title: HCT43-7LuMRRR PDO

source_name: PDO established from surgical specmen HCT43-7LuMRRR


title: WS, Parabola 10 End, replicate 2

status: Public on Apr 01 2021

type: RNA

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

country: USA

institute: University of Florida

hyb_protocol: 3.5 µg of sense DNA was hybridized, with rotation, onto an Affymetrix GeneChip® Arabidopsis Gene 1.0 ST Array for 16 h at 45 °C. Arrays were washed on a Fluidics Station 450 (ThermoFisher Scientific, Catalog # 00-0079) using the Hybridization Wash and Stain Kit (Thermofisher Scientific, Catalog # 900720) and the Washing Procedure FS450_0002.

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files from each microarray experiment were loaded into the RStudio (v1.1.453) environment and normalized with the Robust Multichip Average (RMA) algorithm using the Oligo package. Tests of differential gene expression were performed using the Limma package, with cutoff criteria of: FDR of q < 0.05 and greater than two-fold change. Differentially-expressed genes (DEGs) were output and probe IDs were annotated using the TAIR10 version of the annotation for the AraGene 1.0 ST array. R version 4.0.0 was used. Scripts for microarray differential expression analysis were derived from scripts from the US National Aeronautics and Space Administration (NASA) GeneLab, which have been made publicly-available.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Roots from seedlings fixed at the end of the tenth parabola, replicate 2

label_protocol: cDNA was synthesized from 100 ng of total RNA, and the cDNA was used as a template for in vitro transcription (IVT). The antisense RNA synthesized during the IVT reaction was used to generate sense DNA. Sense strand DNA was fragmented, biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (ThermoFisher Scientific, Catalog # 900670) per the manufacturer’s protocol.

growth_protocol: Petri dishes (100 mm x 15 mm; Fisher Scientific, Pittsburgh, PA, USA), containing 50 mL of a 0.5% Phytagel™-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg’s Vitamin Mixture, were prepared aseptically for planting. Seeds were sterilized via treatment with 70% ethanol for 10 minutes, and then with 50% bleach supplemented with Tween-20 at 2-3 drops per mL for 20 minutes, with seeds being mixed throughout the process. Seeds were washed with sterile water at least 6 times, and stored at 4 °C for 3-5 days. Seeds were dispensed onto the media surface in a laminar flow hood in one row of 12-15 seeds, and plates were sealed with Micropore® tape (3M, Maplewood, MN, USA). Plates were grown vertically at the University of florida in growth rooms at 19 ± 2 °C, and 24-h fluorescent lighting at approximately 80 µmol m-2 s-1 PAR until the time of transport to the experimental location. Plates were transported to Ellington Airport in Houston, Texas, inside a cooler lit with an LED light bank, and maintained onsite in a mobile growth setup consisting of a fluorescent light bank, with room temperature similar to that used for early growth.

extract_protocol: RNALater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3-4 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNALater™ was removed from roots, and RNA was extracted using the QIAshredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA.

treatment_protocol: The morning before the flight, seedlings were transplanted from plates into Kennedy Space Center Fixation Tubes (KFTs) loaded with RNALater™ fixative internally fitted with wetted Kimwipes™ cut into a cylinder. On the flight day, KFTs were taken onboard the C-9 aircraft. Members of the group actuated the KFTs in level flight soon before the first parabola, immediately at the start of the first parabola, mid-way through the first parabola, and after the first, third, and tenth parabolas, fixing seedlings in RNALater™.

tag: tissue

value: Whole Root

tag: cultivar

value: Wassilewskija (WS)

tag: genotype

value: Wild-type

tag: age

value: 12 days, 24h light grown

tag: fixative

value: RNALater-fixed Sample


title: HCT41-4LMR PDO

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: The JFCR-Cancer Institute

description: gene expression data of PDO derived from recurrent tumor

hyb_protocol: Following fragmentation, 5.2 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human transcriptome Array 2. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome analysis console 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Homo sapiens

source_name: PDO established from surgical specmen HCT41-4LMR

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA ( GeneChip WT PLUS Reagent Kit (Affymetrix)).

growth_protocol: PDOs were collected and matrigel were removed using cell recovery solution.

extract_protocol: RNA was extracted using an RNeasy Micro Kit (Qiagen). RNA quality was validated using an Agilent Bioanalyzer.

treatment_protocol: Collected PDOs were directly used for RNA isolation.

value: colorectal cancer

tag: pdo derived from

value: recurrent tumor


title: pCaMV35S:14-3-3κ:GFP Root, Parabola 1, replicate 1

source_name: Roots of seedlings fixed after the first parabola, replicate 1

extract_protocol: RNALater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3-4 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNALater™ was removed from roots, and RNA was extracted using the QIAshredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA

treatment_protocol: The morning before the flight, seedlings were transplanted from plates into Kennedy Space Center Fixation Tubes (KFTs) loaded with RNALater™ fixative internally fitted with wetted Kimwipes™ cut into a cylinder. On the flight day, KFTs were taken onboard the C-9 aircraft. Members of the group actuated the KFTs in level flight before the first parabola, and after the first, third, and tenth parabolas, fixing seedlings in RNALater™.

value: 10 days, 24h light grown


title: WS, Parabola 3 End, replicate 3

source_name: Roots from seedlings fixed at the end of the third parabola, replicate 3


title: HCT38-8LMR PDO

source_name: PDO established from surgical specmen HCT38-8LMR


title: HCT38-9LMR PDO

source_name: PDO established from surgical specmen HCT38-9LMR


title: HCT43-1T PDO

description: gene expression data of PDO derived from primary tumor

source_name: PDO established from surgical specmen HCT43-1T

value: primary tumor


title: HCT41-3LM PDO

description: gene expression data of PDO derived from metastasis tumor

source_name: PDO established from surgical specmen HCT41-3LM

value: metastasis tumor


title: WS, Parabola 1 End, replicate 2

source_name: Roots from seedlings fixed at the end of the first parabola, replicate 2


title: WS, Parabola 1 Midpoint, KFT B, replicate 2

source_name: Roots from seedlings fixed at the peak of the first parabola, at the transition from hyper-g to µg, by member B of the flight crew, replicate 2


title: HCT38-7LMR PDO

source_name: PDO established from surgical specmen HCT38-7LMR


title: WS, Parabola 1 End, replicate 3

source_name: Roots from seedlings fixed at the end of the first parabola, replicate 3


title: HCT38-6LM PDO

source_name: PDO established from surgical specmen HCT38-6LM


title: HCT38-5LM PDO

source_name: PDO established from surgical specmen HCT38-5LM


title: WS, Parabola 1 Midpoint, KFT B, replicate 1

source_name: Roots from seedlings fixed at the peak of the first parabola, at the transition from hyper-g to µg, by member B of the flight crew, replicate 1


title: HCT83-3LM PDO

source_name: PDO established from surgical specmen HCT83-3LM


title: HCT37-5LM PDO

source_name: PDO established from surgical specmen HCT37-5LM


title: HCT38-10LMRR PDO

source_name: PDO established from surgical specmen HCT38-10LMRR


title: HCT38-1T PDO

source_name: PDO established from surgical specmen HCT38-1T


title: WS, Parabola 1 Midpoint, KFT B, replicate 3

source_name: Roots from seedlings fixed at the peak of the first parabola, at the transition from hyper-g to µg, by member B of the flight crew, replicate 3


title: HCT38-3LM PDO

source_name: PDO established from surgical specmen HCT38-3LM


title: WS, Parabola 1 End, replicate 1

source_name: Roots from seedlings fixed at the end of the first parabola, replicate 1


title: HCT37-4LM PDO

source_name: PDO established from surgical specmen HCT37-4LM


title: WS, Parabola 1 Midpoint, KFT A, replicate 2

source_name: Roots from seedlings fixed at the peak of the first parabola, at the transition from hyper-g to µg, by member A of the flight crew, replicate 2


title: WS, Parabola 1 Start, replicate 2

source_name: Roots from seedlings fixed immediately after pitching up from level flight into a hyper-g climb, replicate 2


title: WS, Level Flight, replicate 3

source_name: Roots from seedlings fixed during level flight 1 minute before the beginning of the first parabola, replicate 3


title: HCT38-11LMRRR PDO

source_name: PDO established from surgical specmen HCT38-11LMRRR


title: WS, Parabola 1 Start, replicate 3

source_name: Roots from seedlings fixed immediately after pitching up from level flight into a hyper-g climb, replicate 3


title: HCT37-3LM PDO

source_name: PDO established from surgical specmen HCT37-3LM


title: HCT33-5LMR PDO

source_name: PDO established from surgical specmen HCT33-5LMR


title: WS, Parabola 1 Start, replicate 1

source_name: Roots from seedlings fixed immediately after pitching up from level flight into a hyper-g climb, replicate 1


title: HCT37-2N PDO

description: gene expression data of PDO derived from normal mucosa

source_name: PDO established from surgical specmen HCT37-2N

value: normal mucosa


title: WS, Parabola 1 Midpoint, KFT A, replicate 3

source_name: Roots from seedlings fixed at the peak of the first parabola, at the transition from hyper-g to µg, by member A of the flight crew, replicate 3


title: HCT37-1T PDO

source_name: PDO established from surgical specmen HCT37-1T


title: HCT33-4LMR PDO

source_name: PDO established from surgical specmen HCT33-4LMR


title: WS, Level Flight, replicate 2

source_name: Roots from seedlings fixed during level flight 1 minute before the beginning of the first parabola, replicate 2


title: HCT31-4LMR PDO

source_name: PDO established from surgical specmen HCT31-4LMR


title: pCaMV35S:14-3-3κ:GFP Root, Last-Actuated, Replicate 3

data_processing: CEL files from each microarray experiment were loaded into the RStudio (v1.1.453) environment and normalized with the Robust Multichip Average (RMA) algorithm using the Oligo package. The flight treatment samples were compared to the ground control samples. Tests of differential gene expression were performed using the Limma package, with cutoff criteria of: FDR of q < 0.05 and greater than two-fold change. Differentially-expressed genes (DEGs) between the treatment and control conditions were output and probe IDs were annotated using the TAIR10 version of the annotation for the AraGene 1.0 ST array. R version 4.0.0 was used. Scripts for microarray differential expression analysis were derived from scripts from the US National Aeronautics and Space Administration (NASA) GeneLab, which have been made publicly-available.

