title: T47D_1B.ChIP_rep1

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (1.106) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigwig and bed files of called peaks

source_name: Breast cancer cell line

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s Medium, 100 U/ml penicillin, 100 μg/ml streptomycin and 10% fetal bovine serum (Sigma Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies directed against HIF-1a (rabbit polyclonal, PM14), HIF-2a (rabbit polyclonal, PM9), or HIF-1b (rabbit polyclonal, Novus Biologicals, NB100-110).
Libraries were prepared from immunoprecipitated chromatin using the Illumina ChIP-Seq kit; All ChIP-seq experiments were performed in duplicate in accordance with ENCODE consortium guidelines.

treatment_protocol: Hypoxic incubations were performed for the specified duration and ambient oxygen concentration in an In Vivo2 400 Hypoxia Work Station (Ruskinn Technology).

tag: cell line

value: Breast cancer cell line

tag: ambient o2 concentration

tag: duration of hypoxia

value: 16 hours

tag: tchip antibody

value: HIF1b (Novus NB100-110)


title: T47D_1B.ChIP_rep2

status: Public on Dec 31 2019

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type


title: S176

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

country: USA

institute: University of Arizona

library_source: transcriptomic

data_processing:
Raw fastq data were aligned to mouse transcriptome by Salmon v0.91
Salmon counts were imported through Tximport to get unnormalized gene expressions
Normalized counts were extracted from DESeq2
Genome_build: Mouse ensembl release 95
Supplementary_files_format_and_content: csv file with unnormalized gene counts from Tximport

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

tag: tissue

value: Hippocampus

tag: Sex

value: Male

tag: genotype


title: DO-1195

city: Bar Harbor

first: Yuka

last: Takemon

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

data_processing:
bclfastq v1.8.3 was used for base-calling
EMASE was used to align multi-parent allele specific expression and quantify gene expresison counts from fastq files
GBRS was used to quantify multiway allele specificity to account for DO generation.
EMASE raw counts were rank normalized
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing matrix of gene expression (raw and rank normalized) for all 188 samples.

source_name: Right kidney

extract_protocol:
Pulverized aliquots lysed and homogenized in TRIzol reagent (Ambion, cat#15596026). Total RNA was isolated using miRNeasy Mini kit (Qiagen, cat#217004) according to manufactures’ protocols, including the optional DNase digest step.
Poly(A) RNA-seq libraries were constructed using the TruSeq RNA Library Prep Kit v2 (Illumina), including the addition of unique barcode sequences. Library quality and quantity were assessed using the DNA 1000 LabChip assay (Agilent Technologies) and quantitative PCR (Kapa Biosystems). Libraries were randomized and pool in batches for sequencing at 100 bp single-end on the HiSeq 2500 (Illumina) using TruSeq SBS Kit v4 reagents (Illumina).

treatment_protocol: Whole right kidneys were flash frozen and pulverized.

value: Kidney

tag: generation

value: M


title: PC-3_1B.ChIP_rep2

source_name: Prostate cancer cell line

value: Prostate cancer cell line


title: DO-1191


title: S175


title: PC-3_1B.ChIP_rep1


title: HCT116_1B.ChIP_rep3

source_name: Colorectal cancer cell line

value: Colorectal cancer cell line


title: S168

value: Female


title: HCT-116_1B.ChIP_rep2


title: clec-4_OP_6h-Rep1

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

country: Germany

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text file includes Raw reads counts for each Sample

organism: Caenorhabditis elegans

source_name: whole body

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

treatment_protocol: Worms were exposed to OP50 and BT at the stage L4. The BT strains were diluted in 1:10 (non-pathogenic BT strain BT407). The experiments with BT were performed at 20°C.

tag: treatment

tag: time

value: 6 h

tag: medium

value: mNGM

tag: temperature


title: DO-1182


title: DO-1210

value: F


title: DO-1181


title: S167


title: A549_1B.ChIP_rep3

source_name: Lung cancer cell line

value: Lung cancer cell line


title: DO-1196


title: DO-1179


title: A549_1B.ChIP_rep2


title: DO-1193


title: 786ONGWASCaptureC_rep1

data_processing:
Library strategy: Capture-C
Reads were trimmed using trim galore and then in silico digested with DpnII using dpnII2E.pl (https://github.com/telenius/captureC/releases)
Resulting reads were then algined to genome using bowtie 1.0.0
Interaction frequencies were then determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases)
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigwig files contain interaction frequency from all sites

source_name: VHL defective clear cell kidney cancer cell line

growth_protocol: Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Capture-C libraries were prepared as previously described (Davies et al. 2016 Nature Methods). Cells were fixed with 2% (vol/vol) formaldehyde for 10 min, quenched with 125 mM glycine in PBS and then lysed in cold lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2% Igepal, 1× cOmplete Protease Inhibitor Cocktail (Roche). Chromatin was digested with Dpn2 (New England Biolabs) at 37oC overnight. Fragments were then diluted and ligated with T4 DNA ligase (Thermo Scientific) at 16oC overnight. Crosslinking was reversed by overnight incubation at 60oC with proteinase K (Bioline). The 3C libraries were then purified by phenol-chloroform and chloroform extraction followed by precipitation in ethanol at -80oC overnight. Digestion efficiency was determined by qPCR and gel electrophoresis.
Sequencing libraries were prepared from 5 μg of each 3C library by sonication using a S220 focused-ultrasonicator (Covaris) to a average size of 200bp and indexed using NEBnext reagents (New England Bioloabs) according to protocol. Enrichment of 1-2 μg of indexed library incubated with 13 pmol of a pool of biotinylated oligonucleotides (Intergrated DNA technologies or Sigma) was performed using the SeqCap EZ system (#06953212001, Roche/Nimblegen) following the manufacturer’s instructions. Two rounds of capture employing 48-72 hr and 24 hr hybridizations respectively were used. Capture enrichment was determined by qPCR. Correct library size was confirmed using a Bioanalyzer DNA 1000 or Tapestation D1000 kit (Agilent), and DNA concentrations were determined using a Qubit 2.0 Fluorometer (ThermoFisher Scientific).

value: renal cancer


title: S158


title: S164


title: S165


title: DO-1172


title: DO-1165


title: S166


title: DO-1163


title: DO-1162


title: S174


title: S156


title: S157


title: S155


title: DO-1160


title: 786ONGWASCaptureC_rep2


title: 15Y26Passage5

city: Taiyuan

first: Ruifeng

last: Liu

state: Shanxi

address: No. 1 Dong San Dao Xiang

department: Institute of Dermatology

country: China

institute: Taiyuan City Centre Hospital

data_processing:
RNA-seq reads were mapped to human genome by hisat2 software (v2.0.4) with default parameters. FPKM values were caculated by cufflinks software suite (v2.2.1). Cuffdiff2 software (v2.2.2) was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format with FPKM.

source_name: Mesenchymal stem cells (MSC)

growth_protocol: Skin derived mesenchymal stem cells were cultured in DMDM/F12 medium and adherent cultured

extract_protocol:
Total RNA from each sample was used to prepare the RNA sequencing library
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: Skin-derived MSC

tag: passage

tag: disease state

value: Psoriasis


title: DO-1174


title: 15Y15Passage5


title: DO-1159


title: S154


title: DO-1156


title: 15Y29Passage5


title: 15Z3Passage5

value: Normal


title: 14Z66Passage5


title: 14Z70Passage5


title: DO-1157


title: S147


title: S146


title: DO-1149


title: S145


title: DO-1140


title: DO-1148


title: S144


title: DO-1135


title: S148


title: Melanocytes_1

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description:
Mc_1
Bulk RNA-seq (melanocytes)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.

data_processing:
All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters. Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Excel workbook for all sequencing libraries combined, listing all genes (rows) and FPKMs for all samples. Column name indicates the sorted cell type (each sorted cell type has two biological replicates). The first column lists the official gene symbol.

source_name: Dorsal skin

extract_protocol:
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
From 100ng amplified cDNA sequencing libraries were generated with 6 unique barcoded adapters (3 samples x 2 replicates) using the Ovation Ultralow DR Library System (NuGEN).

value: Dorsal skin

value: Melanocytes


title: DO-1124


title: DO-1131


title: DO-1121


title: Matrix_2

description:
Mx_2
Bulk RNA-seq (matrix)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.

value: Matrix


title: Melanocytes_2

description:
Mc_2
Bulk RNA-seq (melanocytes)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.


title: Outer root sheath_1

description:
ORS_1
Bulk RNA-seq (outer root sheath)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.

value: Outer root sheath


title: Outer root sheath_2

description:
ORS_2
Bulk RNA-seq (outer root sheath)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.


title: Matrix_1

description:
Mx_1
Bulk RNA-seq (matrix)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.


title: DO-1153

value: Kidney


title: DO-1119


title: DO-1118


title: Dermal fibroblasts_2

description:
DF_2
Bulk RNA-seq (dermal fibroblasts)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.

value: Dermal fibroblasts


title: Dermal fibroblasts_1

description:
DF_1
Bulk RNA-seq (dermal fibroblasts)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.


title: Dermal papilla_2

description:
DP_2
Bulk RNA-seq (dermal papilla)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.

value: Dermal papilla


title: Dermal papilla_1

description:
DP_1
Bulk RNA-seq (dermal papilla)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.


title: DO-1115


title: Dermal sheath_2

description:
DS_2
Bulk RNA-seq (dermal sheath)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.

value: Dermal sheath


title: DO-1107


title: DO-1103


title: DO-1114


title: Dermal sheath_1

description:
DS_1
Bulk RNA-seq (dermal sheath)
Bulk RNA-sequencing of sorted populations from P5 backskin; raw data files contain all transcriptome information for DS, DP, and DF populations, processed data file includes transcriptome information for DS, DP, and DF populations used in this study.


