title: Identificaton of abberantly expressed genes in triple negative breast cancer specimens

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from Feature Extraction. Agilent software was used.

source_name: triple negative breast cancer specimens

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions

value: breast cancer


title: pax2a_24hpf_rep1

status: Public on Aug 15 2018

type: SRA

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

library_source: genomic

data_processing:
library strategy: 4C-seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Danio rerio (danRer6 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
A running 51 bins-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), danRer10, mm10
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 2Mb around each viewpoint that can be directly uploaded to UCSC for visualization.

molecule: genomic DNA

organism: Danio rerio

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax2a

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

tag: developmental

tag: tissue

value: whole embryo


title: MDA-MB-231,MKC-8866 treated, 4 hours, biological rep2

type: RNA

city: Galway

first: Afshin

last: Samali

address: Newcastle Road, Dangan

department: Biomedical Sciences

country: Ireland

institute: Apoptosis Research Centre

hyb_protocol: Labeled, fragmented cDNA (5.5ug) (AffymetrixGeneChip® WT Terminal Labeling and Controls Kit, catalogue number 901524) was hybridized to Human Gene 2.0 arrays for 16 hours at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, catalogue number 900720).

scan_protocol: Arrays were washed and stained using the Affymetrix Fluidics Station 450, and scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring (Agilent technologies) software using Affymetrix default analysis settings and Robust Multichip Average (RMA) algorithm as normalization method.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human triple negative breast cancer cell line MDA-MB-231 from ATCC (HTB-26)

label_protocol: Human RNA samples (450ng) were processed and labeled for array hybridization using the Ambion WT Expression kit (Life Technologies, catalogue number 4411974).

growth_protocol: MDA-MB 231 cells were maintained at 37C in 5% CO2, in DMEM High Glucose (4,500 mg/ml), supplemented with 10% FBS and 2mM L-glutamine

extract_protocol: RNA was extracted from cells using a combination of Trizol extraction and Rneasy Columns from Qiagen.

treatment_protocol: MDA-MB 231 cells at passage 16 (repeat 1), 17 (repeat 2) 19, (repeat 3) were seeded at 500,000 cells/T25 flask. The next day the media on cells was replaced with media containing DMSO or MKC-8866 (20 μM). In parallel cells were placed in a hypoxic glovebox (1% O2, Coy Laborartoy) and the media was replaced with hypoxia pre-conditioned media (i.e. media left in hypoxia overnight) containing DMSO or MKC-8866 (20 μM). At appropriate time-points cells were scraped from the flasks, pelleted and resuspended in 1mL Trizol.

tag: cell line

tag: treatment

value: MKC-8866 treated, 4 hours


title: Identificaton of abberantly expressed genes in pooled RNA sample from 15 breast cancer specimens

country: Japan

source_name: 15 breast cancer specimens


title: MDA-MB-231, DMSO treated, 4 hours, biological rep2

value: DMSO treated, 4 hours


title: meox2b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of meox2b


title: meox1_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of meox1


title: MDA-MB-231, DMSO treated, 4 hours, biological rep1


title: Identificaton of abberantly expressed genes in ER negative and HER2 positive breast cancer specimens


title: foxa2_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of foxa2


title: meox1_24hpf_rep1


title: pax3a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax3a


title: eng2a_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of eng2a


title: eng2b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of eng2b


title: foxa1_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of foxa1


title: foxa1_24hpf_rep1


title: muscle_rep2_RRBS

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description:
muscle3
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv

data_processing:
RRBS libraries were sequenced in paired-end mode on the Illumina HiSeqX platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome Branchiostoma lanceolatum (Bl71nemr) using WALT alignment algorithm and MethylDackel to extract cytosine methylation metrics with default parameters.
Genome_build: Branchiostoma lanceolatum: Bl71nemr
Supplementary_files_format_and_content: For "*_bigtable.tsv" processed data files the column headers are as follows: column 1 - assembly (chromosome). column 2 - position: coordinate for the cytosine position on the chromosome. columns 3, 5, 7, 9, 11, 13 (.C) - number of reads depicting a methylated cytosine. columns 4, 6, 8, 10, 12, 14 (.cov) - total number of reads at that position.

organism: Branchiostoma lanceolatum

source_name: muscle

extract_protocol:
Adult tissues were homogenized in 3 volumes STOP buffer (15 mM EDTA, 10 mM Tris-HCl pH7.5, 1% SDS, 0.5 mg/mL proteinase K) after which two phenol:chloroform:isoamylalcohol (PCI, 25:24:1) extractions were performed. DNA was then precipitated in 1/5 volume NH4AC 4M and 3 volumes EtOH and dissolved in 100 uL, treated with RNase and purified by a PCI extraction. The precipitation was done with EtOH and the DNA was resuspended in 50 uL H2O.
RRBS library generation was performed as described previously (Murphy et al, 2018; Cell). Briefly, 125ng of genomic DNA was digested using MspI restriction enzyme. Digested DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Bisulphite conversion of adapter-ligated DNA fragments was performed using EZ DNA Methylation-Gold Kit.  Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 11 cycles of amplification.

tag: developmental stage

value: adult

value: muscle


title: Identificaton of abberantly expressed genes in ER positive and HER2 negative breast cancer specimens


title: dlx6a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx6a


title: dlx4b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx4b


title: dlx5a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx5a


title: dlx4a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx4a


title: dlx3b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx3b


title: dlx2b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx2b


title: dlx2a_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx2a


title: dlx2a_24hpf_rep1


title: gbx2_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of gbx2


title: dlx1a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of dlx1a


title: notochord_rep1_RRBS

description:
notochord1
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv

source_name: notochord

value: notochord


title: gut_rep2_RRBS

description:
gut2
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv

source_name: gut

value: gut


title: dlx1a_24hpf_rep2


title: gut_rep1_RRBS

description:
gut1
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv


title: fezf1_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of fezf1


title: Gcn5AA_Rapa_Med8_ChEC

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

country: Switzerland

institute: Univeristy of Geneva

data_processing:
Library strategy: ChEC-Seq
For ChEC-Seq, Pairs of FASTQ files were mapped to the sacCer3 genome assembly using Novoalign (Novocraft), generating SAM files that were then converted to tag directories with HOMER (PMID 20513432) (homer.ucsd.edu) for further analysis.
processed data files format and content: ChEC-seq data were visualized as reads per million (RPM)-normalized single-base resolution bedgraph tracks.
Genome_build: sacCer3, 972-h pombe

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase before treatment

extract_protocol:
Cells were pelleted at 3,000 x g and washed three times with 1 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), centrifuging as above between washes. Cells were resuspended in 600 µL Buffer A containing 0.1% digitonin and permeabilized at 30C for 5 min. CaCl2 was added to 2 mM and ChEC digests were performed at 30C. 5 min after CaCl2 addition, a 100 µL aliquot of the digest was transferred to a tube containing 100 µL 2X stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA) and 1% SDS. Protein was then was digested with 80 µg proteinase K at 55C for 30 m. Nucleic acids were extracted with an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 2.5 volumes 100% ethanol and 30 µg Glycogen (Roche). Pellets were washed once with 1 mL 100% ethanol, dried, and resuspended in 30 µL 0.1X TE buffer, pH 8.0. RNA was digested with 10 µg RNase A at 37C for 20 m. Prior to generating sequencing libraries, ChEC DNA was subjected to size-selection using Ampure XP beads (ThermoFischer). A beads:sample ratio of 2.5:1 was used and the unbound fraction, containing small DNA fragments, was extracted to remove RNase and precipitated as above, and used for library preparation.
Libraries were constructed as described (PMID 27797823).

treatment_protocol: 60 minutes rapamycin

tag: strain

tag: genotype

value: W303 mat a tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 GCN5-FRB::HIS3 MED8-3XFLAG-MNase::HphMX

tag: antibody


title: Esa1AA_Rapa_Med8_ChEC

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ESA1-FRB::KanMX MED8-3XFLAG-MNase::HphMX


title: Gcn5AA_Veh_Med8_ChEC

treatment_protocol: no rapamycin


title: Esa1AA_Veh_Med8_ChEC


title: Med17AA_Rapa_MNase

data_processing:
For MNase-Seq, raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
For MNase-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For MNase-Seq tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
processed data files format and content: wig and bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)
Genome_build: sacCer3, 972-h pombe

extract_protocol:
Chromatin for MNase digestion was prepared essentially as described in Kubik et al., 2015 (GSE73337) (PMID: 26545077)
Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700)

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 MED17-FRB::HIS3


title: Med17AA_Veh_Med8_ChEC

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 MED17-FRB::HIS3 MED8-3XFLAG-MNase::HphMX


title: IPSI-day16 (#7-107)

city: Dublin 4

first: PATRICK

last: LONERGAN

address: Belfield

institute: University College Dublin

library_source: transcriptomic

data_processing:
Raw sequences (fastq) were subjected to quality control using windowed adaptive quality triming approach implemented in fqtrim (https://ccb.jhu.edu/software/fqtrim/).
Read quallity was checked by Fastqc and quality control was performed by fqtrim.
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/).
Read counts mapping to each gene were determined from the mapping data using FeatureCounts
Differential expression analysis between sample groups was performed by robustly fitting the expression data to a generalized linear model using edgeRrobust
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.

organism: Bos taurus

source_name: Endometrium

extract_protocol:
Total RNA extracted from ~100 mg of endometrial homogenate using Trizol reagent (Invitrogen, Carlsbad, CA) per the manufacturer´s instructions. On-column DNase digestion and RNA clean-up was performed using the Qiagen mini kit (Qiagen).
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

value: IPSI uterus horn

tag: time

value: pregnancy day16


title: Cont-day13 (#6-203)

value: Contra uterus horn

value: pregnancy day13


title: muscle_rep1_RRBS

description:
muscle1
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv


title: IPSI-day13 (#8-275)


title: Med17AA_Veh_MNase


title: Cont-day13 (#5-167)


title: IPSI-day16 (#8-245)


title: Med17AA_Rapa_Med8_ChEC


title: HKC8 PBS 24 hours

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

country: China

institute: Southern Medical University

description: lncRNAs expression after 24 hours treated with PBS

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: total RNA from cell PBS 24 hours

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA was extracted using TRIzol(Invitrogen) accoring to the  manufacturer's recommendations.

treatment_protocol: Cells were serum-starved overnight when they reached at approximately 70% confluence, and then incubated with recombinant TGF-β1(10ng/ml)for 24 hours.