source_name: Roots of seedlings fixed in last-actuated KFT, from flight 1, replicate 3

growth_protocol: Petri dishes (100 mm x 15 mm; Fisher Scientific, Pittsburgh, PA, USA), containing 50 mL of a 0.5% Phytagel™-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg’s Vitamin Mixture, were prepared aseptically for planting. Seeds were sterilized via treatment with 70% ethanol for 10 minutes, and then with 50% bleach supplemented with Tween-20 at 2-3 drops per mL for 20 minutes, with seeds being mixed throughout the process. Seeds were washed with sterile water at least 6 times, and stored at 4 °C for 3-5 days. Seeds were dispensed onto the media surface in a laminar flow hood in one row of 12-15 seeds, and plates were sealed with Micropore® tape (3M, Maplewood, MN, USA). Plates were grown vertically at the University of florida in growth rooms at 19 ± 2 °C, and 24-h fluorescent lighting at approximately 80 µmol m-2 s-1 PAR until the time of transport to the experimental location. Plates were transported to the Kennedy Space Center in Cape Canaveral, Florida, inside a cooler lit with an LED light bank.

extract_protocol: RNAlater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3-4 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNAlater™ was removed from roots, and RNA was extracted using the QIAshredder and RNeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA

treatment_protocol: Seedlings were transplanted from plates into Kennedy Space Center Fixation Tubes (KFTs) loaded with RNAlater™ fixative internally fitted with wetted Kimwipes™ cut into a cylinder. KFTs were either inserted into pockets of the flight suit of the team member performing the in-flight fixation, or held by a member of the team on the ground. The flight profile consisted of a high-speed take-off, acceleration to supersonic speeds at level flight and low-altitude, then a 90° upward climb at 4g for roughly 30 seconds. An inversion of the plane at the peak of the climb created about ten seconds of microgravity during the following descent, and a brief period of hyper-g during the pull-up. One ground control KFT was actuated during the flight, and the two in-flight KFTs were actuated during the low-altitude acceleration and after the parabola.

value: RNAlater-fixed Sample


title: HCT31-2N PDO

source_name: PDO established from surgical specmen HCT31-2N


title: WS, Level Flight, replicate 1

source_name: Roots from seedlings fixed during level flight 1 minute before the beginning of the first parabola, replicate 1


title: pCaMV35S:14-3-3κ:GFP Root, Last-Actuated, Replicate 2

source_name: Roots of seedlings fixed in last-actuated KFT, from flight 1, replicate 2


title: WS, Parabola 1 Midpoint, KFT A, replicate 1

source_name: Roots from seedlings fixed at the peak of the first parabola, at the transition from hyper-g to µg, by member A of the flight crew, replicate 1


title: pCaMV35S:14-3-3κ:GFP Root, Last-Actuated, Replicate 1

source_name: Roots of seedlings fixed in last-actuated KFT, from flight 1, replicate 1


title: HCT31-3LM PDO

source_name: PDO established from surgical specmen HCT31-3LM


title: HCT33-3LM PDO

source_name: PDO established from surgical specmen HCT33-3LM


title: pCaMV35S:14-3-3κ:GFP Root, Ground Control, Replicate 1

source_name: Roots of fixed ground control seedlings, from flight 1, replicate 1


title: pCaMV35S:14-3-3κ:GFP Root, First-Actuated, Replicate 2

source_name: Roots of seedlings fixed in first-actuated KFT, from flight 1, replicate 2


title: HCT33-1T PDO

source_name: PDO established from surgical specmen HCT33-1T


title: pCaMV35S:14-3-3κ:GFP Root, First-Actuated, Replicate 3

source_name: Roots of seedlings fixed in first-actuated KFT, from flight 1, replicate 3


title: HCT31-1T PDO

source_name: PDO established from surgical specmen HCT31-1T


title: pCaMV35S:14-3-3κ:GFP Root, Last-Actuated, replicate 3

data_processing: CEL files from each microarray experiment were loaded into the RStudio (v1.1.453) environment and normalized with the Robust Multichip Average (RMA) algorithm using the Oligo package. The flight treatment samples were compared to the ground control samples. Tests of differential gene expression were performed using the Limma package, with cutoff criteria of: FDR of q < 0.05 and greater than two-fold change. Differentially-expressed genes (DEGs) were output and probe IDs were annotated using the TAIR10 version of the annotation for the AraGene 1.0 ST array. R version 4.0.0 was used. Scripts for microarray differential expression analysis were derived from scripts from the US National Aeronautics and Space Administration (NASA) GeneLab, which have been made publicly-available.

source_name: Roots of seedlings fixed in last-actuated KFT, from flight 2, replicate 3

extract_protocol: RNAlater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNAlater™ was removed from roots, and RNA was extracted using the QIAshredder and RNeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA.

treatment_protocol: Seedlings were transplanted from plates into Kennedy Space Center Fixation Tubes (KFTs) loaded with RNAlater™ fixative internally fitted with wetted Kimwipes™ cut into a cylinder. KFTs were either inserted into pockets of the flight suit of the team member performing the in-flight fixation, or held by a member of the team on the ground. The flight profile consisted of a high-speed take-off, acceleration to supersonic speeds at level flight and low-altitude, then a 90° upward climb at 4g for roughly 30 seconds. An inversion of the plane at the peak of the climb created about ten seconds of microgravity during the following descent, and a brief period of hyper-g during the pull-up. One ground control KFT was actuated during the flight, and the two in-flight KFTs were actuated immediately after the microgravity exposure and after level flight had been maintained for about a minute and a half after the parabola.


title: HCT27-3LuM PDO

source_name: PDO established from surgical specmen HCT27-3LuM


title: pCaMV35S:14-3-3κ:GFP Root, Last-Actuated, replicate 2

source_name: Roots of seedlings fixed in last-actuated KFT, from flight 2, replicate 2


title: HCT27-4LuM PDO

source_name: PDO established from surgical specmen HCT27-4LuM


title: pCaMV35S:14-3-3κ:GFP Root, First-Actuated, replicate 3

source_name: Roots of seedlings fixed in first-actuated KFT, from flight 2, replicate 3


title: pCaMV35S:14-3-3κ:GFP Root, Ground Control, Replicate 3

source_name: Roots of fixed ground control seedlings, from flight 1, replicate 3


title: pCaMV35S:14-3-3κ:GFP Root, First-Actuated, Replicate 1

source_name: Roots of seedlings fixed in first-actuated KFT, from flight 1, replicate 1


title: HCT25-7LMR PDO

source_name: PDO established from surgical specmen HCT25-7LMR


title: HCT26-3LM PDO

source_name: PDO established from surgical specmen HCT26-3LM


title: pCaMV35S:14-3-3κ:GFP Root, Last-Actuated, replicate 1

source_name: Roots of seedlings fixed in last-actuated KFT, from flight 2, replicate 1


title: pCaMV35S:14-3-3κ:GFP Root, Ground Control, Replicate 2

source_name: Roots of fixed ground control seedlings, from flight 1, replicate 2


title: HCT25-8LMRR PDO

source_name: PDO established from surgical specmen HCT25-8LMRR


title: HCT27-1T-2 PDO

source_name: PDO established from surgical specmen HCT27-1T-2


title: HCT26-1T PDO

source_name: PDO established from surgical specmen HCT26-1T


title: HCT25-9LMRR PDO

source_name: PDO established from surgical specmen HCT25-9LMRR


title: CYT_Rep2

type: SRA

city: Hangzhou

first: Jin

last: Zhang

state: Zhejiang

address: yuhangtang road

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using hisat2 default to generate bam file
raw counts for exons are counted by featureCount -M to generate coding gene counts and ERV-repeats were counted by salmon
Genome_build: mm10
Supplementary_files_format_and_content: count for each sample,processed data is divided to exon and repeats

organism: Mus musculus

source_name: mouse embyonic cells

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

treatment_protocol: One replicate was cytarabine treated for 24 hours.

tag: strain

tag: treatment

value: cytarabine treated


title: CYT_Rep1


title: Born from Stressed Mother, Raised by Control Mother 5

city: Irvine, CA

first: Amal

last: Alachkar

address: 355 Med Surge II

institute: University of California Irvine

description: Gene expression data from adult mice brain

hyb_protocol: Following fragmentation, 1 ug of ss-cDNA were hybridized for 20 hr at 48C on GeneChip MoGene-2.1-ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station.

data_processing:
The data were analyzed with Transcriptome Analysis Console (TAC) software (Affymetrix) using Tukey's Biweight Average algorithm and default settings
GC-RMA signal intensity

source_name: adult brain harvested at 13 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Genechip WT Expression Array Manual, 2018).

growth_protocol: Pregnant mice were exposed to treatments at gestational day 17 until delivery, for 1 hour

extract_protocol: Extraction of total RNA was performed according to Qiagen RNeasy kit manufacturer's instructions.

