title: at-endosperm-H3_replicate_2_ler_x_col_osd1

description: Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  osd1 INT (male)

data_processing:
PHE1::PHE1-GFP ChIP: Reads were aligned to the Arabidopsis (TAIR10) genome using Bowtie version 1.2.2, allowing 2 mismatches (-v 2). Only uniquely mapped reads were kept. ChIP-seq peaks were called using MACS2 version 2.1.1, with its default settings. Input samples served as control for their corresponding GFP ChIP sample. Each biological replicate was handled individually, and only the overlapping peak regions between the two replicates were considered for further analysis,
ChIP-Seq of endosperm data: Reads were treated as single-ended. Reads passing a quality control and trimmed to 100-bp long were pooled together replicate-wise and mapped to the to the A. thaliana (TAIR10) genome using Bowtie allowing for up to two mismatches. Parental-of-origin alleles were identified by mapping the reads to the TAIR10 for Col and to the Ler-0 genome and not allowing for mismatches. Only reads aligning exclusively to one of the parental genomes were considered as parental specific. Genomic positions in Ler specific reads were converted to TAIR10 genomic coordinates for further analysis using the liftOver tool from UCSC. Reads that changed more than 10% were removed. Mapped reads were deduplicated and extended to the estimated average length of the genomic fragments (270 bp), coverage was estimated and normalized to 10 millions of reads. ChIP signals were normalized with H3 ChIP by taking the log2 ratio in 50-bp bins across the genome. Enriched regions in any particular histone mark were defined by calculating the log2 ratios in 150-bp bins. These data were standardized and normalized for comparative purposes across samples with a Z score transformation applying a cutoff of z ≥ 1. Enriched regions consisting of bins with low H3 coverage (≤ 1st quartile) and/or situated >150 bp away from another enriched region were not considered.
Genome_build: TAIR10
Supplementary_files_format_and_content: ChIP_Seq of GFP factor: bed files representing peak coordinates, as called by MACS. Format:  <chromosome><peak_start><peak_end><peak_id>
Supplementary_files_format_and_content: ChIP-seq of endosperm data: BedGraph files representing average values of Read per Ten Million Mapped reads for each 50 bp across the genome. Format:  <chromosme><bin_start><bin_end><read_per_ten_million>

source_name: AT F1-Endosperm Landsberg x Columbia

extract_protocol:
INTACT-purified endosperm nuclei from 600-800 mg siliques were cross-linked 8 min with 1% formaldehyde and sonicated in 100 μl of NLB (Nuclei Lysis Buffer, 50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, supplemented with Complete protease inhibitors) using a Bioruptor (Diagenode). 900 μl of ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, containing Complete protease inhibitors (Roche)) was added and chromatin was divided in different aliquots for an overnight incubation with antibodies. The following antibodies were used in this study: anti-Histone H3 (Sigma, #H9289,), anti-H3K27me3 (Millipore, #07-449). Antibodies IP were performed using Dynabeads (Invitrogen). DNA elution, de-crosslinking and purification steps were done using the IPure kit (Diagenode).
ChIP-seq libraries were generated using the Microplex Library Preparation kit (Diagenode) following the manufacturer's protocol using 1 ng of starting material.

treatment_protocol: Material for Ler x Col-osd1 cross was generated by pollinating pi/- mutants with pollen of Col-0 INT osd1-plants.

tag: genotype/variation

value: Ler x Col-osd1

value: endosperm

tag: chip antibody

value: anti-Histone H3 (Sigma, #H9289)


title: Coho smolt Brain_1623 [56095]

status: Public on Dec 03 2019

type: RNA

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description:
Sample array position within slide:
Array3Onkism0809_B_10167
raw data files:
Onkism0809_B_10167.txt
Onkism0809_B_10167_ref.txt
sample name in processed data file:
56095
*ref.txt file is the raw data for channel 2 (pooled reference.

hyb_protocol: Gene expression was quantified using 44K cGRASP salmonid microarrays (Koop et al., 2008) for each of the four tissues. Fragmented sample and reference cRNA (dye coupled aRNA) in GEx Hybridization HI-RPM buffer (Agilent) were hybridized to microarray slides using aHS4800 Pro Hybridization Station (TecanTrading AG), which automatically washed, hybridized, denatured, and dried the slides. To reduce technical variance, hybridizations were performed by a single technician in batches of up to 48 samples during a two-week period.

scan_protocol: Slides were read using a LS Reloaded scanner (TecanTrading AG) and Array- Pro Analyzer software. Images were quantified using ImaGene software (BioDiscovery) with spots being automatically flagged if both dye wavelengths were empty, poor, or negative and manually flagged for reasons such as filaments, blobs, or smears.

data_processing:
Low quality slides (>50% missing spots or spatial problems) and spots (<2 standard deviations from the mean background at both dye wavelengths) were removed using BASE software (Lund University). Local background correction using background mean and a lowess normalization algorithm were also applied.
The file processed_data_brain_withallcontrols.txt includes normalized log2 background-subtracted intensity ratio (each fish/reference) with 'flagged' spots or poor signals removed for all probes including controls. Sample data tables do not include control probes.

label: Alexa 555

molecule: total RNA

organism: Oncorhynchus kisutch

source_name: brain

label_protocol: RNA extracts were amplified for microarray hybridizations using Amino Allyl MessageAmpª II-96 kits (Ambion). Amplified RNA extracts (5?g, aRNA) were labelled with Alexa dyes using Indirect Labelling kits (Invitrogen). Dye coupling reactions were performed using all aRNA samples with Alexa 555 dye and the reference aRNA (a pool of all samples for a tissue) with Alexa 647.

extract_protocol: RNA was extracted from four tissues separately: brain, gill, muscle, and liver. Tissues (10mg) were homogenized in TRI reagent (Ambion) using stainless steel beads on a MM301 mixer mill (Retsch Inc.). Aqueous layer homogenate aliquots (100?L) were transferred to three U-bottom 96 well plates. RNA was extracted from the homogenates using the ÔNo-Spin ProcedureÕ of MagMAX-96 for Microarrays Total RNA Isolation kits (Ambion) and a Biomek NXP automation workstation (Beckman- Coulter). RNA yield and purity were measured by spectrophotometry (A?260 value or A?260/A?280 ratio). RNA extracts were stored in a ?80¡C freezer.

tag: FISH #

tag: fw/sw

value: FW

tag: year

tag: season

tag: origin

value: Hatchery

tag: fork length (cm)

tag: total mass (g)

tag: Sex

value: F

tag: latitude

tag: longitude

value: chehalis

value: Fraser

label: Alexa 647

source_name: brain from all samples in the series

tag: sample type

value: Pooled cRNA reference


title: 200687170029_R03C01

type: genomic

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

country: USA

institute: UCLA

description: colon mucosa

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
Data from 450k and EPIC IDAT files were read in separately with RnBeads and combined, only keeping the probes shared by the two platforms.  Probes were filtered to remove those outside CpG contexts, in SNP, on the sex chromosomes, if they missing values, or if their standard deviation was below 0.005, indicating low variability.  The greedy cut algorithm was used to remove probes with poor detection score p-values.  After filtering of probes, data were normalized using BMIQ with the ENMix oob background correction method.
BMIQ and ENMix oob normalized beta values

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using standard phenol-chloroform extraction with ethanol precipitation

tag: cell type

value: mucosa

tag: age

value: female

tag: batch


title: HMZ008_0.05C_5DAT_rep1

type: SRA

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2 with "-G tair10_ensembl.gtf".
Genome_build: TAIR10
Supplementary_files_format_and_content: The processed file was generated using featureCounts with parameter "-p -t exon -g gene_id -a tair10_ensembl.gtf".

organism: Arabidopsis thaliana

source_name: 5 DAG seedlings treated for 5 days mock

growth_protocol: Wild type Arabidopsis thaliana Col-0  surface sterilized seeds were planted on 1/2-strength Murashige & Skoog medium (0.5MS) with 0.7% (w/v) agar and 1.5% (w/v) sucrose, and were vernalized at 4oC in dark for 2 days. Seedlings were grown under sterile conditions with 200 µmol photons m-2sec-1 light, 21 ± 2 oC, at a 16hr light/8hr dark cycle. Five days after germination, Arabidopsis seedlings were transferred to fresh 0.5 MS medium.

extract_protocol: For experiments with GMVs, plants grown on 0.5 MS and 0.05 MS were harvested at 5 DAT. For experiments with DA, plants were harvested at 48 hours after the seedlings were transferred. RNA was extracted by  Plant RNeasy Kit (Qiagen) and the integrity was monitored using the RNA Nano 6000 Assay of the Agilent BioAnalyzer 2100 system (Agilent). RNA purity and concentration was checked using a Nanodrop ND-1000 spectrophotometer.

treatment_protocol: The GMV treatment: One day before transferring seedlings, Bacillus amyloliquefaciens GB03 was cultured in liquid LB medium at 28 oC overnight. Shortly after 5 DAG seedlings were transferred to new growth medium, 20µL of GB03 suspension culture or double distilled water (DDW) was applied to the non-plant side of tri-partite Petri dish plates, containing 0.5 MS or 0.05 MS medium, with 0.7% (w/v) agar and 1.5% (w/v) sucrose. For Diacetyl treatment:  7 DAG seedlings were transferred to Petri dish plates, containing 0.5 MS medium, with 0.7% (w/v) agar and 1.5% with and without 200µM Diacetyl for mock and treatment, respectively.

tag: tissue

value: seedlings

tag: time point

value: 5 day

tag: agent

value: mock

tag: cultivar


title: 200687170029_R01C01

description: duodenum spheroid

source_name: duodenum

value: spheroid


title: Coho smolt Brain_1622 [56212]

description:
Sample array position within slide:
Array1Onkism0809_B_10170
raw data files:
Onkism0809_B_10170.txt
Onkism0809_B_10170_ref.txt
sample name in processed data file:
56212
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fw/sw


title: at-endosperm-H3k27me3_replicate_2_ler_x_col_osd1

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

library_source: genomic

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

tag: genotype/variation

tag: chip antibody

value: anti-H3K27me3 (Millipore, #07-449)


title: 200687170029_R02C01

description: colon crypt

value: crypt


title: Coho smolt Brain_1684 [56067]

description:
Sample array position within slide:
Array4Onkism0809_B_10105
raw data files:
Onkism0809_B_10105.txt
Onkism0809_B_10105_ref.txt
sample name in processed data file:
56067
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year

tag: season

tag: origin

tag: fork length (cm)

value: U

value: puntledge

value: ECVI


title: 200687170033_R06C02

description: colon crypt

tag: Sex


title: EPI3G1

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.1 (a wrapper for Cutadapt 1.8.1 with parameters  -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCh38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Counts were produced using SeqMonk 0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Separated Value file containing Counts Per Million reads. Rows are genes (rownames are Gene Symbols) and columns are cells.