tag: agent

value: PBS


title: HKC8 TGF-β 24 hours

description: lncRNAs expression after 24 hours treated with TGF-β(10ng/ml)

source_name: total RNA from cell TGF-β 24 hours


title: Gcn5AA_Rapa_MNase

value: W303 mat a tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 GCN5-FRB::HIS3


title: IPSI-day13 (#6-203)


title: HK2 TGF-β 24 hours


title: Gcn5AA_Veh_MNase


title: HK2 PBS 24 hours


title: Esa1AA_Veh_MNase

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ESA1-FRB::KanMX


title: Esa1AA_Rapa_MNase


title: Cont-day13 (#5-140)


title: Med17AA_Rapa_RNAPII

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3 and 972-h pombe genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
For ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For ChIP-Seq, reads that mapped to both sacCer3 and 972-h genomes were discarded.
For ChIP-Seq, the reads were shifted by 100 bp and extended by 50 bp
For ChIP-Seq, reads mapped uniquely to the sacCer3 genome were first normalized to total number of mapped reads in sacCer3 and then to total number of uniquely mapped reads in 972-h pombe in the same sample as described in (Hu et al. 2015)
processed data files format and content: wig and bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)
Genome_build: sacCer3, 972-h pombe

extract_protocol:
H3, H3K9ac, H4ac and RNAPII ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045) with the following modification. A defined amount (5% of total chromatin) of previously cross-linked chromatin from S.pombe was added to S.cerevisiae chromatin prior to immunoprecipitation step.
TruSeq ChIP library preparation kit (Illumina)

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: Gcn5AA_Tra1AA_Rapa_RNAPII

treatment_protocol: 120 minutes rapamycin

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 FRB-TRA1 GCN5-FRB::HIS3


title: Med17AA_Veh_RNAPII


title: Gcn5AA_Tra1AA_Veh_RNAPII


title: IPSI-day13 (#5-167)


title: Cont-day7 (#5-117)

value: pregnancy day7


title: Gcn5AA_Tra1AA_Veh_H4ac

value: Anti-H4 acetylation (Millipore 06-866)


title: Gcn5AA_Tra1AA_Veh_H3K9ac

value: Anti-H3 Lys9 acetylation (Millipore 07-352)


title: IPSI-day5 (#7-300)

value: pregnancy day5


title: Gcn5AA_Tra1AA_Rapa_H3K9ac


title: Cont-day16 (#8-245)


title: Gcn5AA_Tra1AA_Rapa_H3


title: Tra1AA_Veh_RNAPII

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 FRB-TRA1


title: Tra1AA_Rapa_RNAPII


title: Cont-day7 (#4-064)


title: Gcn5AA_Tra1AA_Veh_H3


title: Tra1AA_Rapa_H4ac


title: Cont-day5 (#7-300)


title: Tra1AA_Veh_H4ac


title: Tra1AA_Rapa_H3K9ac


title: Cont-day16 (#7-107)


title: Gcn5AA_Tra1AA_Rapa_H4ac


title: Tra1AA_Veh_H3K9ac


title: IPSI-day5 (#4-184)


title: IPSI-day16 (#5-137)


title: Gcn5AA_Veh_60min_diamide_RNAPII

treatment_protocol: no rapamycin 60 minutes diamide


title: Gcn5AA_Rapa_60min_diamide_RNAPII

treatment_protocol: 120 minutes rapamycin 60 minutes diamide


title: Gcn5AA_Rapa_20min_diamide_RNAPII

treatment_protocol: 80 minutes rapamycin 20 minutes diamide


title: Tra1AA_Rapa_H3


title: Tra1AA_Veh_H3


title: Cont-day13 (#4-1314)


title: Gcn5AA_Veh_20min_diamide_RNAPII

treatment_protocol: no rapamycin 20 minutes diamide


title: Gcn5AA_Rapa_5min_diamide_RNAPII

treatment_protocol: 65 minutes rapamycin 5 minutes diamide


title: eng2a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of eng2a

value: whole embryo


title: IPSI-day13 (#4-1314)


title: Gcn5AA_Veh_0min_diamide_RNAPII

treatment_protocol: no rapamycin no diamide


title: Gcn5AA_Veh_5min_diamide_RNAPII

treatment_protocol: no rapamycin 5 minutes diamide


title: Cont-day5 (#4-184)


title: Esa1AA_Rapa_60min_diamide_RNAPII


title: Gcn5AA_Rapa_0min_diamide_RNAPII

treatment_protocol: 60 minutes rapamycin no diamide


title: IPSI-day7 (#4-064)


title: Esa1AA_Rapa_20min_diamide_RNAPII


title: Esa1AA_Veh_60min_diamide_RNAPII


title: IPSI-day5 (#3-175)


title: Esa1AA_Veh_20min_diamide_RNAPII


title: IPSI-day5 (#1-315)


title: Esa1AA_Veh_5min_diamide_RNAPII


title: Esa1AA_Rapa_5min_diamide_RNAPII


title: Cont-day16 (#5-137)


title: Esa1AA_Rapa_0min_diamide_RNAPII


title: Gcn5AA_Rapa_RNAPII


title: IPSI-day16 (#3-155)


title: Cont-day7 (#2-371)


title: Gcn5AA_Veh_RNAPII


title: Gcn5AA_Rapa_H4ac


title: IPSI-day7 (#2-371)


title: 22Rv1_delSite3_Clone5/6-B8

city: Los Angeles

first: Yu

middle: (Phoebe)

last: Guo

state: California

address: 1450 Biggy Street, NRT 6514

country: USA

institute: Univ. of Southern California

data_processing:
RNA-seq results were aligned to Gencode v19 and reads were counted using STAR
Read count table is generated using STAR as well
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each gene

source_name: 22Rv1 cells

growth_protocol: 22Rv1 cells were grown according to ATCC protocol

extract_protocol:
Total RNA were extracted following the trizol protocol
Libraries were prepared using Kapa Stranded mRNA kit with beads (Kapa #KK8421) according to provided protocol

value: prostate carcinoma cell line 22Rv1

value: Site 3 complete deletion (chr1:154531542-154532455 in hg19)

tag: grna used

tag: clone number


title: Cont-day7 (#2-1337)


title: NONMMUT002667-KO mice 3

city: changsha

first: CHANGJUN

last: LI

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

description: Gene expression after 12hr  in 8Gy-irradiated human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: KO BMSCs replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The sorted mouse Sca-1+ CD29+ CD45− CD11b− BMSCs were cultured to reach 80%–85% confluence. Then, first-passage BMSCs were detached and seeded in culture flasks for the enrichment of cell populations.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Femurs of mice were collected and crushed with a mortar and pestle. The bone was then digested with collagenase A (Sigma) to obtain a single-cell suspension. Cells within the supernatant were collected and incubated with phycoerythrin (PE)-, FITC-, peridinin chlorophyll protein (PerCP)- and allophycocyanin (APC)-conjugated antibodies that recognized mouse Sca-1 (Cat. No. 108108, BioLegend), CD29 (Cat. No. 102206, BioLegend), CD45 (Cat. No. 103132, BioLegend), and CD11b (Cat. No. 101226, BioLegend) for 20 min at 4°C. The acquisition was performed on a fluorescence-activated cell sorting (FACS) Aria model (BD Biosciences), and the analysis was performed using FACS DIVE software version 6.1.3 (BD Biosciences).

tag: cell type

value: Bone marrow stem cells

tag: gender

value: male


title: Gcn5AA_Veh_H4ac


title: Gcn5AA_Veh_H3K9ac


title: Cont-day16 (#3-155)

value: Contra uterus horn

value: pregnancy day16


title: NONMMUT002667-KO mice 1

description: Gene expression after 6hr in 5Gy-irradiated human blood

source_name: KO BMSCs replicate 1


title: Gcn5AA_Rapa_H3


title: Cont-day5 (#1-315)


title: Esa1AA_Veh_0min_diamide_RNAPII


title: Cont-day16 (#2-068)


title: wildtype mice 1

description: Gene expression after 6hr in 0Gy-irradiated human blood

source_name: WT BMSCs replicate 1


title: IPSI-day7 (#6-338)

value: IPSI uterus horn


title: wildtype mice 3

description: Gene expression after 6hr in 2Gy-irradiated human blood

source_name: WT BMSCs replicate 3


title: E.coli 1

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

country: United Kingdom

institute: Newcastle University

data_processing:
Basecalling by standard Illumina pipeline (RTA2 for base calling and filtering, bcl2fastq for producing FASTQ files).
Dataset quality was assessed using FastQC to ensure per base and per tile sequence quality.
Raw reads were quality trimmed using fastx_toolkit allowing a maximum of 50nt and minumum length of 28nt.
Trimmed reads were aligned to the NC_000913.3 genome using Bowtie allowing three mismatched bases and only unique alignments (-n 3 -m 1 -a).
Single base variations between the experimental strain and the reference genome were identified using samtools and bcftools.
Error rate analysis was carried out in R using the BioConductor seqTools, seqInR and IRanges packages. Total error rates were calculated from the alignments as the percentage of total reads with a mismatched base at positions 7-16 in the alignment, thresholded to a Phred quality score of <30. Specific error rates were calculated as the percentage of total reads with a specific mismatch, for example an A incorporated instead of a G (G > A misincorporation), at each read position 7, thresholded to a Phred quality score of <30.  Ambiguous N bases and genomic positions of single base variation were excluded from the error rate calculation.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Alignment files are provided in bowtie format in addition to supplementary text files (E.coli_errors.txt and E.coli_base_errors.txt) containing the calculated error rates for all three samples.

organism: Escherichia coli K-12

source_name: cells

growth_protocol: Total RNA was isolated from mid-exponentially growing cultures of E.coli (OD600 ~ 0.5)

extract_protocol:
Cells were disrupted using the FastRNA Pro Blue Kit (MP Bio). Briefly, cell pellets were resuspended in 1 ml of the supplied phenol lysis solution and added to the Lysing Matrix before disruption in a Precellys 24 homogenizer (Bertin Technologies).
After centrifugation, the supernatant was removed and chloroform extracted. Total RNA was then isolated from the aqueous phase using the Total RNA Purification Plus Kit (Norgen).
Ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Illumina). Samples were fragmented using ultrasound, adapter was ligated to the 3' end of the RNA. First-strand cDNAsynthesis was performed using PrimeScript Reverse Transcriptase (TaKaRa). cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated. cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).