title: DO-1138


title: H3K27ac ChIP-Seq in Mouse E16 Intestine

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: H3K27ac ChIP-Seq in Mouse E16 Intestine

data_processing:
For ChIP-Seq, the filtered single-end reads were aligned to mouse reference genome (GRCm38) using Bowtie2 with default parameters. ChIP-Seq peaks were then called by MACS2 -callpeak with parameters “--keep-dup=1” and “--SPMR”. ENCODE mm10 blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were excluded from the called peaks for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated txt files containing ChIP-Seq peak regions.

source_name: Mouse E16 embryonic tissue

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

extract_protocol:
After isolation of embryonic epithelium using dispase for forestomach and EDTA for the hindstomach, intestine and colon, epithelial pellets were fixed in 1% PFA for 10 minutes at room temperature, quenched with 1/20th volume of 2.5M glycine for 5 minutes, washed twice with cold 1x PBS and flash frozen. When enough sample was acquired (approximately 0.1g of tissue per region), fixed pellets were pooled, dounced in cold PBS with protease inhibitor, and filtered through a 70µm mesh. Samples were then incubated in cold cell membrane and nuclear lysis buffers containing non-denaturating detergents for 30 mins each on a shaker at 4˚C. Washed samples were then pelleted and resuspend in 300µl of sonication buffer containing 0.1% SDS. Sonication was conducted using the Diagenode bioruptor (Diagenode, B01020001) at high power for 40 cycles, 30s ON/OFF. Sonicated samples were cleared with 1:10 dilution of 30% Triton-X and added to antibody bound beads. The next day, beads were washed with high and low salt buffers and treated with Proteinase K overnight at 65˚C. DNA was isolated using phenol/chloroform extraction and 10ng of immunoprecipitated DNA was used for cDNA library construction using the Rubicon DNA-seq Thruplex 48S kit. Libraries were size selected and submitted to be sequenced at 50 base pair read length, single end reads with 15-20 million reads per library.
ThruPLEX DNA-Seq kit

tag: antibody

value: intestine


title: DO-1099


title: H3K27ac ChIP-Seq in Mouse E16 Hindstomach

value: hindstomach


title: DO-1098


title: DO-1078

value: M


title: DO-1077


title: DO-1097

value: F


title: H3K27ac ChIP-Seq in Mouse E16 Colon

description: H3K27ac ChIP-Seq in Mouse E16 Colon

value: colon


title: DO-1076


title: DO-1067


title: DO-1057


title: DO-1058


title: DO-1070


title: DO-1046


title: niche2

city: Baltimore

first: Xin

last: Chen

state: MD

address: 3400 North Charles Street

department: Biology

institute: JHU

data_processing:
Bowtie 0.12.7 was used for alignment against drosophila genome (Flybase dmel_r5.43) with parameter: -a --phred33-quals -n 2 -e 70 -l 28 -m 1 --best –strata
data filtering: only uniquely mapped one with at most two mismatches were used
Assign read to gene: gene exon genomic region were created by merging the annotation of protein, ribosomal RNA etc. An in-house perl script to search and assign the read to the gene. If a read belongs to more than one gene exon region, it will split its count equally into each gene it mapped to.
EdgeR was used to quantitatively measure the level of transcripts normalized across different samples which is termed Corrected Read per Kilobase of gene model per Million mapped reads (cRPKM). This value is used to compare gene expression level among different group of samples (according to their development stage and profile of clustering (which is only for LC stage)
Genome_build: drosophila melanogaster dmel_r5.43
Supplementary_files_format_and_content: Table of Corrected Read per Kilobase of gene model per Million mapped reads (cRPKM) for all genes within each differentiation stages

organism: Drosophila melanogaster

source_name: niche

extract_protocol:
Immediately after isolation, the cysts were treated with mild detergent to permeabilize the plasma membrane while keeping the nucleus intact.
Permeabilization allowed mRNA to be reverse transcribed using poly-dT attached to one universal primer sequence. Poly A was added to the single strand DNA 3’ end using terminal transferase. Second strand DNA was synthesized using poly-dT attached to another universal primer sequence. Finally, the resulting library was amplified using both universal primers.

treatment_protocol: Testes were dissected in S2 insect media.Two Tungsten micro-needles were used to tear the muscle sheath layer, resulting in spilled germ cell cysts into the media.The cysts were viewed using inverted microscope and were picked using glass needle

value: testes

value: germline stem cell (GSC)

tag: Stage

value: niche


title: DO-1042


title: DO-1035


title: DO-1033


title: DO-1041


title: LC2_2

source_name: late spermatocyte

value: late spermatocyte


title: DO-1056


title: DO-1031


title: DO-1100


title: LC1_2


title: DO-1025


title: DO-1029


title: DO-1093


title: H3K27ac ChIP-Seq in Mouse E16 Forestomach

value: forestomach


title: DO-1020


title: DO-1037


title: EC3

source_name: early spermatocyte

value: early spermatocyte


title: DO-1061


title: EC2


title: LC1_1


title: DO-1023


title: DO-1015


title: DO-1007


title: embryo23-24h_E3_C11

city: Basel

first: Jialin

address: biozentrum, Spitalstrasse 41

country: Switzerland

institute: University of Basel

data_processing:
Libraries were sequenced on an Illumina Hi-Seq 2500 with pair-end protocol.
The fastq files were first de-multiplexed by using the “Demultiplex” tool from BRB-seqTools suite (available at https://github.com/DeplanckeLab/BRB-seqTools).
Then, we trimmed the polyA sequences of the de-multiplexed files by using the “Trim” tool.
Next, the STAR aligner (Dobin et al. 2013) was used to map the trimmed reads to the reference genome of fly (BDGP6, Ensembl release 91 )
Genome_build: BDGP6
Supplementary_files_format_and_content: tabular expression matrix, read counts

molecule: polyA RNA

source_name: single embryo

growth_protocol: Fly reared at room temperature on a standard fly medium with 12 hours light dark cycle.

extract_protocol:
For RNA extraction, tubes were thawed on ice, supplemented with 350 µL of 100% Ethanol before homogenizing again with the same parameters. We then used the Direct-zol™ RNA Miniprep R2056 Kit, with the following modifications: we did not perform DNAse I treatment, we added another 2 min centrifugation into an empty column after the RNA Wash step, finally elution was performed by adding 8 µL of RNAse-free water to the column, incubation at room temperature for 2 min and then centrifugation for 2 min. RNA was transferred to a low-binding 96 well plate and stored at -80°C.
RNA quantity was assessed using picogreen (Invitrogen P11496). Samples were then grouped according to their concentration in 96-well plates, and diluted to a final concentration determined by the lowest sample concentration on the plate. RNA was then used for gene expression profiling using BRB-seq. In short, the BRB-seq protocol starts with oligo-dT barcoding, without TSO for the first-strand synthesis (reverse transcription), performed on each sample separately. Then all samples are pooled together, after which the second-strand is synthesized using DNA PolII Nick translation. The sequencing library is then prepared using cDNA augmented by an in-house produced Tn5 transposase preloaded with the same adapters (Tn5-B/B), and further enriched by limited-cycle PCR with Illumina compatible adapters. Libraries are then size-selected (200 - 1000 bp), profiled using High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-474), and measured using Qubit dsDNA HS Assay Kit (Invitrogen, #Q32851).

treatment_protocol: Eggs were harvested using the following protocol. First a 1:1 bleach (Reactolab 99412) 1x PBS mix was poured on the plate and incubated for 2 min. During this incubation, we used a brush to lightly scrape the surface to mobilize the embryos. We then poured the PBS-bleach mixture through a sieve, washed the plate with 1x PBS, and poured the wash on the same sieve. We washed the sieve several time with 1x PBS until the smell of bleach disappeared. Single embryos were then manually transferred to Eppendorf containing 50 µL beads and 350 µL Trizol (lifetechnologies AM9738). The tubes were homogenized in a Precellys 24 Tissue Homogenizer at 6000 rpm for 30 seconds. Samples were then transferred to liquid nitrogen for flash freezing and stored at –80°C.

tag: development stage

value: 23-24 hours

value: whole embryo


title: DO-1010

value: Kidney


title: niche1


title: DO-1000


title: DO-1003


title: LC2_1


title: embryo23-24h_E3_H8


title: EC1


title: WT MEF_3

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

data_processing:
Align RNA-seq reads to reference genome and transcriptome using the STAR program (version 2.5.1b)
Reads uniquely mapped to known genes were counted to obtain a read count matrix
Genes were annotated by unique Entrez IDs
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file inclduing an integer matrix of gene-level read counts. Row names are unique Entriez gene IDs. Data is not normalized.

source_name: WT MEF_3

growth_protocol: typical culture media with high glucose and 10% FBS

extract_protocol:
MEF RNA was extracted using the Trizol method
cDNA library preparation was performed using the TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: no special treatment

value: WT

value: mouse embryonic fibroblasts (MEF)


title: embryo23-24h_E3_F6


title: embryo23-24h_E3_C7


title: DO-0992


title: embryo23-24h_E3_C12


title: embryo23-24h_E3_A6


title: WT MEF_2

source_name: WT MEF_2


title: embryo23-24h_E3_H6


title: DO-0989


title: DO-0995


title: DO-0982


title: embryo23-24h_E3_E10


title: embryo23-24h_E3_G1


title: DO-0980


title: DO-0979


title: DO-0972


title: DO-0969


title: WT MEF_1

source_name: WT MEF_1


title: Prf KO-CD8-1

city: Beijing

first: Tianqi

last: Wang

address: No. 95 Yong-an Road, Xi-cheng District

institute: Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University

description: from MCD-fed perforin knockout mice

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sampl

source_name: Hepatic CD8 T cells

extract_protocol:
Hepatic CD8 T cells were sorted using FACS Aria II from WT or perforin knockout mice after 4 weeks of MCD feeding. And then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult


title: PK MEF_3

source_name: PK MEF_3

tag: cell type


title: embryo23-24h_E3_E1

tag: strain


title: DO-0967

source_name: Right kidney

tag: age


title: WT-CD8-2

description: from MCD-fed WT mice

tag: tissue


title: Prf KO-CD8-2

description: from MCD-fed perforin knockout mice


title: PK MEF_1

source_name: PK MEF_1


title: DO-0960

tag: Sex


title: KA_20_5

city: Dresden

first: Attila

last: Toth

state: Saxony

address: Fiedlerstr. 42

department: Faculty of Medicine

institute: TU Dresden

description:
L1543_KA_20_5
RNA-seq of 20.5 days post coitum fetal gonads

data_processing:
Bcl2fastq 1.8.2
Quantification with Kallisto (0.43.1) by using the mouse transcriptome which was build with the help of Ensembl 87 annotation and mm10 reference
Genome_build: mm10
Supplementary_files_format_and_content: spreadsheet with the TPM values calculated by Kallisto; the first columns are Ensembl ID, Gene name, followed by TPM values of the samples

source_name: Mouse female gonads

extract_protocol: Strand specific RNA-Seq library preparation was performed with Ultra I Directional RNA Library Prep (New England Biolabs)

tag: strain background

value: 20.5 days post coitum

value: whole fetal gonads


title: WT-CD8-1

description: from MCD-fed WT mice


title: embryo23-24h_E3_B12


title: embryo23-24h_E3_D8


title: embryo23-24h_E3_C6


title: DO-0959

tag: generation

value: M


title: embryo23-24h_E3_G5


title: PK MEF_2

source_name: PK MEF_2

tag: genotype


title: KA_18_5

description:
L1542_KA_18_5
RNA-seq of 18.5 days post coitum fetal gonads

value: 18.5 days post coitum


title: DO-0958


title: DO-0957


title: embryo23-24h_E3_D10


title: DO-0956


title: embryo23-24h_E2_C11


title: KA_14_5

description:
L1540_KA_14_5
RNA-seq of 14.5 days post coitum fetal gonads

value: 14.5 days post coitum


title: embryo23-24h_E3_G8


title: embryo23-24h_E3_D12


title: DO-0953


title: KA_12_5

description:
L1539_KA_12_5
RNA-seq of 12.5 days post coitum fetal gonads

value: 12.5 days post coitum


title: KA_11_5

description:
L1538_KA_11_5
RNA-seq of 11.5 days post coitum fetal gonads

value: 11.5 days post coitum


title: DO-0952


title: embryo23-24h_E2_G3


title: embryo23-24h_E2_H4


title: DO-0951


title: AT_11_5

description:
L1537_AT_11_5
RNA-seq of 11.5 days post coitum fetal gonads


title: embryo23-24h_E2_H5


title: embryo23-24h_E2_H6


title: embryo23-24h_E2_C2


title: embryo23-24h_E2_B11


title: DO-0938


title: KA_16_5

description:
L1541_KA_16_5
RNA-seq of 16.5 days post coitum fetal gonads

value: 16.5 days post coitum


title: DO-0941


title: embryo23-24h_E2_G12


title: embryo23-24h_E2_E8


title: DO-0929


title: embryo23-24h_E2_D11


title: DO-0923


title: LC1_3

value: testes

value: germline stem cell (GSC)

value: late spermatocyte


title: embryo23-24h_E2_F7

value: 23-24 hours

value: whole embryo


title: embryo23-24h_E2_E3


title: DO-0936

value: Kidney


title: embryo23-24h_E2_D12


title: DO-0922


title: embryo23-24h_E2_C5


title: DO-0950


title: DO-0911


title: DO-0945


title: embryo23-24h_E2_F9


title: DO-0909


title: embryo23-24h_E2_G7


title: DO-0907


title: P7 Pak2H/H RNA-seq

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Reads were aligned to the mouse genome mm9 and to gene annotations from Refseq gene using TopHat v2.05 (Trapnell et al. 2009).
Cufflinks v2.0.2(Trapnell et al. 2010) was used to quantify FPKM values. Cuffdiff to perform differential expression analysis.
bigwig files were generated by RSeQC.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

source_name: whole cell

growth_protocol: Since complete knockout of Pak2 in mice is embryonic lethal, we have generated Pak2 knockdown mice using a gene-trap strategy, and mice with Pak2 depletion are viable (referring to the H/H as homozygous for the gene trap allele). BubR1+/H mice were provided by Dr. Jan. van Deursen. We cross Pak2+/H mice to BubR1+/H mice to generate Pak2+/H;BubR1+/H mice. We intercrossed Pak2+/H;BubR1+/H mice to generate experimental cohorts of BubR1H/H; Pak2H/H mice. Our control cohorts will include Pak2+/+; BubR1H/H mice. For MEFs culture, we intercrossed Pak2+/H mice to derive Pak2+/+, Pak2+/H, and Pak2H/H MEFs, which were generated from trypsinized carcasses of 13.5-day-old embryos as previously described. They were cultured in 20% oxygen to induce senescence by oxidative stress, frozen at P2 and P3 and used for experimentation at indicated passages (P3, P5, and P7, n=3 MEF lines per genotype).

extract_protocol:
Total RNA was extracted from cells and tissue using Quiagen miRNeasy Mini Kit for RNA-seq library preparation.
RNA-seq libraries were prepared with Ovation RNA-seq system v2 kit (NuGEN) according to the manufacturer’s instruction, and were sequenced on an Illumina HiSeq 2000 at the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

tag: media

value: DMEM

tag: cell cycle stage

value: asynchronization

tag: chip antibody

value: no

value: MEFs


title: DO-0940


title: DO-0937


title: embryo23-24h_E2_B5


title: embryo23-24h_E2_D3


title: DO-0836

value: F


title: P7 WT RNA-seq


title: embryo23-24h_E2_H3


title: DO-0823


title: embryo23-24h_E2_A12


title: P3 Pak2H/H RNA-seq


title: embryo23-24h_E2_C9


title: DO-0831


title: DO-0821


title: DO-0819


title: P3 WT RNA-seq


title: embryo23-24h_E2_F4


title: OX40-1

first: Guangyong

last: Sun

address: Yongan Street 95, Xicheng District

institute: Beijing Friendship Hospital

description: OX40 Fc stimulated

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

source_name: Hepatic monocytes

extract_protocol:
CD11bintF4/80low monocytes were sorted using FACS Aria II in mouse liver, and then stimulated with IgG or OX40 Fc (2ug/ml) for 2 days. And then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: adult


title: DO-0818


title: OX40-2

description: OX41 Fc stimulated


title: DO-0817


title: DO-0809


title: IgG-2

description: IgG stimulated


title: embryo23-24h_E1_1_B3


title: IgG-1

description: IgG stimulated


title: embryo20-21h_E3_A3

value: 20-21 hours


title: embryo23-24h_E1_2_G2


title: embryo20-21h_E3_C4


title: DO-0804


title: embryo20-21h_E3_H7


title: embryo23-24h_E1_2_G3


title: DO-0803


title: DO-0795


title: DO-0816


title: embryo23-24h_E1_2_E3


title: DO-0801


title: DO-0789


title: embryo20-21h_E3_E6


title: embryo20-21h_E3_G11


title: DO-0790


title: DO-0788


title: embryo20-21h_E3_C2


title: embryo20-21h_E3_B7


title: embryo20-21h_E3_G6


title: DO-0787


title: embryo20-21h_E3_D2


title: embryo20-21h_E3_A4


title: DO-0781


title: embryo20-21h_E3_D9


title: embryo20-21h_E3_E2


title: DO-0774


title: DO-0776


title: embryo20-21h_E3_E5


title: DO-0766


title: embryo20-21h_E3_E8


title: DO-0767


title: DO-0779


title: embryo20-21h_E3_E7


title: DO-0763


title: DO-0777


title: embryo20-21h_E3_G9


title: DO-0760


title: DO-0758


title: embryo20-21h_E3_B5


title: embryo20-21h_E3_B10


title: embryo20-21h_E3_B6


title: embryo20-21h_E2_E6


title: embryo20-21h_E3_A11


title: DO-0756


title: DO-0746


title: embryo20-21h_E2_G11


title: embryo20-21h_E2_C4


title: embryo20-21h_E2_F5


title: DO-0744


title: DO-0745


title: DO-0735


title: embryo20-21h_E2_G1


title: DO-0721


title: DO-0996

value: M


title: DO-0765


title: DO-0723


title: DO-0719


title: embryo20-21h_E2_A2


title: embryo20-21h_E1_2_F11


title: DO-0712


title: embryo20-21h_E2_F3


title: DO-0711


title: embryo20-21h_E1_2_E11


title: embryo20-21h_E1_2_F1


title: DO-0704


title: DO-0709


title: DO-0701


title: embryo20-21h_E1_2_F5


title: embryo20-21h_E1_2_F4


title: embryo20-21h_E1_1_D3


title: embryo20-21h_E1_1_A10

value: 17-18 hours


title: DO-0692


title: DO-0698


title: embryo20-21h_E2_F8


title: DO-0685


title: DO-0682


title: embryo17-18h_E3_H11


title: embryo20-21h_E1_2_H2


title: embryo17-18h_E3_D11


title: DO-0693


title: DO-0696


title: DO-0710


title: embryo20-21h_E1_2_G12


title: embryo20-21h_E2_H10


title: embryo20-21h_E1_2_F12


title: DO-0686


title: DO-0683


title: embryo17-18h_E3_E3


title: embryo17-18h_E3_H3


title: DO-0676


title: DO-0674


title: DO-0677


title: DO-0673


title: embryo17-18h_E3_H12


title: DO-0670


title: embryo17-18h_E3_E9


title: DO-0669


title: embryo17-18h_E2_F6


title: embryo17-18h_E2_C8


title: embryo17-18h_E2_B1


title: DO-0661


title: embryo17-18h_E2_A1


title: TissuesTestis

description:
L2805_17_Tissue_plus_Testis
RNA-seq of mouse somatic tissues+mouse testis

source_name: Mouse somatic tissues + mouse testis

value: adult mice

value: whole somatic tissues+whole testis


title: embryo17-18h_E2_G2


title: embryo17-18h_E2_A5


title: Tissues

description:
L2804_17_Tissues
RNA-seq of mouse somatic tissues

source_name: Mouse somatic tissues

value: mouse somatic tissues


title: embryo17-18h_E2_B12


title: ANK-MCM_wt3_23

description:
L26993_ANK-MCM_wt3_23
RNA-seq of Ankrd31+/+ replicate C

data_processing:
Bcl2fastq 2.19.1
Alignment to mouse (mm10) reference with GSNAP (2018-03-11) and support of Ensembl 87 annotation to detect splice sites
FeatureCounts (1.6.0) was used to create fragment to gene counts; mm10 and Ensembl 87 annotation was used
Genome_build: mm10
Supplementary_files_format_and_content: the output of FeatureCounts; the first columns are geneid, chromosom, start, end, strand and length, followed by the raw counts for the 6 samples

source_name: WT_Mouse testis

extract_protocol:
RNA was extracted using the commercial available kit RNeasy Mini (Qiagen)
Strand specific RNA-Seq library preparation was performed with Ultra II Directional RNA Library Prep (New England Biolabs)

tag: genotype/variation

value: wild type; 3xAnkrd31+/+

value: 12 days post-partum

value: whole-testis


title: embryo17-18h_E2_C1

value: whole embryo


title: G3 WT N12 RNA-seq rep2

city: Tianjin

first: Sha

last: Zhou

address: Nankai University

department: The State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

data_processing:
Adaptor sequence and low-quality sequence were trimmed by TrimGalore, then sequence reads were mapped to mm10 genome using STAR.
Reads count were caculated by FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include count values for each Sample.