treatment_protocol: Adult brain tissue collected at 13 weeks

value: 13 week old brain

value: Mother exposed to TMT, raised by mother not exposed to TMT


title: Born from Control Mother, Raised by Stress Mother 1

value: Mother not exposed to TMT, raised by mother exposed to TMT


title: Born from Control Mother, Raised by Stress Mother 4


title: Born from Control Mother, Raised by Stress Mother 3


title: Born from Control Mother, Raised by Stress Mother 2


title: pCaMV35S:14-3-3κ:GFP Root, Ground Control, replicate 2

source_name: Roots of seedlings fixed in ground control KFT, from flight 2, replicate 2


title: Born from Stressed Mother, Raised by Control Mother 4


title: Born from Control Mother, Raised by Stress Mother 5


title: pCaMV35S:14-3-3κ:GFP Root, Ground Control, replicate 1

source_name: Roots of seedlings fixed in ground control KFT, from flight 2, replicate 1


title: pCaMV35S:14-3-3κ:GFP Root, First-Actuated, replicate 2

source_name: Roots of seedlings fixed in first-actuated KFT, from flight 2, replicate 2


title: DMSO_Rep2

value: unteated


title: pCaMV35S:14-3-3κ:GFP Root, First-Actuated, replicate 1

source_name: Roots of seedlings fixed in first-actuated KFT, from flight 2, replicate 1

value: Whole Root


title: CYT_input

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default
Deeptools was used to processed bam file
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deeptools

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Two replicates was cytarabine treated for 24 hours.

tag: chip antibody


title: DMSO_Rep1


title: CTRL_input


title: HCT25-6LM PDO

source_name: PDO established from surgical specmen HCT25-6LM


title: HCT17-1T PDO

source_name: PDO established from surgical specmen HCT17-1T


title: pCaMV35S:14-3-3κ:GFP Root, Ground Control, replicate 3

source_name: Roots of seedlings fixed in ground control KFT, from flight 2, replicate 3

value: Wassilewskija (WS)


title: Born from Stressed Mother, Raised by Control Mother 2


title: Born from Stressed Mother, Raised by Control Mother 1


title: CYT_NCL_K9_Rep1


title: HCT25-2T PDO

source_name: PDO established from surgical specmen HCT25-2T


title: HCT25-10LMRR PDO

source_name: PDO established from surgical specmen HCT25-10LMRR


title: HCT25-3T PDO

source_name: PDO established from surgical specmen HCT25-3T


title: HCT17-3LM PDO

source_name: PDO established from surgical specmen HCT17-3LM


title: Born from Stressed Mother, Raised by Control Mother 3


title: Stress pup from stressed mother 5

value: Mother exposed to TMT


title: Stress pup from stressed mother 3


title: CYT_NCL_K9_Rep2


title: gavaged with DEHP（625 mg/kg bw）for 28 days [WT-DEHP5]

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

data_processing:
Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of mm10 using HISTA. Transcript assembly were performed using Cufflink. DEG analyses were performed using Cuffdiff.
Genome_build: GRCm38（mm10）
Supplementary_files_format_and_content: tab-delimited text files include fpkm for each Sample.

source_name: Liver

growth_protocol: 20-30g C57 male mice, 12 mice per group

extract_protocol:
Liver were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kitwas used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four groups of mice were gavaged with  0.5% CMC or 625 mg/kg bw DEHP for 28 or 90 days.

value: liver

tag: Sex

value: male

value: Wild type

tag: agent

value: DEHP（625 mg/kg bw)

tag: time point

value: 28 days


title: gavaged with DEHP（625 mg/kg bw）for 28 days [WT-DEHP7]


title: gavaged with DEHP（625 mg/kg bw）for 28 days [WT-DEHP6]


title: CTRL_NCL_K9_Rep1


title: Control pup from control mother 2

value: Mother not exposed TMT


title: Control pup from control mother 4


title: Stress pup from stressed mother 4


title: gavaged with DEHP（625 mg/kg bw）for 90 days [WT-DEHP2]

value: 90 days


title: gavaged with DEHP（625 mg/kg bw）for 90 days [WT-DEHP3]


title: Control pup from control mother 1


title: Control pup from control mother 5


title: Stress pup from stressed mother 2


title: Stress pup from stressed mother 1


title: Control pup from control mother 3


title: gavaged with 0.5% CMC for 28 days [WT-CT7]

value: 0.5percent CMC


title: gavaged with 0.5% CMC for 28 days [WT-CT6]


title: gavaged with 0.5% CMC for 28 days [WT-CT5]


title: gavaged with 0.5% CMC for 90 days [WT-CT4]


title: CTRL_NCL_K9_Rep2


title: gavaged with 0.5% CMC for 90 days [WT-CT3]


title: RH4_ACBI1_7d_MYCN_r2

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
adaptor trimming and QC: fastqc v0.11.7
reads alignment: Hisat2 v2.1.0 with options ?--rna-strandness RF --fr?
BAM generation and index: Samtools v1.9
Mapping QC: Qualimap v2.2.1
read fragment count at the gene level: featurecounts v1.6.3 with the options ?-p -B -O -M --fraction?
differential gene expression: DESeq2 v3.7
Genome_build: GRCH38
Supplementary_files_format_and_content: final expression level of genes in text file format

extract_protocol:
After reverse crosslinking, ChIP DNA was purified using MinElute PCR Purification Kit (Qiagen).
ChIPseq Library

treatment_protocol: ChIP assays for SWI/SNF interference studies were performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode) according to the manufacturer’s instructions. Briefly, Cas9 expressing RH4 cells were transduced with indicated sgRNAs. Alternatively, cells were treated with 250nM ACBI1 or cis confirmation negative control compound respectively. After expansion of cells at 7 days post transduction/treatment, cells were fixed using a dual step protocol with ChIP Cross-link Gold (Diagenode, C01019027) for 30min followed by 1% formaldehyde for 15 min, harvested and sonicated with the Bioruptor Pico sonication device (Diagenode) for 13 cycles (30sec ON, 30sec OFF). Sonicated lysates were then quantified and 25µg (35µg for MYCN ChIP) of chromatin were spiked-in with Drosophila Chromatin (Active Motif) and incubated overnight at 4°C with 4µg (7µg for MYCN ChIP) of antibody and an antibody against the Drosophila specific histone variant H2Av (Active Motif). Amounts of spike-in components were calculated according to manufacturers instructions.

tag: cell line

tag: diagnosis

value: rhabdomyosarcoma

value: 7 days treatment with 250nM ACBI1 (active) PROTAC compound (University of Dundee, Institute of Chemical and Structural Biology available at Boehringer Ingelheim (opnMe))

value: wild type

tag: antibody

value: anti-MYCN, Thermo Fisher, MA1-170


title: RH4_sgBRG1_MYCN_r2

value: CRISPR targeting; sgRNA against BRG1; GGGGCAGCAGCATTCGCCAT, RNA collection 7 days post transduction


title: RH4_sgScr_MYCN_r2

value: CRISPR targeting; sgRNA neg crtl (scrambled); GTAGCGAACGTGTCCGGCGT, RNA collection 7 days post transduction


title: RH4_cis_7d_MYCN_r2

value: 7 days treatment with 250nM cis conformation (inactive) PROTAC compound (University of Dundee, Institute of Chemical and Structural Biology available at Boehringer Ingelheim (opnMe))


title: gavaged with DEHP（625 mg/kg bw）for 90 days [WT-DEHP4]


title: gavaged with DEHP（625 mg/kg bw）for 90 days [WT-DEHP1]


title: gavaged with DEHP（625 mg/kg bw）for 28 days [KO-DEHP6]

value: macrophage-specific-Pparg knockout


title: gavaged with DEHP（625 mg/kg bw）for 90 days [KO-DEHP4]


title: gavaged with DEHP（625 mg/kg bw）for 28 days [KO-DEHP7]


title: RH4_sgScr_SMARCC1

value: anti-SMARCC1, Abcam, ab172638


title: RH4_sgBRG1_SMARCC1


title: RH4_ACBI1_7d_SMARCC1


title: RH4_ACBI1_7d_BRG1

value: anti-BRG1, Abcam, ab110641


title: RH4_ACBI1_7d_H3K27ac

value: anti-H3K27ac, Active Motif, 39133


title: gavaged with DEHP（625 mg/kg bw）for 28 days [KO-DEHP5]

value: liver

value: male


title: gavaged with DEHP（625 mg/kg bw）for 90 days [KO-DEHP2]

value: DEHP（625 mg/kg bw)


title: gavaged with DEHP（625 mg/kg bw）for 90 days [KO-DEHP3]


title: RH4_DPF2

extract_protocol:
After DNA purification, library preparation was performed as previously described by Kidder and Zhao 2014.
ChIPseq Library

treatment_protocol: Approximately 10-20 million human RH4 or RH30 cells were fixed with 1% formaldehyde for 10 minutes, following 4h treatment with 2 mM ENTINOSTAT (0.2% DMSO) or 0.2% DMSO. The formaldehyde was quenched by adding glycine to a final concentration of 100 mM, and cells were incubated on ice for 5 minutes. The fixed cells were washed in ice cold PBS, and centrifuged at 1200g for 5 minutes. After decanting the supernatant, the pellets were flash frozen with liquid nitrogen. For ChIP experiments, pellets were resuspended in 1X TE pH 7.4 with protease inhibitors (Active Motif, Cat# 37490), and sheared with Active Motif EpiShear probe sonicator (30 seconds pulse, 30 seconds recovery, for 10-14 minutes of total shearing time). The sonication buffer (TE pH 7.4, protease inhibitors) was adjusted to RIPA buffer with 200 mM NaCl (ChIP IP buffer; Table S5F) and the mixture was centrifuged at 40C for 10 minutes at 16,000g. The supernatant was incubated overnight at 40C with 3 ug antibody (Table S5B), with overhead rotation for approximately 1 hour. After equilibration at 1 hour, 40 mL Protein A Dynabeads (ThermoFisher cat#10002D) were added after buffer exchange into ChIP IP buffer. Spike-in control was used in comparative experiments with Entinostat. The mixture was gently rotated at 40C overnight and subsequently washed twice each with ChIP Wash Buffer, ChIP IP Buffer, LiCl Buffer, and TE pH 7.4 (Table S5F). Beads were resuspended in 100 mL TE pH 7.4, and 2.5 mL SDS (10%), and 5 mL Proteinase K (Active Motive, Cat# 53001) was added and mixed by pipetting. The mixture was incubated in PCR heating blocks for 16 hours at 65 0C.