title: Esa1AA_Veh_RNAPII


title: NONMMUT002667-KO mice 2

description: Gene expression after 6hr in 8Gy-irradiated human blood

source_name: KO BMSCs replicate 2


title: Esa1AA_Rapa_H4ac


title: wildtype mice 2

description: Gene expression after 6hr in 0.5Gy-irradiated human blood

source_name: WT BMSCs replicate 2


title: IPSI-day7 (#2-1337)


title: Esa1AA_Veh_H4ac


title: Esa1AA_Rapa_RNAPII


title: Cont-day5 (#8-1350)


title: IPSI-day5 (#8-1350)


title: Gcn5AA_Rapa_H3K9ac

value: W303 mat a tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 GCN5-FRB::HIS3


title: E.coli 2


title: Esa1AA_Veh_H3K9ac

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ESA1-FRB::KanMX


title: E.coli 3


title: Esa1AA_Rapa_H3


title: Gcn5AA_Veh_H3


title: IPSI-day13 (#5-140)

value: pregnancy day13


title: Esa1AA_Veh_H3


title: Cont-day5 (#3-175)


title: Cont-day7 (#6-338)


title: IPSI-day16 (#2-068)


title: IPSI-day7 (#5-117)


title: sp 2

data_processing:
Basecalling by standard Illumina pipeline (RTA2 for base calling and filtering, bcl2fastq for producing FASTQ files).
Dataset quality was assessed using FastQC to ensure per base and per tile sequence quality.
Raw reads were quality trimmed using fastx_toolkit allowing a maximum of 50nt and minumum length of 28nt.
Trimmed reads were aligned to Ssp.consensus.fa genome using Bowtie allowing three mismatched bases and only unique alignments (-n 3 –m 1 -a).
Error rate analysis was carried out in R using the BioConductor seqTools, seqInR and IRanges packages. Total error rates were calculated from the alignments as the percentage of total reads with a mismatched base at positions 7-16 in the alignment, thresholded to a Phred quality score of <30. Specific error rates were calculated as the percentage of total reads with a specific mismatch, for example an A incorporated instead of a G (G > A misincorporation), at each read position 7, thresholded to a Phred quality score of <30.  Ambiguous N bases were excluded from the error rate calculation.
Genome_build: Ssp_consensus.fa
Supplementary_files_format_and_content: Alignment files are provided in bowtie format in addition to supplementary text files (Ssp_errors.txt, Ssp_base_errors.txt) containing the calculated error rates for all three samples. The genome build Ssp_genome.fa is also provided as a supplementary file.

organism: Synechocystis sp. PCC 6803

growth_protocol: Total RNA was isolated from mid-exponentially growing cultures of Synechocystis sp PCC 6803 (OD730 ~ 0.45)


title: sp 3


title: Esa1AA_Rapa_H3K9ac


title: sp 1


title: Cont-day13 (#8-275)


title: G0

city: Callaghan

first: Ting

last: La

address: University Drive

department: School of Biomedical Sciences & Pharmacy

institute: The University of Newcastle

data_processing:
Hiseq 50nt tags
Filter low quality tags
Mapping to Genome by SOAP or bowtie
Known miRNA alignment by miRBase
Differential expression analysis of known miRNA, Expdiff
Genome_build: mm10
Supplementary_files_format_and_content: Text files include reads values for each sample

source_name: B16 cell lines

growth_protocol: Deliver mVenus-p27K- and  mCherry-hCDT1(30/120) constructs by virus to B16 mouse melanoma cells, distinctive populations of mVenus-p27K-low and mVenus-p27K-high cells positive for mCherry-hCDT1(30/120) were isolated by flow cytometer.

extract_protocol:
Total RNA were extracted by ISOLATE II RNA Mini Kit (Bioline)
BGI small RNA TrueSeq

treatment_protocol: Serum starvation was used to arrest more G0 cells.

tag: facs sorting marker

value: mVenus-p27K-high mCherry-hCDT1(30/120)+


title: G1

value: mVenus-p27K-low mCherry-hCDT1(30/120)+


title: HL004 Ind

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma.

source_name: Human lung epithelial cell culture-method C (Patient 4)

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol:
Feeder-coculture (culture-method A): The primary lung epithelial cells were cultured with with irradiated NIH-3T3 cells in an expansion medium (3:1 mixture of Ham’s F-12 nutrient mix and DMEM supplemented with 5% fetal calf serum, 0.4 µg/mL hydrocortisone , 5 µg/mL recombinant human insulin , 8.4 ng/mL cholera toxin , 24 µg/mL Adenine , and 10 ng/mL recombinant human epidermal growth factor, 9 µM Y27632 and 100 nM dibenzazepine.
Growth protocol after feeder removal used in culture-method B and C: The lung epithelial cells propagated with culture method A were passaged into a cell culture vessel after feeder removal, and cultured in DMEM supplemented with 2mM glutamine, 10mM sodium pyruvate and 10% FCS for another 72 hours.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Pneumocyte phenotype induction applied in culture-method C: The lung epithelial cells were treated with 3 µM CHIR99021, 10 ng/mL keratinocyte growth factor,  100 µM 3-isobutyl-1-methylxanthine, 100 µM 8-bromoadenosine 3’,5’-cyclic monophosphate, 25 nM dexamethasone and 10 ng/mL fibroblast growth factor-10 for three days before feeder removal.

value: lung epithelial cell organoids

tag: patient

value: patient 4

tag: method

value: culture method C


title: OIOneg 5 [YA004]

city: New York

first: Ethan

last: Edwin

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University Medical Center

data_processing:
RTA (Illumina) for base calling
bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming
Map to UCSC/mm9 reference genome using Tophat 2.1 ((--read-mismatches = 4) (--max-multihits = 10)
Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation
We estimate the relative abundance using Htseq 0.6.1 with default settings and the USCS RefSeq gtf file
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files include count values by gene for each sample

source_name: ENSURE_after 24 hours without feeding_perigonadal adipose

extract_protocol:
Tissue was homogenized using a Tissue Tearor (Biospec, Bartlesville, OK) and processed using the Qiagen RNeasy extraction kit as per instructions. We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.
Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center.

tag: diet

value: ENSURE

value: FAST

tag: time point

value: after 24 hours without feeding

value: whole perigonadal adipose tissue

tag: molecule subtype

value: poly-adenylated mRNA >200 bp


title: HL004 NI

source_name: Human lung epithelial cell culture-method B (Patient 4)

tag: tissue

value: culture method B


title: HL004 feeder

source_name: Human lung epithelial cell culture-method A (Patient 4)

value: culture method A


title: OIOneg 7 [YA006]

tag: treatment


title: OIOneg 8 [YA007]

tag: strain


title: OIO 18 [YA017]

source_name: ENSURE_at peak weight_perigonadal adipose

value: FED

value: at peak weight


title: OIOneg 17 [YA016]


title: OIO 16 [YA015]


title: HL002 NI

source_name: Human lung epithelial cell culture-method B (Patient 2)

value: patient 2


title: HL002 Ind

source_name: Human lung epithelial cell culture-method C (Patient 2)


title: OIO 9 [YA008]


title: OIO 1 [YA001]


title: ALOneg 28 [YA025]

source_name: HFD 60%_after 24 hours without feeding_perigonadal adipose

value: HFD 60%


title: OIO 12 [YA011]


title: group 1_CB1

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Mouse Gene 1.0 ST Array (Cat No. 901168); GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.1.1)

data_processing:
Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.5): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); Anova

source_name: clb-b -/- _UV_skin

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Animals were sex and age matched.

extract_protocol: RNA was extracted from dorsal skin tissue using QIAGEN fibrous mini kit (QIAGEN) and cDNA were made by using First strand cDNA synthesis kit (Roche).

treatment_protocol: Mice were exposed to a single dose of 80 mJ/cm2 of UVB radiation. A Waldmann UV236B irradiation system equipped with two fluorescent CF-L 36W/UV6 light tubes (emission range, 280 to 360 nm; peak, 324 nm; Waldmann Medizintechnik, Villingen-Schwenningen, Germany).

tag: genotype/variation

value: clb-b -/-

tag: exposed to

value: dorsal skin

value: 24 hours after exposure


title: HL002 feeder

source_name: Human lung epithelial cell culture-method A (Patient 2)

value: lung epithelial cell organoids


title: group 2_WT3

source_name: wild type_UV_skin

value: wild type

value: single dose of 80 mJ/cm2 of UVB radiation


title: HL002 tissue

source_name: Human lung tissue (Patient 2)

value: lung tissue


title: HL004 tissue

source_name: Human tissue (Patient 4)

value: patient 4


title: group 1_CB3


title: group 2_WT2


title: ALOneg 24 [YA021]

value: FAST

value: after 24 hours without feeding


title: OIOneg 2 [YA002]

value: ENSURE

value: whole perigonadal adipose tissue

value: poly-adenylated mRNA >200 bp


title: ALOneg 23 [YA020]


title: ALO 21 [YA018]

source_name: HFD 60%_at peak weight_perigonadal adipose

value: FED


title: group 1_CB2


title: ALO 27 [YA024]

value: at peak weight


title: ALO 25 [YA022]


title: group 2_WT1


title: OIO 10 [YA009]


title: ALO 22 [YA019]


title: LH93

city: Beijing

first: Shan

last: Li

address: Lincui Road

institute: Insititute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Basecalls performed using BGISEQ-500.
ChIP-seq reads were mapped rice genome with  SOAPaligner/soap2.Clean Parameter: SOAPnuke filter -l 5 -q 0.5 -n 0.1 -Q 2 -c 25
Only uniquely mapping reads were chosen for further analysis, and only a random one was picked for duplicates (reads mapped to the same location).
The coverage distribution on the reference genome and the depth information of the genomic loci were analyzed with the only comparison sequence obtained by comparison, and the depth statistics of the genome were obtained.
Genome_build: Oryza sativa (release 7.0)
Supplementary_files_format_and_content: MACS_peak

organism: Oryza sativa

source_name: Rice

growth_protocol: Hydroponics suitable materials were growing in the greenhouse for ChIP experiments

extract_protocol:
~2 g of two-week-old seedlings of transgenic WYJ7-dep1-1/p35S::Flag-ngr2 rice plants were fixed with 1% formaldehyde under vacuum for 15 min at 20-25°C, and then homogenized in liquid nitrogen. Following isolation and lysing of nuclei, chromatin was isolated and ultrasonically fragmented into fragments of average size of ~500 bp. Immunoprecipitations were performed with anti-Flag antibodies (Sigma, F1804) overnight at 4 °C. The reverse-crosslinked and precipitated DNA.
Libraries were prepared according to Qubit and Agilent 2100's instructions.100-500 bp fragments were selected by gel extraction.

value: two weeks seedling

tag: chip antibody

value: anti-Flag


title: Flag4


title: ALOneg 26 [YA023]

value: HFD 60%


title: notochord_rep2_RRBS

description:
notochord2
Amphioxus-gut_muscle_notochord_RRBS_CHH_bigtable.tsv; Amphioxus-gut_muscle_notochord_RRBS_CpG_bigtable.tsv

source_name: notochord

tag: developmental stage

value: adult

value: notochord


title: Flag3


title: meox2b_24hpf_rep2

data_processing:
library strategy: 4C-seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Danio rerio (danRer6 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
A running 51 bins-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), danRer10, mm10
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 2Mb around each viewpoint that can be directly uploaded to UCSC for visualization.