source_name: ES Cell

growth_protocol: The embryonic stem cells were cultured on feeder in medium consisted of knock-out DMEM (Invitrogen) containing 20% FBS (HyClone), 1,000 U/ml mouse leukemia inhibitory factor (LIF; ESG1107, Millipore), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 μg/ml). For the culture of ESCs, the medium was changed daily, and cells were routinely passaged every two days.

extract_protocol:
For RNA-seq, total RNA was purified using an RNA mini kit (Qiagen) and treated with DNase I (Qiagen).
For RNA-seq, total RNA were poly(A) enriched with oligo(T) beads and RNA libraries were prepared for sequencing using standard Illumina protocols.

value: wild type

value: ESC


title: embryo17-18h_E3_F9


title: embryo17-18h_E1_2_G6


title: G3 Terc-/- F35 RNA-seq rep1

value: Terc knockout


title: embryo17-18h_E3_E11


title: G3 Terc-/- F35 RNA-seq rep2


title: G3 WT N12 RNA-seq rep1


title: embryo17-18h_E1_2_G9


title: embryo17-18h_E1_2_H6


title: embryo17-18h_E1_2_H1


title: embryo17-18h_E2_E2


title: embryo17-18h_E2_E5


title: RNA-seq ZT22 Old-rep2

city: Wuhan

first: Xiaodong

last: Li

state: Hubei Province

address: Luojia Hill, Wuchang District

department: College of Life Sciences

institute: Wuhan University

description: ROF

data_processing:
Illumina Genome Analyzer software was used for basecalling. The fastq files are in the Illumina v1.8+ format (i.e. Phred33 quality score).
Clean reads were mapped to grcm38 mouse genome and transcriptome usin hisat2. The resulted BAM files were used by StringTie to obtain gene expression levels.
Genome_build: grcm38 (genome_tran)
Supplementary_files_format_and_content: tab files of RNA-seq results (gene expression level in FPKM and TPM) produced by StringTie.

source_name: RNA-seq ZT22 Old

extract_protocol:
Livers were removed and flash frozen in liquid nitrogen. Total RNA was later isolated. mRNA was isolated by oligo-dT selection.
strand-specific RNA-seq SE50 libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: ~19 month old

tag: time


title: embryo17-18h_E2_D5

source_name: single embryo


title: embryo17-18h_E1_1_B2


title: RNA-seq ZT18 Old-rep2

description: ROE

source_name: RNA-seq ZT18 Old


title: embryo17-18h_E1_2_H3


title: embryo17-18h_E2_F1


title: embryo17-18h_E1_2_G4


title: embryo17-18h_E1_1_C1


title: embryo17-18h_E1_1_C2


title: RNA-seq ZT14 Old-rep2

description: ROD

source_name: RNA-seq ZT14 Old


title: RNA-seq ZT6 Old-rep2

description: ROB

source_name: RNA-seq ZT6 Old


title: embryo17-18h_E1_1_B6


title: RNA-seq ZT2 Old-rep2

description: ROA

source_name: RNA-seq ZT2 Old


title: embryo14-15h_E3_B4

value: 14-15 hours


title: embryo14-15h_E3_G10


title: embryo14-15h_E3_F2


title: RNA-seq ZT18 Old-rep1

description: OE


title: RNA-seq ZT22 Old-rep1

description: OF


title: RNA-seq ZT14 Old-rep1

description: OD


title: RNA-seq ZT10 Old-rep2

description: ROC

source_name: RNA-seq ZT10 Old


title: RNA-seq ZT10 Old-rep1

description: OC


title: embryo14-15h_E3_C3


title: RNA-seq ZT6 Old-rep1

description: OB


title: embryo14-15h_E3_F10


title: embryo14-15h_E3_H5


title: RNA-seq ZT2 Old-rep1

description: OA


title: RNA-seq ZT22 Young-rep2

description: RYF

source_name: RNA-seq ZT22 Young

value: ~4 month old


title: RNA-seq ZT18 Young-rep2

description: RYE

source_name: RNA-seq ZT18 Young


title: embryo14-15h_E3_A5


title: S1, biological rep1

type: RNA

city: Zhengzhou

first: Ling

last: Fu

address: 100# Science Road

department: School of Pharmaceutical Sciences

institute: Zhengzhou University

description: Gene expression data from esophageal cancer cells acted by Jaridonin

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

source_name: Jaridon 6 on esophageal cancer 109 cell

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The esophageal cancer 109 cells were divided into two group, added Jaridon 6 or not added.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Array hybridization and wash was performed using Affymetrix PrimeView human gene expression

tag: cell line

value: human esophageal cancer cell line

tag: treated with

value: 15 µM Jaridon 6 for 16 h


title: N3, biological rep3

description: Gene expression data from esophageal cancer cells

source_name: esophageal cancer 109 cell

value: none (control)


title: RNA-seq ZT14 Young-rep2

description: RYD

source_name: RNA-seq ZT14 Young


title: S3, biological rep3


title: embryo14-15h_E3_C10

tag: development stage


title: N1, biological rep1


title: N2, biological rep2


title: embryo14-15h_E2_C7


title: embryo14-15h_E2_G6


title: RNA-seq ZT10 Young-rep2

description: RYC

source_name: RNA-seq ZT10 Young


title: embryo14-15h_E3_H2


title: RNA-seq ZT6 Young-rep2

description: RYB

source_name: RNA-seq ZT6 Young


title: CR9

city: Singapore

first: Prakash

last: Arumugam

state: Singapore

address: Biomedical sciences Institute Bioinformatics Institute, A*STAR 30 Biopolis Street, #07-01, Matrix

department: Translational division

country: Singapore

institute: BII

description: 240 minutes,nutrient medium+ rapamycin

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome usinghisat2-2.0.4
Raw counts were calculated using HtSeq-count
Differentially expressed genes were obtained using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample and edgeR output

organism: Saccharomyces cerevisiae

growth_protocol: Purified spores were suspended at approximately 1 OD600 cells/ml in YPD medium and incubated at 30°C with 220rpm shaking.

extract_protocol:
Total RNA was isolated by the “mechanical disruption protocol” using RNeasy MIDI kit (Qiagen), following the instructions of the manufacturer.
Poly-A mRNA was  enriched from ~10 µg of total RNA with oligo dT beads (Invitrogen). ~100 ng of poly-A mRNA recovered was used to construct multiplexed strand-specific RNA-seq libraries as per manufacturer’s instruction (NEXTflexTM Rapid Directional RNA-SEQ Kit, dUTP-Based, v2). Individual library quality was assessed with an Agilent 2100 Bioanalyzer and quantified with a QuBit 2.0 fluorometer before pooling for sequencing on a HiSeq 2000 (1x101 bp read). The pooled libraries were quantified using the KAPA quantification kit (KAPA Biosystems) prior to cluster formation.

treatment_protocol: Purified spores were suspended at approximately 1 OD600 cells/ml in YPD medium with rapamycin (2000 nM) or equivalent volume of DMSO and incubated at 30°C with 220rpm shaking. Samples were collected for analysis at different time points including the zero time point.

tag: treatment

value: spores transferred to nutrient medium with rapamycin for 240 minutes


title: embryo14-15h_E2_C3


title: CR11

description: 360 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 360 minutes


title: RNA-seq ZT22 Young-rep1

description: YF


title: RNA-seq ZT2 Young-rep2

description: RYA

source_name: RNA-seq ZT2 Young


title: CR7

description: 120 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 120 minutes


title: S2, biological rep2

tag: cell type


title: Infected_Rep3

city: Tirupati

first: Guruprasad

middle: Ramarao

last: Medigeshi

state: Andhra Pradesh

address: Panguru (G.P.), Yerpedu Mandal

country: India

institute: Indian Institute of Science Education and Research Tirupati

description:
Gene expression data from embryos in slow phase of cellularisation.
I3.as.rma-Signal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Expression Console and Gene springGX 12.0 using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: Caco-2 cells grown on transwells - Infected With JEV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Caco-2 cells grown on transwells

extract_protocol: Total RNA prepared using Qiagen RNA extraction kit

treatment_protocol: Infected with an MOI of 5 pfu/cell of Japanese encephalitis virus

tag: cell morphology

value: polarized

tag: infection status

value: Japanese encephalitis virus


title: Infected_Rep1

description:
Gene expression data from embryos in slow phase of cellularisation.
I1.as.rma-Signal


title: Infected_Rep2

description:
Gene expression data from embryos in slow phase of cellularisation.
I2.as.rma-Signal


title: Uninfected_Rep3

description:
Gene expression data from embryos in slow phase of cellularisation.
UI3.as.rma-Signal

