene Abundance


title: 201503670049_R08C01

label: Cy5 and Cy260


title: Ctrl.zygote.rep2

description: Gene Abundance


title: 201503670012_R07C01

label: Cy5 and Cy256


title: 201503670012_R08C01

label: Cy5 and Cy257


title: 201503670012_R05C01

label: Cy5 and Cy255


title: 201503670012_R03C01

label: Cy5 and Cy254


title: Ctrl.Late4cell.rep8

description: Gene Abundance


title: Ctrl.Late4cell.rep9

description: Gene Abundance


title: Ctrl.Late4cell.rep7

description: Gene Abundance


title: 201503670005_R06C01

label: Cy5 and Cy252


title: Ctrl.Late4cell.rep6

description: Gene Abundance


title: Ctrl.Late4cell.rep5

description: Gene Abundance


title: 201503670005_R02C01

label: Cy5 and Cy251


title: 201503670136_R07C01

label: Cy5 and Cy264


title: 201496860196_R08C01

label: Cy5 and Cy249


title: Ctrl.Late4cell.rep4

description: Gene Abundance


title: 201503670005_R01C01

label: Cy5 and Cy250


title: 201503670005_R07C01

label: Cy5 and Cy253


title: Ctrl.Late4cell.rep3

description: Gene Abundance


title: 201496860196_R06C01

label: Cy5 and Cy248


title: Ctrl.Late4cell.rep2

description: Gene Abundance


title: 201496860196_R05C01

label: Cy5 and Cy247


title: 201496860196_R02C01

label: Cy5 and Cy245


title: Ctrl.Late4cell.rep15

description: Gene Abundance


title: 201496860196_R03C01

label: Cy5 and Cy246


title: Ctrl.Late4cell.rep13

description: Gene Abundance


title: Ctrl.Late4cell.rep12

description: Gene Abundance


title: Ctrl.Late4cell.rep11

description: Gene Abundance


title: 201496860125_R02C01

label: Cy5 and Cy242


title: 201496860028_R08C01

label: Cy5 and Cy241


title: 201496860028_R07C01

label: Cy5 and Cy240


title: Ctrl.Late4cell.rep1

description: Gene Abundance


title: 201496860028_R02C01

label: Cy5 and Cy238


title: 201496860028_R04C01

label: Cy5 and Cy239


title: Ctrl.4cellEarly.rep7

description: Gene Abundance


title: 201496860028_R01C01

label: Cy5 and Cy237


title: Ctrl.Late4cell.rep16

description: Gene Abundance


title: Ctrl.4cellEarly.rep5

description: Gene Abundance


title: Ctrl.4cellEarly.rep9

description: Gene Abundance


title: 201496860026_R08C01

label: Cy5 and Cy236


title: Ctrl.4cellEarly.rep3

description: Gene Abundance


title: 201496860026_R06C01

label: Cy5 and Cy235


title: 201496860026_R04C01

label: Cy5 and Cy234


title: 201496860026_R03C01

label: Cy5 and Cy233


title: Ctrl.4cellEarly.rep4

description: Gene Abundance


title: 201496860125_R05C01

label: Cy5 and Cy243


title: 201496860026_R01C01

label: Cy5 and Cy232


title: 201496860125_R07C01

label: Cy5 and Cy244


title: 201496850188_R06C01

label: Cy5 and Cy230


title: Ctrl.4cellEarly.rep1

description: Gene Abundance


title: Ctrl.4cellEarly.rep2

description: Gene Abundance


title: 201496850188_R05C01

label: Cy5 and Cy229


title: Ctrl.4cellEarly.rep6

description: Gene Abundance


title: 201496850161_R07C01

label: Cy5 and Cy226


title: 201496850161_R08C01

label: Cy5 and Cy227


title: 5808922083_R05C01

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

data_processing:
GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)
Average Beta (after background-subtraction and colour-correction in GenomeStudio software according to standard Illumina protocol)
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

extract_protocol: Buccal epithelial cells were collected with Isohelix DNA buccal swabs using standard collection procedures and stabilized with Isohelix Dri-Capsules for storage at room temperature prior to genomic DNA extraction (Cell Projects Ltd., Kent, UK). Genomic DNA was purified and concentrated using DNA Clean & Concentrator (Zymo Research, CA, USA).