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of meox2b

tag: developmental

value: whole embryo


title: NT KDM45 DNMT3AB 4-cell 2 (RNA-Seq)

status: Public on Aug 14 2018

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v1.3.3 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.2.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.

source_name: nuclear transfer embryo

extract_protocol:
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. cDNA were synthesized using primers with 24-nt poly(dT),then a universal tail was added to the second strand cDNAs. After 18-20 cyclesof PCR, the PCR product is purified by QIAquick PCR purification kit(28104).
The prepared cDNA are sheared using Covaris S220. Fragment ends are repaired using NEBNext End Repair Module(E6050), then a NEBNext dA-Tailing Module(E6053) was used to yield a protruding 3- 'A' base for ligation of Illumina's adapters.After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles. library fragments of 200-500bp were band isolated from an agarose gel.

treatment_protocol: We separated the blastomeres of lived 2- or 4-cell stage embryos. One blastomere was harvested for single-cell sequencing, and the rest were further cultured in an aggregation plate to record the final development fate

value: nuclear transfer embryo

tag: development stage

tag: knock out

tag: overexpression


title: NT DNMT3AB 2-cell 1 (RNA-Seq)


title: NT DNMT3AB 2-cell 2 (RNA-Seq)


title: NT KDM45 DNMT3AB 2-cell 2 (RNA-Seq)


title: NT DNMT3AB 4-cell 1 (RNA-Seq)


title: NT siDNMT3A+siDNMT3B 4-cell (WGBS-Seq)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter "-s 16 -v 0.1 -n 1 -R -p 10".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
DMRs of diffenrent states called by MOABS mcomp function
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

extract_protocol:
For WGBS, 30-50 cells were used per reaction. All isolated cells were washed three times in 0.5% BSA-PBS solution to avoid possible contamination.
The sequencing libraries were generated using the Pico Methyl-Seq Library Prep Kit following the manufacturer's instructions. Paired-end 150-bp sequencing was performed on a NovaSeq (Illumina) at Berry Genomics Corporation

treatment_protocol: The zona pellucida of injected and control SCNT embryos was removed with 0.5% pronase E (Sigma). After incubating 2- or 4-cell stage embryos in Ca2+-free CZB medium, one blastomere was removed by gently pipetting using a fire-polished glass needle with an inner diameter of 120 μm. The separated blastomeres were prepared for library analysis, and the rest were still cultured at 37 °C in humidified atmosphere of 5% CO2 until the blastocyst stage. The tight junctions of TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm. All samples were washed several times in 0.5% BSA-PBS (Sigma) solution before they were prepared for library generation.

value: trophectoderm


title: NT KDM45 DNMT3AB 4-cell 1 (RNA-Seq)


title: NT siDNMT3A+siDNMT3B 2-cell (WGBS-Seq)

value: inner cell mass


title: NT KDM4B+KDM5B+siDNMT3A+siDNMT3B 2-cell (WGBS-Seq)


title: NT KDM4B+KDM5B+siDNMT3A+siDNMT3B 4-cell (WGBS-Seq)

value: zygote


title: NT KDM45 DNMT3AB 2-cell 1 (RNA-Seq)


title: NT DNMT3AB 2-cell 3 (RNA-Seq)


title: NT KDM4B+KDM5B+siDNMT3A+siDNMT3B 1-cell (WGBS-Seq)


title: NT siDNMT3A+siDNMT3B 1-cell (WGBS-Seq)


title: NT TE (WGBS-Seq)


title: NT 4-cell (to blastocyst) (WGBS-Seq)


title: NT 4-cell (4-cell arrest) (WGBS-Seq)


title: NT 2-cell (2-cell arrest) (WGBS-Seq)


title: NT 2-cell (4-cell arrest) (WGBS-Seq)


title: NT DNMT3AB 4-cell 2 (RNA-Seq)


title: NT 1-cell  (WGBS-Seq)


title: CC (WGBS-Seq)

source_name: cumulus cell

value: cumulus cell


title: SC 4-cell (WGBS-Seq)


title: MEF 4-cell (WGBS-Seq)


title: SC 1-cell (WGBS-Seq)


title: MEF 2-cell (WGBS-Seq)


title: MEF 1-cell (WGBS-Seq)


title: KO3

city: Phoenix

first: Tobias

last: Jakobi

state: Arizona

address: 475 N. 5th Street

department: Internal Medicine

institute: University of Arizona

data_processing:
FLEXBAR 2.5
STAR 2.5.1b
Cufflinks 2.2.1
Genome_build: GRCm38_79
Supplementary_files_format_and_content: Gene expression values produced by Cuffdiff

source_name: OCar1-/- pancreas, mouse 3

growth_protocol: RNA isolation from pancreas without any culturing

extract_protocol:
RNA was isolated from the pancreas of three 3 weeks old male wild type (C57Bl6/N) and OCaR1–/– mice, respectively, using TRIZOL reagent (Thermo Fisher Scientific, Germany). The integrity of the RNA samples was verified using a 2100 Bioanalyzer system (Agilent Technologies, USA) and the RNA integrity number (RIN) was between 8.20 and 9.10.
A cDNA library was generated using the NEB Next RNA Master Mix Library Prep Kit for Illumina with the NEB Next Oligodexoxynucleotides for Illumina (New England Biolabs, Germany). First strand synthesis was conducted employing 2.5 μg RNA that was polyA-RNA selected. The read length of the RNAseq (Hiseq2000 machine using the standard illumina sequencing by synthesis chemistry) was single read 50 base pair reads, SE.

treatment_protocol: no treatment

tag: age

value: age 3 weeks

value: pancreas


title: MEF (WGBS-Seq)

source_name: mouse embryonic fibroblast cell

value: mouse embryonic fibroblast cell


title: KO1

source_name: OCar1-/- pancreas, mouse 1


title: NT ICM (WGBS-Seq)


title: NT 2-cell (to blastocyst) (WGBS-Seq)


title: ML D2 (ML-60218 treatment)

city: Houston

first: Deborah

last: Johnson

state: Texas

address: One Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Sequence analysis was performed using the RNAv9 pipeline developed by EA Q2 Solutions (available at https://github.com/ExpressionAnalysis/ea-utils/).  Fastq-mcf was used to first remove low quality reads, homopolymers, and adapter sequences.
STAR version 2.4 was used to align the clipped and filtered reads to the UCSC mouse mm10 transcriptome definition, and the RNA-Seq quantification software RSEM10, version 1.2.14, was used for transcript quantification. ERCC oligos sequences were used for QC the alignments.
Post-quantification analysis was done for further characterization of reads which align to UTRs, and those which align to intragenic regions.
EA Q2 Solutions' in-house developed software VarPROWL (Variant PROfiling With Logistic regression) was used for calling variants in the RNA-Seq data.
Principal components analysis for identifying outliers and visualization of sample groupings was performed with the statistical language R, and general QC metrics are provided in the Excel file DJ_QC_summary.xls
Genome_build: mm10
Supplementary_files_format_and_content: "DJ_QC_summary.xls", Excel, QC metrics, and "DJ_Genes_summary.xls", Excel, Gene-level data analysis

source_name: 3T3-L1 preadipocytes

growth_protocol: 3T3-L1 cells were maintained in DMEM-HG supplemented with 10% FBS, 2 mM GlutaMax, and 1% penicillin /streptomycin at 37℃ incubators with 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the Zymo Directzol RNA Kit.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

treatment_protocol: To differentiate the 3T3-L1 cells into adipocytes, cells were first grown to confluency. Part of the 2-day post-confluent cells were collected as day 0 (D0) samples. The rest cells were induced to differentiate with the differentiation cocktail which contained 10 µg/mL Insulin, 2 µM Dex, 0.5 mM IBMX and 25 µg/mL AsA for two days. After two days, the cells were collected as day 2 (D2) samples.

tag: agent

tag: cell line

value: 3T3-L1 cells

tag: differentiation stage

value: day 2 after differentiation


title: shBrf1 D2

tag: shRNA

tag: time point


title: ML D0 (ML-60218 treatment)

value: before differentiation


title: shBrf1 D0


title: SC 2-cell (WGBS-Seq)

tag: tissue


title: control D0 (empty shRNA vector)

value: empty shRNA vector


title: KO2

source_name: OCar1-/- pancreas, mouse 2


title: shMaf1 D0


title: shMaf1 D2


title: WT3

source_name: wild type /C56Bl6/N)  pancreas, mouse 3

value: wild type


title: WT2

source_name: wild type /C56Bl6/N)  pancreas, mouse 2


title: SC (WGBS-Seq)

source_name: sertoli cell

value: sertoli cell


title: NT Kdm4b 4-cell 4 (RNA-Seq)


title: NT Kdm5b 2-cell 3 (RNA-Seq)


title: NT Kdm5b ICM 3 (RNA-Seq)


title: NT Kdm5b ICM 1 (RNA-Seq)


title: NT Kdm4b 4-cell 2 (RNA-Seq)


title: NT Kdm5b 2-cell 2 (RNA-Seq)


title: NT Kdm5b ICM 2 (RNA-Seq)


title: NT Kdm4b 4-cell 3 (RNA-Seq)


title: NT Kdm5b 2-cell 1 (RNA-Seq)


title: control D2 (empty shRNA vector)


title: WT1

source_name: wild type /C56Bl6/N) pancreas, mouse 1


title: NT Low Kdm4b+Kdm5b siDnmt3b 4-cell 2 (RRBS-Seq)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “-D C-CGG -w 100 -s 12 -v 0.1 -m 32 -x 1000 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

extract_protocol: none proveided by the submitter


title: NT Kdm4b 4-cell 1 (RNA-Seq)


title: NT Low Kdm4b+Kdm5b siDnmt3b 4-cell 1 (RRBS-Seq)


title: NT Low Kdm4b+Kdm5b 4-cell 3 (RRBS-Seq)


title: NT Low Kdm4b+Kdm5b siDnmt3a 4-cell 1 (RRBS-Seq)


title: NT Kdm4b+Kdm5b TE 4 (RRBS-Seq)


title: NT Low Kdm4b+Kdm5b 4-cell 1 (RRBS-Seq)


title: NT Kdm4b 4-cell 5 (RNA-Seq)


title: NT Kdm4b+Kdm5b TE 3 (RRBS-Seq)


title: NT Kdm4b+Kdm5b TE 1 (RRBS-Seq)


title: NT Kdm4b+Kdm5b ICM 1 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 4-cell 4 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 4-cell 5 (RRBS-Seq)


title: NT Kdm4b+Kdm5b TE 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 4-cell 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 4-cell 3 (RRBS-Seq)


title: NT Low Kdm4b+Kdm5b siDnmt3a 4-cell 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b ICM 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 4-cell 1 (RRBS-Seq)


title: NT Low Kdm4b+Kdm5b 4-cell 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 2-cell 5 (RRBS-Seq)


title: MouseperiCC4: Mouse spinal cord peri central canal region 4

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

country: France

institute: inserm inm u1191

description: biological replica

hyb_protocol: The biotinylated cRNA was hybridized to HT_HG-U133_Plus_PM (human) and HT_MG-430_PM (mouse) Affymetrix microarrays.