source_name: Caco-2 cells grown on transwells - Mock infected

value: mock


title: Uninfected_Rep2

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
UI2.as.rma-Signal


title: Uninfected_Rep1

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
UI1.as.rma-Signal


title: CR6

description: 60 minutes,nutrient medium+ rapamycin

tag: strain

value: spores transferred to nutrient medium with rapamycin for 60 minutes


title: RNA-seq ZT18 Young-rep1

description: YE

tag: tissue

tag: age

value: wild type


title: CR5

description: 30 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 30 minutes


title: CR3

description: 10 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 10 minutes


title: RNA-seq ZT14 Young-rep1

description: YD

value: Liver


title: CR1

description: 0 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 0 minutes


title: RNA-seq ZT6 Young-rep1

description: YB


title: embryo14-15h_E2_D1

value: 14-15 hours

value: whole embryo


title: embryo14-15h_E2_D8


title: embryo14-15h_E2_E9


title: embryo14-15h_E1_2_E12


title: embryo14-15h_E1_2_G8


title: embryo14-15h_E2_C6


title: CD11

description: 360 minutes, nutrient medium

value: spores transferred to nutrient medium for 360 minutes


title: embryo14-15h_E2_G8


title: GFinduction-GFP+

city: Shanghai

first: Lin

last: Cheng

state: Shanghai

address: 808 Building of Sci-Tech, 197 Ruijin 2nd Rd

institute: Shanghai Jiao Tong University

description: Treated with GF

data_processing:
Barcoded RNA-seq libraries were mixed and sequenced by Illumina Hiseq 4000 at the depth of 50-60 million 150 bp pair-end reads. The sequencing reads were pseudoaligned to a transcriptome index file (based on Mus_musculus.GRCm38.rel79.cdna.all) using Kallisto (v0.43.1) (Bray et al., 2016). The output transcript compatibility counts were used for Gene-based clustering and differential gene expression analyses according to Love et.al. (Love et al., 2015).
Barcoded ATAC-seq libraries were mixed and sequenced by Illumina XTEN at the depth of 40-60 million 150 bp paired-end reads per sample. Sequencing reads of each library were mapped to the mouse genome (mm10) using Bowtie2 (v2.2.9) (Langmead and Salzberg, 2012) with default settings. PCR duplicates were removed by samtools (v1.3.1) (Li et al., 2009). Normalized bigwig files were generated by DeepTools (v2.4.2) (Ramirez et al., 2014) for visualization with Integrative Genomics Viewer (Robinson et al., 2011). ATAC-seq peaks were called by MACS2 (v2.1.1.20160309) (Liu, 2014) using the following parameters -f BAMPE -g mm -B -q 0.01. After removing ENCODE blacklisted regions, ATAC-seq peaks of all samples were combined and sorted using bedtools (v2.25.0) (Quinlan and Hall, 2010). MEF ATAC-seq sequencing reads were downloaded from NCBI Sequence Read Archive (SRR5077744), and were processed using the same analysis pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: TPM count table

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were isolated from E13.5 mouse embryos and mouse TTFs were isolated from 8-week-old mice as our previous report (Cheng et al., 2014). Both cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1 mM GlutaMAX, 0.1 mM non-essential amino acid, 100 units/mL penicillin and 100 μg/mL streptomycin at 37 °C with 5% CO2. All cells at early passages (less than 3 passages) were used further experiment.

extract_protocol:
Total RNA was extracted from approximately 1 million cells using Qiagen RNAeasy kit. ATAC-seq (Buenrostro et al., 2015) was performed according to Corces et.al. (Corces et al., 2016). For each sample, 50,000 cells were washed twice with PBS and incubated with 50 ul of tagmentation mix (25 μl of 2x TD buffer, 2.5 μl of TDE1, 0.5 μ l of 1% digitonin, 16.4 μ l of 1x PBS, and 5.6 μ l of nuclease-free water) for 30 min at 37 ℃, after which DNA was purified for PCR amplification using custom-made barcoded primers.
RNA-seq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. ATAC-seq libraries were constructed by PCR with custom-made primers using tagmented genomic DNA as input according to Buenrostro et al., 2015.

treatment_protocol: For chemical-induced conversion from fibroblasts into ciNSCs, initial MEFs or TTFs were cultured in DMEM at 37 °C under 5% CO2 and 21% O2 (Normoxia) for 24 hr, then were transferred into conditional medium containing valproic acid (Sigma-Aldrich), CHIR99021 (Tocris Bioscience) and Repsox (Sigma-Aldrich) under 5% CO2, 21% or 5% O2 (Hypoxia). The conditional medium is as follows: DMEM supplemented with 10% FBS, KnockOut™ DMEM (Thermo Fisher Scientific) with 10% KnockOut™ serum replacement (Thermo Fisher Scientific), Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (Thermo Fisher Scientific) with 10% FBS , neural basal medium (STEMCELL Technologies) with N2 and B27, Roswell Park Memorial Institute RPMI 1640 medium (Thermo Fisher Scientific) with 10% FBS, and MyeloCult™ M5300 (STEMCELL Technologies). Medium containing chemical cocktail was changed every four days. These cells were further cultured in neural basal medium containing 20 ng/ml EGF (STEMCELL Technologies) and 20 ng/ml bFGF (STEMCELL Technologies), which was changed every other day. For growth factor-induced NSC generation, MEFs cultured in DMEM were transferred into M5300 with 50 ng/ml IL6 (PeproTech) for early two days, then with 50 ng/ml FGF5 (R&D Systems) and 100 ng/ml LIF (R&D Systems) for another four days. Growth factors treated MEFs were finally cultured in neural basal medium with 20 ng/ml EGF and 20 ng/ml bFGF. For neurosphere formation, cells were cultured in ultra-low adherent plates (STEMCELL Technologies).

tag: passages

value: Nestin::GFP transgenic mice

tag: facs

value: Yes


title: RNA-seq ZT2 Young-rep1

description: YA

value: ~4 month old

tag: genotype


title: embryo14-15h_E1_2_F9

source_name: single embryo


title: NSC-GFP+

description: Primary cells

source_name: Mouse neural stem cells


title: CD7

description: 120 minutes, nutrient medium

value: spores transferred to nutrient medium for 120 minutes


title: CD9

description: 240 minutes,nutrient medium

value: spores transferred to nutrient medium for 240 minutes


title: embryo14-15h_E1_2_E7


title: CD6

description: 60 minutes,nutrient medium

value: spores transferred to nutrient medium for 60 minutes


title: RNA-seq ZT10 Young-rep1

description: YC


title: embryo14-15h_E1_2_F10


title: Basal-2

first: Wenqian

last: Song

address: Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS

data_processing:
Aligns RNA-Seq reads to the genome using TopHat version 2.0.4
Assembles transcripts using Cufflinks version 2.0.2
Merges transcript assemblies using Cuffmerge
Finds differentially expressed genes and transcripts, detects differential splicing using Cuffdiff version 2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: Basal cells isolated from hormone-treated mammary gland

growth_protocol: Cells were freshly sorted from mouse mammary gland.

extract_protocol:
Approximately 50 cells of Lin-, CD24+, CD29hi, TdTomato+ (normal basal), Lin-, CD24+, CD29hi, GFP+ (LdBC) and Lin-, CD24+, CD29low, GFP+ (normal luminal) were harvested by FACS. Cell samples were lysed in 50 μl of 4 M guanidine isothiocyanate solution (GuSCN; Invitrogen, 15577-018) at 42°C for 10 min. The volume of the lysate was adjusted to 200 μl by nuclease-free water, and was further concentrated by ethanol precipitation in the presence of 1/10 volume of acetate sodium (pH 5.7, 3 M; Ambion) and 2 μl of carrier glycogen (20 mg/ml; Roche). Total RNA pellets were dissolved in lysis solution and reverse-transcribed and amplified with modified Smart-seq2 PCR technique ( Chen, J. et al. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nat Protoc 12, 566-580, doi:10.1038/nprot.2017.003 (2017).
RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina) and then applied to sequencing on Illumina HiSeq 2500.

treatment_protocol: Adult virgin mice were ovariectormized and treated with hormone pellets for 14 days. Cells were freshly sorted from mammary glands of these mice.

tag: mouse condition

value: adult virgin mice ovariectomized and treated with hormone pellets

value: Mouse mammary gland

value: Basal cells


title: Basal-1


title: CD5

description: 30 minutes, nutrient medium

value: spores transferred to nutrient medium for 30 minutes


title: embryo14-15h_E1_2_E4


title: CD3

description: 10 minutes, nutrient medium

value: spores transferred to nutrient medium for 10 minutes


title: LdBC-2

source_name: Luminal-derived basal cells isolated from hormone-treated mammary gland

value: Luminal-derived basal cells


title: embryo14-15h_E1_2_G1


title: CD1

description: 0 minutes, nutrient medium

value: spores transferred to nutrient medium for 0 minutes


title: LdBC-1


title: embryo14-15h_E1_1_B4


title: embryo14-15h_E1_1_D11


title: CS

description: purified spores

value: purified spores


title: Luminal cell

source_name: Luminal cells isolated from hormone-treated mammary gland

value: Luminal cells


title: BR9

description: 240 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 240 minutes


title: embryo14-15h_E1_1_C12

value: 14-15 hours

value: whole embryo


title: embryo14-15h_E1_1_A9


title: NES-GFP+ D8 [ATAC-Seq]