value: anti-DPF2, Abcam, ab134942


title: RH4_cis_7d_SMARCC1


title: RH4_cis_7d_BRG1


title: RH4_cis_7d_H3K27ac


title: RH4_BRD9

value: anti-BRD9, Abcam, ab137245


title: gavaged with 0.5% CMC for 28 days [KO-CT6]

value: 0.5percent CMC

value: 28 days


title: gavaged with 0.5% CMC for 28 days [KO-CT5]


title: gavaged with 0.5% CMC for 90 days [KO-CT4]

value: 90 days


title: RH4_sgBRG1_H3K27ac

value: rhabdomyosarcoma


title: RH4_sgBRG1_HDAC2

value: anti-HDAC2, Abcam, ab7029


title: RH4_sgBRG1_H3K9ac

value: CRISPR targeting; sgRNA against BRG1; GGGGCAGCAGCATTCGCCAT, RNA collection 7 days post transduction

value: anti-H3K9ac, Cell Signaling Technologies, 9649


title: gavaged with 0.5% CMC for 28 days [KO-CT7]


title: gavaged with 0.5% CMC for 90 days [WT-CT1]

value: Wild type


title: gavaged with 0.5% CMC for 90 days [KO-CT3]

value: macrophage-specific-Pparg knockout


title: RH4_sgBRG1_BRG1


title: gavaged with 0.5% CMC for 90 days [KO-CT2]


title: gavaged with DEHP（625 mg/kg bw）for 90 days [KO-DEHP1]


title: gavaged with DEHP (2500 mg/kg bw) [KDEHP3]

data_processing:
Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of mm10 using HISTA. Transcript assembly were performed using Cufflink. DEG analyses were performed using Cuffdiff.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include fpkm for each Sample.

source_name: gavaged with DEHP (2500 mg/kg bw)

treatment_protocol: Two groups of mice were gavaged with  0.5% CMC, 2500 mg/kg bw DEHP, respectively.

tag: strain background

tag: genotype/variation

value: liver-specific-Pparg knockout

value: gavaged with DEHP (2500 mg/kg bw)


title: RH4_sgBRG1_input


title: RH4_sgScr_H3K27ac

value: CRISPR targeting; sgRNA neg crtl (scrambled); GTAGCGAACGTGTCCGGCGT, RNA collection 7 days post transduction

value: anti-H3K27ac, Active Motif, 39133


title: HCT25-1T PDO

source_name: PDO established from surgical specmen HCT25-1T

tag: tissue

value: colorectal cancer

value: primary tumor


title: gavaged with DEHP (2500 mg/kg bw) [KDEHP4]

value: male

value: liver


title: RH4_sgScr_H3K9ac


title: RH4_sgScr_input


title: RH4_sgScr_HDAC2


title: gavaged with 0.5% CMC for 90 days [KO-CT1]

value: 0.5percent CMC


title: gavaged with DEHP (2500 mg/kg bw) [KDEHP2]


title: gavaged with DEHP (2500 mg/kg bw) [KDEHP5]


title: gavaged with 0.5% CMC [KCT5]

source_name: gavaged with 0.5% CMC

value: gavaged with 0.5% CMC


title: gavaged with DEHP (2500 mg/kg bw) [KDEHP1]


title: RH4_Ent_4h_PBRM1

value: 4 hours treatment with 2μM Entinostat (NCI Development Therapeutics Program (DTP), https://dtp.cancer.gov/)  (0.2% DMSO, Sigma, D8418)

value: wild type

value: anti-PBRM1, Active Motif, 61381


title: gavaged with 0.5% CMC [KCT4]


title: RH4_Ent_4h_BRG1

value: rhabdomyosarcoma

value: anti-BRG1, Abcam, ab110641


title: RH4_DMSO_4h_PBRM1

value: 4 hours treatment with 0.2% DMSO (Sigma, D8418)


title: gavaged with 0.5% CMC [KCT2]


title: H3ΔNThr22_monocyte-derived macrophages_donor3

city: Stanford

first: Purvesh

last: Khatri

state: California

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

data_processing:
All data processing was carried out using the PEPATAC pipeline (http://code.databio.org/PEPATAC/) version 0.8.6
In summary: Adapter trimming was performed by Skewer, followed by QC analysis with FastQC
Reads were aligned to human repeats (https://github.com/databio/ref_decoy) and mitochondrial DNA (http://www.ncbi.nlm.nih.gov/nuccore/251831106) using bowtie2 with the following parameters: -p 30 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Remaining unaligned reads were aligned to the human genome (GRCh38) using bowtie2 with the following parameters: -p 30 --very-sensitive -X 2000
Duplicates were removed using Picard tools with the following parameters: VALIDATION_STRINGENCY=LENIENT. BigWig files were then generated using "bamSitesToWig" tool in PEPATAC followed by wigToBigWig (http://hgdownload.cse.ucsc.edu/admin/exe/).
Genome_build: GRCh38
Supplementary_files_format_and_content: Smooth bigWig file output from PEPATAC pipeline for each sample.

source_name: Monocyte-derived macrophages

growth_protocol: U937 cells were cultured in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (ATCC), glutamine (Gibco), and penicillin/streptomycin. Primary monocytes were cross-linked immediately after purification by a magnetic bead-based negative selection kit (Miltenyl Biotec, 130-096-537). Monocytes were cultured in RPMI-1640 media with 30 ng/mL M-CSF for 5 days to obtain monocyte-derived macrophages.

extract_protocol:
Cells were resuspended in ChIP lysis buffer (50mM HEPES-KOH pH 7.5, 140 mM NaCl, 1mM EDTA pH8, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, protease inhibitors) and incubated for 10 mins on ice. Cell lysate was sonicated with Branson Digital Sonifier (Branson) and diluted with RIPA buffer by 10 fold before incubating overnight with antibody/protein-A magnetic complexes. Beads were washed two times with ChIP wash buffer I (20mM Tris pH8, 0.1%SDS, 1% Triton, 0.1% Sodium Deoxycholate, 2mM EDTA, 150mM NaCl) and two times with ChIP wash buffer II ( 20mM Tris pH8, 0.1%SDS, 1% Triton, 0.1% Sodium Deoxycholate, 2mM EDTA, 500 mM NaCl). IPed DNA was eluted from beads, de-crosslinked at 68C and purified using the MinElute PCR Purification Kit (Qiagen).
Purified-DNA was subjected for library preparation using the NEBNext Ultra II DNA library prep kit (NEB) following the manufacturer’s protocol

treatment_protocol: Cells were cross-linked with 1% formaldehyde (Sigma) for 8 mins at room temperature with gentle mixing. Cross-linking reaction was stopped by adding final concentration of 125mM glycine and incubate for 5 mins at room temperature.

value: Monocyte-derived macrophages

value: anti-Cleaved H3 Thr22 (CST) D7J2K #12576


title: gavaged with 0.5% CMC [KCT3]

value: liver-specific-Pparg knockout


title: gavaged with 0.5% CMC [KCT1]


title: Bulk H3_monocyte-derived macrophages_donor3

value: anti-H3 (abcam) ab1791


title: RH4_DMSO_4h_BRG1


title: JMJD3_null_3

city: SAN FRANCISCO

first: John

last: Liu

address: 35 Medical Center Way

institute: UCSF

data_processing:
Reads were aligned to the mouse genome mm9 using Tophat v2.0.10 (Trapnell et al., 2009) with the following flags: --library-type fr-firststrand –transcriptome-index mm9.gtf –prefilter-multihits. Differential expression was analyzed using Cuffdiff v2.1.1 (Trapnell et al., 2010) with the flags: -b genome.fa -u --library-type fr-firststrand.
Genome_build: mm9

molecule: polyA RNA

source_name: Dentate Gyrus

growth_protocol: Jmjd3 F/F mice which contain Jmjd3 alleles with loxP sites flanking the JmjC catalytic domain were maintained and genotyped as described (Iwamori et al., 2013; Park et al., 2014)

extract_protocol:
Trizol followed by DNAse I treatment; QIAGEN Rneasy columns.
Libraries were prepared using illumina Truseq Stranded mRNA kit

treatment_protocol: Dentate gyrus from 3 biological replicates (P7 hGFAP-Cre;Jmjd3F/F and littermate control) was micro-dissected

tag: developmental stage


title: H3ΔNThr22_monocyte-derived macrophages_donor2


title: Bulk H3_monocyte-derived macrophages_donor2


title: JMJD3_null_2

tag: genotype


title: gavaged with 0.5% CMC for 90 days [WT-CT2]

value: Wild type

value: 90 days


title: RH4_sgScr_BRG1

value: CRISPR targeting; sgRNA neg crtl (scrambled); GTAGCGAACGTGTCCGGCGT, RNA collection 7 days post transduction


title: JMJD3_null_1


title: H3ΔNThr22_monocyte-derived macrophages_donor1


title: JMJD3_wt_3

value: littermate controls


title: JMJD3_wt_2


title: Bulk H3_primary monocyte_donor3

source_name: Primary monocytes

value: Peripheral blood monocytes


title: H3ΔNThr22_primary monocyte_donor2


title: clear cell ovarian carcinoma_17

city: Seoul

first: Ha-Yeon

last: Shin

address: 237, Dogok-ro

department: Obstetrics and Gynecology

country: South Korea

institute: Yonsei University

data_processing:
FASTQ format were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using STAR and Bowtie2.
Read counts analysis were conducted using HTSeq and Picard.
Normalization and differential expression were conducted by DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: endometriosis_associated.txt: TXT file contains normalized abundance measurements for each sample.