title: 5808922083_R06C01


title: 5808922083_R01C01


title: 201496850161_R03C01

label: Cy5 and Cy225


title: 201496850161_R01C01

label: Cy5 and Cy223


title: 5808922080_R03C02


title: 201496850188_R08C01

label: Cy5 and Cy231


title: 5808922080_R05C02


title: 5808922080_R02C02


title: 201496710181_R07C01

label: Cy5 and Cy221


title: 5808922080_R01C02


title: 5808922080_R05C01


title: 5808922080_R04C01


title: 5808922080_R03C01


title: 201496850188_R03C01

label: Cy5 and Cy228


title: 201496710181_R01C01

label: Cy5 and Cy218


title: 201503670190_R06C01

label: Cy5 and Cy216


title: 5808922076_R04C02


title: 5808922080_R01C01


title: 201503670190_R07C01

label: Cy5 and Cy217


title: Ctrl.zygote.rep1

description: Gene Abundance


title: 5808922076_R03C02


title: 201496710181_R08C01

label: Cy5 and Cy222


title: 5808922076_R02C02


title: 5808922083_R04C01


title: 201503670190_R04C01

label: Cy5 and Cy214


title: Ctrl.zygote.rep5

description: Gene Abundance


title: 201503670190_R01C01

label: Cy5 and Cy213


title: 5808922076_R01C02


title: 201503670138_R08C01

label: Cy5 and Cy212


title: 201496710181_R04C01

label: Cy5 and Cy219


title: 5808922063_R06C02


title: 5808922063_R05C02


title: 5808922076_R04C01


title: 201503670138_R07C01

label: Cy5 and Cy211


title: Ctrl.Late4cell.rep10

description: Gene Abundance


title: Ctrl.4cellEarly.rep10

description: Gene Abundance


title: 201503670138_R05C01

label: Cy5 and Cy209


title: 201503670138_R02C01

label: Cy5 and Cy208


title: 201503670137_R08C01

label: Cy5 and Cy207


title: 5808922063_R01C02

label: Cy5 and Cy3


title: 5808922063_R02C02


title: 5808922063_R03C01


title: 5808922063_R06C01


title: 201503670137_R06C01

label: Cy5 and Cy205


title: 5808922063_R02C01


title: 201503670125_R08C01

label: Cy5 and Cy203


title: 201503670125_R06C01

label: Cy5 and Cy202


title: 5808922063_R01C01


title: 201503670138_R06C01

label: Cy5 and Cy210


title: 201503670125_R05C01

label: Cy5 and Cy201


title: 5808922083_R03C01


title: 5808922054_R04C02


title: 5808922054_R03C02


title: 5808922054_R02C02


title: 201503670125_R02C01

label: Cy5 and Cy199


title: 5808922054_R01C02


title: 201503670113_R08C01

label: Cy5 and Cy198


title: 201503670113_R04C01

label: Cy5 and Cy196


title: 5808922054_R06C01


title: 201503670113_R03C01

label: Cy5 and Cy195


title: 5808922054_R05C01


title: 5808922054_R01C01


title: 201503670113_R01C01

label: Cy5 and Cy194


title: 201503670091_R08C01

label: Cy5 and Cy193


title: 201503670091_R05C01

label: Cy5 and Cy192


title: 5808922042_R05C02


title: 5808922042_R04C02


title: 201503670091_R04C01

label: Cy5 and Cy191


title: 201503670091_R03C01

label: Cy5 and Cy190


title: 5808922042_R03C02


title: 5808922042_R01C02


title: 201503670091_R01C01

label: Cy5 and Cy189


title: 201503670034_R08C01

label: Cy5 and Cy188


title: 5808922042_R06C01

label: Cy5 and Cy3


title: 5808922042_R05C01


title: 201503670034_R06C01

label: Cy5 and Cy187


title: 5808922063_R05C01


title: 201503670113_R05C01

label: Cy5 and Cy197


title: 5808922042_R04C01


title: 201496710095_R07C01

label: Cy5 and Cy185


title: 5808922042_R01C01


title: 5808922041_R06C02


title: 5808922042_R02C01


title: 5808922041_R05C02


title: 201496710095_R06C01

label: Cy5 and Cy184


title: 5808922041_R03C02


title: 5808922041_R02C02


title: 201496710095_R02C01

label: Cy5 and Cy182


title: 201496710086_R05C01

label: Cy5 and Cy180


title: 5808922041_R01C02


title: 201496850161_R02C01

label: Cy5 and Cy224


title: Ctrl.4cellEarly.rep8

description: Gene Abundance


title: 201496710086_R04C01

label: Cy5 and Cy179


title: 5808922041_R06C01


title: 201496710086_R03C01

label: Cy5 and Cy178


title: 201496710095_R08C01

label: Cy5 and Cy186


title: 5808922041_R05C01


title: 201496710086_R02C01

label: Cy5 and Cy177


title: 5808922041_R03C01


title: 5808922041_R02C01


title: 5808922041_R01C01