data_processing:
Barcoded RNA-seq libraries were mixed and sequenced by Illumina Hiseq 4000 at the depth of 50-60 million 150 bp pair-end reads. The sequencing reads were pseudoaligned to a transcriptome index file (based on Mus_musculus.GRCm38.rel79.cdna.all) using Kallisto (v0.43.1) (Bray et al., 2016). The output transcript compatibility counts were used for Gene-based clustering and differential gene expression analyses according to Love et.al. (Love et al., 2015).
Barcoded ATAC-seq libraries were mixed and sequenced by Illumina XTEN at the depth of 40-60 million 150 bp paired-end reads per sample. Sequencing reads of each library were mapped to the mouse genome (mm10) using Bowtie2 (v2.2.9) (Langmead and Salzberg, 2012) with default settings. PCR duplicates were removed by samtools (v1.3.1) (Li et al., 2009). Normalized bigwig files were generated by DeepTools (v2.4.2) (Ramirez et al., 2014) for visualization with Integrative Genomics Viewer (Robinson et al., 2011). ATAC-seq peaks were called by MACS2 (v2.1.1.20160309) (Liu, 2014) using the following parameters -f BAMPE -g mm -B -q 0.01. After removing ENCODE blacklisted regions, ATAC-seq peaks of all samples were combined and sorted using bedtools (v2.25.0) (Quinlan and Hall, 2010). MEF ATAC-seq sequencing reads were downloaded from NCBI Sequence Read Archive (SRR5077744), and were processed using the same analysis pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by DeepTools (v2.4.2)

tag: timepoint

value: Nestin::GFP transgenic mice

value: Yes

value: Treated with VCR


title: NES-GFP+ D4 [ATAC-Seq]


title: BR11

description: 360 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 360 minutes


title: BR7

description: 120 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 120 minutes


title: NES-GFP- D8 [ATAC-Seq]


title: embryo14-15h_E1_1_A8


title: embryo14-15h_E1_1_B1


title: BR5

description: 30 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 30 minutes


title: NES-GFP- D4 [ATAC-Seq]


title: embryo14-15h_E1_1_B11


title: BR3

description: 10 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 10 minutes


title: NES-GFP+ D4

description: RNA-seq-TPM-count-table.xlsx


title: embryo14-15h_E1_1_D8


title: BR1

description: 0 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 0 minutes


title: NES-GFP- D8

description: RNA-seq-TPM-count-table.xlsx


title: NES-GFP- D4

description: RNA-seq-TPM-count-table.xlsx


title: CR2 UTX Re-expression Replicate 3

first: Kian Leong

last: LEE

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

description:
9701972086_F_Grn.idat
Replicate 3
CR2 UTX 3

hyb_protocol: 750ng of cRNA from each sample was hybridized to HumanHT-12 v4.0 beadchip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina) at scan factor 1 as per manufacturer specifications.

data_processing: Raw intensity values were subjected to background subtraction performed on the BeadStudio Data Analysis software (Illumina) and normalized using the cross-correlation method (Chua et al., 2006, PMID: 16528099). Differential gene expression was identified based on a fold change cutoff of >1.5 in wild type UTX reconstituted HCT116 cells compared to empty vector controls for both clones CR1 and CR2.

source_name: Colorectal Carcinoma Cells

label_protocol: 400ng of total RNA with RNA Integrity Number (RIN) > 7.5 was reverse transcribed into cDNA followed by second strand synthesis and in vitro transcription into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification Kit according to manufacturer recommendations.

growth_protocol: HCT116 cells were cultured in high glucose DMEM (Nacalai, Kyoto, Japan) supplemented with 10% FBS, 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol: Total RNA was extracted from all cells using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number (RIN) >7.5).

treatment_protocol: HCT116 cell lines with endogenous UTX mutated by CRISPR-Cas9 for two independent clones CR1 and CR2 were lentivirally infected with empty vector (CSII-CMV-IRES2-puro) or the same vector containing wild type UTX for reconstitution. Cells were cultured for 4 days in selection medium with 5 μg/ml puromycin post-infection   and subsequently maintained in medium with no puromycin.

tag: endogenous utx

value: CRISPR-Cas9 Mutated

tag: re-expression

value: Wild Type UTX


title: BD11

description: 360 minutes, nutrient medium

value: spores transferred to nutrient medium for 360 minutes


title: CR2 Empty Vector Control Replicate 2

description:
9701972086_I_Grn.idat
Replicate 2
CR2 Vector Control 2

tag: cell line

value: Empty Vector


title: CR2 Empty Vector Control Replicate 3

description:
9701972086_K_Grn.idat
Replicate 3
CR2 Vector Control 3


title: BR6

description: 60 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 60 minutes


title: BD9

description: 240 minutes,nutrient medium

value: spores transferred to nutrient medium for 240 minutes


title: NES-GFP+ D8

description: RNA-seq-TPM-count-table.xlsx


title: embryo11-12h_E3_H4

last: Liu

value: 11-12 hours


title: BD7

description: 120 minutes, nutrient medium

value: spores transferred to nutrient medium for 120 minutes


title: embryo11-12h_E3_B11

value: whole embryo


title: CR2 UTX Re-expression Replicate 1

description:
9701972086_B_Grn.idat
Replicate 1
CR2 UTX 1


title: CR2 UTX Re-expression Replicate 2

description:
9701972086_D_Grn.idat
Replicate 2
CR2 UTX 2


title: BD6

description: 60 minutes,nutrient medium

value: spores transferred to nutrient medium for 60 minutes


title: CR1 UTX Re-expression Replicate 2

description:
7963862066_D_Grn.idat
Replicate 2
CR1 UTX 2


title: embryo11-12h_E3_C5


title: embryo11-12h_E3_F1


title: BD5

description: 30 minutes, nutrient medium

value: spores transferred to nutrient medium for 30 minutes


title: NSD2 KO_pretreated_2h_Rep_2

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

data_processing:
bcl2fastq/2.15 was used to demultiplex the sequence run from a illumina HiSeq 2500  run
Alignment and Ht-seq count analysis was performed using STAR/2.5.2b and Ht-seq count tool
Genome_build: mm9
Supplementary_files_format_and_content: Ht-Seq Counts

source_name: Murine embryonic fibroblasts (MEFs)

growth_protocol: MEFs were grown in Dulbucco’s minimal essential medium (DMEM) containing 10% donor bovine serum at 37°C.

extract_protocol:
RNA from MEFs was extracted using TRIzol regent (Invitrogen) according to manufacturer’s protocol.
Library preparation including ligating barcode was conducted using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN).  Fragments were selected ranging from 250 to 450 bp and subjected to paired-end sequencing on a HiSeq2000 (Illumina).

treatment_protocol: WT MEFs and NSD2 KO MEFs were treated with mouse recombinant IFNβ (100 units/ml, PBL Interferon Source) for 2h. About pretreated cells, cells were treated with IFN for 3h, washed and left without IFN for 24h. Pretreated cells were re-stimulated with IFN for 2h.

tag: genotype/variation

value: NSD2 KO

tag: group

value: pretreated

tag: time point


title: embryo11-12h_E3_F7

data_processing:
Libraries were sequenced on an Illumina Hi-Seq 2500 with pair-end protocol.
The fastq files were first de-multiplexed by using the “Demultiplex” tool from BRB-seqTools suite (available at https://github.com/DeplanckeLab/BRB-seqTools).
Then, we trimmed the polyA sequences of the de-multiplexed files by using the “Trim” tool.
Next, the STAR aligner (Dobin et al. 2013) was used to map the trimmed reads to the reference genome of fly (BDGP6, Ensembl release 91 )
Genome_build: BDGP6
Supplementary_files_format_and_content: tabular expression matrix, read counts

tag: development stage


title: NSD2 KO_pretreated_0h_Rep_2


title: BD3

description: 10 minutes, nutrient medium

tag: treatment

value: spores transferred to nutrient medium for 10 minutes


title: CR1 UTX Re-expression Replicate 1

description:
7963862066_B_Grn.idat
Replicate 1
CR1 UTX 1


title: CR1 UTX Re-expression Replicate 3

description:
7963862066_F_Grn.idat
Replicate 3
CR1 UTX 3


title: WT_pretreated_2h_Rep_2

value: WT


title: embryo11-12h_E3_F3


title: BD1

description: 0 minutes, nutrient medium

value: spores transferred to nutrient medium for 0 minutes


title: CR1 Empty Vector Control Replicate 2

description:
7963862066_I_Grn.idat
Replicate 2
CR1 Vector Control 2


title: BS

description: purified spores

value: purified spores


title: AR11

description: 360 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 360 minutes


title: MEFs D1

description: RNA-seq-TPM-count-table.xlsx

value: Nestin::GFP transgenic mice

value: No

value: Treated with VCR


title: embryo11-12h_E3_A9


title: CR2 Empty Vector Control Replicate 1

description:
9701972086_G_Grn.idat
Replicate 1
CR2 Vector Control 1

value: CRISPR-Cas9 Mutated

value: Empty Vector


title: WT_pretreated_0h_Rep_2


title: MEFs D0

description: RNA-seq-TPM-count-table.xlsx

value: Primary cells


title: embryo11-12h_E3_A1

value: 11-12 hours


title: MEFs D2

description: RNA-seq-TPM-count-table.xlsx


title: embryo11-12h_E2_B4

value: whole embryo


title: embryo11-12h_E3_B8


title: embryo11-12h_E2_G10


title: NSD2 KO_pretreated_2h_Rep_1


title: AR9

description: 240 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 240 minutes


title: WT_pretreated_2h_Rep_1


title: CR1 Empty Vector Control Replicate 1

description:
7963862066_G_Grn.idat
Replicate 1
CR1 Vector Control 1


title: NSD2 KO_pretreated_0h_Rep_1


title: AR6

description: 60 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 60 minutes


title: embryo11-12h_E2_F12


title: WT_pretreated_0h_Rep_1


title: embryo11-12h_E2_F11


title: AR5

description: 30 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 30 minutes


title: WT_naive_2h_Rep_2

value: naive


title: embryo11-12h_E2_A8


title: WT_naive_0h_Rep_2


title: AD9

description: 240 minutes,nutrient medium

value: spores transferred to nutrient medium for 240 minutes


title: WT_naive_2h_Rep_1

value: WT


title: NSD2 KO_naive_0h_Rep_2

value: NSD2 KO


title: AD11

description: 360 minutes, nutrient medium

value: spores transferred to nutrient medium for 360 minutes


title: embryo11-12h_E2_B9


title: AR7

description: 120 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 120 minutes


title: AD7

description: 120 minutes, nutrient medium

value: spores transferred to nutrient medium for 120 minutes


title: embryo11-12h_E2_B10


title: NSD2 KO_naive_2h_Rep_1


title: embryo11-12h_E2_H2


title: embryo11-12h_E1_2_E8


title: NSD2 KO_naive_0h_Rep_1


title: AD5

description: 30 minutes, nutrient medium

value: spores transferred to nutrient medium for 30 minutes


title: ZMYND11 KO_2h_Rep_2

data_processing:
bcl2fastq/2.15 was used to demultiplex the sequence run from a illumina HiSeq 2500  run
Alignment and Ht-seq count analysis was performed using STAR/2.5.2b
Genome_build: mm9
Supplementary_files_format_and_content: Ht-Seq Counts

growth_protocol: NIH3T3 were grown in Dulbucco’s minimal essential medium (DMEM) containing 10% donor bovine serum at 37°C.