source_name: paraffin-embedded tissue

extract_protocol:
All FFPE tissue slides were stained with hematoxylin and reviewed by an experienced gynecological pathologist. The selected lesions from whole tissues were excised by laser capture microdissection. For LCM, the FFPE tissues were sectioned and placed on slides with polyethylene terephthalate membrane (Leica Microsystems Inc., IL, USA). LCM was performed using a Leica AS LMD laser microdissection system (Leica Microsystems Inc.) according to the manufacturer’s instructions. An RNeasy FFPE kit (Qiagen, Valencia, CA, USA) was used to isolate total RNA from FFPE tissues according to the manufacturer’s instructions.
Sample emulsion PCR, emulsion breaking, and enrichment were performed using an Ion PITM Template OT2 200 Kit v3 (Life Technologies, Part #4488318 Rev. B.0) according to the manufacturer’s instructions. Multiple barcoded libraries were combined with equal molar ratios for one Ion PITM v2 chip. Two-pooled Ion AmpliSeqTM Exome libraries were loaded onto a single Ion PITM v2 chip. Five-pooled Ion AmpliSeq™ Transcriptome libraries were loaded onto a single Ion PITM v2 chip. Subsequent emulsion PCR and enrichment of the sequencing beads of the pooled libraries were performed using the Ion OneTouchTM system (Life Technologies) within approximately 7 h, according to the manufacturer’s protocol. Finally, 520 Flows sequencing was done on the Ion PITM v2 chip using Ion PITM Sequencing 200 Kit v3 (Life Technologies, Part #4488315 Rev. B.0) on the Ion ProtonTM sequencer (Life Technologies).

value: clear cell ovarian carcinoma


title: clear cell ovarian carcinoma_15


title: clear cell ovarian carcinoma_16


title: endometrioid ovarian carcinoma_11

value: endometrioid ovarian carcinoma


title: H3ΔNThr22_rep1

source_name: Monocytic cell line


title: clear cell ovarian carcinoma_13


title: clear cell ovarian carcinoma_12


title: H3ΔNThr22_primary monocyte_donor3


title: Bulk H3_rep2


title: H3ΔNThr22_rep2


title: Bulk H3_monocyte-derived macrophages_donor1


title: Bulk H3_rep1


title: clear cell ovarian carcinoma_14


title: Huh7_shARID1A_RNA-seq

city: Guangzhou

first: Shanshan

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.
Reads of each sample were aligned to the GRCh38/hg38 reference genome using BWA.
RPKM (Reads Per Kb per Million reads) is used to calculate gene expression.
Genome_build: GRCh 38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: cell line

growth_protocol: DMEM plus 10% fetal bovine serum

extract_protocol:
Total RNA was extracted from cells using TRIZOL (Invitrogen, USA) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shControl Huh7 and shARID1A Huh7 cells without or with 100nM rapamycin treatment for 6 hours

value: liver cancer

value: DMSO


title: endometrioid ovarian carcinoma_10


title: Huh7_shARID1A_Rapa_RNA-seq

value: Rapa


title: endometrioid ovarian carcinoma_8


title: JMJD3_wt_1


title: Huh7_shControl_Rapa_RNA-seq

value: control


title: clear cell ovarian carcinoma_11


title: Huh7_shControl_RNA-seq


title: Bulk H3_primary monocyte_donor2


title: Huh7_shARID1A_Rapa_ATAC-seq

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.
Reads of each sample were aligned to the GRCh38/hg38 reference genome using BWA.
Peaks of ATAC-seq were identified using MACS v2.0 with cutoff q<0.05.
Genome_build: GRCh 38
Supplementary_files_format_and_content: peak text files

extract_protocol:
Nuclei isolated from 50,000 counted cells were used for transposition reaction with transposase. Column-purified DNA was amplified in 20μl reactions with high-fidelity 2×PCR Master Mix using primers with unique barcodes to setup library.
libraries were constructed following the NEB kit


title: endometrioid ovarian carcinoma_7


title: H3ΔNThr22_primary monocyte_donor1


title: endometrioid ovarian carcinoma_12


title: Bulk H3_primary monocyte_donor1


title: clear cell ovarian carcinoma_10


title: clear cell ovarian carcinoma_8


title: Huh7_shControl_Rapa_ATAC-seq


title: Huh7_shARID1A_ATAC-seq


title: endometrioid ovarian carcinoma_6


title: endometrioid ovarian carcinoma_9


title: Huh7_shControl_ATAC-seq


title: clear cell ovarian carcinoma_7


title: endometrioid ovarian carcinoma_5


title: clear cell ovarian carcinoma_6


title: endometrioid ovarian carcinoma_3


title: sibetamcat_pos_24h_2

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

country: France

institute: Institut Imagine

data_processing:
Mapping with hisat2 2.0.4
Sort with samtools 1.4
Deduplication with Picard 1.9.2 MarkDuplicates
Sort with samtools 1.4
Assign to features (Ensembl-annotated genes) using featureCounts 1.5.0
Genome_build: Human v37 (hg19)
Supplementary_files_format_and_content: Tab-delimited table of raw read counts for Ensembl genes and for each sample (Final_gene_count_table.txt)
Supplementary_files_format_and_content: Tab-delimited table with the layout for processing (Matrix_layout.txt)

source_name: H1299 cell line

growth_protocol: Human non-small cell lung carcinoma H1299 cells carrying a doxycycline (DOX)-inducible BRCA2 shRNA (Lai et al., 2017), were cultivated in monolayers in Dulbecco’s Modified Eagle Medium (DMEM, Sigma-Aldrich) supplemented with 10% tetracycline-free foetal bovine serum (Clontech). For induction of BRCA2 shRNA, 2 µg/mL DOX (Sigma-Aldrich, D9891) was added to growth medium for 3 days.

extract_protocol:
Cells were collected for RNA extraction using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s guidelines. RNA samples were quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and RNA size profile and integrity were analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RNA integrity number estimates for all samples were between 9.0 and 10.0.
Poly(A) transcript enrichment and strand specific library preparation were performed using TruSeq Stranded mRNA kit (Illumina) following manufacturer’s instructions. Libraries were amplified (15 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (Lamble et al., 2013). Individual libraries were normalized using Qubit and size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were pooled together and diluted to ~10 nM for storage. Each library aliquot was denatured and further diluted prior to loading on the sequencer.

treatment_protocol: H1299 cells were cultured in presence or absence of DOX for 3 days. A day after the addition of DOX both cultures were transfected with control siRNA or siβ-catenin. The following day 250 nM LY2090314 was added to the media for 24 hours.

tag: brca2 status


title: clear cell ovarian carcinoma_5


title: sibetamcat_pos_unt_3

value: siBeta-catenin


title: sibetamcat_pos_24h_1


title: sibetamcat_pos_24h_3


title: sibetamcat_pos_unt_2


title: sibetamcat_pos_unt_1


title: Allstar_pos_24h_2


title: Allstar_pos_24h_3


title: clear cell ovarian carcinoma_4


title: endometrioid ovarian carcinoma_2


title: clear cell ovarian carcinoma_3


title: clear cell ovarian carcinoma_9


title: Allstar_pos_24h_1


title: clear cell ovarian carcinoma_2


title: Allstar_pos_unt_1


title: endometrioid ovarian carcinoma_1


title: Allstar_pos_unt_2


title: endometrioid ovarian carcinoma_4


title: sibetamcat_neg_24h_3

value: WT


title: adjacent endometriosis to endometrioid ovarian carcinoma_3


title: clear cell ovarian carcinoma_1


title: adjacent endometriosis to endometrioid ovarian carcinoma_1


title: adjacent endometriosis to endometrioid ovarian carcinoma_2


title: sibetamcat_neg_unt_3


title: adjacent endometriosis to clear cell ovarian carcinoma_7


title: sibetamcat_neg_24h_2


title: sibetamcat_neg_unt_2


title: Allstar_neg_24h_3


title: adjacent endometriosis to clear cell ovarian carcinoma_4


title: adjacent endometriosis to clear cell ovarian carcinoma_6


title: Allstar_neg_24h_1


title: adjacent endometriosis to clear cell ovarian carcinoma_5


title: Allstar_neg_24h_2


title: Allstar_pos_unt_3


title: Allstar_neg_unt_3


title: Allstar_neg_unt_2


title: adjacent endometriosis to clear cell ovarian carcinoma_2


title: adjacent endometriosis to clear cell ovarian carcinoma_3


title: atypical endometriosis_18

value: atypical endometriosis


title: U937 cells, ELANE_rep1 (ChIP-seq)

description: Neutrophil Elastase IP

data_processing:
All data processing was carried out using the PEPATAC pipeline (http://code.databio.org/PEPATAC/) version 0.8.6
In summary: Adapter trimming was performed by Skewer, followed by QC analysis with FastQC
Reads were aligned to human repeats (https://github.com/databio/ref_decoy) and mitochondrial DNA (http://www.ncbi.nlm.nih.gov/nuccore/251831106) using bowtie2 with the following parameters: -p 30 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Remaining unaligned reads were aligned to the human genome (GRCh38) using bowtie2 with the following parameters: -p 30 --very-sensitive -X 2000
Duplicates were removed using Picard tools with the following parameters: VALIDATION_STRINGENCY=LENIENT. Peaks were then called using MACS2 callpeak using the following parameters: -f BAMPE -q 0.25 --call-summits --nomodel --keep-dup all. The comparison/control (-c) parameter was supplied with the input sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.narrowPeak files are the narrowPeak file outputs from MACS2 (TSVs). Columns are: 'chromosome', 'start', 'end', 'peak name', 'int_neglogqval', '', 'FoldChange'

growth_protocol: U937 cells were cultured in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (ATCC), glutamine (Gibco), and penicillin/streptomycin.Primary monocytes were cross-linked immediately after purification by a magnetic bead-based negative selection kit (Miltenyl Biotec, 130-096-537). Monocytes were cultured in RPMI-1640 media with 30 ng/mL M-CSF for 5 days to obtain monocyte-derived macrophages.

treatment_protocol: U937 cells were cross-linked with 1% formaldehyde (Sigma) for 8 mins at room temperature with gentle mixing. Cross-linking reaction was stopped by adding final concentration of 125mM glycine and incubate for 5 mins at room temperature.