source_name: engineered epicardial cell

extract_protocol:
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.

value: hPSC-derived epicardium

tag: es line


title: Coho smolt Brain_1624 [56039]

description:
Sample array position within slide:
Array4Onkism0809_B_10139
raw data files:
Onkism0809_B_10139.txt
Onkism0809_B_10139_ref.txt
sample name in processed data file:
56039
*ref.txt file is the raw data for channel 2 (pooled reference.

value: FW

value: Hatchery

tag: total mass (g)

tag: latitude

tag: longitude

tag: sample type


title: EPI3F9

tag: cell type


title: Coho smolt Brain_1619 [56203]

description:
Sample array position within slide:
Array1Onkism0809_B_10185
raw data files:
Onkism0809_B_10185.txt
Onkism0809_B_10185_ref.txt
sample name in processed data file:
56203
*ref.txt file is the raw data for channel 2 (pooled reference.

value: M

value: chehalis


title: EPI3F6


title: at-endosperm-input_replicate_2_ler_x_col_osd1

value: Ler x Col-osd1

tag: tissue

value: endosperm

value: none (input)


title: at-endosperm-input_replicate_1_ler_x_col_osd1


title: genomic DNA from decidual tissue 5

first: Li

last: Pi

address: Xietu Road

institute: Shanghai Institute of Planned Parenthood Research

description: control 2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 array Beadchip using standard Illumina protocol

data_processing: All data were processed via Beta Mixture Quantile dilation. Linear models were developed to calculate P-values using the Limma package of the R software (Smyth 2005)

source_name: control decidual tissue 2

extract_protocol: DNA was extracted from the decidual tissues using the DNeasy Blood and Tissue Kit (TransGen, China) after the samples were digested via proteinase K and treated with Rnase

tag: gender

value: female

value: decidual tissue


title: Coho smolt Brain_1621 [56143]

description:
Sample array position within slide:
Array2Onkism0809_B_10184
raw data files:
Onkism0809_B_10184.txt
Onkism0809_B_10184_ref.txt
sample name in processed data file:
56143
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: Fraser

value: Pooled cRNA reference


title: EPI3F8


title: 200687170033_R05C02

description: duodenum mucosa

value: mucosa

tag: age

tag: batch


title: EPI3F7


title: at-endosperm-H3k27me3_replicate_1_ler_x_col_osd1

tag: genotype/variation

tag: chip antibody

value: anti-H3K27me3 (Millipore, #07-449)


title: silique.input.wt_rep2

description: Arabidopsis thaliana F1-silique of  PHE1::PHE1-GFP

source_name: AT F1-Silique Columbia

extract_protocol:
Crosslinking of plant material was done by collecting 600 mg of 2DAP PHE1::PHE1-GFP siliques, and vacuum infiltrating them with a 1% formaldehyde solution in PBS. The vacuum infiltration was done for two periods of 15 min, with a vacuum release between each period. The crosslinking was then stopped by adding 0.125 mM glycine in PBS and performing a vacuum infiltration for a total of 15 min, with a vacuum release each 5 min. The material was then ground in liquid nitrogen, resuspended in 5mL Honda buffer (Moreno-Romero et al., 2017), and incubated for 15 min with gentle rotation. This mixture was filtered twice through Miracloth and one time through a CellTrics filter (30 µm), after which a centrifugation for 5 min, at 4°C and 1,500 g was performed. The nuclei pellet was then resuspended in 100 µL of nuclei lysis buffer(Moreno-Romero et al., 2017), and the ChIP protocol was continued as described before(Moreno-Romero et al., 2017). GFP Tag Antibody (A-11120, Thermo Fisher Scientific) was used in this ChIP.
Libraries were prepared using the Ovation Ultralow v2 Library System (NuGEN), with a starting material of 1 ng, following the manufacturer’s instructions

treatment_protocol: Plant material was generated by self-pollination of PHE1::PHE1-GFP plants

value: silique


title: Coho smolt Brain_1615 [56199]

description:
Sample array position within slide:
Array1Onkism0809_B_10201
raw data files:
Onkism0809_B_10201.txt
Onkism0809_B_10201_ref.txt
sample name in processed data file:
56199
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

tag: year

tag: season


title: 200687170033_R02C02

description: colon crypt

value: crypt

tag: Sex


title: genomic DNA from decidual tissue 6

description: control 3

source_name: control decidual tissue 3


title: silique.gfp.wt_rep2

value: GFP Tag Antibody (A-11120, Thermo Fisher Scientific)


title: genomic DNA from decidual tissue 4

description: control 1

source_name: control decidual tissue 1


title: Coho smolt Brain_1617 [56112]

description:
Sample array position within slide:
Array3Onkism0809_B_10120
raw data files:
Onkism0809_B_10120.txt
Onkism0809_B_10120_ref.txt
sample name in processed data file:
56112
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

tag: fork length (cm)


title: genomic DNA from decidual tissue 1

description: case 1

source_name: case decidual tissue 1


title: Coho smolt Brain_1547 [56097]

description:
Sample array position within slide:
Array3Onkism0809_B_10139
raw data files:
Onkism0809_B_10139.txt
Onkism0809_B_10139_ref.txt
sample name in processed data file:
56097
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Wild

tag: total mass (g)

value: U

tag: latitude

value: capilano


title: EPI3F3

value: hPSC-derived epicardium

tag: es line


title: 200687170033_R01C02

description: colon mucosa

tag: cell type


title: genomic DNA from decidual tissue 2

description: case 2

source_name: case decidual tissue 2

tag: tissue


title: genomic DNA from decidual tissue 3

description: case 3

source_name: case decidual tissue 3

tag: gender


title: 200687170033_R04C02

description: duodenum crypt


title: 200687170033_R03C02

description: colon mucosa


title: at-endosperm-H3_replicate_1_ler_x_col_osd1

value: anti-Histone H3 (Sigma, #H9289)


title: EPI3F5


title: EPI3F4


title: 200687170033_R05C01

description: colon crypt

value: male


title: Coho smolt Brain_1548 [56035]

description:
Sample array position within slide:
Array4Onkism0809_B_10170
raw data files:
Onkism0809_B_10170.txt
Onkism0809_B_10170_ref.txt
sample name in processed data file:
56035
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: FW

tag: longitude

tag: sample type


title: silique.gfp.wt_rep1

tag: genotype/variation


title: EPI3F11


title: S30_2

city: Beijing

first: guo

last: wenbin

address: No. 20, East Street, Fengtai District, Beijing

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to human whole genome GRCh38 (hg38)  using STAR v2.5.1b
Fagments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.

source_name: skin

extract_protocol:
Total DNA and RNA extraction from skin biopsies were performed using AllPrep DNA/RNA Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin


title: EPI3F12


title: silique.input.wt_rep1

tag: chip antibody

value: none (input)


title: Coho smolt Brain_1544 [56036]

description:
Sample array position within slide:
Array4Onkism0809_B_10169
raw data files:
Onkism0809_B_10169.txt
Onkism0809_B_10169_ref.txt
sample name in processed data file:
56036
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw


title: S30_1


title: Coho smolt Brain_1536 [56093]

description:
Sample array position within slide:
Array3Onkism0809_B_10169
raw data files:
Onkism0809_B_10169.txt
Onkism0809_B_10169_ref.txt
sample name in processed data file:
56093
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year

value: Hatchery


title: EPI3F1


title: Coho smolt Brain_1620 [56231]

description:
Sample array position within slide:
Array1Onkism0809_B_10123
raw data files:
Onkism0809_B_10123.txt
Onkism0809_B_10123_ref.txt
sample name in processed data file:
56231
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

value: F

value: chehalis

value: Fraser


title: 200687170033_R01C01

description: colon mucosa

value: mucosa

tag: age

tag: Sex

value: female

tag: batch


title: Coho smolt Brain_1534 [56168]

description:
Sample array position within slide:
Array2Onkism0809_B_10125
raw data files:
Onkism0809_B_10125.txt
Onkism0809_B_10125_ref.txt
sample name in processed data file:
56168
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

tag: fork length (cm)

tag: total mass (g)

value: Pooled cRNA reference


title: EPI3E9

tag: cell type

tag: es line


title: 200687170033_R06C01

description: duodenum spheroid

value: spheroid


title: EPI3E7


title: 200514090006_R05C02

description: duodenum mucosa


title: EPI3F2


title: 200687170033_R04C01

description: colon crypt

value: crypt


title: EPI3F10


title: 200687170033_R03C01

description: duodenum crypt


title: Coho smolt Brain_1443 [56233]

description:
Sample array position within slide:
Array1Onkism0809_B_10121
raw data files:
Onkism0809_B_10121.txt
Onkism0809_B_10121_ref.txt
sample name in processed data file:
56233
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Wild

value: M

tag: latitude

value: salmon


title: Coho smolt Brain_1528 [56170]

description:
Sample array position within slide:
Array2Onkism0809_B_10123
raw data files:
Onkism0809_B_10123.txt
Onkism0809_B_10123_ref.txt
sample name in processed data file:
56170
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: U

value: capilano


title: Coho smolt Brain_1535 [56230]

description:
Sample array position within slide:
Array1Onkism0809_B_10124
raw data files:
Onkism0809_B_10124.txt
Onkism0809_B_10124_ref.txt
sample name in processed data file:
56230
*ref.txt file is the raw data for channel 2 (pooled reference.

value: FW

tag: longitude


title: Coho smolt Brain_1530 [56140]

description:
Sample array position within slide:
Array2Onkism0809_B_10198
raw data files:
Onkism0809_B_10198.txt
Onkism0809_B_10198_ref.txt
sample name in processed data file:
56140
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: sample type


title: s18_2

tag: tissue

value: skin


title: Coho smolt Brain_1442 [56144]

description:
Sample array position within slide:
Array2Onkism0809_B_10183
raw data files:
Onkism0809_B_10183.txt
Onkism0809_B_10183_ref.txt
sample name in processed data file:
56144
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_1533 [56086]

description:
Sample array position within slide:
Array3Onkism0809_B_10184
raw data files:
Onkism0809_B_10184.txt
Onkism0809_B_10184_ref.txt
sample name in processed data file:
56086
*ref.txt file is the raw data for channel 2 (pooled reference.


title: EPI3E6

value: hPSC-derived epicardium


title: S28RNA_2


title: s18_1


title: 200687170033_R02C01

description: duodenum spheroid


title: S28RNA_1


title: 200514090006_R06C02

description: colon crypt

value: male


title: EPI3E8


title: s24_2


title: s24_1


title: EPI3E4


title: Coho smolt Brain_1440 [56213]

description:
Sample array position within slide:
Array1Onkism0809_B_10169
raw data files:
Onkism0809_B_10169.txt
Onkism0809_B_10169_ref.txt
sample name in processed data file:
56213
*ref.txt file is the raw data for channel 2 (pooled reference.

value: F


title: s17_1


title: 200514090006_R01C02

description: duodenum spheroid


title: EPI3E5


title: 200514090006_R03C02

description: duodenum crypt


title: Coho smolt Brain_1532 [56156]

description:
Sample array position within slide:
Array2Onkism0809_B_10139
raw data files:
Onkism0809_B_10139.txt
Onkism0809_B_10139_ref.txt
sample name in processed data file:
56156
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Hatchery


title: s17_2


title: EPI3E2


title: S16RNA_1


title: 200514090006_R05C01

description: duodenum crypt


title: s15_2


title: 200514090006_R04C01

description: jejunum mucosa

source_name: jejunum


title: EPI3E11


title: Coho smolt Brain_1438 [56214]

description:
Sample array position within slide:
Array1Onkism0809_B_10168
raw data files:
Onkism0809_B_10168.txt
Onkism0809_B_10168_ref.txt
sample name in processed data file:
56214
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Fraser


title: Coho smolt Brain_1441 [56087]

description:
Sample array position within slide:
Array3Onkism0809_B_10183
raw data files:
Onkism0809_B_10183.txt
Onkism0809_B_10183_ref.txt
sample name in processed data file:
56087
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_1437 [56088]

description:
Sample array position within slide:
Array3Onkism0809_B_10180
raw data files:
Onkism0809_B_10180.txt
Onkism0809_B_10180_ref.txt
sample name in processed data file:
56088
*ref.txt file is the raw data for channel 2 (pooled reference.


title: 200514090006_R02C02

description: colon mucosa

value: mucosa


title: EPI3E10


title: 200514090006_R04C02

description: duodenum crypt

value: female


title: EPI3E3


title: 200514090006_R02C01

description: duodenum mucosa


title: s11_2


title: EPI3D9


title: 200514090006_R06C01

description: duodenum mucosa


title: S16RNA_2


title: s6_2


title: s15_1


title: 200514090006_R03C01

description: duodenum spheroid


title: EPI3E12


title: 200514090016_R04C02

description: colon mucosa


title: s11_1


title: 200514090006_R01C01

description: duodenum mucosa


title: EPI3E1


title: Coho smolt Brain_1016 [56216]

description:
Sample array position within slide:
Array1Onkism0809_B_10162
raw data files:
Onkism0809_B_10207.txt
Onkism0809_B_10207_ref.txt
sample name in processed data file:
56216
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW

value: WCVI

value: Pooled cRNA reference


title: 200514090016_R05C02

description: duodenum spheroid

value: spheroid


title: S4RNA_2


title: 200514090016_R06C02

description: colon crypt

value: crypt


title: EPI3D7


title: EPI3D8


title: EPI3D6


title: s6_1


title: Coho smolt Brain_1020 [56239]

description:
Sample array position within slide:
Array1Onkism0809_B_10112
raw data files:
Onkism0809_B_10112.txt
Onkism0809_B_10112_ref.txt
sample name in processed data file:
56239
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Wild

value: North


title: Coho smolt Brain_1436 [56028]

description:
Sample array position within slide:
Array4Onkism0809_B_10185
raw data files:
Onkism0809_B_10185.txt
Onkism0809_B_10185_ref.txt
sample name in processed data file:
56028
*ref.txt file is the raw data for channel 2 (pooled reference.

value: U

value: salmon


title: Coho smolt Brain_1435 [56052]

description:
Sample array position within slide:
Array4Onkism0809_B_10123
raw data files:
Onkism0809_B_10123.txt
Onkism0809_B_10123_ref.txt
sample name in processed data file:
56052
*ref.txt file is the raw data for channel 2 (pooled reference.

value: FW


title: EPI3D5

value: hPSC-derived epicardium


title: Coho smolt Brain_1014 [56119]

description:
Sample array position within slide:
Array3Onkism0809_B_10109
raw data files:
Onkism0809_B_10109.txt
Onkism0809_B_10109_ref.txt
sample name in processed data file:
56119
*ref.txt file is the raw data for channel 2 (pooled reference.

value: M


title: Coho smolt Brain_1015 [56193]

description:
Sample array position within slide:
Array1Onkism0809_B_10211
raw data files:
Onkism0809_B_10211.txt
Onkism0809_B_10211_ref.txt
sample name in processed data file:
56193
*ref.txt file is the raw data for channel 2 (pooled reference.

value: F


title: Coho smolt Brain_1434 [56053]

description:
Sample array position within slide:
Array4Onkism0809_B_10122
raw data files:
Onkism0809_B_10122.txt
Onkism0809_B_10122_ref.txt
sample name in processed data file:
56053
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_1019 [56076]

description:
Sample array position within slide:
Array3Onkism0809_B_10211
raw data files:
Onkism0809_B_10211.txt
Onkism0809_B_10211_ref.txt
sample name in processed data file:
56076
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Columbia


title: Coho smolt Brain_1012 [56063]

description:
Sample array position within slide:
Array4Onkism0809_B_10109
raw data files:
Onkism0809_B_10109.txt
Onkism0809_B_10109_ref.txt
sample name in processed data file:
56063
*ref.txt file is the raw data for channel 2 (pooled reference.


title: 200514090016_R03C02

description: duodenum mucosa


title: EPI3D4


title: S4RNA_1

value: skin


title: EPI3D3


title: 200514090016_R01C02

description: ileum mucosa

source_name: ileum

value: mucosa


title: hKRT_Mi2KDD5_Exp1_RNA_rep2

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) or hg19 (human genome) assembly using the genome mappers Bowtie2 for ATACseq and STAR for RNAseq and ChIPseq.
For RNA-seq, read normalization, RPKM and differential gene expression, were performed using the HOMER scripts analyzeRepeats.pl and getDiffExpression.pl with implementation of DESeq2 through R.
Peak calling for ATAC-seq was perfomed using MACS2 call peaks  with --keep-dup all --nomodel --shift 37 --extsize 73.
Peak calling for ChIP-seq was performed using the Homer findPeaks algorithm.
Genome_build: mm10, hg19

source_name: neonatal foreskin

extract_protocol:
Primary human epidermal keratinocytes were incubated for 6 hours with the infection medium containing lentiviral particles derived from shRNA lentiviral constructs for Mi-2β or control, and then selected for 3-5 days in puromycin.
Trueseq stranded mRNA sample prep kit (Illumina)

tag: cell types

value: keratinocytes

tag: genotype


title: hKRT_Mi2KDD5_Exp1_RNA_rep1


title: EPI3D2


title: Coho smolt Brain_825 [56057]

description:
Sample array position within slide:
Array4Onkism0809_B_10115
raw data files:
Onkism0809_B_10115.txt
Onkism0809_B_10115_ref.txt
sample name in processed data file:
56057
*ref.txt file is the raw data for channel 2 (pooled reference.

source_name: brain

tag: fw/sw

value: SW

tag: year

value: Fraser


title: Coho smolt Brain_826 [56116]

description:
Sample array position within slide:
Array3Onkism0809_B_10112
raw data files:
Onkism0809_B_10112.txt
Onkism0809_B_10112_ref.txt
sample name in processed data file:
56116
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

value: Hatchery

source_name: brain from all samples in the series

value: Pooled cRNA reference


title: 200514090016_R05C01

description: jejunum crypt

value: crypt

tag: age

tag: Sex

value: female


title: EPI3D12


title: 200514090016_R06C01

description: small intestine mucosa

source_name: small intestine

value: male

tag: batch


title: hKRT_CTR_Exp1_RNA_rep1

value: CTR


title: 200514090016_R04C01

description: duodenum crypt


title: EPI3D10


title: Coho smolt Brain_824 [56073]

description:
Sample array position within slide:
Array4Onkism0809_B_10091
raw data files:
Onkism0809_B_10091.txt
Onkism0809_B_10091_ref.txt
sample name in processed data file:
56073
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

tag: fork length (cm)


title: hKRT_Mi2KDD3_Exp1_RNA_rep1


title: hKRT_Mi2KD_cJUN_ChIP_rep1

extract_protocol:
Primary human epidermal keratinocytes were incubated for 6 hours with the infection medium containing lentiviral particles derived from shRNA lentiviral constructs for Mi-2β or control, and then selected for 3-5 days in puromycin.
As detailed in Hu et al. Genes Dev (2016)


title: Coho smolt Brain_811 [56176]

description:
Sample array position within slide:
Array2Onkism0809_B_10114
raw data files:
Onkism0809_B_10114.txt
Onkism0809_B_10114_ref.txt
sample name in processed data file:
56176
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)


title: 200514090016_R03C01

description: duodenum crypt

tag: cell type


title: Coho smolt Brain_797 [56235]

description:
Sample array position within slide:
Array1Onkism0809_B_10116
raw data files:
Onkism0809_B_10116.txt
Onkism0809_B_10116_ref.txt
sample name in processed data file:
56235
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude


title: EPI3D11

tag: es line


title: hKRT_CTR_cJUN_ChIP_rep1


title: EPI3D1


title: 200514090016_R02C02

description: duodenum crypt


title: Coho smolt Brain_786 [56071]

description:
Sample array position within slide:
Array4Onkism0809_B_10093
raw data files:
Onkism0809_B_10093.txt
Onkism0809_B_10093_ref.txt
sample name in processed data file:
56071
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: Wild

tag: longitude


title: 200514090016_R02C01

description: jejunum spheroid

value: spheroid


title: hKRT_Mi2KDD3_Exp1_RNA_rep2


title: Coho smolt Brain_785 [56237]

description:
Sample array position within slide:
Array1Onkism0809_B_10114
raw data files:
Onkism0809_B_10114.txt
Onkism0809_B_10114_ref.txt
sample name in processed data file:
56237
*ref.txt file is the raw data for channel 2 (pooled reference.

value: North

tag: sample type


title: 101178130064_R06C02

description: duodenum spheroid


title: hKRT_Mi2KD_RNApII_ChIP_rep1

tag: cell types


title: hKRT_CTR_Exp1_RNA_rep2

tag: genotype


title: EPI3C8

value: hPSC-derived epicardium


title: hKRT_CTR_RNApII_ChIP_rep1


title: 101178130064_R04C02

description: duodenum crypt


title: Coho smolt Brain_766 [56178]

description:
Sample array position within slide:
Array2Onkism0809_B_10112
raw data files:
Onkism0809_B_10112.txt
Onkism0809_B_10112_ref.txt
sample name in processed data file:
56178
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

value: F


title: EPI3C7


title: 101178130064_R02C02

description: duodenum spheroid


title: hKTR_Mi2KD_H3K4me3_ChIP_rep1


title: Coho smolt Brain_796 [56059]

description:
Sample array position within slide:
Array4Onkism0809_B_10113
raw data files:
Onkism0809_B_10113.txt
Onkism0809_B_10113_ref.txt
sample name in processed data file:
56059
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year


title: hKRT_CTR_H3K4me3_ChIP_rep1


title: 101178130064_R05C01

description: duodenum crypt


title: 101178130064_R01C02

description: duodenum crypt


title: EPI3C4


title: EPI3C5


title: EPI3C9


title: hKRT_CTR_H3K27Ac_ChIP_rep1


title: EPI3C3


title: Coho smolt Brain_666 [56056]

description:
Sample array position within slide:
Array4Onkism0809_B_10116
raw data files:
Onkism0809_B_10116.txt
Onkism0809_B_10116_ref.txt
sample name in processed data file:
56056
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

value: U


title: Coho smolt Brain_576 [56244]

description:
Sample array position within slide:
Array1Onkism0809_B_10107
raw data files:
Onkism0809_B_10107.txt
Onkism0809_B_10107_ref.txt
sample name in processed data file:
56244
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_661 [56253]

description:
Sample array position within slide:
Array1Onkism0809_B_10089
raw data files:
Onkism0809_B_10089.txt
Onkism0809_B_10089_ref.txt
sample name in processed data file:
56253
*ref.txt file is the raw data for channel 2 (pooled reference.

value: M


title: hKTR_Mi2KD_input_rep1


title: hKRT_CTR_input_rep2


title: Coho smolt Brain_579 [56019]

description:
Sample array position within slide:
Array4Onkism0809_B_10211
raw data files:
Onkism0809_B_10211.txt
Onkism0809_B_10211_ref.txt
sample name in processed data file:
56019
*ref.txt file is the raw data for channel 2 (pooled reference.


title: EPI3C2


title: Coho smolt Brain_552 [56018]

description:
Sample array position within slide:
Array4Onkism0809_B_10212
raw data files:
Onkism0809_B_10212.txt
Onkism0809_B_10212_ref.txt
sample name in processed data file:
56018
*ref.txt file is the raw data for channel 2 (pooled reference.


title: EPI3C6


title: Coho smolt Brain_531 [56240]

description:
Sample array position within slide:
Array1Onkism0809_B_10111
raw data files:
Onkism0809_B_10111.txt
Onkism0809_B_10111_ref.txt
sample name in processed data file:
56240
*ref.txt file is the raw data for channel 2 (pooled reference.

value: ECVI


title: EPI3C11


title: EPI3C12


title: hKTR_Mi2KD_H3K27Ac_ChIP_rep1

value: keratinocytes


title: hKRT_CTR_input_rep1


title: EPI3C10


title: hKRT_Mi2_ChIP_rep2

extract_protocol:
Primary human epidermal keratinocytes were isolated from neonatal foreskins. Cells were cultured and expanded under serum-free conditions with keratinocyte growth medium.
As detailed in Hu et al. Genes Dev (2016)


title: EPI3C1


title: HaCaT_Mi2ChIP

source_name: cell line

extract_protocol:
HaCaT cells were cultured in DMEM supplemented with 10% FCS.
As detailed in Schmidl et al. Nat Methods (2015)


title: hKRT_Mi2_ChIP_rep1-2


title: EPI3B9


title: EPI3B8


title: hKRT_Mi2_ChIP_rep1-1


title: 200795790097_K

description: duodenum crypts

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data were read in from IDAT files and probe IDs were converted to nuIDs with lumi.  Intensities were normalized using variance-stabilizing transform, and interarray normalization was done using robust spline regression.  Probes with detection score p-values greater than 0.01 or missing a gene symbol annotation were dropped.  nuIDs were converted to gene symbols, and duplicate probes mapping to the same gene were dropped using collapseRows, with only the probe with the highest mean expression for each gene symbol being kept.
VST and RSN-normalized expression

label: biotin

source_name: duodenum

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was isolated using RNA Clean & Concentrator kit (Zymo Research).

value: crypts

value: Male

tag: age


title: EPI3B7

source_name: engineered epicardial cell


title: Coho smolt Brain_363 [56064]

description:
Sample array position within slide:
Array4Onkism0809_B_10108
raw data files:
Onkism0809_B_10108.txt
Onkism0809_B_10108_ref.txt
sample name in processed data file:
56064
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW

tag: Sex

value: WCVI

value: Oregon


title: 200795790097_J

description: colon crypts

source_name: colon

value: Female


title: Coho smolt Brain_572 [56192]

description:
Sample array position within slide:
Array1Onkism0809_B_10212
raw data files:
Onkism0809_B_10212.txt
Onkism0809_B_10212_ref.txt
sample name in processed data file:
56192
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Hatchery

value: Fraser

value: Pooled cRNA reference


title: Coho smolt Brain_516 [56065]

description:
Sample array position within slide:
Array4Onkism0809_B_10107
raw data files:
Onkism0809_B_10107.txt
Onkism0809_B_10107_ref.txt
sample name in processed data file:
56065
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_365 [56113]

description:
Sample array position within slide:
Array3Onkism0809_B_10115
raw data files:
Onkism0809_B_10115.txt
Onkism0809_B_10115_ref.txt
sample name in processed data file:
56113
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Washington


title: KPTC26 - Tumor Region 2

city: Baltimore

first: Noushin

last: Niknafs

state: MD

address: 3400 N Charles St, Hackerman 220

institute: Johns Hopkins University

hyb_protocol: The Agilent Oligo aCGH/ChIP-on-Chip hybridization kit was used for the hybridization.

scan_protocol: Slides were scanned on the Agilent Micoarray scanner G2505C US83903565, and images were quantified using Agilent Feature Extraction Software.

data_processing: Background subtraction and within array loess normalization were performed using limma package (v3.22.7) in R statistical computing environment (v3.2.3).

organism: Mus musculus

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC26 - region 3

label_protocol: Agilent's Genomic DNA ULS Labeling Kit was used for labeling genomic DNA: Cy5 for all tumor samples; Cy3 for normal kidney gDNA.

growth_protocol: The normal and tumor tissues were harvested and frozen down immediately after the mice were sacrificed.

extract_protocol: Genomic DNA were extracted using DNeasy Blood & Tissue Kit (QIAGEN, Cat No./ID: 69506)

tag: strain

value: K-rasLSL.G12D/+; p53R172H/+; Tgfbr2tm1Hlm; Ptf1a-Cre (KPTC)

value: 171 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPTC26


title: 200795790097_I

description: duodenum crypts


title: KPTC26 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC26 - region 1


title: KPTC24 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC24 - region 2

value: 173 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPTC24


title: EPI3B6

value: hPSC-derived epicardium


title: Coho smolt Brain_358 [56126]

description:
Sample array position within slide:
Array3Onkism0809_B_10094
raw data files:
Onkism0809_B_10094.txt
Onkism0809_B_10094_ref.txt
sample name in processed data file:
56126
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

value: Wild

value: M

value: North


title: Coho smolt Brain_502 [56243]

description:
Sample array position within slide:
Array1Onkism0809_B_10108
raw data files:
Onkism0809_B_10108.txt
Onkism0809_B_10108_ref.txt
sample name in processed data file:
56243
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fork length (cm)


title: KPTC13 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC13 - region 2

value: 134 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPTC13


title: KPTC13 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC13 - region 1


title: Coho smolt Brain_349 [56127]

description:
Sample array position within slide:
Array3Onkism0809_B_10093
raw data files:
Onkism0809_B_10093.txt
Onkism0809_B_10093_ref.txt
sample name in processed data file:
56127
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)

value: F


title: KPTC13 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC13 - region 3


title: 200795790097_H

description: duodenum crypts

tag: cell type

value: crypts


title: Coho smolt Brain_526 [56242]

description:
Sample array position within slide:
Array1Onkism0809_B_10109
raw data files:
Onkism0809_B_10109.txt
Onkism0809_B_10109_ref.txt
sample name in processed data file:
56242
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW

tag: latitude

value: ECVI


title: EPI3B4

tag: es line


title: 200795790097_G

description: duodenum crypts

value: Male


title: EPI3B5


title: EPI3B3


title: KPTC24 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC24 - region 3


title: 200795790097_F

description: colon crypts

value: Female


title: KPTC24 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC24 - region 1


title: EPI3B2


title: 200795790097_E

description: duodenum crypts


title: EPI3B12


title: Coho smolt Brain_334 [56189]

description:
Sample array position within slide:
Array2Onkism0809_B_10092
raw data files:
Onkism0809_B_10092.txt
Onkism0809_B_10092_ref.txt
sample name in processed data file:
56189
*ref.txt file is the raw data for channel 2 (pooled reference.

source_name: brain

tag: FISH #

value: WCVI

source_name: brain from all samples in the series


title: EPI3B11


title: KPTC12 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC12 - region 2

source_name: cells from tumor-free kidney (matched normal tissue) of KPTC12


title: 200795790097_C

description: duodenum crypts

source_name: duodenum


title: Coho smolt Brain_359 [56129]

description:
Sample array position within slide:
Array3Onkism0809_B_10091
raw data files:
Onkism0809_B_10091.txt
Onkism0809_B_10091_ref.txt
sample name in processed data file:
56129
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Hatchery

tag: longitude

value: Pooled cRNA reference


title: Coho smolt Brain_300 [56188]

description:
Sample array position within slide:
Array2Onkism0809_B_10093
raw data files:
Onkism0809_B_10093.txt
Onkism0809_B_10093_ref.txt
sample name in processed data file:
56188
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Washington

tag: sample type


title: KPTC12 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC12 - region 1

value: K-rasLSL.G12D/+; p53R172H/+; Tgfbr2tm1Hlm; Ptf1a-Cre (KPTC)


title: EPI3B10

source_name: engineered epicardial cell


title: 200795790097_B

description: duodenum crypts


title: 200795790097_D

description: colon crypts

source_name: colon


title: Coho smolt Brain_298 [56115]

description:
Sample array position within slide:
Array3Onkism0809_B_10113
raw data files:
Onkism0809_B_10113.txt
Onkism0809_B_10113_ref.txt
sample name in processed data file:
56115
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_319 [56175]

description:
Sample array position within slide:
Array2Onkism0809_B_10115
raw data files:
Onkism0809_B_10115.txt
Onkism0809_B_10115_ref.txt
sample name in processed data file:
56175
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Columbia


title: KPTC12 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC12 - region 3


title: EPI3A9

value: hPSC-derived epicardium


title: 200795790093_L

description: duodenum crypts


title: EPI3B1


title: Coho smolt Brain_101 [56179]

description:
Sample array position within slide:
Array2Onkism0809_B_10111
raw data files:
Onkism0809_B_10111.txt
Onkism0809_B_10111_ref.txt
sample name in processed data file:
56179
*ref.txt file is the raw data for channel 2 (pooled reference.