scan_protocol: The microarrays were scanned using the Affymetrix Gene Atlas scanner.

data_processing: The data files were generated with Affymetrix Expression Console v1.2.1 and gene expression data were normalized with GC-RMA algorithm.

label: biotin

source_name: mouse 4

label_protocol: RNA profiling was performed using affymetrix microarray technology.Hybridization targets were obtained following a double amplification procedure according to the protocol developed by Affymetrix (GeneChipTwo-Cycle Eukaryotic Target Labeling Assay; Affymetrix, USA). A hybridization mixture containing 10 µg of biotinylated cRNA was generated.

extract_protocol: Tissue Microdissection: For Human and mouse, after collection, spinalcords were flash frozen in N2 without chemical fixation. Frozen sections (30 µm thick) were obtained at –23°C to prevent RNA degradation using a CM3050S microtome (Leica Microsystems, Wetzlar, Germany) and were mounted on PEN-membrane 1 mm glass slides (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) that had been pretreated to inactivate RNase. Sections were then fixed in a series of pre-cooled ethanol baths (40s in 95%, 75% and 30s in 50%), stained with cresyl violet 1% for 30s and dehydrated in a series of pre-cooled ethanol baths (30s in 50%, 75% and 40s in 95% and 100%). Immediately after dehydration laser microdissection was performed using a PALM MicroBeam microdissection system version 4.6 equipped with a P.A.L.M. RoboSoftware (P.A.L.M. Microlaser Technologies AG, Bernried, Germany). Laser power and duration were adjusted to optimize capture efficiency and microdissection was performed at 63X magnification. Samples were collected in adhesives caps (P.A.L.M. Microlaser Technologies AG, Bernried, Germany).To limit RNA degradation, samples were collected for up to 15 minutes per slide and microdissected tissue was lysed with 250 µl of lysis buffer (Promega). The samples were stored at −80°C until extraction was performed using the ReliaPrep RNA cell Miniprep System (Promega, Madison, USA) according to the manufacturer’s protocol and eluted with 14 μl of RNAse-free water. The concentration of RNA was determined using Nanodrop 1000 and the integrity of RNA was determined using RNA 6000 Pico Kit and Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The RNA integrity number (RIN) was above 7/8.

value: spinal cord peri central canal region

value: 3 months


title: MouseperiCC1: Mouse spinal cord peri central canal region 1

source_name: mouse 1


title: MouseperiCC2: Mouse spinal cord peri central canal region 2

description: biological replica

source_name: mouse 2


title: MouseCC3: Mouse spinal cord central canal region 3

description: biological replica

source_name: mouse 3

value: spinal cord central canal region


title: MouseCC4: Mouse spinal cord central canal region 4

description: biological replica


title: MouseCC2: Mouse spinal cord central canal region 2

description: biological replica


title: MouseCC1: Mouse spinal cord central canal region 1


title: MouseperiCC3: Mouse spinal cord peri central canal region 3

description: biological replica


title: NT Kdm4b+Kdm5b 2-cell 3 (RRBS-Seq)


title: NT Kdm4b+Kdm5b ICM 3 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 2-cell 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 2-cell 1 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 1-cell 3 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 1-cell 2 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 1-cell 1 (RRBS-Seq)


title: NT Kdm4b+Kdm5b 2-cell 4 (RRBS-Seq)


title: Df/+ DCV replicate 2

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

institute: CNRS

description:
Gene expression of control (Df/+) flies at 3 days after DCV injection
Control-DCV2

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Agilent “Drosophila (V2) Gene Expression Microarray” 4x44K (Design ID 018972), for 17 hrs, at 65°C under 10 rpm.

scan_protocol: Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 5 µm resolution in a 20-bit scan mode, according to the “AgilentHD_GX_1Color” protocol

data_processing:
Raw .tif images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol.
Median raw expression values where further normalized by quantile method

organism: Drosophila melanogaster

source_name: Adult flies

label_protocol: Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 100 ng of total RNA.

growth_protocol: Fly cultures were grown on standard medium at 25°C. To avoid genetic background effect, we generated control designated as Df/+ and hemizygote IKKb (Ird5) null mutant designated as Df/Ird5[1] by crossing Df(3R)Exel7328 and wild-type (cnbw) or IKKb null mutant (Ird5[1]). These control and IKKb (Ird5) null mutant fly lines were tested for Wolbachia infection, and cured whenever necessary.

extract_protocol: RNA was extracted and treated with DNAse, using RNA Spin kit (Macherey Nagel). RNA quality was checked by Eukaryote Total RNA Pico assay (Agilent) and validated. 200 ng of RNA were used to perform micro-array (Agilent DNA microarrays Drosophila).

treatment_protocol: After generating the control (Df/+) and IKKb null (Df/Ird5[1]) flies, the flies were infected by DCV (500 pfu/fly) at 22C for 3 days. We also injected Tris-HCl ph7.5 buffer as control.

value: Df/+

value: control

tag: infection

value: DCV

tag: replicate

value: adult

value: whole fly


title: NT Kdm5b TE 3 (RRBS-Seq)

value: trophectoderm

tag: strain


title: NT Kdm5b TE 4 (RRBS-Seq)


title: Df/Ird5[1] DCV replicate 1

description:
Gene expression of IKKb (Ird5) null mutant (Df/Ird5[1]) flies at 3 days after DCV injection
IKKb-null-mutant-DCV-1

tag: genotype/variation

value: IKKb null mutant


title: Df/Ird5[1] DCV replicate 2

description:
Gene expression of IKKb (Ird5) null mutant (Df/Ird5[1]) flies at 3 days after DCV injection
IKKb-null-mutant-DCV-2


title: Df/+ DCV replicate 1

description:
Gene expression of control (Df/+) flies at 3 days after DCV injection
Control-DCV1


title: Df/Ird5[1] Tris replicate 2

description:
Gene expression of IKKb (Ird5) null mutant (Df/Ird5[1]) flies at 3 days after Tris injection
IKKb-null-mutant-Tris2

value: control (Tris)


title: NT Kdm5b TE 2 (RRBS-Seq)


title: NT Kdm5b TE 1 (RRBS-Seq)


title: NT Kdm5b ICM 4 (RRBS-Seq)

value: inner cell mass


title: Df/+ Tris replicate 1

description:
Gene expression of control (Df/+) flies at 3 days after Tris injection
Control-Tris1


title: Df/+ Tris replicate 2

description:
Gene expression of control (Df/+) flies at 3 days after Tris injection
Control-Tris2


title: Df/Ird5[1] Tris replicate 1

description:
Gene expression of IKKb (Ird5) null mutant (Df/Ird5[1]) flies at 3 days after Tris injection
IKKb-null-mutant-Tris1


title: NT Kdm5b ICM 1 (RRBS-Seq)


title: NT Kdm5b ICM 2 (RRBS-Seq)


title: NT Kdm5b TE 5 (RRBS-Seq)


title: NT Kdm5b ICM 3 (RRBS-Seq)


title: NT Kdm5b 4-cell 7 (RRBS-Seq)


title: NT Kdm5b 4-cell 6 (RRBS-Seq)


title: NT Kdm5b 4-cell 3 (RRBS-Seq)


title: NT Kdm5b 4-cell 2 (RRBS-Seq)


title: NT Kdm5b 4-cell 5 (RRBS-Seq)


title: Normal stomach 1b engineered control

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

institute: Keio University

description: Batch 2

hyb_protocol: Affymetrics GeneChip® 3 ' IVT PLUS Reagent Kit or 3 ' IVT Express Reagent Kit procedure

scan_protocol: GeneChip Scanner 3000 7G procedure

data_processing: The data was normalized by RMA (R package affy). Batch effect was compensated by ComBat (R package sva).

source_name: Patient 46

label_protocol: Affymetrix

extract_protocol: QIAGEN RNeasy Plus Mini Kit procedure

tag: individual

value: Patient 46

tag: sample type

value: Normal stomach 1b engineered control

value: Stomach


title: Normal stomach 1b CDH1/TP53 double knockout #2 R-spondin(-)

description: Batch 2


title: NT Kdm5b 4-cell 4 (RRBS-Seq)

source_name: nuclear transfer embryo


title: Normal stomach 1b CDH1/TP53 double knockout #1 R-spondin(-)

description: Batch 2


title: NT Kdm5b 4-cell 1 (RRBS-Seq)


title: Normal stomach 1b CDH1/TP53 double knockout #2 R-spondin(+)

description: Batch 2


title: Normal colon engineered control

description: Batch 2

source_name: CRC Patient

value: CRC Patient

value: Normal colon engineered control

value: Colon


title: Normal stomach 1b CDH1/TP53 double knockout #1 R-spondin(+)

description: Batch 2


title: Normal colon CDH1/TP53 double knockout

description: Batch 2

value: Normal colon CDH1/TP53 double knockout


title: NT Kdm5b 2-cell 3 (RRBS-Seq)


title: Normal stomach 2c

description: Batch 2

source_name: Patient 47

value: Patient 47

value: Normal stomach


title: NT Kdm5b 2-cell 4 (RRBS-Seq)


title: NT Kdm5b 2-cell 2 (RRBS-Seq)


title: Normal stomach 1c

description: Batch 2


title: Normal stomach 2b

description: Batch 2


title: Normal stomach 2a

description: Batch 2


title: Normal stomach 1b

description: Batch 2


title: NT Kdm5b 2-cell 1 (RRBS-Seq)


title: Gastric cancer organoid 2 normal counterpart

description: Batch 2

source_name: Patient 2

value: Patient 2

value: Gastric cancer organoid normal counterpart


title: Gastric cancer organoid normal like 9

description: Batch 2

source_name: Patient 34

value: Patient 34

value: Gastric cancer organoid normal like


title: NT Kdm5b 1-cell 3 (RRBS-Seq)

value: zygote


title: Normal stomach 1a

description: Batch 2


title: Gastric cancer organoid normal like 8

description: Batch 2

source_name: Patient 44

value: Patient 44


title: Normal stomach 1b CDH1 knockout

description: Batch 2

value: Normal stomach 1b CDH1 knockout


title: Gastric cancer organoid normal like 6

description: Batch 2

source_name: Patient 42

value: Patient 42


title: Gastric cancer organoid normal like 5

description: Batch 2

source_name: Patient 41

value: Patient 41


title: Intestinal metaplasia 1

description: Batch 1

source_name: Patient 45

value: Patient 45

value: Intestinal metaplasia


title: Gastric cancer organoid normal like 7

description: Batch 2

source_name: Patient 43

value: Patient 43

value: Stomach


title: NT Kdm4b TE 10 (RRBS-Seq)