value: anti-Neutrophil Elastase (abcam) ab21595 lot# GR3201583-14


title: atypical endometriosis_16


title: atypical endometriosis_17


title: U937 cells, CTSG_rep1 (ChIP-seq)

description: Cathepsin G IP

value: anti-Cathepsin G (abcam) ab49854 lot# GR298953-6


title: sibetamcat_neg_24h_1


title: U937 cells, PRTN3_rep1 (ChIP-seq)

description: Proteinase 3 IP

value: anti-PR3 (abcam) EPR6277 ab133613


title: U937 cells, H3ΔNThr22_rep1 (ChIP-seq)

description: Cleaved H3 Thr22 CST IP

value: anti-Cleaved H3 Thr22 (CST) D7J2K #12576


title: atypical endometriosis_15


title: atypical endometriosis_14


title: U937 cells, Bulk H3_rep1 (ChIP-seq)

description: Total H3 antibody IP

value: anti-H3 (abcam) ab1791


title: U937 cells, Input DNA_rep1 (ChIP-seq)

description: Input DNA replicate 1


title: atypical endometriosis_13


title: sku5 Root, Ground Control, Blue Origin, replicate 3

data_processing:
Fastq files containing the reads were trimmed using Trimmomatic (v0.36) for removal of adapters and low-quality bases
Before and after trimming, QC of the reads was performed with FastQC (v0.11.4) and MultiQC (v1.1)
Reads were aligned to the WS transcriptome using the STAR aligner (v2.7.3a)
Transcripts were quantified using RSEM (v1.2.31)
Differential expression analysis was carried out using DESeq2 with cutoffs of an FDR of q < 0.05 and greater than 2-fold change
Genome_build: Arabidopsis thaliana ecotype Wassilewskija (WS) Transcriptome; Gan et al., 2011. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419.
Supplementary_files_format_and_content: The differential expression output are provided as sheets in an XLSX workbook (VG_BO_FLTvGC_DEGs.xlsx). Each sheet contains a FLT vs. GC comparison for a different genotype and flight platform combination. Data for all genes with greater than 2-fold change, and with a q-value < 0.05, are provided. A file containing the non-normalized RSEM-output expression values has also been provided (VG_BO_Expression.xlsx). In this expression file, the VG Col-0 expression values are separated from the VG & BO WS and sku5 values, as each was aligned to a different reference genome before quantification.

source_name: solid 0.5x MS media plates; ground control for the Blue Origin NS-12 flight, 11-day-old plants harvested to RNALater post-flight

growth_protocol: Petri dishes (100 mm x 15 mm; Fisher Scientific, Pittsburgh, PA, USA), containing 50 mL of a 0.5% Phytagel™-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg’s Vitamin Mixture, were prepared aseptically for planting. Seeds were sterilized via treatment with 70% ethanol for 10 minutes, and then with 50% bleach supplemented with Tween-20 at 2-3 drops per mL for 20 minutes, with seeds being mixed throughout the process. Seeds were washed with sterile water at least 6 times, and stored at 4 °C for 3-5 days. Seeds were dispensed onto the media surface in a laminar flow hood in one row of 12-15 seeds, and plates were sealed with Micropore® tape (3M, Maplewood, MN, USA). Plates were maintained vertically in a growth room at 19 ± 2 °C, with 24-h fluorescent lighting at approximately 80 µmol m-2 s-1 PAR, until the time of transport to the experimental location. At the VG site, plates were maintained in the ambient conditions of the payload facility, under an LED light bank. At the BO site, plates were maintained in the payload processing facility in a Danby herb cultivator at 26 °C (Danby, Ontario, CA; Catalog # DFG17A1B). For each experiment, flight plates were wrapped in Duvetyne Black-Out Cloth (Seattle Fabrics) and this package was Velcro-mounted to the inner wall of the FLEX imaging payload as a piggyback payload.

extract_protocol:
RNALater™-fixed samples were removed from -80 °C storage, and thawed overnight at 4°C. Seedlings were disentangled, and roots were dissected from shoots. Root tissues were used for RNA extraction, and shoots were restored to -80 °C storage. For each experimental condition, 3-4 biological replicates, derived from roots fixed in a single KFT, were used. Excess RNALater™ was removed from roots, and RNA was extracted using the QIAshredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA), using the manufacturer’s instructions. RNase-free DNase (QIAGEN GmbH, Hilden, Germany) was used for on-column digestion and removal of DNA.
The BO and VG RNA extracts were submitted for RNA-Seq analysis. The total RNA concentration was determined with a Qubit® 2.0 Fluorometer (ThermoFisher Scientific, Grand Island, NY, USA), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The RINs of the total RNA used for RNA-Seq library construction were between 7.1 and 9.4. RNA-Seq libraries were constructed at the UF ICBR Gene Expression Core using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s recommendations. Two ERCC controls were used for the experiment: ERCC Mix 1 was used for flight samples and ERCC 2 was used for ground control samples. Briefly, 1 µl of 1:2000 diluted RNA spike-in ERCC (half the amount suggested in the ERCC user guide) spike to 50 ng of total RNA followed by mRNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs, Catalog # E7490). RNA-Seq libraries were then constructed with the NEBNext Ultra Directional Library Prep Kit (New England Biolabs, catalog #E7420) according to the manufacturer's user guide. Briefly, RNA was fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for the desired time. This step was followed by first strand cDNA synthesis using reverse transcriptase and oligo(dT) primers. Synthesis of double-stranded cDNA was performed using the 2nd strand master mix provided in the kit, followed by end-repair and Illumina adaptor ligation. Finally, the uniquely-barcoded libraries were enriched by 10 cycles of PCR amplification, and purified by Agencourt AMPure beads (Beckman Coulter, catalog # A63881). 24 barcoded libraries were sized on the Bioanalyzer, and quantitated via the Qubit 2.0 Fluorometer. Finally, the 24 individual libraries were pooled equimolarly.

treatment_protocol: The VG VP-03 flight launched on December 13th, 2018 from the Mojave Air and Spaceport in California. The VSS Unity detached from its mothership one hour after takeoff, to begin the suborbital portion of the flight. The one minute ascent was characterized by hyper-g which increased steadily to nearly 4.5g over 30 seconds, and then decreased. This was followed by three minutes of microgravity, and one minute of hyper-g on descent, increasing to around 3.5g and decreasing again. A glide of about nine minutes followed, containing a mixture of short hyper- and hypo-g spikes. The VSS Unity landed, and access was provided to the cabin for opening of the FLEX payload. The plates were removed and transported from the runway to a nearby vehicle with a harvest station set up in the rear bay. The BO payload was transported to the launch pad, and loaded into the payload stack of the New Shepard capsule. The NS-12 mission launched at 12:53 PM EST on December 11th, 2019 from the BO West Texas Launch Site. The ascent took about two minutes, reaching a maximum of near 3g before engine cutoff. After a three minute window of microgravity was a one minute hyper-g portion of the descent, with a peak of 5.7g measured. The release of the capsules’ drogue and primary parachutes generated short spikes between 3g and 3.5g, but otherwise this portion of the descent was around 1g, and lasted for four minutes. The FLEX payload was removed from the capsule after landing, and before capsule recovery operations. Plates were removed from the FLEX payload, and carried briefly to a nearby area set up for harvest. The 11-day-old seedlings were harvested and fixed in the same manner as in the VG experiment. The fixation was 33 minutes after landing, with an elapsed time of 43 minutes for the experiment. GC seedlings, which were maintained in the BO Payload Processing Facility during the flight , were removed from the Danby unit and harvested one hour after the FLT seedlings.

tag: cultivar

value: Wassilewskija (WS)

value: Whole roots

tag: age

value: 11 days

tag: biosource type

value: RNALater fixed_sample

tag: flight platform

value: Blue Origin

value: ground control


title: sku5 Root, Ground Control, Blue Origin, replicate 2

tag: treatment


title: sku5 Root, Ground Control, Blue Origin, replicate 1


title: atypical endometriosis_11


title: atypical endometriosis_10


title: atypical endometriosis_8


title: sku5 Root, Flight, Blue Origin, replicate 2

source_name: solid 0.5x MS media plates; flown on the Blue Origin NS-12 flight, 11-day-old plants harvested to RNALater post-flight

value: flown


title: atypical endometriosis_9


title: adjacent endometriosis to clear cell ovarian carcinoma_1


title: WS Root, Ground Control, Blue Origin, replicate 3

value: Wild-type


title: WS Root, Ground Control, Blue Origin, replicate 1


title: atypical endometriosis_5


title: sku5 Root, Flight, Blue Origin, replicate 3


title: atypical endometriosis_7


title: WS Root, Ground Control, Blue Origin, replicate 2


title: atypical endometriosis_4


title: atypical endometriosis_3


title: atypical endometriosis_6


title: atypical endometriosis_2


title: atypical endometriosis_12


title: WS Root, Flight, Blue Origin, replicate 2


title: WS Root, Flight, Blue Origin, replicate 3


title: atypical endometriosis_1


title: WS Root, Flight, Blue Origin, replicate 1


title: endometriosis_7

value: endometriosis


title: WS Root, Ground Control, Virgin Galactic, replicate 3

source_name: solid 0.5x MS media plates; ground control for the Virgin Galactic VP-03 flight, 10-day-old plants harvested to RNALater post-flight

value: 10 days

value: Virgin Galactic


title: WS Root, Ground Control, Virgin Galactic, replicate 2


title: WS Root, Ground Control, Virgin Galactic, replicate 1


title: sku5 Root, Flight, Blue Origin, replicate 1


title: endometriosis_6


title: WS Root, Flight, Virgin Galactic, replicate 2

source_name: solid 0.5x MS media plates; flown on the Virgin Galactic VP-03 flight, 10-day-old plants harvested to RNALater post-flight