value: FW

value: Wild

value: U

value: chilliwack


title: 200795790097_A

description: duodenum crypts


title: KPTC9 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC9 - region 3

value: 91 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPTC9


title: KPTC9 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC9 - region 2


title: KPTC11 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC11 - region 3

value: 131 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPTC11


title: 200795790093_K

description: colon crypts

value: crypts


title: EPI3A7


title: KPTC11 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC11 - region 2


title: 200795790093_J

description: duodenum crypts


title: Coho smolt Brain_100 [56117]

description:
Sample array position within slide:
Array3Onkism0809_B_10111
raw data files:
Onkism0809_B_10111.txt
Onkism0809_B_10111_ref.txt
sample name in processed data file:
56117
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_299 [56190]

description:
Sample array position within slide:
Array2Onkism0809_B_10091
raw data files:
Onkism0809_B_10091.txt
Onkism0809_B_10091_ref.txt
sample name in processed data file:
56190
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW

value: M


title: Coho smolt Brain_98 [56062]

description:
Sample array position within slide:
Array4Onkism0809_B_10110
raw data files:
Onkism0809_B_10110.txt
Onkism0809_B_10110_ref.txt
sample name in processed data file:
56062
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_99 [56183]

description:
Sample array position within slide:
Array2Onkism0809_B_10107
raw data files:
Onkism0809_B_10107.txt
Onkism0809_B_10107_ref.txt
sample name in processed data file:
56183
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_260 [56181]

description:
Sample array position within slide:
Array2Onkism0809_B_10109
raw data files:
Onkism0809_B_10109.txt
Onkism0809_B_10109_ref.txt
sample name in processed data file:
56181
*ref.txt file is the raw data for channel 2 (pooled reference.


title: KPC19 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC19 -  region 3

value: 211 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC19


title: EPI3A6


title: 200795790093_I

description: duodenum crypts

value: Male


title: KPTC11 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC11 - region 1


title: KPC19 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC19 -  region 2


title: KPC18 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC18 -  region 3

value: 259 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC18


title: KPTC9 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPTC9 - region 1


title: EPI3A8


title: EPI3A5


title: EPI3A4


title: 200795790093_H

description: duodenum crypts

source_name: duodenum


title: 200795790093_F

description: colon crypts

value: Female


title: 200795790093_G

description: duodenum crypts


title: EPI3A2

source_name: engineered epicardial cell


title: 200795790093_C

description: duodenum crypts


title: EPI3A3


title: 200795790093_A

description: duodenum crypts


title: KPC18 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC18 -  region 2


title: 200795790093_D

description: colon crypts

source_name: colon


title: Coho smolt Brain_39 [56131]

description:
Sample array position within slide:
Array2Onkism0809_B_10212
raw data files:
Onkism0809_B_10212.txt
Onkism0809_B_10212_ref.txt
sample name in processed data file:
56131
*ref.txt file is the raw data for channel 2 (pooled reference.

source_name: brain

value: Hatchery

source_name: brain from all samples in the series

value: Pooled cRNA reference


title: KPC18 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC18 -  region 1


title: Coho smolt Brain_38 [56118]

description:
Sample array position within slide:
Array3Onkism0809_B_10110
raw data files:
Onkism0809_B_10110.txt
Onkism0809_B_10110_ref.txt
sample name in processed data file:
56118
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_34 [56194]

description:
Sample array position within slide:
Array1Onkism0809_B_10210
raw data files:
Onkism0809_B_10210.txt
Onkism0809_B_10210_ref.txt
sample name in processed data file:
56194
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_36 [56077]

description:
Sample array position within slide:
Array3Onkism0809_B_10210
raw data files:
Onkism0809_B_10210.txt
Onkism0809_B_10210_ref.txt
sample name in processed data file:
56077
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_9 [56098]

description:
Sample array position within slide:
Array3Onkism0809_B_10138
raw data files:
Onkism0809_B_10138.txt
Onkism0809_B_10138_ref.txt
sample name in processed data file:
56098
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_31 [56133]

description:
Sample array position within slide:
Array2Onkism0809_B_10210
raw data files:
Onkism0809_B_10210.txt
Onkism0809_B_10210_ref.txt
sample name in processed data file:
56133
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_10 [56080]

description:
Sample array position within slide:
Array3Onkism0809_B_10204
raw data files:
Onkism0809_B_10204.txt
Onkism0809_B_10204_ref.txt
sample name in processed data file:
56080
*ref.txt file is the raw data for channel 2 (pooled reference.


title: EPI3A11


title: KPC9 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC9 -  region 3

value: 125 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC9


title: Coho smolt Brain_8 [56022]

description:
Sample array position within slide:
Array4Onkism0809_B_10206
raw data files:
Onkism0809_B_10206.txt
Onkism0809_B_10206_ref.txt
sample name in processed data file:
56022
*ref.txt file is the raw data for channel 2 (pooled reference.


title: 200795790093_B

description: duodenum crypts


title: EPI3A12

value: hPSC-derived epicardium


title: KPC9 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC9 -  region 1


title: EPI3A10


title: daf-2(-);daf-12(-)-Replicate-2

city: Delhi

first: Arnab

last: Mukhopadhyay

state: Delhi

address: Aruna asaf ali marg

country: India

institute: National Institute of Immunology

data_processing:
Demultiplexing and conversion of BCL file format reads to FASTQ file format was done with Illumina CASAVA v1.8.2 software package
Reads were trimmed off to remove adapter sequence, if any, and to filter out the reads ≤ 15 bp using CLC Genomics Workbech v6.5.1
Quality filtered reads were aligned to the C. elegans annotated reference genome (W230) using CLC Genomics Workbench v6.5.1
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using default parameters. Biological replicates of different samples were compared  with two group comparison as independent measurement (one group of genes are controls and another group of genes as treat) by using the gene RPKM. Significant fold changes (P≤ 0.05, fold change ≥ 2) were selected by applying beta-binomial Baggerley’s test
Supplementary_files_format_and_content: abundance measurement

organism: Caenorhabditis elegans

source_name: mix stage culture

growth_protocol: Wild-type (N2), daf-2 (e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20)mutant worm strains were obtained from Caenorhabditis Genetics Centre (Minneapolis,  MN, USA). Mixed culture of worms were grown on 15-20 OP50 E coli. seeded 150 X 15 mm NGM (Nematode Growth Media)  petri-plates maintained at 20 °C.

extract_protocol:
Worms were grown for mixed culture from different strains on OP50 E coli. seeded 90 mm plates for RNA isolation.  The pellet was forzen in 250 µl TRIzol reagent (Invitrogen part # 15596-026) and kept at -80 °C after washing four times in M9 buffer. Total RNA was isolated as per manufacturer protocol from the frozen pellet
RNA quality was checked on a 2100 Bioanalyzer by using the RNA 6000 Nano Kit (Agilent Technologies, USA). RNA with RNA integrity number (RIN) > 9 was selected for library preparation.  The RNA library was prepared using the TrueSeq RNA SamplePrep V2 kit (Illumina, USA) according to manufacturer-provided specifications.

tag: culture

value: Mix Culture

tag: temperature

value: 20 °C


title: KPC8 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC8 -  region 3

value: 126 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC8


title: KPC 8- Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC8 -  region 2


title: EPI3A1


title: KPC9 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC9 -  region 2


title: daf-2(-);daf-12(-)-Replicate-1

tag: genotype


title: KPC6 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC6 -  region 3

value: 214 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC6


title: S_EV_6

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

institute: Imperial College

description: Mnase digested DNA

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were first trimmed with trimgalore to remove adapters and low quality bases.
The trimmed reads were then mapped to the E.coli K-12 MG1655 genome (GCA_000005845.2) using Bowtie2 (--no-discordant --no-mix). Multimappers were filtered out to retain only reads mapping uniquely.
Coverage tracks were computed using the coverage function in the rtracklayer package for R.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: bigWig

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: Escherichia coli cells were obtained from DSMZ (https://www.dsmz.de/) and grown at 37C in LB medium under constant agitation (180rpm). Expression of HMf histonesin E.coli cells was triggered by Rhamnose induction to a final working concentration of 15mM. The cells were harvested in late exponential and stationary phase, which means 2 hours and 17 hours after induction, respectively.

extract_protocol:
DNA was extracted by phenol chloroform extraction and precipitated with ethanol.
For MNase digestion experiments single-end reads were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: An equal number of bacteria were harvested by centrifugation (4000rpm - 15 minutes - 4C), the supernatant was discarded and the pelleted cells resuspended in chilled 1x PBS. Cells were fixed by adding a fixation solution (100mM NaCl, 50mMTris-HCl pH 8.0, 10% formaldehyde) to a final concentration of 1% formaldehyde for 10 minutes (slow rotation) at room temperature. 140mM Glycine for 10 minutes at room temperature (rotating slowly) inhibited formaldehyde and avoided over-fixation. Formaldehyde and glycine residues were washed away by centrifugation (4000 rpm - 5 min - 4C) then bacteria were washed with 10 ml chilled 1x PBS, twice. Incubation in a lysozyme buffer (120mM Tris-HCl pH 8.0, 50mM EDTA, 4mg/ml Lysozyme) for 10 minutes at 37C increased protoplasts forming efficiency. After incubation cells were centrifuged and the pellet was resuspended in 500 ul of lysis buffer (10mM NaCl, 10mM Tris-HCl pH 7.4, 3mM MgCl2, 0.5% NP-40, 1x Pi, 0.15mM Spermine, 0.5mM Spermidine), transferred in a new microcentrifuge tube and incubated for 20 minutes on ice.  The lysate was spinned down and the pelletwas washed with 500 ul of -CA buffer (15mM NaCl, 10mM Tris-HCl pH 7.4, 60mM KCl, 1x Pi, 0.15mM Spermine, 0.5mM Spermidine) without resuspending. The washed pellet was finally resuspended in 500 ul of +CA Buffer (15mM NaCl, 10mM Tris-HCl pH 7.4, 60mM KCl, 1mM CaCl2,  0.15mM Spermine, 0.5mM Spermidine) to a uniform suspension. 50 ul of this suspension were digested with the wanted concentration of micrococcal nuclease (MN) for 10 minutes (20 minutes for cells in stationary phase) at room temperature and finally blocked with a STOP solution containing calcium-chelating agents (100mM EDTA, 10mM EGTA). Each sample was further diluted with -CA buffer  (without Pi, spermine and spermidine) and treated with 10% SDS and 150ng/ml proteinase K overnight at 65C shaking (~500 rpm).

tag: time point

value: 17 hours after induction


title: S_EV_5

description: Mnase digested DNA


title: EPI2H7

source_name: engineered epicardial cell


title: EPI2H9


title: EPI2H6


title: EPI2H8


title: EPI2H5


title: S_EV_3

description: Mnase digested DNA


title: KPC8 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC8 -  region 1


title: S_B_4

description: Mnase digested DNA


title: HOTTIP-KO-H3K27me3-ChIP-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq , ChIP-seq and CHIRP-seq.

growth_protocol: Total bone marrow cells were isolated from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers.  Human MOLM13 leukemia cells were culture at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3 and H3K79me2 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449;  Anti-H3K79me2, Abcam, Cat No. ab3594.).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    CHIRP-seq library constructs with the illumina Truth CHIP DNA library kt.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK and MOLM13 cells without any treatment

tag: cell line

tag: cell types

value: Human-derived acute myeloid leukemia cells

tag: tissue origin

value: peripheral blood

tag: genotype/variation

value: HOTTIP-KO

tag: chip antibody

value: Anti-H3K27me3, Millipore, Cat. #07-449


title: Coho smolt Brain_6 [56079]

description:
Sample array position within slide:
Array3Onkism0809_B_10206
raw data files:
Onkism0809_B_10206.txt
Onkism0809_B_10206_ref.txt
sample name in processed data file:
56079
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

value: FW

tag: year

tag: season

tag: origin

tag: fork length (cm)

tag: Sex

value: U

value: chilliwack


title: EPI2H4

tag: cell type

tag: es line


title: HOTTIP-KO-H3K4me3-ChIP-seq

value: Anti-H3K4me3, Millipore, Cat. #04-745


title: EPI2H3


title: S_B_3

description: Mnase digested DNA


title: HOTTIP-KO-H3K79me2-ChIP-seq

value: Anti-H3K79me2, Abcam, Cat. #ab3594


title: S_B_1

description: Mnase digested DNA


title: Coho smolt Brain_7 [56157]

description:
Sample array position within slide:
Array2Onkism0809_B_10138
raw data files:
Onkism0809_B_10138.txt
Onkism0809_B_10138_ref.txt
sample name in processed data file:
56157
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: Hatchery

tag: total mass (g)

tag: latitude

tag: longitude

tag: sample type

value: Pooled cRNA reference


title: EPI2H2

value: hPSC-derived epicardium


title: Coho smolt Brain_5 [56218]

description:
Sample array position within slide:
Array1Onkism0809_B_10138
raw data files:
Onkism0809_B_10138.txt
Onkism0809_B_10138_ref.txt
sample name in processed data file:
56218
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_4 [56136]

description:
Sample array position within slide:
Array2Onkism0809_B_10204
raw data files:
Onkism0809_B_10204.txt
Onkism0809_B_10204_ref.txt
sample name in processed data file:
56136
*ref.txt file is the raw data for channel 2 (pooled reference.


title: KPC6 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC6 -  region 2

tag: strain

tag: age


title: Coho smolt Brain_3 [56134]

description:
Sample array position within slide:
Array2Onkism0809_B_10207
raw data files:
Onkism0809_B_10207.txt
Onkism0809_B_10207_ref.txt
sample name in processed data file:
56134
*ref.txt file is the raw data for channel 2 (pooled reference.

source_name: brain


title: KPC6 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC6 -  region 1


title: HOTTIP-VP160-ATAC-seq-2

tag: cell line

tag: cell types

tag: tissue origin

tag: genotype/variation


title: S_A_3

description: Mnase digested DNA

tag: time point


title: Coho smolt Brain_1 [56135]

description:
Sample array position within slide:
Array2Onkism0809_B_10206
raw data files:
Onkism0809_B_10206.txt
Onkism0809_B_10206_ref.txt
sample name in processed data file:
56135
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

tag: year

tag: season

tag: origin

value: Mainland

source_name: brain from all samples in the series


title: KPC5 - Tumor Region 2

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC5 -  region 2

value: 91 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC5


title: KPC5 - Tumor Region 3

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC5 -  region 3


title: EPI2H11

tag: cell type

tag: es line


title: HOTTIP-VP160-ATAC-seq-1


title: EPI2H10


title: KPC5 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC5 -  region 1


title: EPI2H1


title: S_A_1

description: Mnase digested DNA


title: S_A_2

description: Mnase digested DNA


title: EPI2G9


title: HOTTIP-VP160-RNA-seq-1


title: HOTTIP-KO-RNA-seq-2

source_name: HOTTIP-KO-RNA-seq


title: Coho smolt Brain_2 [56061]

description:
Sample array position within slide:
Array4Onkism0809_B_10111
raw data files:
Onkism0809_B_10111.txt
Onkism0809_B_10111_ref.txt
sample name in processed data file:
56061
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fork length (cm)

tag: total mass (g)

tag: Sex


title: E_EV_2

description: Mnase digested DNA

value: 2 hours after induction


title: HOTTIP-KO-RNA-seq-1


title: EPI2G8


title: E_EV_1

description: Mnase digested DNA


title: HOTTIP-VP160-RNA-seq-2


title: ESRRG gene expression profile in gastric cancer cells [ESRRGOE_2_MKN45]

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

country: South Korea

institute: ChuangAng University

description: Over-expression in gastric cancer cell

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing: GenomeStudio was used for data processing and quantile normalization method was used.

source_name: gastric cancer cell

label_protocol: Extracted RNA was amplified and labeled with Amplification kit (AMIL1797; Ambion)

growth_protocol: The cells were grown in RPMI1640 media.

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Cells were treated with indicated lenti-viral ventor

value: ESRRG over-expression


title: ESRRG gene expression profile in gastric cancer cells [Con_3_MKN45]

description: control

value: Control


title: ESRRG gene expression profile in gastric cancer cells [ESRRGOE_1_MKN45]

description: Over-expression in gastric cancer cell


title: ESRRG gene expression profile in gastric cancer cells [ESRRGOE_3_MKN45]

description: Over-expression in gastric cancer cell


title: ESRRG gene expression profile in gastric cancer cells [Con_2_MKN45]

description: control


title: EPI2G7


title: Coho smolt Brain_95 [56182]

description:
Sample array position within slide:
Array2Onkism0809_B_10108
raw data files:
Onkism0809_B_10108.txt
Onkism0809_B_10108_ref.txt
sample name in processed data file:
56182
*ref.txt file is the raw data for channel 2 (pooled reference.

extract_protocol: RNA was extracted from four tissues separately: brain, gill, muscle, and liver. Tissues (10mg) were homogenized in TRI reagent (Ambion) using stainless steel beads on a MM301 mixer mill (Retsch Inc.). Aqueous layer homogenate aliquots (100?L) were transferred to three U-bottom 96 well plates. RNA was extracted from the homogenates using the ÔNo-Spin ProcedureÕ of MagMAX-96 for Microarrays Total RNA Isolation kits (Ambion) and a Biomek NXP automation workstation (Beckman- Coulter). RNA yield and purity were measured by spectrophotometry (A?260 value or A?260/A?280 ratio). RNA extracts were stored in a ?80¡C freezer.

value: Wild

tag: latitude

tag: longitude

tag: sample type


title: WT-RNA-seq-2

source_name: WT-RNA-seq

tag: cell line

tag: cell types

value: Human-derived acute myeloid leukemia cells

value: peripheral blood

value: WT


title: ESRRG gene expression profile in gastric cancer cells [Con_1_MKN45]

description: control

tag: genotype/variation


title: E_EV_4

description: Mnase digested DNA

tag: time point


title: E_B_4

description: Mnase digested DNA


title: WT-RNA-seq-1

tag: tissue origin


title: EPI2G6


title: KPC19 - Tumor Region 1

source_name: tumor cells from primary pancreatic ductal adenocarcinoma KPC19 -  region 1

tag: strain

tag: age

value: 211 Days

source_name: cells from tumor-free kidney (matched normal tissue) of KPC19


title: ESRRG gene expression profile in gastric cancer cells [ESRRGOE_3_AGS]

description: Over-expression in gastric cancer cell

value: AGS


title: EPI2G5


title: E_B_3

description: Mnase digested DNA


title: EPI2G4


title: E_B_1

description: Mnase digested DNA


title: E_A_5

description: Mnase digested DNA


title: EPI2G2


title: E_A_3

description: Mnase digested DNA


title: EPI2G11


title: E_A_1

description: Mnase digested DNA


title: EPI2G10


title: Coho smolt Brain_96 [56020]

description:
Sample array position within slide:
Array4Onkism0809_B_10210
raw data files:
Onkism0809_B_10210.txt
Onkism0809_B_10210_ref.txt
sample name in processed data file:
56020
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

value: FW

tag: year

tag: season

tag: origin

value: U

value: chilliwack


title: adr-1(zw96)-2

city: Denton

first: Bojun

last: Chen

state: TX

address: 1511 W Sycamore St

department: Biological Sciences

institute: University of North Texas

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads are filtered to remove reads containing adapters or reads of low quality. The filtering process is as follows: 1)Discard reads with adaptor contamination.2)Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%). 3)Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
Filtered reads are mapped to the reference genome using Tophat v2.0.12. The mismatch parameter is set to two, and other parameters are set to default.
Gene expression level is estimated by counting the reads that map to exons using DEGSeq 1.12.0. The input data for differential gene expression analysis are readcounts from gene expression level analysis. The differential gene expression analysis contains three steps: 1)Readcounts Normalization; 2)Model dependent p-value estimation; 3)FDR value estimation based on multiple hypothesis testing.
Genome_build: ce11
Supplementary_files_format_and_content: Tab-delimited text files include Readcount, log2.Fold change, p-value, and q-value for each sample.

source_name: whole worm

extract_protocol:
Worms were washed off the culture plates and washed three times with M9 buffer. Total RNA was extracted using TRIzol Reagent (Invitrogen) and treated with TURBO DNase (Ambion).
RNA libraries were constructed using standard Illumina protocols.

value: N2 (Bristol)

tag: genotype

tag: developmental stage

value: young adult


title: adr-1(zw96)-3


title: Pancreatitis, rectus abdominis muscle biopsy 7

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from rectus abdominis muscle biopsy of male patient with chronic pancreatitis.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

source_name: rectus abdominis muscle biopsy

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Biopsies from the rectus abdominis muscle were harvested from patients at the beginning of surgery, and a portion to be used for RNA isolation was immediately snap-frozen in liquid nitrogen followed by storage at -80⁰C.  Muscles were minced and homogenized in TRIzol for RNA extraction.

tag: diagnosis

value: chronic pancreatitis

tag: Sex

value: M

tag: tnm

tag: bw loss in 6 months prior to surgery

value: n.d. (not determined)

tag: neoadjuvant therapy (y/n)

tag: survival post-surgery (or days elapsed since surgery, if still alive at time of censor)

tag: tissue

value: rectus abdominis muscle


title: control

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description: 71293_CTGAAGCTCAGGACGT_CCRE8ANXX_1_20180810B_20180810

data_processing:
alignment to genome using STAR v.2.5.0c
pileup files prepared with Samtools v1.3
occurrences of high quality nucleotides counted using custom scripts
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: text file containing the pileups created by samtools

source_name: control

growth_protocol: Mouse protocols were reviewed by institutional preclinical core facility (PCF) at IST Austria and all breeding and experimentation was performed under a license approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and EU animal laws. Mice were maintained and housed in animal facilities with a 12-hour day/night cycle and adequate food/water conditions according to IST Austria institutional regulations. Inbreed mouse lines: CAST/EiJ (JAX stock # 000928) and C57BL/6J (JAX stock # 000664).

extract_protocol:
Upon cell sorting, samples were incubated for 30min at 37°C. Total volume was adjusted to 250µl using RNase-free H2O (Thermo Fisher Scientific) followed by addition of 750µl Trizol LS (Thermo Fisher Scientific). Samples were mixed by inverting 5 times. After a 5min incubation step at RT, the entire solution was transferred into a MaXtract tube (Qiagen). 200µl chloroform (Sigma-Aldrich) were added, followed by 3 times 5sec vortexing and 2min incubation at RT. Samples were centrifuged for 2min with 12000rpm at 18°C. Supernatant was transferred to a new tube and isopropanol (Sigma-Aldrich) was added in a 1:1 ratio. For better visibility of the RNA pellet 1µl GlycoBlue (Thermo Fisher Scientific) was added and entire solution was mixed by vortexing (3x 5sec). Samples were left for precipitation o/n at -20°C. After precipitation samples were centrifuged for 20min with 14000rpm at 4°C. Supernatant was removed and RNA pellet was washed with 70% ethanol, followed by a 5min centrifugation step (14000rpm at 4°C). RNA pellet was resuspended in 12,5µl RNase-free H2O. RNA quality was analyzed using Bioanalyzer RNA 6000 Pico kit (Agilent) following the manufacturer’s instructions. RNA samples were stored at -80°C until further use.
RNA was isolated from 10.000 sorted cells using Trizol LS (Thermo Fisher Scientific), DNAse1 treated (DNA free KIT, Ambion) and converted to cDNA (SuperScript VILO, Invitrogen). Genomic DNA was prepared from the carcass of one embryo used for FACS sorting. For deep sequencing, regions of interest were amplified with different primers that produce fragments where the SNP of interest is located within 50bp of one end, with a high fidelity DNA polymerase. PCR fragments were purified (Ampure XP, Beckman Coulter) and pooled per sample of origin. Each pool was prepared for deep sequencing (VBCF GmbH, Vienna) and sequenced on a HiSeq 2500 (Illumina) using v4 chemistry.
targeted sequencing of cDNA

treatment_protocol: Single cell suspension was prepared using Neural Tissue Dissociation Kit (Miltenyi #130-092-628) following the manufacturer’s instructions. Pregnant females were sacrificed by cervical dislocation. Embryos were isolated and directly transferred into 1x PBS and kept on ice. Region of interest (neocortex) was dissected and used for single cell suspension preparation. Enrichment for neurons and RGPs (progenitors) was performed according to a protocol described previously (Johnson et al. 2015, PMID: 25734491). The following antibodies were used for FACS: Prominin-1-PEVio770 1:100 (Miltenyi, Clone: MB9-3G8, #130-102-891), CD15-BV421 (5µl per sample) (BD, Clone: W6D3, #740086), CD11b-APCR700 1:100 (BD, Clone: m1/70, #564985), CD31-APCR700 1:100 (BD, Clone MEC13.3, #565509) and CD45-APCR700 1:100 (BD, Clone: 30-F11, #565478). In order to avoid contamination of non-neuronal and non-progenitor cell populations an initial gating was performed where cells positive for CD11b, CD31 and CD45 were eliminated. The cell population negative for these markers was then used further. The progenitor cell population which was Prominin+, CD15+ was collected. The neuronal population was negative for both markers. Cell sorting was performed at 4°C using the 100 nozzle and on a FACS Aria III, BD Biosciences. Cells were collected in a custom made RNA extraction buffer (30nM TRIS pH 8, 10nM EDTA pH 8, 1% SDS and 200 µg/µL Proteinase K).

tag: mother strain

tag: father strain

value: CAST/EiJ

value: carcass


title: RGP replicate 2

description: 71292_GAATTCGTTAATCTTA_CCRE8ANXX_1_20180810B_20180810

source_name: RGP

value: cortex

tag: cell type

value: radial glia progenitors

tag: purification

value: antibody based FACS


title: ESRRG gene expression profile in gastric cancer cells [Con_3_AGS]

description: control

tag: cell line

tag: genotype/variation

value: Control


title: ESRRG gene expression profile in gastric cancer cells [ESRRGOE_1_AGS]

description: Over-expression in gastric cancer cell

value: ESRRG over-expression


title: ESRRG gene expression profile in gastric cancer cells [ESRRGOE_2_AGS]

description: Over-expression in gastric cancer cell

value: AGS


title: Pancreatitis, rectus abdominis muscle biopsy 6

description: Gene expression data from rectus abdominis muscle biopsy of female patient with chronic pancreatitis.

value: F

tag: age


title: adr-1(zw96)-1

tag: strain


title: EPI2F8

source_name: engineered epicardial cell

extract_protocol:
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.

value: hPSC-derived epicardium

tag: es line


title: RGP replicate 1

description: 71291_ATTCAGAAAGGCGAAG_CCRE8ANXX_1_20180810B_20180810


title: EPI2G1


title: EPI2F9


title: Pancreatitis, rectus abdominis muscle biopsy 8


title: Neuron replicate 2

description: 71290_GAGATTCCGGCTCTGA_CCRE8ANXX_1_20180810B_20180810

source_name: Neuron

value: cortical projection neurons


title: wild type-3

value: N2 (Bristol)

tag: genotype

value: wild type

tag: developmental stage


title: ESRRG gene expression profile in gastric cancer cells [Con_2_AGS]

description: control


title: wild type-2

value: young adult


title: ESRRG gene expression profile in gastric cancer cells [Con_1_AGS]

description: control


title: Pancreatitis, rectus abdominis muscle biopsy 5

tag: diagnosis

value: chronic pancreatitis

tag: Sex


title: EPI2F7


title: Pancreatitis, rectus abdominis muscle biopsy 4

tag: tnm

tag: bw loss in 6 months prior to surgery

value: n.d. (not determined)


title: Pancreatitis, rectus abdominis muscle biopsy 3

value: M

tag: neoadjuvant therapy (y/n)

tag: survival post-surgery (or days elapsed since surgery, if still alive at time of censor)

value: rectus abdominis muscle


title: wild type-1


title: Neuron replicate 1

description: 71289_TCCGGAGACCTATCCT_CCRE8ANXX_1_20180810B_20180810

tag: mother strain

value: CAST/EiJ

tag: tissue


title: Pancreatitis, rectus abdominis muscle biopsy 1


title: EPI2F6

tag: cell type


title: mKRT_Mi2ChIP

source_name: neonatal skin

extract_protocol:
Primary  mouse  keratinocytes were isolated from newborn back skins and expanded in culture under serum-free conditions with keratinocyte growth medium.
As detailed in Hu et al. Genes Dev (2016)

tag: cell types

value: keratinocytes

value: WT


title: Pancreatitis, rectus abdominis muscle biopsy 2


title: EPI2F5


title: E13_yellow_Replicate 6 [94769]

data_processing:
All libraries were sequenced 3x (technical replicates) to increase read depth. Raw reads were delivered as unaligned BAM files and technical replicates were combined using samtools (v1.8) and converted to fastq format using bamToFastq (bedtools suite v2.26.0) for alignment. Reads within transcripts were counted using STAR_2.5.0c with an index prepared from GRCm38 and Gencode M16 gene annotation. Note that for optimal representation of the long non-coding RNA Meg3 the spliced ENSMUST00000143836.7 transcript was modified to represent a single exon transcript. Parameters used for STAR alignment: --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Read counts in transcripts as reported by STAR as tab delimited text

molecule: polyA RNA

growth_protocol: Mouse protocols were reviewed by institutional preclinical core facility (PCF) at IST Austria and all breeding and experimentation was performed under a license approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and EU animal laws. Mice were maintained and housed in animal facilities with a 12-hour day/night cycle and adequate food/water conditions according to IST Austria institutional regulations. Mouse lines with chromosome 7 MADM cassettes: MADM-7-GT JAX stock # 021457, MADM-7-TG JAX stock # 021458, Emx1-Cre: JAX stock # 005628. All MADM-based analyses were carried out in a mixed C57BL/6J, CD1 genetic background.

extract_protocol:
sorted cells were directly processed without RNA extraction
Smart-Seq2 (VBCF GmbH Vienna)

treatment_protocol: Pregnant females were sacrificed and E13/E16 embryos were collected. Neocortex area was dissected. Single individuals were used as replicates. Single cell suspensions were prepared by using Papain containing L-cysteine and EDTA (vial 2, Worthington), DNase I (vial 3, Worthington), Ovomucoid protease inhibitor (vial 4, Worthington), EBSS (Thermo Fisher Scientific), DMEM/F12 (Thermo Fisher Scientific), FBS and HS. All vials from Worthington kit were reconstituted according to the manufacturer’s instructions using EBSS. The dissected brain area was directly placed into Papain-DNase solution (20units/ml papain and 1000 units DNase). Enzymatic digestion was performed for 30min at 37°C in a shaking water bath. Next, solution 2 (EBSS containing 0.67mg Ovomucoid protease inhibitor and 166.7 U/ml DNase I) was added, the whole suspension was thoroughly mixed and centrifuged for 5min at 1000rpm at RT. Supernatant was removed and cell pellet was resuspended in solution 2. Trituration with p1000 pipette was performed to mechanically dissolve any remaining tissue parts. DMEM/F12 was added to the cell suspension as a washing solution, followed by a centrifugation step of 5min with 1500rpm at RT. Cells were resuspended in media (DMEM/F12 containing 10% FBS and 10% HS) and kept on ice until sorted. Right before sorting, cell suspension was filtered using a 40µm cell strainer. FACS was performed on a BD FACS Aria III using 100 nozzle and keeping sample and collection devices (0.8ml PCR tubes) at 4°C. Duplet exclusion was performed to ensure sorting of true single cells. Cells were sorted into 4µl lysis buffer (0.2% Triton X-100, 2U/µl RNase Inhibitor [Clonetech]). Immediately after sorting was completed samples were transferred into a 96 well plate (Bio-Rad) that was kept on dry ice. GFP+, tdT+ and GFP+/tdT+ cells (200-400 cells) were collected.

tag: color

value: yellow

value: cortex

tag: cre

tag: madm

value: Chr. 7

tag: replicate

value: Replicate 6


title: EPI2F4

tag: es line


title: Mi2_ATAC_rep2

source_name: adult epidermis

extract_protocol:
Dorsal epidermis was separated from the dermis by digestion with 0.25% trypsin overnight at 4C to obtain a single cell suspension. ITGA6+, CD45-, CD34- cells were sorted with FACS Aria.
Nextera DNA sample prep kit (Illumina)

tag: strain

tag: genotype


title: Non-cachectic PDAC, rectus abdominis muscle biopsy 5

description: Gene expression data from rectus abdominis muscle biopsy of non-cachectic male patient with pancreatic ductal adenocarcinoma.