value: trophectoderm


title: NT Kdm5b 1-cell 1 (RRBS-Seq)


title: Gastric cancer organoid normal like 4

description: Batch 2

source_name: Patient 40

value: Patient 40


title: NT Kdm5b 1-cell 2 (RRBS-Seq)


title: NT Kdm4b TE 8 (RRBS-Seq)


title: NT Kdm4b TE 9 (RRBS-Seq)


title: NT Kdm4b TE 7 (RRBS-Seq)


title: NT Kdm4b TE 5 (RRBS-Seq)


title: NT Kdm4b TE 6 (RRBS-Seq)


title: NT Kdm4b TE 4 (RRBS-Seq)


title: Gastric cancer organoid normal like 1

description: Batch 2

source_name: Patient 37

value: Patient 37


title: Gastric cancer organoid 36

description: Batch 2

source_name: Patient 36

value: Patient 36

value: Gastric cancer organoid


title: Gastric cancer organoid normal like 2

description: Batch 2

source_name: Patient 38

value: Patient 38


title: Gastric cancer organoid normal like 3

description: Batch 2

source_name: Patient 39

value: Patient 39


title: NT Kdm4b TE 3 (RRBS-Seq)


title: Gastric cancer organoid 1 normal counterpart

description: Batch 2

source_name: Patient 1

value: Patient 1

value: Gastric cancer organoid normal counterpart


title: NT Kdm4b TE 2 (RRBS-Seq)


title: Gastric cancer organoid 34

description: Batch 2

source_name: Patient 33

value: Patient 33


title: Gastric cancer organoid 35

description: Batch 2

source_name: Patient 35

value: Patient 35


title: NT Kdm4b TE 1 (RRBS-Seq)

source_name: nuclear transfer embryo


title: Gastric cancer organoid 30

description: Batch 2

source_name: Patient 30

value: Patient 30


title: NT Kdm4b ICM 2 (RRBS-Seq)

value: inner cell mass


title: NT Kdm4b 4-cell 3 (RRBS-Seq)


title: NT Kdm4b ICM 1 (RRBS-Seq)


title: NT Kdm4b 4-cell 1 (RRBS-Seq)


title: NT Kdm4b 4-cell 2 (RRBS-Seq)


title: NT Kdm4b 2-cell 6 (RRBS-Seq)


title: NT Kdm4b 2-cell 5 (RRBS-Seq)


title: Gastric cancer organoid 33

description: Batch 2


title: Gastric cancer organoid 31

description: Batch 2

source_name: Patient 31

value: Patient 31


title: NT Kdm4b 2-cell 3 (RRBS-Seq)


title: Gastric cancer organoid 22

description: Batch 2

source_name: Patient 22

value: Patient 22


title: NT Kdm4b 2-cell 4 (RRBS-Seq)


title: Gastric cancer organoid 29

description: Batch 2

source_name: Patient 29

value: Patient 29


title: NT Kdm4b 2-cell 2 (RRBS-Seq)


title: Gastric cancer organoid 25

description: Batch 2

source_name: Patient 25

value: Patient 25

value: Stomach


title: Gastric cancer organoid 27

description: Batch 2

source_name: Patient 27

value: Patient 27


title: Gastric cancer organoid 26

description: Batch 2

source_name: Patient 26

value: Patient 26


title: Gastric cancer organoid 23

description: Batch 2

source_name: Patient 23

value: Patient 23


title: Gastric cancer organoid 20

description: Batch 2

source_name: Patient 20

value: Patient 20

value: Gastric cancer organoid


title: Gastric cancer organoid 28

description: Batch 2

source_name: Patient 28

value: Patient 28


title: Gastric cancer organoid 19

description: Batch 2

source_name: Patient 19

value: Patient 19


title: NT Kdm4b 1-cell 1 (RRBS-Seq)

value: zygote


title: NT TE 3 (RRBS-Seq)

value: trophectoderm


title: Gastric cancer organoid 21

description: Batch 2

source_name: Patient 21

value: Patient 21


title: Gastric cancer organoid 24

description: Batch 2

source_name: Patient 24

value: Patient 24


title: Gastric cancer organoid 32

description: Batch 2

source_name: Patient 32

value: Patient 32


title: NT Kdm4b 1-cell 3 (RRBS-Seq)


title: NT TE 1 (RRBS-Seq)


title: NT Kdm4b 2-cell 1 (RRBS-Seq)


title: Gastric cancer organoid 18

description: Batch 2

source_name: Patient 18

value: Patient 18


title: NT ICM 3 (RRBS-Seq)

value: inner cell mass


title: Gastric cancer organoid 15

description: Batch 2

source_name: Patient 15

value: Patient 15


title: Gastric cancer organoid 14

description: Batch 2

source_name: Patient 14

value: Patient 14


title: Gastric cancer organoid 17

description: Batch 2

source_name: Patient 17

value: Patient 17

value: Stomach


title: Gastric cancer organoid 16

description: Batch 2

source_name: Patient 16

value: Patient 16


title: Gastric cancer organoid 13

description: Batch 2

source_name: Patient 13

value: Patient 13


title: NT ICM 2 (RRBS-Seq)

source_name: nuclear transfer embryo


title: Gastric cancer organoid 12

description: Batch 2

source_name: Patient 12

value: Patient 12


title: Gastric cancer organoid 11

description: Batch 2

source_name: Patient 11

value: Patient 11

value: Gastric cancer organoid


title: NT 4-cell arrest in 2-cell stage 5 (RRBS-Seq)


title: Gastric cancer organoid 10

description: Batch 2

source_name: Patient 10

value: Patient 10


title: NT ICM 1 (RRBS-Seq)


title: NT 4-cell arrest in 2-cell stage 4 (RRBS-Seq)


title: Gastric cancer organoid 9

description: Batch 1

source_name: Patient 9

value: Patient 9


title: NT 4-cell arrest in 2-cell stage 2 (RRBS-Seq)


title: NT 1-cell 3 (RRBS-Seq)

value: zygote


title: NT 4-cell arrest in 2-cell stage 1 (RRBS-Seq)


title: NT 4-cell arrest in 2-cell stage 3 (RRBS-Seq)


title: NT 1-cell 2 (RRBS-Seq)


title: NT 1-cell 1 (RRBS-Seq)


title: WT TE 3 (RRBS-Seq)

source_name: fertilzed embryo

value: trophectoderm


title: WT TE 2 (RRBS-Seq)


title: Patient 133

city: Aarhus N

first: Karina

middle: Dalsgaard

last: Sørensen

state: Aarhus N

address: Palle Juul-Jensens Boulevard 99

department: Molecular Medicine

country: Denmark

institute: Aarhus University

hyb_protocol: 40 ng of total RNA was reversed transcribed in 40 µl reactions using the miRCURY LNATM miRNA PCR, polyadenylation and cDNA synthesis kit II (Exiqon). cDNA was diluted x100 and analysed in 10 µl PCR reactions. Negative controls (no template in reverse transcription reaction) were run in parallel.

scan_protocol: Amplification was performed using the LightCycler® 480 Real-Time PCR System (Roche) and ExiLENT SYBR® Green Master mix (Qiagen). Amplification curves and melting curves were analysed for quantification cycles (Cq) using the Roche LC software

data_processing:
Background substraction, for ratio model training the raw data Cq values were used
normalized Cq values (Cq Global mean - Cq miRNA)

label: SYBR® Green

source_name: prostate

label_protocol: The ExiLENT SYBR Green master mix was used.

extract_protocol: Total RNA was isolated from 1.5mm punch biopsies from the FFPE tissue samples using miRNeasy FFPE Kit (Qiagen), according to manufacturer's instructions. The 260/280 mm absorbance ratio (optimal ratio: 2.0) was used as quality assurance for the RNA samples. RNA samples with a ratio <1.75 were excluded from further analysis. The purified RNA was stored at -80C.

value: benign prostate tissue


title: Patient 134


title: Patient 135


title: Gastric cancer organoid 8

description: Batch 1

source_name: Patient 8

value: Patient 8


title: Gastric cancer organoid 6

description: Batch 2

source_name: Patient 6

value: Patient 6


title: Gastric cancer organoid 3

description: Batch 1

source_name: Patient 3

value: Patient 3


title: Patient 136


title: Gastric cancer organoid 5

description: Batch 1

source_name: Patient 5

value: Patient 5


title: Gastric cancer organoid 2

description: Batch 1

source_name: Patient 2

value: Patient 2


title: ash-1(Y888F) RNAseq

city: Eugene

first: Vincent

middle: T

last: Bicocca

state: OR

address: 1229 University of Oregon

department: Biology

institute: University of Oregon

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011) and bigwig files were generated using DeepTools (Ramirez et al., 2016) using a window size of 20 -200bp (tdf and bigwig files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).
Supplementary_files_format_and_content: For Poly-A mRNA files: Text files contain counts for every gene as outlined in process above.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: none provided by the submitter

tag: cell type

value: conidium


title: Patient 132


title: WT TE 1 (RRBS-Seq)

tag: development stage


title: Gastric cancer organoid 1

description: Batch 1

source_name: Patient 1

value: Patient 1

value: Stomach


title: BRBS388_H12_P4

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

description:
PolyA RNA
processed data file: CAS_Seurat_norm_n3_5000g.txt

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to human genome hg38 using STAR version 2.2.1 with default parameters except --sjdbOverhang 49 --outSAMstrandField intronMotif --outFilterMultimapNmax 1 (The max number of multiple alignments allowed for a read is 1. If exceeded, the read is considered unmapped).
Read counting was performed using HTSeq-Count (version 0.9.1) with parameters --stranded=no -m union, and using the annotations of human genome hg38 release 87 downloaded from the ENSembl website. In short, our RNA-Seq data has not been made with a strand-specific protocol. When a read was mapped to more than one gene, it was considered as ambiguous and assigned to none of them.
Raw counts were normalized using the Setup fonction of the Seurat package (version 1.4.0.16) with the following parameters : min.cells = 3, do.logNormalize=T, total.expr = 1e6, min.genes=5000, is.expr = 0. We thus selected the cells expressing at least 5000 genes (86), and selected the genes expressed in at least 3 selected cells (18017).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CAS_Seurat_norm_n3_5000g.txt: Text file with tab delimiters including normalized gene counts for each sample.

source_name: Cord blood CD34+ cell-derived dendritic cell cultures

growth_protocol: CD34+ progenitor cells, isolated from human cord blood, were expanded with Flt3L, SCF, TPO and IL7 for 7 days and then induced to differentiation upon plating on OP9+OP9_DLL1 stromal cells for additional 18 days in the presence of Flt3L, TPO and IL7.