title: 201496710036_R07C01

label: Cy5 and Cy175


title: 201496710036_R04C01

label: Cy5 and Cy174


title: 5808922040_R05C02


title: 201496710086_R06C01

label: Cy5 and Cy181


title: 201496710036_R02C01

label: Cy5 and Cy173


title: 201496710036_R01C01

label: Cy5 and Cy172


title: 5808922040_R04C02

label: Cy5 and Cy3


title: 201492570153_R07C01

label: Cy5 and Cy171


title: 5808922040_R02C02


title: 5808922040_R03C02


title: 201492570153_R06C01

label: Cy5 and Cy170


title: 5808922040_R04C01


title: 5808922040_R02C01


title: 201492570153_R05C01

label: Cy5 and Cy169


title: 201492570153_R04C01

label: Cy5 and Cy168


title: 201496710036_R08C01

label: Cy5 and Cy176


title: 201492570153_R01C01

label: Cy5 and Cy167


title: 5808922042_R06C02


title: 201492560198_R08C01

label: Cy5 and Cy166


title: 5808922040_R01C01


title: 201492560198_R06C01

label: Cy5 and Cy164


title: 201492560198_R07C01

label: Cy5 and Cy165


title: 9296930145_R02C02


title: Ctrl.Late4cell.rep14

description: Gene Abundance


title: 201503670125_R03C01

label: Cy5 and Cy200


title: 9296930145_R01C02


title: 201492560198_R05C01

label: Cy5 and Cy163


title: 5808922076_R03C01


title: 9296930145_R06C01


title: 201490030241_R08C01

label: Cy5 and Cy161


title: 9296930145_R05C01


title: 5808922063_R04C02


title: 5808922040_R05C01


title: 201503670137_R03C01

label: Cy5 and Cy204


title: 9296930145_R01C01


title: 201490030241_R07C01

label: Cy5 and Cy160


title: 9296930127_R04C02


title: 9296930127_R03C02


title: 201490030241_R03C01

label: Cy5 and Cy159


title: 9296930145_R06C02


title: 9296930127_R01C02


title: 9296930127_R06C01


title: 201490030241_R01C01

label: Cy5 and Cy157


title: 201490030196_R08C01

label: Cy5 and Cy156


title: 9296930127_R04C01

label: Cy5 and Cy3


title: 201490030241_R02C01

label: Cy5 and Cy158


title: 201490030196_R04C01

label: Cy5 and Cy154


title: 201490030196_R06C01

label: Cy5 and Cy155


title: 201496710095_R04C01

label: Cy5 and Cy183


title: 201492560198_R04C01

label: Cy5 and Cy162


title: 9296930127_R03C01


title: 201490030196_R02C01

label: Cy5 and Cy153


title: 9296930127_R01C01


title: 9296930118_R06C02


title: 201490030196_R01C01

label: Cy5 and Cy152


title: 9296930118_R05C02


title: 9296930118_R04C02


title: 201490030153_R04C01

label: Cy5 and Cy149


title: 201490030153_R03C01

label: Cy5 and Cy148


title: 9296930118_R02C02


title: 9296930118_R01C02


title: 201490030153_R01C01

label: Cy5 and Cy147


title: 201490030018_R07C01

label: Cy5 and Cy146


title: 201490030018_R06C01

label: Cy5 and Cy145


title: 201490030018_R04C01

label: Cy5 and Cy144


title: 9296930118_R03C01


title: 201490030018_R03C01

label: Cy5 and Cy143


title: 9296930115_R05C02


title: 9296930115_R04C02


title: 9296930127_R02C01


title: 9296930118_R02C01


title: 201490030016_R04C01

label: Cy5 and Cy141


title: 201490030018_R01C01

label: Cy5 and Cy142


title: 9296930115_R02C02

label: Cy5 and Cy3


title: 201490030153_R07C01

label: Cy5 and Cy151


title: 9296930115_R01C02


title: 201490030153_R06C01

label: Cy5 and Cy150


title: 201490020133_R07C01

label: Cy5 and Cy138


title: 201490030016_R01C01

label: Cy5 and Cy139


title: 9296930115_R04C01


title: 201490020133_R06C01

label: Cy5 and Cy137


title: 9296930115_R03C01


title: 9296930115_R02C01


title: 9296930115_R01C01


title: 201490020133_R05C01

label: Cy5 and Cy136


title: 9296930118_R06C01


title: 201490020133_R04C01

label: Cy5 and Cy135


title: 9296930108_R06C02


title: 9296930108_R05C02


title: 201490020116_R07C01

label: Cy5 and Cy133


title: 201490020133_R01C01

label: Cy5 and Cy134


title: 9296930115_R03C02


title: 201490020116_R05C01

label: Cy5 and Cy132


title: 9296930108_R03C02


title: 9296930108_R06C01


title: 9296930108_R02C02


title: 201490020116_R02C01

label: Cy5 and Cy130


title: 201490020116_R04C01

label: Cy5 and Cy131


title: 201490030016_R03C01