extract_protocol:
RNA from MEFs was extracted using TRIzol regent (Invitrogen) according to manufacturer’s protocol.
Library preparation including ligating barcode was conducted using a Neoprep library prep station from illumina. Fragments were selected ranging from 250 to 450 bp and subjected to paired-end sequencing on a HiSeq2000 (Illumina).

treatment_protocol: WT NIH3T3 and ZMYND11 crispr KO NIH3T3 were treated with mouse recombinant IFNβ (100 units/ml, PBL Interferon Source) for 2h.

value: ZMYND11 KO

tag: agent

value: IFNB

value: Swiss albino


title: AD3

description: 10 minutes, nutrient medium

tag: strain

value: spores transferred to nutrient medium for 10 minutes


title: WT_2h_Rep_2


title: WT_naive_0h_Rep_1


title: embryo11-12h_E1_1_A11

extract_protocol:
For RNA extraction, tubes were thawed on ice, supplemented with 350 µL of 100% Ethanol before homogenizing again with the same parameters. We then used the Direct-zol™ RNA Miniprep R2056 Kit, with the following modifications: we did not perform DNAse I treatment, we added another 2 min centrifugation into an empty column after the RNA Wash step, finally elution was performed by adding 8 µL of RNAse-free water to the column, incubation at room temperature for 2 min and then centrifugation for 2 min. RNA was transferred to a low-binding 96 well plate and stored at -80°C.
RNA quantity was assessed using picogreen (Invitrogen P11496). Samples were then grouped according to their concentration in 96-well plates, and diluted to a final concentration determined by the lowest sample concentration on the plate. RNA was then used for gene expression profiling using BRB-seq. In short, the BRB-seq protocol starts with oligo-dT barcoding, without TSO for the first-strand synthesis (reverse transcription), performed on each sample separately. Then all samples are pooled together, after which the second-strand is synthesized using DNA PolII Nick translation. The sequencing library is then prepared using cDNA augmented by an in-house produced Tn5 transposase preloaded with the same adapters (Tn5-B/B), and further enriched by limited-cycle PCR with Illumina compatible adapters. Libraries are then size-selected (200 - 1000 bp), profiled using High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-474), and measured using Qubit dsDNA HS Assay Kit (Invitrogen, #Q32851).

value: 11-12 hours

tag: tissue


title: embryo11-12h_E1_1_A1

value: whole embryo


title: AR3

description: 10 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 10 minutes


title: AR1

description: 0 minutes,nutrient medium+ rapamycin

value: spores transferred to nutrient medium with rapamycin for 0 minutes


title: AD1

description: 0 minutes, nutrient medium

value: spores transferred to nutrient medium for 0 minutes


title: embryo11-12h_E1_1_A6


title: embryo11-12h_E1_2_E5


title: embryo11-12h_E1_2_F6


title: AD6

description: 60 minutes,nutrient medium

value: spores transferred to nutrient medium for 60 minutes


title: WT_0h_Rep_2


title: WT_2h_Rep_1


title: embryo11-12h_E1_1_C7


title: ZMYND11 KO_0h_Rep_2


title: embryo11-12h_E1_1_D6


title: embryo11-12h_E1_1_B5


title: embryo11-12h_E1_1_A5


title: WT_0h_Rep_1


title: TICs, ATRA and SAHA treated

city: Los Angeles

first: Keigo

last: Machida

state: CA

address: 2011 Zonal Ave., HMR503C

department: Molecular Microbiology and Immunology

institute: University of Southern California

description: TICs treated with ATRA and SAHA

data_processing:
Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping them to the mouse genome (mm10) with SHRiMP2.2.3 ( http://compbio.cs.toronto.edu/shrimp/ ).
Then used cufflinks2.0.2 (cuffdiff2 - Running Cuffdiff) to perform differential expression analysis with an FDR cutoff of 0.05 (95% confidence interval).
A Perl script was used after differential expression analysis to make the results files more human readable.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Mouse liver tumor-initiating stem-like cells (TICs)

growth_protocol: Mouse TICs were isolated from mouse liver tumors and cultured in DMEM/F12 medium supplemented with 10% FBS, Glutamine, NEAA, mouse EGF, nucleosides, dexamethasone and penicillin/streptomycin.

extract_protocol:
Total RNA for RNA sequencing was extracted using RNeasy Plus Mini Kit (Qiagen), DNase I treatment and rRNA depletion with Tibozero technology were performed before RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse TICs were treated with 5ug/ml of ATRA, 0.5ug/ml of SAHA, or combination of ATRA and SAHA for 16 hours.

value: liver


title: embryo11-12h_E1_1_A7


title: embryo11-12h_E1_1_A4


title: TICs, SAHA treated

description: TICs treated with 0.5ug/ml of SAHA


title: embryo11-12h_E1_1_C9


title: TICs, ATRA treated

description: TICs treated with 5ug/ml of ATRA


title: ZMYND11 KO_2h_Rep_1


title: embryo11-12h_E1_1_D1


title: AS

description: purified spores

value: purified spores


title: TICs, Control

description: TICs treated with vehicle control


title: embryo8-9h_E3_E12

value: 8-9 hours


title: ZMYND11 KO_0h_Rep_1


title: 19619 BrKo_ GFP-negativ

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
3098
norm_gene_counts_GFP

data_processing:
CASAVA v1.82
STARaligner
DESeq2

source_name: brain

extract_protocol:
Nugen Ovation SoLo
Qiagen miRNeasy

tag: population

value: microglia


title: 19619 BrKo_ GFP-positiv

description:
3099
norm_gene_counts_GFP

value: monocytes


title: 18889 BrKo_ GFP-positiv

description:
3093
norm_gene_counts_GFP


title: embryo8-9h_E3_D7

first: Jialin

address: biozentrum, Spitalstrasse 41

institute: University of Basel


title: 18889 BrKo_ GFP-negativ

description:
3092
norm_gene_counts_GFP


title: 5xpool BrKo_ GFP-positiv

description:
2639
norm_gene_counts_GFP


title: embryo8-9h_E3_B3


title: embryo8-9h_E3_H1


title: embryo8-9h_E2_A6


title: 5xpool BrKo_ GFP-negativ

description:
2638
norm_gene_counts_GFP


title: embryo8-9h_E2_D4


title: 18774+18772 BrKo_ GFP-positiv

description:
2637
norm_gene_counts_GFP


title: 18774+18772 BrKo_ GFP-negativ

description:
2636
norm_gene_counts_GFP


title: embryo8-9h_E2_F2


title: embryo8-9h_E2_H9


title: embryo8-9h_E2_B2


title: embryo8-9h_E2_E4


title: embryo8-9h_E2_E7


title: embryo8-9h_E2_C10


title: embryo8-9h_E2_H12


title: G4-1

city: Seoul

first: Sang Yean

last: Kim

state: Select

address: 222 BANPO-DAERO SEOCHO-GU, SEOUL

country: South Korea

institute: The Catholic university of korea

description: sample 21

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenPlex 3.0.

source_name: Human pericardial fluid

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment, The quality of total RNA was analyzed with the RNA StdSens Chips on the Experion system.

tag: cytology

value: unknown

tag: pathology


title: G4-2

description: sample 22


title: G1-4

description: sample 4

value: positive

value: cancer


title: G2-4

description: sample 13

value: negative


title: G4-3

description: sample 23


title: embryo8-9h_E2_G5


title: G3-1

description: sample 15

value: non-cancer


title: SK-NL-SETDB1_SETDB1 OE_2

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: melanoma metastasis

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: expression

value: SETDB1 overexpressing


title: G2-5

description: sample 14


title: CR1 Empty Vector Control Replicate 3

description:
7963862066_K_Grn.idat
Replicate 3
CR1 Vector Control 3

value: CRISPR-Cas9 Mutated

value: Empty Vector


title: G3-3

description: sample 18


title: G1-5

description: sample 5


title: G2-3

description: sample 12


title: G3-2

description: sample 17


title: G2-2

description: sample 9


title: embryo8-9h_E2_A10

value: whole embryo


title: embryo8-9h_E1_2_F8


title: embryo8-9h_E1_2_G7


title: embryo8-9h_E1_2_H12


title: MSC060616-GFP P5

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

source_name: human mesenchymal stroma/stem-like cells

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

tag: cell type

value: mesenchymal stroma/stem-like cells


title: embryo8-9h_E1_2_H9


title: embryo8-9h_E1_2_G5


title: embryo8-9h_E1_2_H4


title: embryo8-9h_E1_2_E1


title: embryo8-9h_E1_2_E9


title: MCF10A-cherry P147

source_name: human MCF10A-cherry neoplastic breast epithelial cell line

value: neoplastic breast epithelial cell line


title: embryo8-9h_E1_2_H10


title: G1-6

description: sample 6


title: G3-5

description: sample 20


title: G1-3

description: sample 3


title: G1-2

description: sample 2


title: embryo8-9h_E1_1_C5


title: SK-NL-SETDB1_empty vector_2

value: empty vector


title: G1-1

description: sample 1


title: non treat, biological rep3

first: Mi Ran

last: Yun

address: 50-1 Yonsei-Ro Seodaemun-Gu

department: Yonsei Cancer Research Institute

institute: JE-UK Laboratory of Molecular Cancer Therapeutics

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: H3122 lung cancer cell line