tag: diagnosis

value: pancreatic ductal adenocarcinoma

tag: age

value: Y


title: mKRT_input


title: EPI2F3

value: hPSC-derived epicardium


title: E13_green_Replicate 6 [94768]

value: green


title: E13_red_Replicate 6 [94767]

value: red


title: Non-cachectic PDAC, rectus abdominis muscle biopsy 4

description: Gene expression data from rectus abdominis muscle biopsy of non-cachectic female patient with pancreatic ductal adenocarcinoma.

tag: Sex

value: F

tag: tnm

value: N


title: E13_green_Replicate 5 [94765]

value: Replicate 5


title: EPI2F2


title: Mi2_ATAC_rep1


title: TS24hr_ATAC_rep2


title: E13_red_Replicate 5 [94764]


title: EPI2F11


title: EPI2F12


title: Non-cachectic PDAC, rectus abdominis muscle biopsy 2

value: M

tag: bw loss in 6 months prior to surgery

tag: neoadjuvant therapy (y/n)


title: Non-cachectic PDAC, rectus abdominis muscle biopsy 3

tag: survival post-surgery (or days elapsed since surgery, if still alive at time of censor)

value: rectus abdominis muscle


title: TS24hr_ATAC_rep1


title: TS6hr_ATAC_rep2


title: EPI2F10


title: E13_yellow_Replicate 4 [94763]

tag: tissue

value: Replicate 4


title: Non-cachectic PDAC, rectus abdominis muscle biopsy 1


title: E13_yellow_Replicate 5 [94766]


title: E13_green_Replicate 4 [94762]


title: Cachectic PDAC, rectus abdominis muscle biopsy 16

description: Gene expression data from rectus abdominis muscle biopsy of cachectic male patient with pancreatic ductal adenocarcinoma.

value: Stage IV


title: TS6hr_ATAC_rep1

value: keratinocytes

value: WT


title: Cachectic PDAC, rectus abdominis muscle biopsy 17

description: Gene expression data from rectus abdominis muscle biopsy of cachectic female patient with pancreatic ductal adenocarcinoma.


title: WT_ATAC_rep2


title: WT_ATAC_rep1


title: EPI2E8

tag: cell type


title: E16_yellow_Replicate 7 [94760]

value: yellow

value: cortex

value: Replicate 7


title: E13_red_Replicate 4 [94761]

value: Chr. 7


title: E16_green_Replicate 7 [94759]


title: EPI2E7


title: EPI2E6


title: TS24hr_RNA_rep2

extract_protocol:
Dorsal epidermis was separated from the dermis by digestion with 0.25% trypsin overnight at 4C to obtain a single cell suspension. ITGA6+, CD45-, CD34- cells were sorted with FACS Aria.
Trueseq stranded mRNA sample prep kit (Illumina)

tag: cell types


title: E16_red_Replicate 7 [94758]

tag: color


title: Cachectic PDAC, rectus abdominis muscle biopsy 15

value: pancreatic ductal adenocarcinoma


title: E16_yellow_Replicate 6 [94757]

tag: cre

value: Replicate 6


title: EPI2E9

value: hPSC-derived epicardium


title: TS24hr_RNA_rep1


title: EPI2F1


title: E16_green_Replicate 6 [94756]

value: green

tag: madm


title: EPI2E4


title: EPI2E3


title: Cachectic PDAC, rectus abdominis muscle biopsy 12

value: F


title: Cachectic PDAC, rectus abdominis muscle biopsy 14

value: N


title: E16_red_Replicate 6 [94755]

value: red

tag: replicate


title: TS6hr_RNA_rep1


title: E16_yellow_Replicate 5 [94754]

value: Replicate 5


title: Cachectic PDAC, rectus abdominis muscle biopsy 13

value: M

value: rectus abdominis muscle


title: WT_RNA_rep2


title: Cachectic PDAC, rectus abdominis muscle biopsy 11


title: Cachectic PDAC, rectus abdominis muscle biopsy 8


title: EPI2E2

tag: es line


title: Cachectic PDAC, rectus abdominis muscle biopsy 10


title: Cachectic PDAC, rectus abdominis muscle biopsy 7


title: E16_green_Replicate 5 [94753]

tag: strain


title: EPI2E12


title: WT_RNA_rep1

tag: genotype


title: E16_red_Replicate 5 [94752]


title: EPI2E11


title: Cachectic PDAC, rectus abdominis muscle biopsy 6

tag: diagnosis


title: Cachectic PDAC, rectus abdominis muscle biopsy 9

value: Stage IV

tag: age


title: E16_yellow_Replicate 4 [94751]

value: Replicate 4


title: 861_SPLN_2

city: Cambridge

first: Rebecca

middle: H

last: Herbst

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options. Estimated counts from rsem were upper-quartile normalized where the 75th percentile was set to 1000.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample; Supplementary data file includes normalized counts.

source_name: Sorted CD103-KLRG1- Tregs

extract_protocol:
Cells were directly sorted into TCL buffer. Whole transcriptome amplication was performed with Smartseq v2 protocol.
RNA libraries were prepared for sequencing with the Illumina Nextera kit according to the manufacturer's instructions.

value: LSL-KrasG12D, p53fl/fl, Foxp3RFP


title: EPI2E10


title: Cachectic PDAC, rectus abdominis muscle biopsy 4

tag: Sex


title: E16_green_Replicate 4 [94750]


title: 861_SPLN_1


title: EPI2E1


title: E16_red_Replicate 4 [94749]


title: 946_LN_103P

source_name: Sorted CD103+KLRG1- Tregs


title: Cachectic PDAC, rectus abdominis muscle biopsy 3

tag: tnm


title: 946_LN_103N


title: 861_SPLN_3


title: E16_yellow_Replicate 3 [94748]

value: yellow

value: Replicate 3


title: EPI2D8


title: 943_LN_103P


title: Cachectic PDAC, rectus abdominis muscle biopsy 5

tag: bw loss in 6 months prior to surgery

value: Y


title: E16_green_Replicate 3 [94747]

value: cortex

value: Chr. 7


title: 943_LN_103N


title: EPI2D6


title: TS96hr_RNA

value: keratinocytes

value: WT


title: E16_red_Replicate 3 [94746]


title: EPI2D5

value: hPSC-derived epicardium


title: Non-cancer control, rectus abdominis muscle biopsy 16

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with IPMN.

value: IPMN

value: F

tag: neoadjuvant therapy (y/n)

value: n.d. (not determined)


title: Cachectic PDAC, rectus abdominis muscle biopsy 1

value: pancreatic ductal adenocarcinoma

tag: survival post-surgery (or days elapsed since surgery, if still alive at time of censor)


title: E16_green_Replicate 2 [94744]

value: green

tag: tissue

value: Replicate 2


title: Non-cancer control, rectus abdominis muscle biopsy 15

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with choledochal cyst.

value: choledochal cyst

value: rectus abdominis muscle


title: 869_LN_103P

value: LSL-KrasG12D, p53fl/fl, Foxp3RFP


title: E16_yellow_Replicate 2 [94745]

value: yellow


title: EPI2D7

tag: cell type


title: Non-cancer control, rectus abdominis muscle biopsy 14

description: Gene expression data from rectus abdominis muscle biopsy of male non-cancer control with common bile duct injury.

value: common bile duct injury

value: M


title: EPI2D9


title: EPI2D3


title: E16_red_Replicate 2 [94743]

value: red

value: cortex


title: E16_yellow_Replicate 1 [94742]

value: Chr. 7

value: Replicate 1


title: Cachectic PDAC, rectus abdominis muscle biopsy 2

value: Y


title: 861_LN_103N


title: EPI2D4

value: hPSC-derived epicardium


title: 869_LN_103N


title: Non-cancer control, rectus abdominis muscle biopsy 12

description: Gene expression data from rectus abdominis muscle biopsy of male non-cancer control with cholecystitis.

value: cholecystitis


title: EPI2D12


title: 946_SP


title: E16_green_Replicate 1 [94741]


title: EPI2D2


title: Non-cancer control, rectus abdominis muscle biopsy 13

description: Gene expression data from rectus abdominis muscle biopsy of male non-cancer control with stricture of choledochojejunostomy.

value: stricture of choledochojejunostomy

value: n.d. (not determined)


title: Non-cancer control, rectus abdominis muscle biopsy 11

description: Gene expression data from rectus abdominis muscle biopsy of male non-cancer control with sclerosing cholangitis.

value: sclerosing cholangitis


title: Non-cancer control, rectus abdominis muscle biopsy 10

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with acute pancreatic necrosis.

value: acute pancreatic necrosis

value: F


title: 869_SP


title: 861_LN_103P


title: EPI2D1


title: E13_yellow_Replicate 3 [94739]

value: Replicate 3


title: 861_SP

value: LSL-KrasG12D, p53fl/fl, Foxp3RFP


title: Non-cancer control, rectus abdominis muscle biopsy 8

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with bile duct injury and acute pancreatic necrosis.

value: rectus abdominis muscle


title: E13_green_Replicate 3 [94738]

value: green


title: 946_DN


title: EPI2C9


title: Non-cancer control, rectus abdominis muscle biopsy 9

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with open cholecystectomy.

value: open cholecystectomy


title: EPI2C8


title: E13_yellow_Replicate 2 [94736]

value: yellow

value: Replicate 2


title: E13_red_Replicate 3 [94737]

value: red

value: cortex

value: Chr. 7


title: 943_DN


title: Non-cancer control, rectus abdominis muscle biopsy 7

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with cholecystitis.


title: EPI2C7

value: hPSC-derived epicardium


title: E13_green_Replicate 2 [94735]


title: EPI2C6


title: E13_red_Replicate 2 [94734]


title: EPI2D11


title: Non-cancer control, rectus abdominis muscle biopsy 4

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with bile duct injury.

value: bile duct injury


title: 869_DN


title: 943_SP


title: E16_red_Replicate 1 [94740]

value: Replicate 1


title: Non-cancer control, rectus abdominis muscle biopsy 6

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with common bile duct stricture.

value: common bile duct stricture

value: n.d. (not determined)


title: EPI2C5


title: 861_DN


title: Non-cancer control, rectus abdominis muscle biopsy 3

value: IPMN


title: 946_DP

source_name: Sorted CD103+KLRG1+ Tregs


title: Non-cancer control, rectus abdominis muscle biopsy 5

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with choledocholithiasis s/p cholecystectomy.

value: choledocholithiasis s/p cholecystectomy

value: F


title: Non-cancer control, rectus abdominis muscle biopsy 2

description: Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with squamoid cyst.

value: squamoid cyst


title: E13_yellow_Replicate 1 [94733]


title: E13_green_Replicate 1 [94732]


title: 943_DP

value: LSL-KrasG12D, p53fl/fl, Foxp3RFP


title: EPI2C3


title: EPI2E5


title: 869_DP


title: EPI2C2