label: Cy5 and Cy140


title: 201490020055_R07C01

label: Cy5 and Cy129


title: 9296930108_R03C01


title: 9296930108_R05C01


title: 201490020055_R04C01

label: Cy5 and Cy128


title: 9296930108_R02C01


title: 9296930108_R01C01


title: 201496710181_R05C01

label: Cy5 and Cy220


title: 201490020055_R02C01

label: Cy5 and Cy126


title: 201490020055_R03C01

label: Cy5 and Cy127


title: 9296930080_R03C02

label: Cy5 and Cy3


title: 201490020055_R01C01

label: Cy5 and Cy125


title: 9296930080_R06C01


title: 201490020016_R06C01

label: Cy5 and Cy123


title: 201490020016_R05C01

label: Cy5 and Cy122


title: 201490020016_R07C01

label: Cy5 and Cy124


title: 9296930080_R05C01


title: 201490020010_R08C01

label: Cy5 and Cy120


title: 201490020016_R04C01

label: Cy5 and Cy121


title: 9296930080_R04C01


title: 9296930029_R02C02


title: 9296930029_R05C02


title: 201490020010_R07C01

label: Cy5 and Cy119


title: 201490020010_R04C01

label: Cy5 and Cy118


title: 9296930029_R05C01


title: 201490020010_R03C01

label: Cy5 and Cy117


title: 9296930029_R01C02


title: 201503670184_R08C01

label: Cy5 and Cy115


title: 201490020010_R01C01

label: Cy5 and Cy116


title: 9296930029_R02C01


title: 201503670184_R03C01

label: Cy5 and Cy113


title: 201503670184_R04C01

label: Cy5 and Cy114


title: 201503670184_R02C01

label: Cy5 and Cy112


title: 9285451063_R04C02


title: 9296930080_R06C02


title: 9296930080_R02C02


title: 9285451063_R03C02


title: 201503670184_R01C01

label: Cy5 and Cy111


title: 201503670183_R08C01

label: Cy5 and Cy110


title: 9285451063_R06C01

label: Cy5 and Cy3


title: 9285451063_R05C01


title: 201503670183_R07C01

label: Cy5 and Cy109


title: 201503670190_R05C01

label: Cy5 and Cy215


title: 9285451063_R03C01


title: 201503670183_R05C01

label: Cy5 and Cy108


title: 201503670137_R07C01

label: Cy5 and Cy206


title: 9285451030_R05C01


title: 201503670183_R03C01

label: Cy5 and Cy106


title: 201503670140_R07C01

label: Cy5 and Cy104


title: 9285451030_R06C02


title: 9285451063_R05C02


title: 9285451030_R04C01


title: 9285451030_R01C01


title: 201503670140_R01C01

label: Cy5 and Cy101


title: 201503670140_R02C01

label: Cy5 and Cy102


title: 9285451009_R03C02


title: 9285451009_R06C01


title: 201503470065_R07C01

label: Cy5 and Cy99


title: 201503470065_R06C01

label: Cy5 and Cy98


title: 9285451009_R03C01


title: 201503470065_R04C01

label: Cy5 and Cy97


title: 9285451009_R02C01


title: 9285451063_R02C01


title: 9285451063_R01C01


title: 201503470038_R03C01

label: Cy5 and Cy94


title: 201503670140_R08C01

label: Cy5 and Cy105


title: 9285451003_R04C02


title: 201503470038_R01C01

label: Cy5 and Cy92


title: 201503470038_R02C01

label: Cy5 and Cy93


title: 9285451030_R02C01


title: 9285451003_R02C02


title: 201503670183_R04C01

label: Cy5 and Cy107


title: 201503470027_R07C01

label: Cy5 and Cy90


title: 201503470027_R08C01

label: Cy5 and Cy91


title: 9285451115_R05C02

label: Cy5 and Cy3


title: 9285451009_R06C02


title: 9285451115_R06C02


title: 201503670140_R03C01

label: Cy5 and Cy103


title: 9285451003_R05C02


title: 201503470027_R04C01

label: Cy5 and Cy89


title: 201503470027_R03C01

label: Cy5 and Cy88


title: 9285451115_R04C02


title: 9285451115_R05C01


title: 9285451115_R04C01


title: 201503470003_R08C01

label: Cy5 and Cy87


title: 9285451003_R06C02


title: 201503470038_R08C01

label: Cy5 and Cy95


title: 201503470065_R01C01

label: Cy5 and Cy96


title: 201503470003_R04C01

label: Cy5 and Cy86


title: 201503470003_R03C01

label: Cy5 and Cy85


title: 9285451115_R02C01


title: 9285451115_R01C01


title: 9285451115_R03C01


title: 201496860130_R06C01

label: Cy5 and Cy81


title: 9285451096_R05C02


title: 9285451096_R06C02


title: 201496860130_R08C01

label: Cy5 and Cy82


title: 201503470003_R02C01

label: Cy5 and Cy84


title: 9285451096_R02C02


title: 9285451096_R03C02


title: 201496860130_R05C01

label: Cy5 and Cy80