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit


title: MCF10A-hyb1 P3

source_name: MCF10A/MSC-derived hybrid cells

value: MCF10A/MSC-derived hybrid cells


title: SK-NL-SETDB1_SETDB1 OE_3


title: SK-NL-SETDB1_SETDB1 OE_1


title: embryo8-9h_E1_1_A3


title: G3-4

description: sample 19


title: Crizotinib resistance cell, biological rep2

value: Crizotinib


title: G2-1

description: sample 7


title: HT144_HC/KA-SETDB1 OE_3

value: mutant HC/KA-SETDB1 overexpressing


title: HT144_HC/KA-SETDB1 OE_1


title: HT144_SETDB1 OE_1


title: SK-NL-SETDB1_empty vector_1


title: embryo8-9h_E1_1_C4

value: 8-9 hours


title: Crizotinib resistance cell, biological rep1


title: HT144_HC/KA-SETDB1 OE_2


title: embryo8-9h_E3_F8


title: HT144_empty vector_2


title: embryo8-9h_E1_1_C11


title: embryo8-9h_E1_1_B9


title: HT144_SETDB1 OE_2


title: embryo8-9h_E1_1_B8


title: embryo8-9h_E1_1_C8


title: embryo8-9h_E1_1_A12


title: MCF10A-hyb2


title: embryo8-9h_E1_1_C3


title: embryo8-9h_E1_1_D7


title: embryo8-9h_E1_1_D5


title: embryo5-6h_E3_F12

value: 5-6 hours


title: HT144_empty vector_1


title: Human PAX8 1

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

description: Gene expression data from human pancreatic islets isolated from healthy donors

hyb_protocol: Following fragmentation, 3.8 µg of single-stranded cDNA were hybridized for 16 hr at 45ºC on GeneChip® Human Gene 2,0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

source_name: Human PAX8 1 pancreatic islets from healthy donor

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2ng total RNA Labeling Protocol (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression ArraysWT Pico Reagent Kit, ©2015 Affymetrix Inc.)

growth_protocol: Pancreatic iselts from healthy donors were isolated, cultured and processed

extract_protocol: Total RNA was extracted using the RNAeasy plus micro kit (Qiagen) following the instructions of the manufacturer.

treatment_protocol: Islet preparations were washed, handpicked and subsequently maintained in CMRL-1066 (Gibco) containing 5.6 mM glucose supplemented with 10% FCS, 100 Units/ml penicillin, 100 μg/ml streptomycin and 100 μg/ml gentamycin. At 16 hours upon reception islets  were invected with a control P SIN Dual-GFP lentiviral vector. Islets were processed for RNA exptraction at 96 hours post infection.

value: Human pancreatic islets

tag: lentivirus

value: over-expression of the PAX8 gene


title: embryo5-6h_E3_D4


title: EMF exposed, biological rep1

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: U-87 MG EMF exposed control cells

hyb_protocol: labeled samples were hybridized to Human Gene 2.0  ST Array (Affymetrix) using standard protocol

scan_protocol: The arrays were scanned on a GCS3000 7G scanner using standard Affymetrix protocols

data_processing: The CEL files were converted to CHP files using RMA in Expression Console 3.0 and used for statistical analysis (ANOVAp<0.05) in Transcriptome Analysis Console 3.0

source_name: U-87 MG EMF exposed cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: U-87 MG cells were plated at a density of 4x10^5 cells/100-mm dish in Minimum Essential Medium with Earle’s salts and non-essential amino acids (Gibco/Life Technologies, Grand Island, NY) containing 10% fetal bovine serum (FBS) (Atlanta Biologicals, Norcross, GA) and 1mM sodium pyruvate (Gibco) in a humidified 5% CO2 incubator at 37°C.

extract_protocol: total RNA was isolated using RNEasy protocol with an on column DNase step. The RNA was checked for quality using a nanodrop and a bioanalyzer nanochip (Agilent).

treatment_protocol: 24 h after seeding, the plates were randomized to the treatment culture box inside the Faraday chamber and exposed continuously for 54 h to  RGFIELDS™ targeting four specific molecules [hsa-miRNA-381; mutated alpha-kinase 2 gene; HSP70 (70 kDa heat shock protein); CHI3L1 (chitinase-3-like protein 1)], or to the control culture box outside the Faraday chamber, to serve as the unexposed controls.  The culture boxes contained a continuous supply of 5% CO2/95% air mixture at 37°C.

value: U-87 MG

value: glioblastoma cells


title: embryo5-6h_E3_G3

city: Basel

source_name: single embryo


title: embryo5-6h_E3_B1


title: Crizotinib resistance cell, biological rep3


title: HT144_empty vector_3


title: non treat, biological rep2


title: unexposed, biological rep1

description: U-87 MG unexposed control cells

source_name: U-87 MG unexposed control cells


title: Human Control3

source_name: Human Control3 pancreatic islets from healthy donor

value: control


title: Human Control1

source_name: Human Control1 pancreatic islets from healthy donor


title: EMF exposed, biological rep2

description: U-87 MG EMF exposed control cells


title: embryo5-6h_E3_E4


title: embryo5-6h_E3_H10


title: Jingpo from Huyu, Ruili, Yunnan, China X1 rep 2

type: genomic

city: Kunming

first: Ya-ping

last: Zhang

state: Yunnan

address: 32 Jiaochang Donglu

department: State Key Laboratory of Genetic Resources and Evolution

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

description:
JYHRX1_2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48oC, single-base extension and allele-specific staining was performed according to the manufacturer's protocols.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 50-55 min at 0.68 bar and scanned on iScan system.

data_processing:
Genomic DNA extracted from whole blood was genotyped using Infinium Human OmniZhongHua-8 Genotyping BeadChips (Illumina).
1. kizwangwz-geo_matrix.xy.txt.gz: the genotype matrix file for chromosome X and Y.   2. kizwangwz-geo_matrix.txt.gz: the genotype matrix file for autosomal chromosomes.
Genotype: AA,AB,BB,or NC (no call)

label: Cy3 and Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37oC using multi-sample amplification mixs 1 and 2 (MA1 and MA2) and multi-sample amplification master mix (MSM). After incubation the amplified DNA was fragmented with fragmentation solution (FMS), precipitated with precipitation solution (PM1) and isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAmp DNA Blood Mini Kit (Qiagen) according to the manufacturer’s protocols.

tag: gender

value: Male

tag: ethnic group

value: Jingpo

tag: location

value: Huyu, Ruili, Yunnan, China


title: Jingpo from Huyu, Ruili, Yunnan, China Y1

description:
JYHRY1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Female


title: Jingpo from Huyu, Ruili, Yunnan, China SC2

description:
JYHSC2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China S1

description:
JYHRS1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China W2

description:
JYHRW2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China R1

description:
JYHRR1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China L2

description:
JYHRL2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China V1

description:
JYHRV1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China X1 rep 1

description:
JYHRX1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China Q2

description:
JYHRQ2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China M3

description:
JYHRM3
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China SB2

description:
JYHSB2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China SA2

description:
JYHSA2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo5-6h_E3_D5

value: whole embryo


title: unexposed, biological rep2

description: U-87 MG unexposed control cells

tag: cell line


title: Human PAX8 2

source_name: Human PAX8 2 pancreatic islets from healthy donor


title: embryo5-6h_E3_G7


title: embryo5-6h_E3_A2


title: embryo5-6h_E3_B9


title: Human Control2

source_name: Human Control2 pancreatic islets from healthy donor


title: BT474 sensitive, non-treated, n1

city: Madrid

first: Juan

last: Madoz-Gúrpide

state: Madrid

address: Avda. Reyes Católicos, 2

department: Anatomical Pathology

institute: Health Research Institute Fundación Jiménez Díaz

hyb_protocol: Hybridized to Human Exon 1.0 ST Array for 16h at 45ºC in a GeneChip Hybridization Oven 640

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Raw data was normalized by the RMA method using the oligo package (available at Bioconductor). Probes were mapped to gene ids using the hugene20sttranscriptcluster.db package (available at Bioconductor). The normalized expression value of multiple probes mapped to the same gene was merged taken the average value.

source_name: breast cancer cell line BT-474

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: BT-474 cells were maintained in DMEM-F12 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mmol/L glutamine, and 1% penicillin G-streptomycin.

extract_protocol: RNeasy mini Kit (Qiagen)

treatment_protocol: The trastuzumab-conditioned BT-474.R cell lines were established by culturing the BT-474 cell line in the appropriate media supplemented with 15 μg/ml of recombinant humanized monoclonal HER2 antibody, trastuzumab (Herceptin, Genentech, USA). Trastuzumab was dissolved in sterile water at a stock concentration of 20 mg/ml. Resistant populations were obtained for the four cell lines through lifetime exposure to the drug for a minimum of 8 months.


title: BT474 sensitive, trastuzumab-treated, n1


title: Human PAX8 3

source_name: Human PAX8 3 pancreatic islets from healthy donor


title: non treat, biological rep1


title: EMF exposed, biological rep3

description: U-87 MG EMF exposed control cells


title: embryo5-6h_E2_E12


title: embryo5-6h_E3_G2


title: embryo5-6h_E3_D6


title: Jingpo from Huyu, Ruili, Yunnan, China H2

description:
JYHRH2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China I1

description:
JYHRI1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China J1

description:
JYHRJ1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BT474 sensitive, trastuzumab-treated, n2


title: Jingpo from Huyu, Ruili, Yunnan, China G2

description:
JYHRG2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Yebawgyi, Thandwe, Rakhine, Myanmar 854

description:
RRY854
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Rakhine

value: Yebawgyi, Thandwe, Rakhine, Myanmar


title: Jingpo from Huyu, Ruili, Yunnan, China A2

description:
JYHRA2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China B1

description:
JYHRB1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Yebawgyi, Thandwe, Rakhine, Myanmar 853

description:
RRY853
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China E1

description:
JYHRE1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Jingpo from Huyu, Ruili, Yunnan, China C2

description:
JYHRC2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).