title: endometriosis_5


title: endometriosis_4


title: endometriosis_3


title: Col-0 Root, Ground Control, Virgin Galactic, replicate 3

value: Columbia (Col-0)


title: endometriosis_2


title: endometriosis_9


title: Col-0 Root, Flight, Virgin Galactic, replicate 3


title: endometriosis_8


title: Col-0 Root, Ground Control, Virgin Galactic, replicate 1


title: Col-0 Root, Flight, Virgin Galactic, replicate 2


title: Col-0 Root, Ground Control, Virgin Galactic, replicate 2


title: C017_Adipose

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

description:
Ion AmpliSeq Transcriptome
Subcutaneous_adipose_variance_stabilized_counts

data_processing:
Raw reads were obtained by mapping the sequence to the human genome build, hg19.
DESeq2 was used to identify the differentially expressed (DE) genes between the control and PDAC
For discovery purpose, a fold change of 1.2 and FDR of 0.15 were used to identify DE genes.
For PCA and performing correlation with CAWL, variance stabilization counts generated from DESeq2 were used
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for all the muscle samples
Supplementary_files_format_and_content: tab-delimited text files include raw counts for all the adipose samples

source_name: Control adipose

extract_protocol:
Muscle and adipose tissues were homogenized using TissueRuptor homogenizer. RNA was isolated from both the tissue types using AllPrep DNA-RNA-miRNA Universal Kit.
For muscle, library preparation was done in accordance with AmpliSeq Transcriptome Human Gene Expression Kit (A26325, Thermo-Fisher Scientific, MAN00010742 Rev. A.0). 10 ng of RNA was used as the starting material. Libraries for all samples were prepared simultaneously.  Libraries were barcoded using Ion Xpress Barcode 1-16 Kit (4471250, Thermo-Fisher Scientific).  Libraries were quantified using the Ion TaqMan Quantitation Kit (4468802, Thermo-Fisher Scientific) in Fast Mode using the 7900HT (Thermo-Fisher Scientific).  Libraries were diluted to 75pM for sequencing.
For adipose, automated library preparation was completed according to the protocol available with the Ion Chef (MAN0013432). 10 ng of RNA was used as the starting material. Libraries were barcoded using the plates available with the Chef Kit. Libraries were diluted to 50pM for sequencing.
Template prep and sequencing were performed using the Ion PI Hi-Q Chef Kit with template quantitation using the IonSphere Quality Control Kit

treatment_protocol: RNA isolation, sequencing for all muscle and adipose samples were done at one time.

value: Subcutaneous adipose

tag: Sex

value: Male


title: Col-0 Root, Flight, Virgin Galactic, replicate 1


title: ESSEX HL 24 (HY5_HL_4)

city: Colchester

first: Ellie

middle: Jane

last: Stallard

state: Essex

address: University of Essex

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

data_processing:
Sequence data was generated on a Illumina NovaSeq 6000 (model identifier HWI-ST1276; FlowCell ID- C1162ACXX). Raw unfiltered data deposited as FASTQ files (single-read).  Raw sequence reads ranged from from 19861503 to 27395835. Sequence reads base calling using Illumina CASAVA software calculated from the Phred score to have an error rate of 0.03% in all reads and Q30 values of 92.83% to 94.2%.
Raw sequence data filtering to remove adapter sequences (5'Adapter (RA5) 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' ; 3' Adpter (RA3) 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(6-nucleotide index)ATCTCGTATGCCGTCTTCTGCTTG-3 ; 6 nucleotide index sequence CGATGT), reads where >10% of base calls were uncertain and >50% of nucleotides in a sequence were of low qulaity (base quality call >20). Cleaned sequence reads ranged from 19826717 to 27063004.
Read alignment to reference genome (TAIR 10) conducted using the program HISAT2 v2.0.5 using the default parameters. >98% of filtered reads were mapped to the genome and of these 98.57% of aligned reads mapped to exons. Outputs are  files are in BAM files for each sample.
Transcript abundance is the measure of gene expression and is expressed as Fragments Per Kilobase of transcript sequence per Million base pairs sequenced (FPKM) and is scored on reads that map to exons. The software used was HTSeq v0.6.1 in -m union mode.Within each treatment/genotype group of 4 the square of the Pearson correlation coefficient >0.92, with the exception of BBX32_HL_2 and BBX32_HL_4 comparison for which the value was 0.82.
Differential expression analysis between treatments used normalised mean values from each group  (e.g. COL0,  COL0_HL etc.) and was determined using the program DESeq2 v1.20.0 (normalisation method DEseq) to generate log2 fold change and p values determined using a negative binomial distribution  estimation model. False discovery rate (Benajmini-Hochberg) generated padj. values ,which were regarded as significant at <0.05.
Genome_build: TAIR 10

source_name: fully expanded leaf

growth_protocol: Arabidopsis thaliana plants (Col-0; BBX32-10; hy5-2 )  were grown under a 8:16-h light:dark cycle at 23°C, 60% relative humidity, and light intensity of 150 µmol m-2 s-1. Individual Arabidopsis seed were sown  onto a soil mix (Scotts Levingtons F2+S compost) in round pots (2.5 cm diameterx x 5cm) and placed for 3 d at 4°C for stratification before transferring to growth conditions for germination and growth . The Col-0 and hy5-2 genotypes were obtained from the Euorpean Arabidopsis Stock Centre, BBX32-10 seed was a kind gift from  Dr Rajnish Khanna (then at Mendel Biotechnology Inc., Cailfornia, USA).

extract_protocol:
Total RNA was isolated from four individual plants (4 leaves per plant) per treatment (8 in total)  using TRIzol reagent according to manufactuere's protocol  (Invitrogen), followed by DNAase1 treatment, further phenol extraction, ethanol precipitation and re-suspension in sterile distilled water after brief drying. Concnetration of RNA was deterimined initially using a nanodrop spectrophotomer. Quality of the RNA and its concentration was checked on a Agilent 2100 Bioanalyzer using RNA 6000 nanochip according to the manufacter's protocol. The 24 samples (represneting 6 goups of  biological replicates  were confirmed by quantitative real time PCR as having no significant differences between them in the cDNA levels of transcripts of a PP2A reference housekeeping gene. Samples were delivered frozen on dry ice within 24h to the sequence service provider (Novogene, Cambridge).
This was conducted by Novogene (Cambridge, UK). The total RNA was enriched for mRNA using oligo-dT magnetic beads. After recovery of the enriched mRNA fraction, the RNA was fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamer primers and revrse transcriptase.After first-strand synthesis, a custom second-strand synthesis buffer  (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The ds cDNA was purified from the  reaction solution, end repaired and a 3' A added. Adaptors were then ligated onto the tailed cDNA fragments. Sequencing adaptors were a standard Illumina design. Adaptor - fragments were size selected (250-300 bp insert size) and enriched by PCR amplification. Librar concentration was initially quantified using a Qubit 2.0 fluorimeter (Life Technologies). Insert size was checked on an Agilent 2100 Bioanalyzer and quantified using quantitative PCR.

treatment_protocol: The HL exposure was a light intensity of 1100 (± 100) µmol m-2 s-1 from a white light emitting diode (LED) array (Isolight; Technologica Ltd, Colchester UK).  Six plants, at 35 days post-germination, were exposed to HL for 3.5h. The same number of plants were selected to be LL controls. The HL exposure began 1h after subjective dawn and was carried out in the chamber the plants were grown in. At the end of  HL exposure, one exposed plant, not destined to be sampled, was monitored for its response to HL by determining the degree of decline in the dark-adapted chlorophyll fluoerescence (CF) parameter Fv/Fm using a CF imager (Technologica Ltd., Colchester, UK) and compared with a LL control plant. This confirmed that the HL exposure and plants' responses proceeded as expected.

value: fully expanded leaf

value: 3.5 h high light


title: C016_Adipose


title: endometriosis_1


title: ESSEX HL 23 (HY5_HL_3)


title: WS Root, Flight, Virgin Galactic, replicate 3


title: C010_Adipose


title: C011_Adipose

value: Female


title: C014_Adipose


title: ESSEX HL 22 (HY5_HL_2)


title: ESSEX HL 19 (HY5_3)

value: low light control


title: ESSEX HL 20 (HY5_4)


title: C005_Adipose


title: WS Root, Flight, Virgin Galactic, replicate 1

value: Wassilewskija (WS)

value: Whole roots


title: ESSEX HL 21 (HY5_HL_1)


title: ESSEX HL 18 (HY5_2)


title: ESSEX HL 17 (HY5_1)


title: C004_Adipose


title: C003_Adipose


title: S031_Adipose

source_name: PDAC adipose

value: Pancreatic ductal adenocarcinoma


title: C013_Adipose


title: ESSEX HL 15 (BBX32_HL_3)


title: ESSEX HL 16 (BBX32_HL_4)


title: S029_Adipose


title: C009_Adipose


title: S028_Adipose


title: ESSEX HL 14 (BBX32_HL_2)


title: S027_Adipose


title: ESSEX HL 13 (BBX32_HL_1)


title: ESSEX HL 10 (BBX32_2)


title: S025_Adipose


title: S023_Adipose


title: ESSEX HL 12 (BBX32_4)


title: ESSEX HL 11 (BBX32_3)


title: ESSEX HL 9 (BBX32_1)


title: ESSEX HL 8 (COL0_HL_4)


title: S021_Adipose


title: S020_Adipose


title: ESSEX HL 7 (COL0_HL_3)


title: ESSEX HL 6 (COL0_HL_2)


title: M018_Adipose


title: S018_Adipose


title: ESSEX HL 5 (COL0_HL_1)


title: S017_Adipose


title: ESSEX HL 4 (COL0_4)


title: S015_Adipose


title: ESSEX HL 3 (COL0_3)


title: S014_Adipose


title: S012_Adipose


title: S024_Adipose


title: S011_Adipose


title: ESSEX HL 2 (COL0_2)


title: S009_Adipose


title: ESSEX HL 1 (COL0_1)


title: S007_Adipose


title: S006_Adipose


title: S005_Adipose


title: S019_Adipose


title: S008_Adipose


title: S004_Adipose


title: C017_Muscle

description:
Ion AmpliSeq Transcriptome
Rectus_Abdominis_Muscle_variance_stabilized_counts

source_name: Control muscle

value: Rectus abdominis muscle


title: S002_Adipose


title: C014_Muscle


title: WT Striatum 2 months male mRNA rep3 [10_19_24_mo]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
mRNA
Q1300006_04_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615787

data_processing:
Libraries for RNA-seq were sequenced using an Illumina NovaSeq6000.
Sequenced reads were trimmed for adaptor sequence using Omitsoft aligner and then mapped to rat genome Rat.B6.0.
a) Trimmed low-quality bases from the reads, aligned reads to the rat reference genome (Ensembl R89) with OmicSoft Aligner and quantitated the reads per gene with OmicSoft Quantitate. b) Fragments Per Kilobase of exon model per million reads mapped were calculated with OmicSoft. c) Generated the QC plots (PCA, Volcano, Bar charts of QC metrics).
Genome_build: Rat.B6.0
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM and Count values for each Sample.