title: 9285451096_R01C02


title: 201503470003_R01C01

label: Cy5 and Cy83


title: 201496860130_R04C01

label: Cy5 and Cy79


title: 9285451096_R04C01


title: 201496860130_R03C01

label: Cy5 and Cy78


title: 9285451096_R03C01


title: 201496860030_R07C01

label: Cy5 and Cy76


title: 201496860030_R08C01

label: Cy5 and Cy77


title: 9285451096_R02C01

label: Cy5 and Cy3


title: 201496860030_R06C01

label: Cy5 and Cy75


title: 9285451096_R01C01


title: 201496860030_R04C01

label: Cy5 and Cy74


title: 9285451076_R04C02


title: 9285451076_R06C02


title: 201496860030_R02C01

label: Cy5 and Cy73


title: 201496850187_R07C01

label: Cy5 and Cy72


title: 9285451076_R03C02


title: 201496850187_R06C01

label: Cy5 and Cy71


title: 9285451076_R02C02


title: 201496850187_R04C01

label: Cy5 and Cy69


title: 201496850130_R07C01

label: Cy5 and Cy67


title: 201496850187_R02C01

label: Cy5 and Cy68


title: 9285451076_R05C01


title: 9285451076_R04C01


title: 9285451076_R02C01


title: 9285451076_R06C01


title: 9285451076_R01C01


title: 9285451068_R02C02


title: 201496850130_R03C01

label: Cy5 and Cy65


title: 9285451068_R06C02


title: 9285451068_R06C01


title: 201496850130_R01C01

label: Cy5 and Cy63


title: 9285451067_R06C02


title: 9285451067_R05C02


title: 201496860063_R08C01

label: Cy5 and Cy62


title: 201496860063_R03C01

label: Cy5 and Cy60


title: 201496860063_R01C01

label: Cy5 and Cy59


title: 9285451067_R03C02


title: 201496850089_R07C01

label: Cy5 and Cy58


title: 9285451067_R04C01


title: 9285451067_R02C01


title: 201496850130_R06C01

label: Cy5 and Cy66


title: 201496850089_R06C01

label: Cy5 and Cy57


title: 201496850089_R04C01

label: Cy5 and Cy56


title: 201496850008_R06C01

label: Cy5 and Cy53


title: 9285451067_R01C01

label: Cy5 and Cy3


title: 201496850008_R07C01

label: Cy5 and Cy54


title: 9285451052_R04C02


title: 201496850130_R02C01

label: Cy5 and Cy64


title: 9285451052_R02C02


title: 201496850089_R02C01

label: Cy5 and Cy55


title: 9285451068_R02C01


title: 9285451052_R01C02


title: 201496850008_R04C01

label: Cy5 and Cy52


title: 201496850008_R01C01

label: Cy5 and Cy50


title: 9285451052_R05C01


title: 201492560190_R08C01

label: Cy5 and Cy49


title: 9285451052_R04C01


title: 201492560190_R06C01

label: Cy5 and Cy48


title: 201496850008_R03C01

label: Cy5 and Cy51


title: 9285451052_R03C02


title: 201496860063_R04C01

label: Cy5 and Cy61


title: 9285451050_R06C02


title: 201492560190_R05C01

label: Cy5 and Cy47


title: 201492560190_R01C01

label: Cy5 and Cy45


title: 9285451050_R05C02


title: 9285451052_R03C01


title: 9285451050_R03C02


title: 201492560138_R08C01

label: Cy5 and Cy44


title: 201492560138_R06C01

label: Cy5 and Cy42


title: 201492560138_R07C01

label: Cy5 and Cy43


title: 9285451052_R06C01


title: 9285451050_R06C01


title: 9285451050_R02C02


title: 201492560137_R08C01

label: Cy5 and Cy40


title: 9266441073_R06C02


title: 201496850187_R05C01

label: Cy5 and Cy70


title: 9285451050_R02C01

label: Cy5 and Cy3


title: 201492560137_R06C01

label: Cy5 and Cy38


title: 9266441073_R05C02


title: 201492560137_R07C01

label: Cy5 and Cy39


title: 201492560137_R03C01

label: Cy5 and Cy37


title: 9285451050_R04C01


title: 9266441073_R04C02


title: 9266441073_R03C02


title: 201492560137_R02C01

label: Cy5 and Cy36


title: 201492560136_R08C01

label: Cy5 and Cy35


title: 9266441073_R02C02


title: 201492560190_R03C01

label: Cy5 and Cy46


title: 9266441073_R01C02


title: 9296930029_R01C01


title: 201492560136_R07C01

label: Cy5 and Cy34


title: 9266441073_R06C01


title: 201492560136_R06C01

label: Cy5 and Cy33


title: 9266441073_R05C01


title: 9266441073_R02C01


title: 9274651204_R05C02


title: 201492560073_R07C01

label: Cy5 and Cy29


title: 201492560136_R01C01

label: Cy5 and Cy31


title: 201492560073_R04C01

label: Cy5 and Cy28


title: 9274651204_R04C02


title: 9274651204_R03C02


title: 201492560054_R07C01

label: Cy5 and Cy25


title: 9274651204_R01C02


title: 9274651204_R02C02


title: 201492560073_R01C01

label: Cy5 and Cy26


title: 201492560138_R05C01

label: Cy5 and Cy41


title: 201492560054_R06C01

label: Cy5 and Cy24


title: 9274651204_R03C01


title: 9266441073_R01C01


title: 201492560054_R04C01

label: Cy5 and Cy23


title: 9274651149_R03C02

label: Cy5 and Cy3


title: 9274651149_R04C02


title: 201492560136_R04C01

label: Cy5 and Cy32


title: 201492560054_R01C01

label: Cy5 and Cy21


title: 9274651149_R05C01


title: 201490030052_R08C01

label: Cy5 and Cy20


title: 9274651117_R06C02


title: 201490030052_R06C01

label: Cy5 and Cy19


title: 201490030052_R05C01

label: Cy5 and Cy18


title: 201492560054_R03C01

label: Cy5 and Cy22


title: 9274651117_R03C02


title: 201492560073_R02C01

label: Cy5 and Cy27


title: 9274651117_R04C02


title: 201490030052_R02C01

label: Cy5 and Cy16


title: 9274651204_R06C01


title: 201490020091_R07C01

label: Cy5 and Cy15


title: 9274651117_R05C01


title: 9274651104_R05C02


title: 201490020091_R02C01

label: Cy5 and Cy13


title: 201490020091_R04C01

label: Cy5 and Cy14


title: 9285451003_R03C02


title: 9274651117_R01C01


title: 9274651104_R03C02


title: 9274651104_R04C02


title: 201503670165_R08C01

label: Cy5 and Cy12


title: 201503670165_R03C01

label: Cy5 and Cy10


title: 201503670165_R06C01

label: Cy5 and Cy11


title: 9274651104_R02C02


title: 9274651104_R05C01


title: 9274651104_R04C01


title: 9274651104_R06C01


title: 9274651104_R01C01


title: 201503670165_R01C01

label: Cy5 and Cy8


title: 9266441188_R06C02


title: 201490030052_R04C01

label: Cy5 and Cy17


title: 9266441188_R05C02

label: Cy5 and Cy3


title: 201503470078_R05C01

label: Cy5 and Cy6


title: 9266441188_R04C02


title: 201503470078_R02C01

label: Cy5 and Cy4


title: 9266441188_R03C02


title: 201503470025_R07C01


title: 9266441188_R02C02


title: 201503670165_R02C01

label: Cy5 and Cy9


title: 201503470065_R08C01

label: Cy5 and Cy100


title: 201503470025_R03C01


title: 201503470078_R03C01

label: Cy5 and Cy5


title: 201503470025_R02C01


title: 9266441188_R01C02


title: 201492560073_R08C01

label: Cy5 and Cy30


title: 201503470025_R05C01


title: 9266441188_R05C01


title: 9266441188_R06C01


title: 201503470025_R04C01


title: 9266441188_R04C01


title: 201503470078_R06C01

label: Cy5 and Cy7


title: 9266441144_R04C02


title: 201496860101_R01C01


title: 201496860101_R05C01


title: 9266441144_R05C02


title: 9266441144_R02C02


title: 9266441144_R01C02


title: 201496860101_R08C01


title: 201496710107_R08C01


title: 201496860101_R02C01


title: 9266441144_R05C01


title: 201496710107_R05C01


title: 9266441144_R04C01


title: 201496710107_R04C01


title: 201496710107_R01C01


title: 9266441144_R03C01


title: 9266441144_R01C01


title: 201496710047_R08C01


title: 201496710047_R07C01


title: 9266441124_R06C02


title: 201496710047_R05C01


title: 201496710010_R06C01


title: 9266441188_R02C01


title: 9266441124_R06C01


title: 9266441124_R03C02


title: 201496710047_R02C01


title: 201496710010_R05C01


title: 9266441124_R04C02


title: 9266441124_R01C02


title: 9266441124_R02C01


title: 9266441124_R05C01


title: 9266441124_R04C01


title: 201496710010_R03C01


title: 201496710010_R02C01


title: 201496710107_R07C01


title: 9266441119_R05C02


title: 201496710010_R01C01


title: 201492560223_R06C01


title: 201492560223_R07C01


title: 9266441119_R03C01


title: 201492560223_R02C01


title: 9266441119_R04C01


title: 9266441119_R02C01


title: 201492560167_R08C01


title: 9266441119_R01C01


title: 201492560167_R02C01


title: 201492560167_R01C01


title: 201492560060_R08C01


title: 3998568023_R02C02

extract_protocol: Buccal swabs were collected using Catch-All Swabs (Epicentre, USA).  Genomic DNA was extracted using the Masterpure system (Epicentre, USA), and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).


title: 3998568023_R02C01


title: 3998568023_R04C02


title: 3998568004_R06C02


title: 201492560167_R04C01


title: 3998568023_R05C01


title: 201492560167_R05C01


title: 201492560060_R07C01


title: 201492560060_R03C01


title: 201492560060_R05C01


title: 201492560060_R01C01


title: 201492560223_R08C01


title: 3998568004_R02C01


title: 3998568004_R04C01


title: 3998568004_R05C02


title: 3998568004_R01C02


title: 201492560223_R01C01


title: 201490030177_R03C01


title: 201490030177_R05C01


title: 3998568004_R01C01


title: 201490030177_R02C01


title: 3998568004_R06C01


title: 3998567077_R05C02


title: 3998567077_R05C01


title: 201496860191_R08C01


title: 3998568023_R01C01


title: 201496860191_R05C01


title: 201496860191_R04C01


title: 201496860176_R08C01


title: 201496860176_R04C01


title: 3998568004_R04C02


title: 3998567077_R01C01


title: 201496860176_R06C01


title: 3998567077_R02C01


title: 3998567077_R01C02


title: 3998567077_R04C01


title: 3998567077_R04C02


title: 3998567024_R04C01


title: 201496860165_R07C01


title: 3998567024_R03C01


title: 3998567024_R01C02


title: 100946150149_R06C01


title: 201496860165_R06C01


title: 201496860165_R01C01


title: 201496860165_R02C01


title: 100946150149_R06C02


title: 3998567024_R06C02


title: 201496860176_R07C01


title: 201496860112_R05C01


title: 201496860112_R07C01


title: 201496860112_R04C01


title: 201496860176_R02C01


title: 201496860045_R04C01


title: 100946150149_R02C01


title: 201496860045_R08C01


title: 100946150149_R01C02


title: 100946150122_R05C01


title: 201496860045_R03C01


title: 100946150122_R04C02


title: 201496860112_R01C01


title: 201496860165_R05C01


title: 100946150122_R02C02


title: 100946150122_R01C02


title: 201496850129_R07C01


title: 100946150149_R05C02


title: 201496860045_R01C01


title: 100946150122_R01C01


title: 100946150121_R06C01


title: 201496860045_R02C01


title: 100946150149_R04C01


title: 100946150149_R05C01


title: 100946150121_R05C01


title: 201496850129_R04C01


title: 201496850129_R02C01


title: 100946150121_R04C01


title: 201496850129_R01C01


title: 201496850129_R05C01


title: 100946150149_R03C02


title: 100946150121_R02C02


title: 201496860112_R02C01


title: 201496850064_R08C01


title: 100946150122_R03C01


title: 100946150121_R02C01


title: 201496850064_R07C01


title: 201496850064_R06C01


title: 100946150108_R05C02


title: 100946150121_R01C01


title: 100946150108_R05C01


title: 201496850064_R02C01


title: 100946150108_R03C02


title: 201490030081_R05C01


title: 201490030081_R08C01


title: 201490030081_R06C01


title: 100946150107_R04C01


title: 100946150108_R01C02


title: 100946150107_R03C02


title: 201490030081_R03C01


title: 100946150107_R02C02


title: 201490030079_R06C01


title: 201490030081_R02C01


title: 201490030079_R08C01


title: 201490030079_R04C01


title: 100946150106_R04C02


title: 201490030009_R05C01


title: 100946150106_R06C02


title: 201490030009_R02C01


title: 100946150106_R02C01


title: 100946150106_R01C02


title: 100946150106_R02C02


title: 100946150097_R06C02


title: 201496850064_R03C01


title: 201490020184_R04C01


title: 201503670201_R07C01


title: 100946150097_R05C01


title: 201490020184_R01C01


title: 201490030009_R07C01


title: 201503670201_R05C01


title: 201503670201_R06C01


title: 100946150097_R03C01


title: 201503670201_R03C01


title: 100946150106_R05C01


title: 100946150106_R06C01


title: 100946150097_R04C01


title: 201490030009_R06C01


title: 100946150097_R02C01


title: 100946150097_R01C02


title: 201503670191_R08C01


title: 201490020184_R05C01


title: 201503670191_R06C01


title: 100946150061_R05C02


title: 201503670191_R04C01


title: 100946150061_R05C01


title: 100946150107_R01C01


title: 100946150097_R05C02


title: 201503670191_R02C01


title: 100946150097_R06C01


title: 100946150097_R01C01


title: 201503670167_R05C01


title: 201490030009_R01C01


title: 100946150061_R04C01


title: 100946150061_R03C02


title: 100946150061_R03C01


title: 201503670167_R04C01


title: 201503670167_R02C01


title: 100946150061_R02C01


title: 100946150061_R02C02


title: 100946150061_R01C02


title: 201503670006_R06C01


title: 201503670191_R05C01


title: 9407210042_R01C01


title: 201503670006_R03C01


title: 9407210038_R05C02


title: 9407210038_R03C02


title: 201503670167_R01C01


title: 201496860177_R07C01


title: 201496860177_R08C01


title: 201503670006_R01C01


title: 9407210038_R01C02


title: 201496860177_R04C01


title: 201496860177_R03C01


title: 9407210035_R04C02


title: 9407210035_R05C02


title: 9407210035_R06C01


title: 201503670167_R03C01


title: 201496860133_R07C01


title: 201496860133_R05C01


title: 9407210035_R03C01


title: 9407210035_R02C02


title: 9407210035_R02C01


title: 201496850138_R07C01


title: 201496860133_R08C01


title: 201503670006_R05C01


title: 9407210021_R06C02


title: 201496850138_R04C01


title: 9407210021_R05C02


title: 9407210038_R02C02


title: 201496850138_R03C01


title: 100946150107_R05C01


title: 9407210042_R04C02


title: 201496850138_R02C01


title: 9407210021_R02C01


title: 201496850127_R08C01


title: 9407210021_R02C02


title: 201496850127_R05C01


title: 9407210021_R01C02


title: 9407201158_R06C01


title: 201496850127_R04C01


title: 201496850127_R03C01


title: 201496850127_R02C01


title: 201496850138_R08C01


title: 201492560135_R08C01


title: 201492560135_R06C01


title: 9407201158_R02C01


title: 9407201158_R02C02


title: 9407201158_R03C02


title: 201492560135_R02C01


title: 9407201158_R05C02


title: 9407201158_R01C01


title: 9407201158_R04C01


title: 201492560135_R01C01


title: 9407201156_R06C01


title: 201490020139_R08C01


title: 9407210021_R04C01


title: 201490020139_R07C01


title: 201492560135_R05C01


title: 9407201156_R05C02


title: 9407201156_R02C02


title: 9407201156_R04C02


title: 201490020139_R02C01


title: 201490020139_R04C01


title: 201490020139_R01C01


title: 9407201156_R01C02


title: 9407201156_R01C01


title: 201490020011_R08C01


title: 201490020011_R03C01


title: 9407201155_R05C01


title: 9407201155_R06C01


title: 9407201155_R02C01


title: 201490020011_R02C01


title: 9407201155_R01C02


title: 201490020011_R01C01


title: 9407201155_R01C01


title: 201503670201_R04C01


title: 201490030177_R07C01


title: 9407201146_R06C02


title: 201496850089_R01C01


title: 201496860101_R03C01


title: 9407201146_R05C01


title: 201492560199_R08C01_Buccal12

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

extract_protocol: Genomic DNA was extracted using the Gentra Puregene Buccal Cell Kit (Qiagen #158845) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).


title: 201492560199_R06C01_Buccal


title: 9407201146_R01C02


title: 9407201146_R02C02


title: 201492560199_R05C01_Buccal


title: 9407201145_R06C02


title: 201492560144_R08C01_Buccal12


title: 9407201146_R01C01


title: 201490020011_R05C01


title: 201492560144_R06C01_Buccal12


title: 9407201145_R04C02


title: 9407201145_R05C01


title: 201492560144_R05C01_Buccal


title: 9407201155_R04C01


title: 201492560144_R04C01_Buccal12


title: 9407201145_R02C01


title: 201492560144_R02C01_Buccal


title: 9407201145_R02C02


title: 201492560018_R07C01_Buccal


title: 9407201145_R01C02


title: 201492560018_R03C01_Buccal


title: 9407201143_R06C02


title: 9407201156_R03C02


title: 201492560018_R05C01_Buccal12


title: 9407201143_R04C02


title: 201492560018_R02C01_Buccal


title: 9407201143_R06C01


title: 201492560199_R02C01_Buccal


title: 9407201143_R05C02


title: 201490030017_R08C01_Buccal


title: 9407201143_R04C01


title: 9407201143_R02C02


title: 201490030017_R04C01_Buccal


title: 201490030017_R07C01_Buccal12


title: 9407201141_R06C01


title: 9407201145_R05C02


title: 9407201141_R04C02


title: 200925700207_R06C01_Buccal


title: 200925700207_R04C01_Buccal


title: 9407201141_R03C02


title: 9407201141_R02C02


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title: iBC_MSC_rep2

city: CUHK, Shatin

first: Hoi-Hung

last: Cheung

address: Rm.708A, LKS Integrated Biomedical Sciences Bldg.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.
Algorithm for mapping sequences: appropriate software is chosen according to the characteristics of the reference genome. In general, TopHat2 is chosen for animal and plant genomes.
Files are provided in BAM format, a standard file format that contains mapping results, and the corresponding reference genome and gene annotation file for some species.
Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used. In RNA-seq, FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, is the most commonest method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010).
To compare gene expression levels under different conditions, an FPKM distribution diagram and violin Plot are used. For biological replicates, the final FPKM would be the mean value.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes FPKM values for all samples

source_name: MSC

growth_protocol: MSC was grown in MSC medium (10% MSC-qualified FBS in low-glucose DMEM) and passed every 4-5 days when cells became confluent.

extract_protocol:
Trizol reagent
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: No specific treatment.

value: iPSC-derived

value: WRN+/+


title: C24_MSC_rep2


title: C24_MSC_rep1


title: 200923040024_R08C01_Buccal12

value: M