extract_protocol:
Cells from cord blood CD34+ hematopoietic progenitor cultures were FACS sorted in 96-well plates (single cell sorted) containing lysis buffer (TCL together with 1% of 2-Mercaptoethanol).
Single cell RNA-sequencing libraries were generated using an adaptation of Smart-Seq2 (Villani et al., Science, 2017) and the Illumina Nextera XT DNA library preparation kit. Full-length RNA-sequencing was performed.

value: Putative cDC2

tag: phenotype


title: Patient 131


title: Gastric cancer organoid 7

description: Batch 1

source_name: Patient 7

value: Patient 7


title: WT ICM 3 (RRBS-Seq)

value: inner cell mass


title: BRBS385_E12_P3

value: Cord blood CD34+ cell-derived dendritic cell cultures

value: Putative pre-cDC2


title: BRBS384_D12_P4


title: WT ICM 2 (RRBS-Seq)


title: BRBS386_F12_P4


title: BRBS383_C12_P3


title: Patient 130


title: Gastric cancer organoid 4

description: Batch 1

source_name: Patient 4

value: Patient 4

value: Gastric cancer organoid


title: WT ICM 1 (RRBS-Seq)


title: BRBS381_A12_P3


title: BRBS382_B12_P4


title: Patient 128


title: BRBS387_G12_P3


title: BRBS380_H11_P4


title: WT 1-cell 3 (RRBS-Seq)

value: zygote


title: BRBS379_G11_P3


title: BRBS377_E11_P3


title: BRBS378_F11_P4


title: Patient 127

value: radical prostatectomy


title: Patient 126


title: BRBS372_H10_P4


title: WT 1-cell 1 (RRBS-Seq)


title: BRBS374_B11_P4


title: WT 1-cell 2 (RRBS-Seq)


title: BRBS376_D11_P4


title: BRBS373_A11_P3


title: BRBS371_G10_P3


title: BRBS370_F10_P4


title: BRBS369_E10_P3


title: BRBS368_D10_P4


title: Patient 123


title: Patient 129

value: benign prostate tissue


title: BRBS367_C10_P3


title: BRBS366_B10_P4


title: Patient 120


title: Patient 121


title: BRBS364_H09_P4


title: BRBS362_F09_P2

value: Putative pDC


title: BRBS363_G09_P3


title: BRBS365_A10_P3


title: NT TE 2 (RRBS-Seq)

source_name: nuclear transfer embryo

value: trophectoderm


title: Patient 125


title: BRBS359_C09_P3


title: Patient 119


title: Patient 124


title: Patient 118


title: BRBS358_B09_P2


title: BRBS353_E08_P1

value: Putative cDC1


title: BRBS354_F08_P2


title: BRBS356_H08_P4


title: BRBS357_A09_P1


title: Patient 116


title: BRBS352_D08_P4


title: 14mig_3_HiC

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
first principle component of pooled libraries (*PC1only.bed)
TAD binsignal of pooled libraries
Called domains, boundaries, and gaps of pooled libraries (*domains.txt)
Total significant contacts (*significant_ints.csv)
Decreased contacts compared to control (unmigrated) (*down_filtered.csv)
Increased contacts compared to control (unmigrated) (*up_filtered.csv)

data_processing:
Read quality was confirmed with FastQC v0.11.4
Libraries were pooled and downsampled so that the three conditions (control, 5µm pores, 14µm pores) had the same number of valid reads (144,382,298)
HiCUP output was converted to HOMER input using the hicuptohomer script provided by HiCUP
The first principle component of the correlation matrix of each chromosome was found in HOMER v4.9.1 at 300kb resolution, 500kb super-resolution on a matrix normalised with the HOMER default
Significant and differential contacts were identified in HOMER at 40kb resolution, 100kb super-resolution with default normalisation, minimum distance 100kb, maximum distance 5Mb
HOMER was used to generate chromosomal matrices at 50kb resolution for topologically associated domain (TAD) analysis in TopDom v0.0.2 using a window size of 5
Genome_build: hg38
Supplementary_files_format_and_content: bedfile of the frst principle component of each condition. Total significant contacts in each condition (csv). Contacts with significantly increased and decreased frequency in 5mig and 14mig compared to control (csv). Binsignal output from TopDom in each condition (tsv)

source_name: Myeloid leukaemia

growth_protocol: A seed-lot store was generated of cells at 4 passages. Cells were grown in suspension in RPMI 1640 (ThermoFisher, 11875119) with 10% FBS (medi’Ray, MG-FBS0820-500ML-GEN), 1% pen/strep (ThermoFisher, 15140122), and 1% GlutaMAXTM (ThermoFisher, 35050061). Cells were differentiated into a granulocytic phenotype with 1µm all trans retinoic acid (ATRA)(Sigma Aldrich, R2625-50MG) for four days.

extract_protocol:
Hi-C protocol as described in Rao et al 2014 with MboI restriction enzyme
Illumina Truseq Nano kit (Truseq Nano DNA LT Sample Preparation Kit, FC-121-4001) was used, following kit instructions

tag: differentiation

value: neutrophil-like (4 days all-trans retinoic acid)

tag: passages

tag: migration pore size

value: 14 micrometer diameter


title: Patient 122


title: BRBS351_C08_P3


title: Patient 114


title: BRBS350_B08_P2


title: 5mig_3_HiC

tag: cell line

value: 5 micrometer diameter


title: Patient 112


title: BRBS349_A08_P1


title: BRBS355_G08_P3


title: Patient 117


title: BRBS348_H07_P4


title: Patient 115


title: Patient 110


title: BRBS346_F07_P2


title: ctrl_3_HiC

description:
first principle component of pooled libraries (*PC1only.bed)
TAD binsignal of pooled libraries
Called domains, boundaries, and gaps of pooled libraries (*domains.txt)
Total significant contacts (*significant_ints.csv)


title: 5mig_1_HiC


title: ctrl_2_HiC


title: Patient 109


title: BRBS347_G07_P3


title: 14mig_2_HiC


title: 14mig_1_HiC


title: BRBS345_E07_P1


title: Patient 113


title: 5mig_2_HiC


title: ctrl_1_HiC

description:
first principle component of pooled libraries (*PC1only.bed)
TAD binsignal of pooled libraries (*.binSignal)
Called domains, boundaries, and gaps of pooled libraries (*domains.txt)
Total significant contacts (*significant_ints.csv)


title: Patient 108


title: Patient 111


title: BRBS344_D07_P4


title: BRBS343_C07_P3


title: Control_symptomatic_rep8

city: Oxford

first: Laurienne

last: Edgar

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

institute: University of Oxford

hyb_protocol: Hybridization was varied out in random order on two Illumina Human HT12 v4.0 BeadChips (Illumina, USA) to minimise batch / chip effects.

scan_protocol: Standard Illumina scanning protocol

data_processing:
Illumina BeadArrays were processed with the Bioconductor beadarray package (v.2.24.0) using normal exponential normalization. Probe sets were collapsed per gene based on maximum interquartile range to avoid extreme values but capture variability across all samples. Unannotated and control probe sets were excluded from further analysis.
Normalised using normal exponential normalization with the Bioconductor beadarray package (v.2.24.0).

source_name: Control (non-diabetic) plaque macrophage, symptomatic

label_protocol: Amplification and biotinylation was performed using Ovation Pico WTA V2 kit (Nugen Technologies Inc, USA).

extract_protocol: RNA extracted using Qiagen's RNEasy micro kit, according to manufacturer's protocol.

tag: disease state

value: Control

tag: Sex

value: M

tag: age

tag: cva / tia

value: CVA

tag: medication

value: Asp, Simva, Dig, Bisop


title: Control_symptomatic_rep2

value: TIA

value: Asp, Simva, Amlodipine


title: Diabetic_symptomatic_rep9

source_name: Diabetic plaque macrophage, symptomatic

value: Diabetic

value: Warfarin, Simva, Sotalol, Amlodipine, Doxazosin, Lisin, Glic, Met


title: Control_asymptomatic_rep16

source_name: Control (non-diabetic) plaque macrophage, asymptomatic

value: Asymptomatic

value: Asp, simva, rami, bisoprolol, amlodipine, ISMN


title: Patient 106

tag: tissue

value: radical prostatectomy


title: Control_symptomatic_rep14

value: Asp, Clop, Atorva


title: Patient 105


title: BRBS341_A07_P1

value: Cord blood CD34+ cell-derived dendritic cell cultures


title: BRBS342_B07_P2

value: Putative pDC


title: Patient 103


title: Patient 107


title: NT Kdm4b 1-cell 2 (RRBS-Seq)

value: zygote

tag: strain


title: BRBS338_F06_P2


title: BRBS339_G06_P3

value: Putative pre-cDC2


title: NT 4-cell arrest in 2-cell stage 6 (RRBS-Seq)


title: Control_symptomatic_rep6

value: Asp, simva, atenolol


title: Patient 104


title: BRBS340_H06_P4

value: Putative cDC2


title: Patient 101


title: Control_symptomatic_rep12

value: Control

value: M

value: Asp, Clop, Atorva, Amlodipine, Ramipril


title: BRBS337_E06_P1

value: Putative cDC1


title: BRBS336_D06_P4


title: Diabetic_asymptomatic_rep8

source_name: Diabetic plaque macrophage, asymptomatic

value: Asp, statin, lisinopril, metformin, insulin humalog


title: Patient 100

source_name: prostate


title: Patient 99


title: Diabetic_asymptomatic_rep6

value: Diabetic

value: Asp, Clop, Atorva, Bisop, Rami, Metformin, ISMN


title: Diabetic_symptomatic_rep4

value: TIA

value: Asp, Atorva, Lisonopril, metformin, BFZ, COPD inhalers, lansoprazole


title: Control_symptomatic_rep11

value: Asp, Simva


title: Diabetic_asymptomatic_rep3

value: Asymptomatic

value: Asp, Clopo, simva, indapamide, metformin


title: BRBS335_C06_P3

value: Cord blood CD34+ cell-derived dendritic cell cultures


title: HumanperiCC2: Human peri spinal cord central canal region from patient 2 (46 year old)

source_name: patient 2

value: peri spinal cord central canal region

value: 46 years


title: HumanCC2: Human spinal cord central canal region from patient 2 (46 year old)

value: spinal cord central canal region


title: Patient 102

value: radical prostatectomy


title: Patient 98


title: HumanperiCC1: Human spinal cord peri central canal region from patient 1 (17 year old)

source_name: patient 1

value: spinal cord peri central canal region

value: 17 years


title: Control_asymptomatic_rep2

value: Control

value: M

value: Clopi, lisinopril, atorvastatin


title: Control_asymptomatic_rep10

value: F

value: Clopi, Atenolol, Rami, Amlodipine, Adcal


title: Patient 97


title: BRBS334_B06_P2

value: Putative pDC


title: BRBS333_A06_P1

value: Putative cDC1


title: Patient 96


title: BRBS332_H05_P4

value: Putative cDC2


title: HumanCC1: Human central spinal cord canal region from patient 1 (17 year old)

value: central spinal cord canal region


title: Patient 95


title: Patient 94


title: Patient 93


title: BRBS330_F05_P2


title: BRBS331_G05_P3

value: Putative pre-cDC2


title: BRBS329_E05_P1

value: Cord blood CD34+ cell-derived dendritic cell cultures


title: Patient 92


title: BRBS328_D05_P4


title: CnAb1 Knockdown in mESCs differentiation_siRNA 1 rep3

city: Madrid

first: Jesus

middle: Maria

last: Gómez-Salnero

address: Melchor Fernández Almagro, 3

institute: CNIC

hyb_protocol: One-Color MicroArray-Based Gene Expression Analysis Protocol (Agilent Technologies). Samples were hibridice for 17hours with 1.65μg of Cy3 at 65ºC in a hybridization oven.

scan_protocol: Arrays were scanned at 5μm resolution on an Agilent DNA Microarray Scanner (G2565BA) using default setting for 4x44k format one-color arrays. Images were analyzed using Feature Extraction software version 9.5.3.1 (Agilent Technologies)

data_processing: Data was normaliced with RMA in GeneSpring software.

source_name: mESCs analysis 48 hours after transfection with siRNAs

growth_protocol: R1 mESCs were differentiated in EB during 48 hours

extract_protocol: Qiagen RNeasy Mini Kit using DNAse treatment

treatment_protocol: R1 mESCs were transfected with siRNAS against CnAb1 or control

value: mESCs R1

tag: time

value: 48 hours after transfection


title: CnAb1 Knockdown in mESCs differentiation_siRNA 2 rep1

label_protocol: One-Color MicroArray-Based Gene Expression Analysis Protocol (Agilent Technologies)


title: BRBS327_C05_P3


title: Diabetic_asymptomatic_rep5

value: Diabetic

value: Asymptomatic

value: Asp, Clop, Atorva, Bisop, Rami, Metformin, ISMN


title: CnAb1 Knockdown in mESCs differentiation_siRNA 2 rep2


title: CnAb1 Knockdown in mESCs differentiation_siRNA 1 rep1


title: BRBS326_B05_P2


title: Patient 90

value: radical prostatectomy


title: Patient 89


title: CnAb1 Knockdown in mESCs differentiation_Control rep3


title: Control_symptomatic_rep13

value: Control

value: CVA

value: Asp, Clop, Atorva, Amlodipine, Ramipril


title: Diabetic_asymptomatic_rep1

value: F

value: Insulin, lisinopril, clopi, atorva 80, bisop, BFZ, amitrityline, gabapentine, fluoxetine


title: Control_symptomatic_rep7

value: M

value: TIA

value: Warfarin, Clop, Simva, Bisop, Thyroxine, Dig, Amiloride, Fruse


title: Diabetic_asymptomatic_rep7

value: Asp, simva, candesartan, fruse, metformin, thyroxine, insulin


title: CnAb1 Knockdown in mESCs differentiation_siRNA 1 rep2


title: Control_asymptomatic_rep3

value: Atorva, Naproxen + Omeprazole


title: Control_asymptomatic_rep15

value: Clop, Atorva 80, felodipine


title: Patient 91


title: BRBS325_A05_P1

value: Cord blood CD34+ cell-derived dendritic cell cultures

value: Putative cDC1


title: Control_symptomatic_rep1

value: Asp, Simva, Amlodipine


title: CnAb1 Knockdown in mESCs differentiation_Control rep2

value: mESCs R1

value: 48 hours after transfection


title: Control_asymptomatic_rep4

value: Asymptomatic


title: BRBS324_H04_P4

value: Putative cDC2


title: Patient 86

value: radical prostatectomy


title: Patient 87


title: BRBS323_G04_P3

value: Putative pre-cDC2


title: Patient 88


title: Patient 85


title: BRBS321_E04_P1


title: Patient 84


title: BRBS320_D04_P4


title: BRBS319_C04_P3


title: Patient 83


title: whole blood_primary ESCC tumors without LN metastases (N-)_864974

city: Chengdu

first: sen

last: qin

address: Tianhui Ave

institute: Chengdu military general hospital

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from ESCC patients was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Peripheral Blood


title: CnAb1 Knockdown in mESCs differentiation_Control rep1


title: whole blood_primary ESCC tumors without LN metastases (N-)_850050


title: Patient 81


title: BRBS318_B04_P2

value: Putative pDC


title: BRBS317_A04_P1


title: Patient 82


title: BRBS316_H03_P4


title: Patient 80


title: whole blood_primary ESCC tumors with LN metastases (N+)_865044


title: BRBS315_G03_P3


title: whole blood_primary ESCC tumors with LN metastases (N+)_850103


title: BRBS314_F03_P2


title: Patient 79


title: Control_symptomatic_rep5

value: Control

value: M

value: Indapamide, omeprazole, Doxazosin, Spiron, inhalers


description: Gene Expression analysis in mESCs after CnAb1 (2) siRNA transfection

hyb_protocol: Affimetrix Exon Expression Analysis Protocol following manufacturer instructions. Cy3 labeling.

growth_protocol: R1 mESCs were culture in pluripotent conditions


title: Patient 77


title: Patient 76


title: whole blood_primary ESCC tumors with LN metastases (N+)_845788


title: BRBS312_D03_P4


title: whole blood_primary ESCC tumors without LN metastases (N-)_850049


title: BRBS311_C03_P3


description: Gene Expression analysis in mESCs after CnAb1 (1) siRNA transfection

scan_protocol: Affimetrix Exon Expression Analysis Protocol following manufacturer instructions


title: BRBS310_B03_P2


title: Patient 78


label_protocol: Affimetrix Exon Expression Analysis Protocol following manufacturer instructions


title: BRBS313_E03_P1


title: Patient 74


title: Patient 73


title: BRBS309_A03_P1


description: Gene Expression analysis in mESCs after Control siRNA transfection


title: BRBS308_H02_P4


title: dsIrd5 CrPV 6h replicate 2

description:
Gene expression of S2 cells knocked down for Ird5 and 6h after CrPV induction
dslrd5-CrPV6h2

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Agilent “Drosophila (V2) Gene Expression Microarray” 4x44K (Design ID 021791), for 17 hrs, at 65°C under 10 rpm.

source_name: S2 cells

growth_protocol: S2 cells were cultured at 25 °C in Schneider's medium (Biowest) supplemented with 10% fetal calf serum (FCS), penicillin/streptomycin (50 μg/ml of each) and 2 mM glutamax.

treatment_protocol: To perform micro-array, 2x10^6 S2 cells (10^6/mL) were seeded in 6-wells plates in serum-free medium and mixed with 30 μg of dsRNAs against GFP or Ird5. After 2h, the medium was supplemented with 10% FCS. Four days after dsRNA soaking, the cells were infected by CrPV for 2h or 6h or non-infection (NI). The cells were collected for total RNA extraction.

tag: genotype/variation

value: IKKb (Ird5) knockdown

tag: infection

value: CrPV

tag: replicate

value: S2 cells


title: Patient 75


tag: cell type


title: MEF_KO_rep3

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

hyb_protocol: End labeled cDNA was hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix, #902118) for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol.

scan_protocol: GeneChip Scanner 3000 7G and AGCC (Affymetrix)

data_processing: All analysis was done in R. Standard quality control checks were performed, including: checking raw images and RNA degradation plots; confirming that hybridization of probes was uniform, and that correlations and signal intensities across chips were similar; and performing PCA analysis. Normalization was performed using the “gcrma” package. For analysis, post-normalization relative expression values were used.  probe group file: MoGene-2_0-st.pgf  meta-probeset file: MoGene-2_0-st.mps

source_name: MEF, KO, Cre adenovirus infected

label_protocol: The Ambion WT Expression Kit (#4411973) was used to generate amplified sense-strand cDNA, and fragmentation and labeling was performed with the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, #901525). Microarray expression analysis was performed using GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix, #902118) following the manufacturer’s instructions.

growth_protocol: We isolated murine embryonic fibroblasts (MEFs) using standard protocols from conditional Pbrm1 mice we had generated, where Cre-mediated recombination would cause a frame-shift mutation of the Pbrm1 allele and loss of Pbrm1 expression. MEFs were cultured in DMEM (Cellgro) supplemented with 10% (v/v) fetal bovine serum and 1 mM glutamine.

extract_protocol: Total RNA was collected for microarray analysis using the Qiagen RNeasy kit according to the manufacturer´s protocol.

treatment_protocol: MEFs were infected with either control GFP adenovirus (Vector Biolabs, #1060) or Cre adenovirus (Vector Biolabs, #1045) in 6-well plates. MEFs were passaged 3 times after infection before RNA collection.

value: MEF

tag: adenovirus

value: Cre

value: loss of Pbrm1 expression


title: Patient 72


title: MEF_control_rep2

source_name: MEF, control, GFP adenovirus infected

value: GFP

value: control


title: dsGFP CrPV 6h replicate 2

description:
Gene expression of S2 cells knocked down for GFP and 6h after CrPV induction
dslrd5-CrPV2h2


value: mESCs R1


title: BRBS307_G02_P3

value: Cord blood CD34+ cell-derived dendritic cell cultures

tag: phenotype


title: Patient 71

value: radical prostatectomy


title: d3EB_Smad23DKO_clone_KT15.1F11

first: Anna

middle: Dorothea

last: Senft

address: South Parks Road

department: Sir William Dunn School of Pathology

description: d3EB_Smad23DKO_biological replicate 4

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Bead-Station data were extracted using the Gene Expression Analysis Module V1.6.0 of GenomeStudio V2009.2 (Illumina) and imported into the R-based Illumina pre-processing module (http://www.arrayanalysis.org/  (Eijssen et al., 2015)). Hierarchical clustering identified three outlier samples in ESCs that were excluded from subsequent analysis.

source_name: Smad2/3 KO day 3 embryonic bodies

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol:
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)
ESCs (see ESC samples) were trypsinized, resuspended in ESC medium (see ESC samples) without LIF (EB medium), pelleted, washed in PBS (w/o MgCl2) and counted. A single-cell solution of 4 x 10^4 cells/ml in EB medium was pipetted into 10μl drops onto square 12cm plates and the plates carefully inverted onto lids containing a 3cm dish filled with PBS (w/o MgCl2) to maintain humidity of hanging drops. Cells were left to form embryoid bodies for 48h after which EBs were harvested in EB medium and  kept in suspension for another 24h.
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)

extract_protocol: RNA was extracted with QIAGEN Rneasy micro kit and DNase I treatment on-column in accordance with the prescribed protocol provided with the kit.

treatment_protocol: ~5000 EBs were collected in EB medium, washed once in PBS (w/o MgCl2) and RNA isolated.

value: Smad2/3 KO day 3 embryonic bodies


title: MEF_KO_rep2