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen mRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Corpus Striatum

value: Wild type

value: 2 months

value: male


title: Q130 KI Striatum 2 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300006_02_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615777

value: Q130 KI Het


title: Q130 KI Striatum 6 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300015_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615855

value: 6 months


title: WT Striatum 2 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300006_03_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615785


title: Q130 KI Striatum 6 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300014_02_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615857


title: WT Striatum 6 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300016_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615866


title: WT Striatum 6 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300015_02_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615865


title: WT Striatum 6 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300010_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615867


title: WT Striatum 2 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300007_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615786


title: C016_Muscle


title: Q130 KI Striatum 6 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300014_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615856


title: Q130 KI Striatum 2 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300007_03_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615776


title: C013_Muscle


title: Q130 KI Striatum 2 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300006_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
re-analysis of GSM4615775


title: C011_Muscle


title: WT Striatum 24 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300150_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: 24 months


title: C010_Muscle


title: WT Striatum 24 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300163_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: C009_Muscle


title: WT Striatum 24 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300153_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: female


title: C005_Muscle


title: WT Striatum 24 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300168_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 24 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300143_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: C003_Muscle

description:
Ion AmpliSeq Transcriptome
Rectus_Abdominis_Muscle_variance_stabilized_counts

value: Male


title: C004_Muscle


title: Q130 KI Striatum 24 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300142_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: C001_Muscle


title: Q130 KI Striatum 24 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300170_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S031_Muscle

source_name: PDAC muscle


title: S029_Muscle


title: Q130 KI Striatum 24 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300167_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 24 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300148_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S023_Muscle


title: S028_Muscle


title: S027_Muscle


title: WT Cortex 24 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300150_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

source_name: Cortex

value: Cerebral Cortex


title: S025_Muscle


title: Q130 KI Striatum 24 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300169_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 24 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300168_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 24 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300170_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: M018_Muscle


title: Q130 KI Cortex 24 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300169_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S019_Muscle


title: WT Cortex 24 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300163_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S018_Muscle


title: Q130 KI Cortex 24 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300148_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 24 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300142_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S017_Muscle


title: S015_Muscle


title: Q130 KI Cortex 24 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300146_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S014_Muscle


title: S012_Muscle


title: Q130 KI Striatum 24 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300146_01_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S011_Muscle


title: WT Cerebellum 24 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300150_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

source_name: Cerebellum

value: Cerebellum


title: S024_Muscle

value: Female


title: WT Cortex 24 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300153_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cerebellum 24 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300168_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S007_Muscle

description:
Ion AmpliSeq Transcriptome
Rectus_Abdominis_Muscle_variance_stabilized_counts


title: S009_Muscle


title: WT Cerebellum 24 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300153_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S020_Muscle


title: WT Cerebellum 24 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300163_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S006_Muscle


title: S008_Muscle


title: Q130 KI Cortex 24 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300143_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cerebellum 24 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300169_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S005_Muscle


title: Q130 KI Cerebellum 24 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
Q1300142_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S004_Muscle


title: Q130 KI Cerebellum 24 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300143_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cerebellum 24 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300170_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: S002_Muscle


title: Q130 KI Cerebellum 24 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
Q1300167_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Thrombin_1_HUVEC

city: Milwaukee

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
Illumina RNA sequence data were demultiplexed using bcl2fastq v2.20.0.422
Data were quality controlled, aligned, and gene expression was quantified using the ARMOR pipeline v1.2.2
Salmon expression quantifications were imported into R v3.5.3 and were summarized at the gene level using tximport v1.10.0
All samples were normalized and gene expression was compared between conditions using Wald tests within DESeq2 v1.22.1
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files containing raw read counts and FPKM values per gene per sample

source_name: HUVEC

growth_protocol: Pooled HUVEC (Lonza; Cat. C2517A, Walkersville, MD, USA) were cultured in endothelial basal medium (Cat. CC-3162, Lonza), containing 1 μg/mL hydrocortisone, 10 ng/mL epidermal growth factor (EGF), 10 ng/mL basic fibroblast growth factor (bFGF), and 5% (vol/vol) fetal calf serum (FCS).

extract_protocol:
RNA was isolated using Priazol method
Libraries were prepared using the the NEBNext Ultra RNA Library Prep Kit (NEB #E7530),

treatment_protocol: Cells were treated with Poly(I:C) and/or thrombin for 3h

tag: primary cell type

value: Healthy Endothelial cells

value: Thrombin treated


title: Q130 KI Cerebellum 24 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300148_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Thrombin_3_HUVEC


title: Q130 KI Cerebellum 24 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
Q1300146_01_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 19 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7438_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: 19 months


title: PolyIC-Thr_3_HUVEC

value: Poly(I:C) plus thrombin treated


title: WT Striatum 19 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7416_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: PolyIC-Thr_1_HUVEC


title: WT Striatum 19 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7440_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: PolyIC_3_HUVEC

value: Poly (I:C) treated


title: PolyIC-Thr_2_HUVEC


title: PolyIC_2_HUVEC


title: PolyIC_1_HUVEC


title: WT Striatum 19 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7448_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Corpus Striatum


title: Control_3_HUVEC

value: Untreated


title: Control_2_HUVEC


title: WT Striatum 19 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7391_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Wild type


title: WT Striatum 19 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7388_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 19 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7373_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 19 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7413_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 19 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7362_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: male


title: Control_1_HUVEC


title: HT-29_T28_T2

city: Shanghai

first: Dean

last: Li

address: Haike Road 100

institute: Chinese Academy of Science

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to human with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

source_name: Colon tumor cell

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01)

value: Human Caucasian colon adenocarcinoma

value: TNFa+Smac+zVAD


title: Q130 KI Cortex 24 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
Q1300167_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Q130 KI Het

value: 24 months


title: Q130 KI Striatum 19 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7372_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_T28_T1


title: Q130 KI Striatum 19 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7429_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_T28_D3

value: vehicle


title: Q130 KI Striatum 19 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7383_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Thrombin_2_HUVEC


title: HT-29_T28_D2


title: Q130 KI Striatum 19 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7378_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 19 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7381_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_T28_D1


title: HT-29_KO_T3


title: HT-29_KO_T2


title: Q130 KI Striatum 19 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7399_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: female


title: Q130 KI Striatum 19 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7455_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 19 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7442_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_T28_T3


title: Q130 KI Striatum 19 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7470_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_KO_D3


title: WT Cortex 19 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7438_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Cerebral Cortex


title: WT Cortex 19 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7448_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Striatum 19 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7412_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_KO_D2


title: HT-29_KO_D1


title: HT-29_D_T3


title: WT Cortex 19 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7440_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_D_T2


title: HT-29_D_D3


title: HT-29_D_T1


title: WT Cortex 19 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7416_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 19 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7362_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 19 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7391_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_D_D2


title: HT-29_A_T3


title: HT-29_A_T2


title: WT Cortex 19 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7413_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 19 months female mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7412_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 19 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7372_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Striatum 19 months female mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7472_Striatum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: WT Cortex 19 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7388_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_A_D3


title: HT-29_KO_T1


title: Q130 KI Cortex 19 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7472_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 19 months male mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7378_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 19 months female mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7455_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 19 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7381_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 19 months male mRNA rep1 [10_19_24_mo]

description:
mRNA
C50118_7383_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Q130 KI Cortex 19 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7429_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: Sulfopin treated 2

city: Rehovot

first: Efrat

last: Resnick

address: Herzel 234

department: Chemical and structural biology

country: Israel

institute: Weizmann institute of science

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters
RSEM was used to calculate gene-level FPKM
DESeq2 was used for calling differential expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mino cell line

growth_protocol: Mino cells were at 37°C in a 5% CO2 humidified incubator and cultured in RPMI-1640 supplemented with 15% Fetal bovine serum and 1% pen strep solution

extract_protocol:
Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 11×106 cells incubated for 6 h

value: B cell non-Hodgkin's lymphoma

value: sulfopin


title: Sulfopin treated 1


title: Sulfopin treated 3


title: Non treated control 1

value: untreated


title: Non treated control 2


title: WT Cortex 19 months female mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7373_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: 19 months


title: Non treated control 3


title: HT-29_D_D1


title: Q130 KI Cortex 19 months female mRNA rep2 [10_19_24_mo]

description:
mRNA
C50118_7442_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_A_T1


title: WT Cerebellum 19 months male mRNA rep4 [10_19_24_mo]

description:
mRNA
C50118_7440_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt

value: Cerebellum


title: WT Cerebellum 19 months male mRNA rep5 [10_19_24_mo]

description:
mRNA
C50118_7438_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt


title: HT-29_A_D1


title: WT Cerebellum 19 months male mRNA rep3 [10_19_24_mo]

description:
mRNA
C50118_7362_Cerebellum
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt