title: Foxk1_Control_replicate2_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1_ControlOE_r2


title: Foxk2_Control_replicate1_knockdown_RNA-seq

status: Public on Dec 01 2018

type: SRA

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2_ControlKD_r1

library_source: transcriptomic

data_processing:
Obtained raw reads were aligned using HISAT2 v2.1.0 aligner against mm10 as reference genome with default parameters
Insert size calculations are done using CollectInsertSizeMetrics from Picard v1.141
Quantification for transcripts from GENCODE vM10 was done using featureCounts from Subread v1.5.1 package
Considered only uniquely mapped exonic reads while quantification (mapping quality MAPQ, 40)
Quantified reads are RPKM normalized using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: Matrix containing tab-delimited data includes normalized expression RPKM values for transcripts in each Sample.

molecule: total RNA

organism: Mus musculus

source_name: 3T3-L1 adipocytes

growth_protocol: 3T3-L1 cells were growth and differentiated into adipocytes using standard protocol. Differentiation medium contained 1 µM dexamethasone, 0.5 mM isobutyl methylxanthine, 5 µg/ml insulin, 10 µM troglitazone. Cells were cultured in medium containing only 5 µg/ml insulin from day 4. From day 6 the cells were kept in growth medium

extract_protocol:
Total RNA from cells was extracted using TRI reagent and isolated using RNeasy mini kit (Quagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ectopic overexpression or downregulation of Foxk1 and Foxk2 in 3T3-L1 adipocytes

tag: cell line

tag: cell type

value: adipocytes

tag: strain

value: Swiss mouse

tag: expression construct

value: scrambled shRNA control


title: Foxk2_replicate2_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2OE_r2

value: constituent overexpression of FOXK2


title: Foxk2_replicate2_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2KD_r2

value: Foxk2 shRNA


title: Foxk2_replicate1_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2KD_r1


title: Foxk1_Control_replicate1_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1_ControlOE_r1

value: empty vector control


title: Foxk2_replicate1_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2OE_r1


title: Foxk2_Control_replicate2_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2_ControlOE_r2


title: Foxk1_Control_replicate2_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1_ControlKD_r2


title: Foxk1_replicate2_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1KD_r2

value: Foxk1 shRNA


title: Foxk2_Control_replicate1_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2_ControlOE_r1


title: Input

city: Portland

first: Michael

middle: R

last: Rountree

state: OR

address: 3429 NE Sandy Blvd. #330

country: USA

institute: Nzumbe, Inc.

description: IgG ChIP’d DNA

library_source: genomic

data_processing:
Sequencing reads (fastq) were mapped to the mouse mm10 genome using Bowtie2 with default settings
The output files in SAM format were converted to BAM format, PCR artifacts removed (rmdup tool), files sorted and index files created using SAMtools (http://samtools.sourceforge.net)
BAM files converted to BED files using BEDTools
Genome_build: Mouse mm10
Supplementary_files_format_and_content: BED files which contain read count (column 5).

molecule: genomic DNA

source_name: liver

growth_protocol: Adult male C57BL/6J mice at 3 months of age were purchased from Jax Labs (Bar Harbor, ME) and allowed to acclimate for 1 month in 12:12 light:dark conditions (LD, lights on 0600-1800 PST) before the start of experiments.  For all experimental groups except Baseline 2), the mice were maintained under usual lights conditions (lights on 0600-1800) and collection occurred around the clock, as necessary.  For the Baseline 2 group, upon arrival half of the mice were immediately switched to a reverse light cycle (lights on 1800-0600) and then maintained under these conditions for one month to allow full entrainment. All mice were housed four to a cage in an environmental chamber (Percival Scientific, Perry, IA) maintained at 20 - 21°C, with food and water available ad lib because food restriction can alter circadian rhythms (Mukherji et al., 2015a;  Mukherji et al., 2015b).  Housing light intensity was approximately 300 lux.  Zeitgeber time (ZT) was used to define lights-on and dark phases during the LD cycle.  By convention, ZT12 was defined as lights-off.

extract_protocol:
For collections, mice were deeply anesthetized with isoflurane, killed by cervical dislocation, the eyes removed to prevent any postmortem light effect, and the livers removed for processing. Liver tissue from each mouse was cut with a scalpel into small pieces (~ 0.5 mm3 size) and crosslinked with a freshly made formaldehyde solution (a protease inhibitor [PI] cocktail tablet (Complete Mini, EDTA-free, Roche, Indianapolis, IN, USA) dissolved in 1% formaldehyde in PBS)  at a ratio of 10 ml solution/1 g of tissue by rotation (Mini-Tube Rotator, Fisher Scientific) at room temp for 5 minutes. The reaction was quenched by adding 2.5 M glycine to a final concentration of 0.125 M and rotating at room temp for another 5 minutes.  The suspension was centrifuged for 5 minutes at 4°C in  Beckman Coulter GPKR centrifuge (84RCF) and the precipitant washed with 10 ml of cold PBS with PI, spun down, and the supernatant removed. The tissue was then homogenized on ice with a glass Dounce homogenizer (loose) for cell disruption in 5 ml PBS with PI, centrifuged 5 minutes at 1000 rpm at 4°C, re-suspended in 5 ml of Cell Lysis Buffer (5 mM PIPES, 85 mM KCL, 0.5% IGEPAL, 1 PI tablet) and incubated on ice for 15 minutes.  The tissue was then homogenized on ice with Dounce glass homogenizer (tight) with 10 strokes. Suspension was centrifuged for 5 minutes at 2000 g at 4°C, the supernatant removed, and isolated nuclei were checked under a microscope and then frozen at -80°C until sonicated.  Isolated nuclei were re-suspended in SDS Shearing Buffer (10 mM Tris HCl, 0.25% SDS, 1 mM EDTA, 1x Halt protease inhibitor cocktail (Thermo Scientific, Rockford, IL, USA), approximately 0.15 mg tissue per 1 µl of the buffer, and sonicated for 10 min (Duty Cycle 2%, Intensity 3, Peak Incident Power 105 Watts, Cycles per Burst 200).  Initial experiments were performed with isolated DNA to ensure a size range of approximately 200-700 bp.  After sonication, the sheared chromatin was centrifuged 5 minutes at 4°C at 10,000 RCF (Forma Scientific Micromax benchtop centrifuge) and supernatant was transferred to a new tube. Next, 100 µl of the chromatin prep (approximately 17 µg of DNA), was diluted with 200 µl of 1.5 x ChIP buffer (75 mM Tris HCl, 0.21 M NaCl, 1.5 mM EDTA, 1.5 % Triton-X, 0.15 % Deoxyholate) with PI and 3 µl of each sample was saved as input.  3 µl of histone H3 trimethyl Lys4 antibody (H3K4me3, Active Motif, Carlsbad, CA) was added to each experimental sample and the samples were incubated overnight at 4°C with rotation.  The chromatin prep from each liver was processed separately. Magnetic beads (Magna ChIP™ Protein A+G Magnetic Beads, Millipore), 20 µl per sample, were washed twice with 2 mL of 1x CHIP buffer (50 mM Tris HCl, 0.14 M NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % Deoxyholate) with PI and returned to an original volume of 20 µl.  The magnetic beads were added to each 100 µl sample and incubated for 2 hours at 4°C with rotation. The beads were then washed twice with 1 ml ChIP buffer (without PI) and incubated for 10 min at 4°C with rotation, followed by two washes with NaCl ChIP buffer (50 mM Tris HCl, 0.5 M NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % Deoxyholate), two washes with LiCl wash buffer (10 mM Tris HCl, 0.25 M LiCl, 1 mM EDTA, 0.5 % NP-40, 0.5 % Deoxyholate) and two washes with TE buffer (10 mM Tris HCl, 1 mM EDTA). After washing, 62.5 µl of TES buffer (50 mM Tris HCl, 1 % SDS , 10 mM EDTA) were added to each sample and the samples were incubated at 65°C for 10 minutes with mixing. The supernatants from each sample were saved in screw top cap vials.  The incubation step was then repeated and the supernatants combined. TES (113 µl ) was added to the input samples (total of 12 µl after combining samples from 4 livers). Next, 5.2 µl of 5 M NaCl and 6.25 µl of RNase A (4 µg/µl) were added to 125 µl of IP and input samples. The samples were then incubated for 30 - 60 min at 37°C.  After incubation, 5 µl of proteinasae K (20 µg/µl) was added to all samples and the samples decrosslinked overnight at 65°C.  After decrosslinking DNA from proteins, each DNA sample was purified with the MinElute PCR Purification Kit ( Qiagen, Valencia, CA ),  according to manufacturer's protocol and the samples representing each time point pooled.
Illumina TrueSeq kit following manufacture’s protocol

treatment_protocol: Baseline = no phase advance.  Immediate = 6 hr. phase advance.  Recovery = 6 hr. phase advance followed by 1 week recovery.  Chronic =  6 hr. phase advance each week for 8 weeks followed by 1 week of recovery.

tag: tissue

value: liver

tag: gender

value: male

tag: chip target


title: Chronic_ZT20

description: H3K4me3 ChIP’d DNA

tag: zeitgeber time

value: 20 hrs.

tag: circadian shift/recovery time

value: 6 hr. every wk for 8 wks / 1 wk


title: Recovery_ZT3

description: H3K4me3 ChIP’d DNA

value: 3 hrs.

value: 6 hr. / 1 wk


title: Recovery_ZT15

description: H3K4me3 ChIP’d DNA

value: 15 hrs.


title: Recovery_ZT8

description: H3K4me3 ChIP’d DNA

value: 8 hrs.


title: Chronic_ZT8

description: H3K4me3 ChIP’d DNA


title: Chronic_ZT15

description: H3K4me3 ChIP’d DNA


title: Immediate_ZT20

description: H3K4me3 ChIP’d DNA

value: 6 hr. / none


title: Recovery_ZT20

description: H3K4me3 ChIP’d DNA


title: Baseline2_ZT20

description: H3K4me3 ChIP’d DNA

value: none/none


title: Immediate_ZT8

description: H3K4me3 ChIP’d DNA


title: Immediate_ZT3

description: H3K4me3 ChIP’d DNA


title: Baseline2_ZT15

description: H3K4me3 ChIP’d DNA


title: Immediate_ZT15

description: H3K4me3 ChIP’d DNA


title: Baseline2_ZT8

description: H3K4me3 ChIP’d DNA


title: Baseline2_ZT3

description: H3K4me3 ChIP’d DNA


title: Baseline1_ZT20

description: H3K4me3 ChIP’d DNA


title: Baseline1_ZT8

description: H3K4me3 ChIP’d DNA


title: Chronic_ZT3

description: H3K4me3 ChIP’d DNA


title: Baseline1_ZT3

description: H3K4me3 ChIP’d DNA


title: Baseline1_ZT15

description: H3K4me3 ChIP’d DNA


title: SUDHL4 RR plus NK Replicate 3

type: RNA

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

description: Gene expression data from SUDHL4 RR plus NK

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were corrected through COMBAT correction, quantile normalized, collapsed to genes from probes, then imported into MultiExperiment Viewer, MeV for analysis. Statistically significant genes were determined by applying a one-way ANOVA with an adjusted Bonferroni correction and false discovery rate (FDR) < 0.05 that resulted in a list of significant genes.

label: biotin

organism: Homo sapiens

source_name: SUDHL4 RR plus NK

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

growth_protocol: DLBCL cell lines SU-DHL4 and SU-DHL10, Burkitt’s cell line Raji, Follicular lymphoma cell line HF1 were purchased from American Type Culture Collection (Manassas, VA, USA) and maintained in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum and 1% antibiotic-antimycotic solution (Corning Cellgro, Manassas, VA, USA). Rituximab (RR) and obinutuzumab (OR) resistant cells were established by continuously culturing SU-DHL4 and SU-DHL10 with increasing concentration of rituximab and obinutuzumab (5-20μg/mL) for over a period of 8 weeks. Development of acquired resistance to anti-CD20 antibody drugs coincided with decreased CD20 expression in these cells, observed by flow cytometry (data not shown). These cells were cultured and maintained in RPMI medium, as described above. Primary human lymphoma cells (EL-2 and EL-5) were isolated from discarded tissue specimens of patients with DLBCL obtained through Tufts Tumor Repository under IRB exempt protocol, as described previously. Activated NK-92 (aNK) and CD19.TaNK cells were provided as generous gift from Nantkwest, Inc. (Woburn, MA, USA). aNK was maintained in X-Vivo 10 media (Lonza, NJ, USA) supplemented with 5% human serum and GFP expressing CD19.TaNK was maintained in MyeloCult H5100 (STEMCELL Technologies) supplemented with recombinant human IL-2 (500IU/ml) (STEMCELL Technologies). Peripheral blood mononuclear cells (PMBC) were purchased from (STEMCELL Technologies), activated using cell culture plates pre-coated with anti-CD3 (clone OKT3) 10g/ml (eBiosciences) and addition of anti-CD28 (clone CD28.2) 2g/ml (eBiosciences) and recombinant IL-2 (10ng/ml), IL-4 (20ng/ml) (Peprotech), following 5 day activation protocol and final stimulation with PMA (5ng/ml) and ionomycin (500ng/ml) for 4 hours prior to the experiment.  All cells were grown at 37°C and 5% CO2 in a humidified atmosphere. Cells were routinely passaged every 3 days and harvested at a density of 1 × 106 viable cells/mL.

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)

treatment_protocol: SU-DHL4, SU-DHL4 RR, SU-DHL4 OR, SU-DHL10, SU-DHL10 RR, SU-DHL10 OR, Raji, EL-2 and EL-5 cell lines were co-cultured with CD19.TaNK  for two hours at effector:target (E:T) ratio 1:1, followed by flow sorting of CD19 positive target bNHL cells preloaded with cell-tracking dye QDOT655 (Molecular Probes), as per instructions supplied by the manufacturer, and by gating out GFP+ CD19.TANK  cells.

tag: treatment

value: CD19.TaNK cells Co-culture

value: SUDHL4 rituximab resistant


title: SUDHL4 plus NK Replicate 1

description: Gene expression data from SUDHL4 plus NK

source_name: SUDHL4 plus NK


title: SUDHL4 RR Replicate 2

description: Gene expression data from SUDHL4 RR

source_name: SUDHL4 RR

value: Controls


title: SUDHL4 plus NK Replicate 3


title: SUDHL4 RR plus NK Replicate 2


title: SUDHL4 RR plus NK Replicate 1


title: SUDHL4 RR Replicate 3

description: Gene expression data from SUDHL4 RR


title: SUDHL4 Replicate 1  (dataset 2)

description: Gene expression data from SUDHL4


title: SUDHL4 plus NK Replicate 2


title: SUDHL4 Replicate 3 (dataset 2)

description: Gene expression data from SUDHL4


title: SUDHL10 RR plus NK Replicate 2

description: Gene expression data from SUDHL10 RR plus NK

source_name: SUDHL10 RR plus NK

value: SUDHL10 rituximab resistant


title: SUDHL10 RR plus NK Replicate 1


title: SUDHL10 Replicate 3 (dataset 2)

description: Gene expression data from SUDHL10


title: SUDHL10 plus NK Replicate 1

description: Gene expression data from SUDHL10 plus NK

source_name: SUDHL10 plus NK


title: SUDHL10 RR plus NK Replicate 3


title: SUDHL10 plus NK Replicate 2


title: EL-2 Replicate 2

description: Gene expression data from EL-2


title: SUDHL10 RR Replicate 3

description: Gene expression data from SUDHL10 RR

source_name: SUDHL10 RR


title: SUDHL10 RR Replicate 1

description: Gene expression data from SUDHL10 RR


title: SUDHL10 RR Replicate 2

description: Gene expression data from SUDHL10 RR


title: EL-2 Replicate 3

description: Gene expression data from EL-2


title: EL-2 OR plus NK Replicate 1

description: Gene expression data from EL-2 plus NK

source_name: EL-2 plus NK


title: SUDHL10 Replicate 1 (dataset 2)

description: Gene expression data from SUDHL10


title: EL-2 OR plus NK Replicate 3

description: Gene expression data from EL-2 plus NK


title: SUDHL4 RR Replicate 1

description: Gene expression data from SUDHL4 RR


title: SUDHL4 Replicate 2  (dataset 2)

description: Gene expression data from SUDHL4


title: EL-2 Replicate 1

description: Gene expression data from EL-2


title: SUDHL10 plus NK Replicate 3


title: EL-2 OR plus NK Replicate 2

description: Gene expression data from EL-2 plus NK


title: SUDHL10 Replicate 2 (dataset 2)

description: Gene expression data from SUDHL10


title: SUDHL10 OR plus NK Replicate 3

description: Gene expression data from SUDHL10 OR plus NK

source_name: SUDHL10 OR plus NK

value: SUDHL10 obinutuzumab resistant


title: Raji Replicate 3

description: Gene expression data from Raji

source_name: Raji

value: Raji


title: Raji OR plus NK Replicate 3

description: Gene expression data from Raji plus NK

source_name: Raji plus NK


title: SUDHL10 OR plus NK Replicate 1


title: Raji Replicate 1

description: Gene expression data from Raji


title: SUDHL10 OR Replicate 1

description: Gene expression data from SUDHL10 OR

source_name: SUDHL10 OR


title: SUDHL10 Replicate 3

description: Gene expression data from SUDHL10


title: SUDHL4 OR plus NK Replicate 2

description: Gene expression data from SUDHL4 OR plus NK

source_name: SUDHL4 OR plus NK

value: SUDHL4 obinutuzumab resistant


title: SUDHL10 OR plus NK Replicate 2


title: SUDHL10 Replicate 2

description: Gene expression data from SUDHL10


title: SUDHL4 OR Replicate 1

description: Gene expression data from SUDHL4 OR

source_name: SUDHL4 OR


title: SUDHL10 OR Replicate 3

description: Gene expression data from SUDHL10 OR


title: SUDHL4 Replicate 3

description: Gene expression data from SUDHL4


title: SUDHL4 OR Replicate 2

description: Gene expression data from SUDHL4 OR


title: EL-5 Replicate 3

description: Gene expression data from EL-5


title: EL-5 Replicate 2

description: Gene expression data from EL-5


title: SUDHL4 OR plus NK Replicate 1


title: EL-5 Replicate 1

description: Gene expression data from EL-5


title: Raji OR plus NK Replicate 1

description: Gene expression data from Raji plus NK


title: SUDHL4 OR Replicate 3

description: Gene expression data from SUDHL4 OR


title: EL-5 OR plus NK Replicate 1

description: Gene expression data from EL-5 plus NK

source_name: EL-5 plus NK


title: SUDHL10 Replicate 1

description: Gene expression data from SUDHL10


title: EL-5 OR plus NK Replicate 2

description: Gene expression data from EL-5 plus NK


title: SUDHL4 OR plus NK Replicate 3


title: SUDHL4 Replicate 1

description: Gene expression data from SUDHL4


title: SUDHL4 Replicate 2

description: Gene expression data from SUDHL4


title: EL-5 OR plus NK Replicate 3

description: Gene expression data from EL-5 plus NK


title: Raji OR plus NK Replicate 2

description: Gene expression data from Raji plus NK


title: SUDHL10 OR Replicate 2

description: Gene expression data from SUDHL10 OR


title: Raji Replicate 2

description: Gene expression data from Raji


title: LNCaP siEZH2 Rep #1

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 16

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: ATCC

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol: Total RNA was isolated from cells using PureLinkTM RNA Mini Kit (Life Tech).  The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: LNCaP/C4-2B cells were treated with DMSO or EPZ6438 (1uM) for 3 days. LNCaP/C4-2B cells were transfected with sicontrol or siEZH2 (CDS) for 3 days

value: LNCaP

tag: transfected with


title: C4-2B siControl Rep #3

description: SAMPLE 21

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

source_name: Derived from metastatic site: Left supraclavicular lymph node [PMID 8168083]

value: siCONT


title: C4-2B siEZH2 Rep #3

description: SAMPLE 24

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.


title: LNCaP siEZH2 Rep #3

description: SAMPLE 18


title: LNCaP siControl Rep #2

description: SAMPLE 14


title: C4-2B EPZ6438 Rep #1

description: SAMPLE 10

tag: treated with


title: LNCaP EPZ6438 Rep #2

description: SAMPLE 5


title: C4-2B siEZH2 Rep #2

description: SAMPLE 23


title: C4-2B siControl Rep #2

description: SAMPLE 20


title: LNCaP siEZH2 Rep #2

description: SAMPLE 17


title: C4-2B DMSO Rep #2

description: SAMPLE 8

value: DMSO


title: C4-2B EPZ6438 Rep #2

description: SAMPLE 11


title: C4-2B DMSO Rep #3

description: SAMPLE 9


title: C4-2B siControl Rep #1

description: SAMPLE 19


title: C4-2B siEZH2 Rep #1

description: SAMPLE 22


title: LNCaP EPZ6438 Rep #1

description: SAMPLE 4


title: LNCaP siControl Rep #3

description: SAMPLE 15


title: C4-2B DMSO Rep #1

description: SAMPLE 7


title: LNCaP EPZ6438 Rep #3

description: SAMPLE 6


title: C4-2B EPZ6438 Rep #3

description: SAMPLE 12


title: LNCaP DMSO Rep #3

description: SAMPLE 3


title: LNCaP siControl Rep #1

description: SAMPLE 13


title: 404848_C1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Hybridisation was performed according to the Illumina standard protocol.

scan_protocol: Arrays were imaged using Illumina default settings

data_processing: NA probes were removed and remaining data were log2 transformed and normalised using quantile normalisation

source_name: Patient 404848; Tissue mucosa

label_protocol: According to the Illumina HumanHT-12 v4 Expression BeadChip

extract_protocol: Tissue samples were collected from patients undergoing surgery at the University Hospital of Heidelberg, and were reviewed by pathologists of the Tissue Bank of the National Center for Tumor Diseases to ensure their quality and origin. Tissue RNA was extracted from fresh-frozen tissue using the QIAamp AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Gene expression was performed at the Genomic and Proteomics Core Facilities, German Cancer Research Center, Heidelberg, Germany, by using Illumina HumanHT-12 v4 Expression BeadChip.

tag: patientid

value: M

tag: age

value: mucosa

tag: disease state

value: Colorectal cancer patient


title: 404768_C1

source_name: Patient 404768; Tissue mucosa


title: 404848_A

source_name: Patient 404848; Tissue tumor

value: tumor


title: 404456_C2

source_name: Patient 404456; Tissue mucosa


title: LNCaP DMSO Rep #1

description: SAMPLE 1


title: LNCaP DMSO Rep #2

description: SAMPLE 2


title: 404656_A

source_name: Patient 404656; Tissue tumor


title: 404656_C2

source_name: Patient 404656; Tissue mucosa


title: 404480_C1

source_name: Patient 404480; Tissue mucosa


title: 404456_A

source_name: Patient 404456; Tissue tumor


title: 404360_C

source_name: Patient 404360; Tissue mucosa


title: 404360_A

source_name: Patient 404360; Tissue tumor


title: 404352_C1

source_name: Patient 404352; Tissue mucosa


title: 404368_C1

source_name: Patient 404368; Tissue mucosa

value: F


title: 404352_A

source_name: Patient 404352; Tissue tumor


title: 404344_A

source_name: Patient 404344; Tissue tumor


title: 404344_C1

source_name: Patient 404344; Tissue mucosa


title: 404328_C1

source_name: Patient 404328; Tissue mucosa


title: 404312_C1

source_name: Patient 404312; Tissue mucosa


title: 404304_C1

source_name: Patient 404304; Tissue mucosa


title: 404296_C1

source_name: Patient 404296; Tissue mucosa


title: 404312_A

source_name: Patient 404312; Tissue tumor


title: 404200_A

source_name: Patient 404200; Tissue tumor


title: 404280_C

source_name: Patient 404280; Tissue mucosa


title: 404096_A

source_name: Patient 404096; Tissue tumor


title: 404304_A

source_name: Patient 404304; Tissue tumor


title: 404264_A

source_name: Patient 404264; Tissue tumor


title: 403976_C

source_name: Patient 403976; Tissue mucosa


title: 404336_C2

source_name: Patient 404336; Tissue mucosa


title: 404096_C1

source_name: Patient 404096; Tissue mucosa


title: 404056_A

source_name: Patient 404056; Tissue tumor


title: 404088_A

source_name: Patient 404088; Tissue tumor


title: 404208_A

source_name: Patient 404208; Tissue tumor


title: 404296_A

source_name: Patient 404296; Tissue tumor


title: 404264_C1

source_name: Patient 404264; Tissue mucosa


title: 404200_C2

source_name: Patient 404200; Tissue mucosa


title: 404208_C1

source_name: Patient 404208; Tissue mucosa


title: 404088_C1

source_name: Patient 404088; Tissue mucosa


title: 403968_C

source_name: Patient 403968; Tissue mucosa


title: 404056_C2

source_name: Patient 404056; Tissue mucosa


title: 403968_A

source_name: Patient 403968; Tissue tumor


title: 404328_A

source_name: Patient 404328; Tissue tumor


title: 404280_A

source_name: Patient 404280; Tissue tumor


title: 403888_C1

source_name: Patient 403888; Tissue mucosa


title: 403928_A

source_name: Patient 403928; Tissue tumor


title: 403976_A

source_name: Patient 403976; Tissue tumor


title: 403944_C1

source_name: Patient 403944; Tissue mucosa


title: 403888_A

source_name: Patient 403888; Tissue tumor


title: 403848_A

source_name: Patient 403848; Tissue tumor


title: 403840_C1

source_name: Patient 403840; Tissue mucosa


title: 403848_C1

source_name: Patient 403848; Tissue mucosa


title: 403704_C1

source_name: Patient 403704; Tissue mucosa


title: 403744_C1

source_name: Patient 403744; Tissue mucosa


title: 403752_A

source_name: Patient 403752; Tissue tumor


title: 403664_C1

source_name: Patient 403664; Tissue mucosa


title: 403416_C

source_name: Patient 403416; Tissue mucosa


title: 403392_C1

source_name: Patient 403392; Tissue mucosa


title: 403320_A

source_name: Patient 403320; Tissue tumor


title: 403752_C1

source_name: Patient 403752; Tissue mucosa


title: 403176_C1

source_name: Patient 403176; Tissue mucosa


title: 403080_A

source_name: Patient 403080; Tissue tumor


title: 403064_C1

source_name: Patient 403064; Tissue mucosa


title: 403800_C1

source_name: Patient 403800; Tissue mucosa


title: 403456_C2

source_name: Patient 403456; Tissue mucosa


title: 403176_A

source_name: Patient 403176; Tissue tumor


title: 403672_C1

source_name: Patient 403672; Tissue mucosa


title: 403320_C1

source_name: Patient 403320; Tissue mucosa


title: 403080_C1

source_name: Patient 403080; Tissue mucosa


title: 403368_A

source_name: Patient 403368; Tissue tumor


title: 403064_A

source_name: Patient 403064; Tissue tumor


title: 403432_C1

source_name: Patient 403432; Tissue mucosa


title: 403840_A

source_name: Patient 403840; Tissue tumor


title: 403056_C1

source_name: Patient 403056; Tissue mucosa


title: 403032_C1

source_name: Patient 403032; Tissue mucosa


title: 402992_A

source_name: Patient 402992; Tissue tumor


title: 402768_C1

source_name: Patient 402768; Tissue mucosa


title: 402968_C2

source_name: Patient 402968; Tissue mucosa


title: 402992_C

source_name: Patient 402992; Tissue mucosa


title: 402744_C1

source_name: Patient 402744; Tissue mucosa


title: 403368_C

source_name: Patient 403368; Tissue mucosa


title: 402672_A

source_name: Patient 402672; Tissue tumor


title: 402800_A

source_name: Patient 402800; Tissue tumor


title: 402760_A

source_name: Patient 402760; Tissue tumor


title: 402672_C1

source_name: Patient 402672; Tissue mucosa


title: 402648_A

source_name: Patient 402648; Tissue tumor


title: 402760_C1

source_name: Patient 402760; Tissue mucosa


title: 402536_C1

source_name: Patient 402536; Tissue mucosa


title: 402872_C1

source_name: Patient 402872; Tissue mucosa


title: 402608_C

source_name: Patient 402608; Tissue mucosa


title: 402576_C1

source_name: Patient 402576; Tissue mucosa


title: 402424_C

source_name: Patient 402424; Tissue mucosa


title: 402512_A

source_name: Patient 402512; Tissue tumor


title: 402440_A

source_name: Patient 402440; Tissue tumor


title: 402536_A

source_name: Patient 402536; Tissue tumor


title: 402440_C2

source_name: Patient 402440; Tissue mucosa


title: 402432_A

source_name: Patient 402432; Tissue tumor


title: 402408_C1

source_name: Patient 402408; Tissue mucosa


title: 402512_C1

source_name: Patient 402512; Tissue mucosa


title: 402408_A

source_name: Patient 402408; Tissue tumor


title: 402376_C1

source_name: Patient 402376; Tissue mucosa


title: 402264_A

source_name: Patient 402264; Tissue tumor


title: 402392_C2

source_name: Patient 402392; Tissue mucosa


title: 402400_C1

source_name: Patient 402400; Tissue mucosa


title: 402400_A

source_name: Patient 402400; Tissue tumor


title: 402296_C2

source_name: Patient 402296; Tissue mucosa


title: 402216_C1

source_name: Patient 402216; Tissue mucosa


title: 402384_C

source_name: Patient 402384; Tissue mucosa


title: 402240_C1

source_name: Patient 402240; Tissue mucosa


title: 402256_C1

source_name: Patient 402256; Tissue mucosa


title: 402096_C1

source_name: Patient 402096; Tissue mucosa


title: 402200_A

source_name: Patient 402200; Tissue tumor


title: 402096_A

source_name: Patient 402096; Tissue tumor


title: 402256_A

source_name: Patient 402256; Tissue tumor


title: 402232_A

source_name: Patient 402232; Tissue tumor


title: 402200_C2

source_name: Patient 402200; Tissue mucosa


title: 402168_C

source_name: Patient 402168; Tissue mucosa


title: 402152_C1

source_name: Patient 402152; Tissue mucosa


title: 402048_C

source_name: Patient 402048; Tissue mucosa


title: 402048_A

source_name: Patient 402048; Tissue tumor


title: 401976_C1

source_name: Patient 401976; Tissue mucosa


title: 402016_C1

source_name: Patient 402016; Tissue mucosa


title: 401864_A

source_name: Patient 401864; Tissue tumor


title: 401816_A

source_name: Patient 401816; Tissue tumor


title: 401728_C1

source_name: Patient 401728; Tissue mucosa


title: 401896_C1

source_name: Patient 401896; Tissue mucosa


title: 401728_A

source_name: Patient 401728; Tissue tumor


title: 401864_C1

source_name: Patient 401864; Tissue mucosa


title: 401696_C1

source_name: Patient 401696; Tissue mucosa


title: 401976_A

source_name: Patient 401976; Tissue tumor


title: 401816_C1

source_name: Patient 401816; Tissue mucosa


title: 401984_C

source_name: Patient 401984; Tissue mucosa


title: 401696_A

source_name: Patient 401696; Tissue tumor


title: 401664_A

source_name: Patient 401664; Tissue tumor


title: 401984_A

source_name: Patient 401984; Tissue tumor


title: 401664_C1

source_name: Patient 401664; Tissue mucosa


title: 401648_A

source_name: Patient 401648; Tissue tumor


title: 401624_C

source_name: Patient 401624; Tissue mucosa


title: 401648_C

source_name: Patient 401648; Tissue mucosa


title: 401624_A

source_name: Patient 401624; Tissue tumor


title: 401424_A

source_name: Patient 401424; Tissue tumor


title: 401424_C1

source_name: Patient 401424; Tissue mucosa


title: 401464_C1

source_name: Patient 401464; Tissue mucosa


title: 401504_C

source_name: Patient 401504; Tissue mucosa


title: 401368_C

source_name: Patient 401368; Tissue mucosa


title: 401352_C

source_name: Patient 401352; Tissue mucosa


title: 401464_A

source_name: Patient 401464; Tissue tumor


title: 401368_A

source_name: Patient 401368; Tissue tumor


title: 401848_C

source_name: Patient 401848; Tissue mucosa


title: 401304_A

source_name: Patient 401304; Tissue tumor


title: 401144_C

source_name: Patient 401144; Tissue mucosa


title: 401288_C

source_name: Patient 401288; Tissue mucosa


title: 401176_A

source_name: Patient 401176; Tissue tumor


title: 402880_C1

source_name: Patient 402880; Tissue mucosa


title: 401120_C

source_name: Patient 401120; Tissue mucosa


title: 402648_C1

source_name: Patient 402648; Tissue mucosa


title: 401248_C

source_name: Patient 401248; Tissue mucosa


title: 401200_C

source_name: Patient 401200; Tissue mucosa


title: 401144_A

source_name: Patient 401144; Tissue tumor


title: 400896_A

source_name: Patient 400896; Tissue tumor


title: 401000_A

source_name: Patient 401000; Tissue tumor


title: 400992_C

source_name: Patient 400992; Tissue mucosa


title: 400896_C1

source_name: Patient 400896; Tissue mucosa


title: 400872_C

source_name: Patient 400872; Tissue mucosa


title: 400728_A

source_name: Patient 400728; Tissue tumor


title: 400728_C

source_name: Patient 400728; Tissue mucosa


title: 401000_C

source_name: Patient 401000; Tissue mucosa


title: 400704_C

source_name: Patient 400704; Tissue mucosa


title: 401248_A

source_name: Patient 401248; Tissue tumor


title: 400712_A

source_name: Patient 400712; Tissue tumor


title: 400600_C

source_name: Patient 400600; Tissue mucosa


title: 400688_C

source_name: Patient 400688; Tissue mucosa


title: 400688_A

source_name: Patient 400688; Tissue tumor


title: 400704_A

source_name: Patient 400704; Tissue tumor


title: 400448_C

source_name: Patient 400448; Tissue mucosa


title: 400456_C1

source_name: Patient 400456; Tissue mucosa


title: 400488_A

source_name: Patient 400488; Tissue tumor


title: 400992_A

source_name: Patient 400992; Tissue tumor


title: 401088_A

source_name: Patient 401088; Tissue tumor


title: 400280_C

source_name: Patient 400280; Tissue mucosa


title: 400216_A

source_name: Patient 400216; Tissue tumor


title: 400264_C

source_name: Patient 400264; Tissue mucosa


title: 400240_C

source_name: Patient 400240; Tissue mucosa


title: 400072_C

source_name: Patient 400072; Tissue mucosa


title: 400240_A

source_name: Patient 400240; Tissue tumor


title: 400200_C

source_name: Patient 400200; Tissue mucosa


title: 400288_A

source_name: Patient 400288; Tissue tumor


title: 400408_A

source_name: Patient 400408; Tissue tumor


title: 400072_A

source_name: Patient 400072; Tissue tumor


title: 400296_C

source_name: Patient 400296; Tissue mucosa


title: 400152_C

source_name: Patient 400152; Tissue mucosa


title: 400152_A

source_name: Patient 400152; Tissue tumor


title: 400408_C

source_name: Patient 400408; Tissue mucosa


title: 402800_C1

source_name: Patient 402800; Tissue mucosa


title: 400216_C

source_name: Patient 400216; Tissue mucosa


title: 16HBE-pQCXIP/SCH772984-n2

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
ERKi_2

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: 16HBE, pQCXIP infected (stable), 1uM SCH772984 treated (4 days)

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

treatment_protocol: pQCXIP cells were treated with DMSO (control), 500nM GSK1120212 (MEK inhibitor) or 1uM SCH772984 (ERK inhibitor) for 4 days

value: bronchial epithelial immortalised cell line


title: 16HBE-pQCXIP/GSK1120212-n3

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
GSK_3

source_name: 16HBE, pQCXIP infected (stable), 500nM GSK1120212 treated (4 days)


title: 16HBE-pQCXIP.DN Ras N17-n2

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
DN_Ras_2

source_name: 16HBE, pQCXIP-DN Ras infected (stable)


title: 16HBE-pQCXIP/DMSO-n2

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
Control_2

source_name: 16HBE, pQCXIP infected (stable), DMSO treated (4 days)


title: 16HBE-pQCXIP/DMSO-n1

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
Control_1


title: 16HBE-pQCXIP/GSK1120212-n1

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
GSK_1


title: 16HBE-pQCXIP/SCH772984-n3

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
ERKi_3


title: 16HBE-pQCXIP/GSK1120212-n2

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
GSK_2


title: 16HBE-pQCXIP.DN Ras N17-n3

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
DN_Ras_3


title: gvs1_O3

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

hyb_protocol: Microarray chips were hybridized using Agilent's Gene Expression Hybridization Kit and washed with Agilent's Gene Expression Wash Buffer Kit.

scan_protocol: An Agilent SureScan Microarray Scanner.

data_processing:
Scanned images were analyzed and quantified using Agilent Feature Extraction software (version 11.5). Log2 intensities of the probes were first normalized using quantile normalization. Applicable cutoffs for reliable signals in probes were determined by Gaussian curve fitting (Signal ≥ 6.0379).
Probes targeting multiple genes were ignored and data was analyzed based on gene expression, not on transcript expression.

organism: Arabidopsis thaliana

source_name: gvs1-1, DAE28

label_protocol: Total RNA was amplified and labeled using Agilent's one-color Low Input Quick Amp Labeling kit.

growth_protocol: Arabidopsis was grown on the soil for 23 and 37 days in 16:8 light-dark (LD) cycle.

extract_protocol: Total RNA was isolated using WelprepTM Total RNA Isolation Reagent.

treatment_protocol: Plants were harvested at 5 h after light-on.

tag: genotype/variation

tag: developmental stage

value: third and fourth leaves


title: 16HBE-pQCXIP.DN Ras N17-n1

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
DN_Ras_1

tag: cell line


title: 16HBE-pQCXIP/SCH772984-n1

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
ERKi_1

tag: cell type


title: 16HBE-pQCXIP/DMSO-n3

description:
Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells
Control_3


title: Col_O2

source_name: Col, DAE28

tag: ecotype

value: Col


title: gvs1_Y1

source_name: gvs1-1, DAE14


title: gvs1_O1


title: gvs1_O2


title: Col_Y3

source_name: Col, DAE14


title: Col_O1


title: gvs1_Y2


title: Col_Y1


title: gvs1_Y3


title: 4: Flesh-6d

city: Yangzhou

first: Xuewen

last: Xu

state: Jiangsu

address: 48 wenhui east road

country: China

institute: Yangzhou University

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:ATCC 35984）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: cucumber Chinese long genome v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Cucumis sativus

source_name: Flesh of  the cucumber inbred line ‘YB’ at 6 days after slef-pollination

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA, China) and a RNeasy Mini Kit (Cat#74106, Qiagen) following the manufacturer’s instructions, the RIN number was subsequently determined to evaluate RNA integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Qualified total RNA was further purified using a RNeasy Micro Kit (Cat#74004, QIAGEN, GmBH, Germany) and a RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). The purified total RNA was then subjected to mRNA isolation, removal of rRNA, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, terminal repair, 3' end addition of an ‘A’, ligation and enrichment. Finally, sample libraries were constructed. The nucleic acid concentrations of the libraries were measured using a Qubit® 2.0 Fluorometer, and the Agilent 2100 system was used to determine the size of the library.

treatment_protocol: For RNA-Seq, the peels and flesh of 'YB' at 3, 6, 9d of pollination were used and each sample were mixed by 3 fruits.

tag: line

value: YB

value: Flesh

value: 6 days after slef-pollination


title: 3: Peel-6d

source_name: Peel of  the cucumber inbred line ‘YB’ at 6 days after slef-pollination

tag: tissue

value: Peel


title: Col_Y2


title: 5: Peel-9d

source_name: Peel of  the cucumber inbred line ‘YB’ at 9 days after slef-pollination

value: 9 days after slef-pollination


title: 2: Flesh-3d

source_name: Flesh of  the cucumber inbred line ‘YB’ at 3 days after slef-pollination

value: 3 days after slef-pollination


title: spleen_monocytes_3

city: Singapore

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description:
Primary isolate from mouse
Spleen4

hyb_protocol: Fragmented cRNAs were hybridized to the standard arrays for 17 hours at 45°C, the arrays were then washed and stained using the fluidics station according to genechip array manufacturer's protocol

scan_protocol: The chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality control analyses were carried out according to the instructions provided by Affymetrix.

data_processing: Data was analyzed with RMA/quantile normalization in r v 2.13.0 in bioconductor using the oligo package

source_name: spleen monocytes

label_protocol: cDNA were prepared according to the Ambion® WT Expression Kit's protocol from 100ng Total RNA. 5.5ug of cDNA were fragmented and labelled according to Affymetrix GeneChip® WT Terminal Labeling and Hybridization kit's protocol.

growth_protocol: Wild type C57BL/6 mice were bred in the specific pathogen-free NTU animal facility.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kits (Qiagen). RNA Integrity Number (RIN) was assessed by Agilent Bioanalyzer (Agilent Technologies). All RNA samples were RIN≥9.2.

treatment_protocol: For tissue processing, 10mL of PBS were used to perfuse the mice after CO2 euthanasia and brains were dissected out and minced followed by 30-60 minutes incubation at 37oC with 1mg/mL Collagenase (Roche, 11088882001) and 20u/mL DNase I (Life Technologies, 18047-019). To prepare single cells from brain, digested suspensions were passed through 19-gauge syringe. Brain leukocytes were enriched through two-layer (40%-80%) Percoll (GE Healthcare, 17-0891-01).Enriched  brain leukocytes were incubated with Fc receptor binding inhibitor (14-0161-86 from eBioscience) for 15 minutes. Unbound Fc receptor binding inhibitors were washed away. Antibody mix were added and incubated for 15 minutes. Following antibodies were used for mouse cells: CD45 (clone: 30F11), CD11b (clone: M1/70), EMR1 (also known as F4/80) (clone: BM8), Ly6C (HK1.4), MHC II (clone:M5/114.15.2).Cell sorting was performed with FACS Aria II.

tag: strain

value: spleen monocytes


title: spleen_monocytes_1

description:
Primary isolate from mouse
Spleen2


title: Col_O3


title: 1: Peel-3d

source_name: Peel of  the cucumber inbred line ‘YB’ at 3 days after slef-pollination


title: 400288_C

source_name: Patient 400288; Tissue mucosa

tag: gender


title: rMC-1 rep3

city: Adelaide

first: Daniel

middle: John

last: Peet

state: SA

address: Molecular Life Sciences Building, University of Adelaide, North Terrace

department: Molecular and Biomedical Sciences

country: Australia

institute: University of Adelaide

data_processing:
Basecalling was performed using default Illumina scripts.
Reads were first trimmed of adapter sequences using cutadapt v1.8.1 (--minimum-length 18 --error-rate 0.2 --overlap=5). Adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. (Marcel, M. 2011)
Reads were then mapped to the rn6 genome and counted using STAR v2.5.3a with default parameters (--runThreadN 8 -- runMode alignReads --chimSegmentMin 20 --twopassMode None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outSAMunmapped Within KeepPairs) (Dobin et al. 2013).
Genes that were either not expressed or expressed at very low levels (not detected at greater than one count per million reads (cpm) for all samples of at least one group) were filtered out of the analysis. Counts for the remaining genes were log2-transformed and normalized to library size and composition using the “TMM” method in Bioconductor’s EdgeR package v3.18.1 (McCarthy et al. 2012; Robinson et al. 2010).
Genome_build: rn6
Supplementary_files_format_and_content: Raw unflitered counts per gene for each sample are provided as csv files. The supplementary tsv file is a matrix table output from EdgeR containing the TMM-normalized log2 cpm values for all samples.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Retinal cell culture

growth_protocol:
Cells were cultured in MEM (#11090, Life Technologies Australia) containing 10% (for rMC-1s) or 20% (for primary MCs and SIRMu-1s) fetal bovine serum, 25 mM glucose and 2 mM L-glutamine. Cultures were maintained in a humidified incubator at 37°C, 5% CO2.
No antibiotics or antifungals

extract_protocol:
Cells were trypsinized, pelleted and total RNA extracted with a mirVana miRNA Isolation Kit (#AM1561, Life Technologies Australia). RNA samples were submitted to the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility (Adelaide, SA, Australia), quality determined with an Agilent RNA 6000 Nano kit (#5067-1511, Agilent Technologies, Santa Clara, CA, USA) on an Agilent 2100 bioanalyzer, confirming RIN values were above 7, and concentrations determined using a Qubit RNA HS assay kit (#Q32852, Life Technologies Australia).
250 ng of total RNA of each sample was subjected to polyA selection with oligo dT beads. 5 ng of enriched polyA RNA was used for library preparation using a KAPA stranded RNAseq Hyperprep kit (#KK8544, KAPA, Cape Town, South Africa) according to the manufacturer’s guidelines. Briefly, RNA was fragmented (approximate insert length: 200bps) and converted to cDNA, followed by end-repair and A-tailing. Adapters compatible with Illumina sequencing were ligated to the cDNA using a concentration of 1.5 µM with an approximate adapter to molar insert ratio of 200:1, and a post-ligation clean-up was performed to remove excess adapters. The libraries were amplified with 10 cycles of PCR and cleaned with 1X ratio of beads. Library sizes and yields were confirmed using an Agilent High Sensitivity DNA kit (#5067-4626) with an Agilent 2100 bioanalyser and diluted to 4 nM stocks. Libraries were pooled in equimolar ratios and sequenced on the Illumina NextSeq500 using a 75-cycle high output kit (#FC-404-2005, Illumina).

value: Sprague-Dawley

value: adult

tag: passages


title: SIRMu-1 rep1

value: postnatal day 2-4


title: 401320_C

source_name: Patient 401320; Tissue mucosa

value: M

value: mucosa


title: Primary MC rep4

growth_protocol:
Cells were cultured in MEM (#11090, Life Technologies Australia) containing 10% (for rMC-1s) or 20% (for primary MCs and SIRMu-1s) fetal bovine serum, 25 mM glucose and 2 mM L-glutamine. Cultures were maintained in a humidified incubator at 37°C, 5% CO2.
Cultured with 87 mg/L gentamicin and 2.2 mg/L amphotericin B

value: Primary MC


title: SIRMu-1 rep3


title: SIRMu-1 rep2


title: SIRMu-1 rep4


title: spleen_monocytes_2

description:
Primary isolate from mouse
Spleen3


title: Primary MC rep3


title: rMC-1 rep2


title: microglia_Ly6CLow_2

description:
Primary isolate from mouse
Ly6C_L9

source_name: microglia Ly6CLow

value: bulk microglia cells

value: Low


title: microglia_Ly6CLow_1

description:
Primary isolate from mouse
Ly6C_L8


title: rMC-1 rep1


title: microglia_Ly6Chigh_2

description:
Primary isolate from mouse
Ly6C_H11

source_name: microglia Ly6Chigh

value: MgSCs

value: High


title: microglia_Ly6CLow_3

description:
Primary isolate from mouse
Ly6C_L11


title: Primary MC rep2


title: SIRMu-1 rep5


title: microglia_Ly6Chigh_3

description:
Primary isolate from mouse
Ly6C_H12


title: Primary MC rep1


title: microglia_Ly6Chigh_1

description:
Primary isolate from mouse
Ly6C_H8


title: 6: Flesh-9d

source_name: Flesh of  the cucumber inbred line ‘YB’ at 9 days after slef-pollination

value: YB


title: 72

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 1129 Farm Lane

department: Biochemistry and Molecular Biology

institute: Michigan State University

description: Rats given a dose by oral gavage every 4 days for 28 days

data_processing:
FASTQC v0.11.2 was used for quality control
FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads
TopHat v1.4.1 was used for alignment
SAMTools v0.1.2 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: RGSC release 74
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified and examined for purity and quality by nanodrop, Qubit, Bioanalyzer and visualization on a denaturing gel.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Female SD rats were gavaged with sesame oil vehicle or 0.01, 0.03, 0.1, 0.3, 1, 3, or 10 ug/kg TCDD every 4 days for 28 days and livers were collected on day 28.

tag: Sex

value: Female

tag: age unit

value: days

value: TCDD

tag: dose

tag: dose unit

value: ug/kg

tag: duration

tag: duration unit

tag: replicate


title: 70

tag: age

tag: treatment


title: 62


title: 61


title: group6 rep4

city: Amsterdam

first: Vanesa

last: Muncan

address: Meibergdreef 69

department: Gastroenterology and Hepatology

country: Netherlands

institute: Tytgat institute for Liver and Intestinal research

hyb_protocol: fragmented cDNa was hybridized on mouse Clariom D pico assay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Data were analysed using Affimetrix expression console, RMA as normalization method

source_name: intestine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Thermofisher:Gene Chip High Throughput kit).

growth_protocol: organoids were grown in a standard orgnaoid growth medium ENR

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

value: tissue intestine

tag: Stage

tag: day of culture


title: 60


title: group5 rep3


title: group6 rep2


title: group6 rep3


title: group3 rep1

value: organoids intestine


title: 71

value: Sprague-Dawley


title: group2 rep4


title: group3 rep2

value: adult


title: group2 rep2


title: group4 rep3


title: group1 rep2


title: group6 rep1


title: group1 rep4


title: 56


title: group2 rep3


title: group4 rep4


title: group4 rep2


title: group3 rep4


title: group5 rep1


title: 52


title: group3 rep3


title: 48


title: 46


title: group2 rep1


title: group5 rep2


title: 55


title: 45


title: 40


title: group4 rep1


title: group1 rep1


title: group1 rep3


title: 22


title: group5 rep4


title: 24


title: 32


title: 29


title: 13

value: Vehicle


title: 16


title: IGG-L8

description: Rats gavaged once and livers collected 2 hours following exposure

data_processing:
Quality control FASTQC v0.11.2
Adaptor sequence removal Cutadapt v1.4.1
Cleaning of low complexity reads FASTX v0.0.14
Mapping Bowtie 2.0.0
Normalization and peak calling CisGenome
Genome_build: RGSC 5.0 release 76
Supplementary_files_format_and_content: bigWig file showing relative enrichment to IgG control (log2fold-change)

extract_protocol:
ChIP was performed as previously described (Dere et al., 2001. BMC Genomics 12, 365; Lo and Matthews, 2012. Toxicol Sci 130(2), 349-61). Briefly, rat livers (~100 mg) were homogenized in 1% formaldehyde and incubated at room temperature for 10 minutes. Homogenates were centrifuged at 10,000 RPM for 3 minutes at 4°C and pellets washed with cold PBS followed by resuspension in TSEI with Protease Inhibitor Cocktail. Samples were sonicated 12 times for 10 seconds and supernatants transferred to new tubes and incubated with rabbit IgG and anti-AhR or just rabbit IgG overnight at 4°C.  Protein A/G-Sepharose was added and samples incubated for 1.5h.  Pellets were washed for 10 minutes in buffer 1, buffer 2, LiCl buffer, and TE. Protein-DNA complexes were then eluted using TE and cross-links reversed by overnight incubation at 65°C followed by DNA purification.
Libraries were prepared using the MicroPlex kit (Diagenode) according to manufacturer's instructions

treatment_protocol: Female Sprague-Dawley rats were gavaged once with sesame oil vehicle or 10 ug/kg TCDD and livers collected 2 hours following treatment.

value: Liver

value: hours

tag: chip antibody

tag: antibody vendor


title: 38


title: IGG-L9

tag: tissue


title: 20

tag: strain


title: 28


title: AHR-L10

value: Enzo Life Sciences


title: 15


title: 37


title: IGG-L6


title: IGG-L7


title: IGG-L10


title: AHR-L6


title: AHR-L9


title: AHR-L7


title: RNA-seq, Primary stromal cells from BM osteoblast diff 9d donor 2

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description:
BM_Ob_2
RNA_HumanPrimaryStromalCells.txt

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
RNA-seq reads were aligned to hg19 genome using STAR aligner and default settings. Only one read per position and read length was kept.
Genome_build: hg19
Supplementary_files_format_and_content: raw and normalized gene counts with statistics

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) or adipose tissue origin (AT-hMSC-TERT) as well as non-mesenchymal cells were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S). Primary stromal cells were gron in DMEM/F12 supplemented with 15 mM HEPES, 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S)

extract_protocol:
RNA-seq: RNA was extracted from 6-well dishes using TRI Reagent (Sigma) follwed by chloroform extraction and purification of RNA using Econo Spin columns (Epoch Life Sciences).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 2 µg RNA for preparation of cDNA libraries.

treatment_protocol:
Immortalized cells and non-mesenchymal cells: Two days post confluency cells were induced to undergo osteoblast or adipocyte differentiation by switched to α-MEM supplemented with 10% FCS, 10 mM dexamethasone, 10 nM vitamin D, 10 mM β-glycerolphosphate, and 50 µg/ml ascorbic acid or to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine. Media was replaced on day 2, 4, 7, 9 and 11.
Human primary stromal cells: Primary cells were expanded prior to the induction of differentiation with DMEM/F-12 supplemented with 10 % FCS, 1 % P/S, 15 mM HEPES and 1 nM FGF-1. Osteogenic induction was similar as for the immortalized cells while the adipogenic induction cocktail contained DMEM/F12 supplemented with 1 % P/S, 15 mM HEPES, 500 µM isobutylmethylxanthine, 100 nM dexamethasone, 10 µg/mL insulin and transferrin, 2 nM T3 and 200 mM rosiglitazone. Both induction cocktails were replaced every third day, while dexamethasone and isobutylmethylxanthine were withdrawn at day three and rosiglitazone at day 6 of adipogenic differentiation

tag: cell line

value: Primary stromal cells from BM

tag: differentiation status

value: osteoblast

tag: timepoint


title: RNA-seq, Primary stromal cells from MUS osteoblast diff 9d donor 2

description:
MUS_Ob_2
RNA_HumanPrimaryStromalCells.txt

value: Primary stromal cells from MUS


title: RNA-seq, Primary stromal cells from WAT osteoblast diff 9d donor 2

description:
WAT_Ob_2
RNA_HumanPrimaryStromalCells.txt

value: Primary stromal cells from WAT


title: RNA-seq, Primary stromal cells from BM adipocyte diff 9d donor 3

description:
BM_Ad_3
RNA_HumanPrimaryStromalCells.txt

value: adipocyte


title: RNA-seq, Primary stromal cells from BM adipocyte diff 9d donor 2

description:
BM_Ad_2
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT osteoblast diff 9d donor 3

description:
WAT_Ob_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS adipocyte diff 9d donor 3

description:
MUS_Ad_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from BM osteoblast diff 9d donor 1

description:
BM_Ob_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from BM osteoblast diff 9d donor 3

description:
BM_Ob_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT osteoblast diff 9d donor 1

description:
WAT_Ob_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from BM adipocyte diff 9d donor 1

description:
BM_Ad_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS osteoblast diff 9d donor 1

description:
MUS_Ob_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS osteoblast diff 9d donor 3

description:
MUS_Ob_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS adipocyte diff 9d donor 2

description:
MUS_Ad_2
RNA_HumanPrimaryStromalCells.txt


title: AHR-L8

tag: Sex

value: Female

tag: age unit


title: RNA-seq, Primary stromal cells from MUS adipocyte diff 9d donor 1

description:
MUS_Ad_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT adipocyte diff 9d donor 3

description:
WAT_Ad_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT adipocyte diff 9d donor 2

description:
WAT_Ad_2
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from BM undifferentiated donor 2

description:
BM_Msc_2
RNA_HumanPrimaryStromalCells.txt

value: undifferentiated


title: RNA-seq, Primary stromal cells from WAT undifferentiated donor 3

description:
WAT_Msc_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from BM undifferentiated donor 3

description:
BM_Msc_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS undifferentiated donor 3

description:
MUS_Msc_3
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from BM undifferentiated donor 1

description:
BM_Msc_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT adipocyte diff 9d donor 1

description:
WAT_Ad_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS undifferentiated donor 2

description:
MUS_Msc_2
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT undifferentiated donor 2

description:
WAT_Msc_2
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from MUS undifferentiated donor 1

description:
MUS_Msc_1
RNA_HumanPrimaryStromalCells.txt


title: RNA-seq, Primary stromal cells from WAT undifferentiated donor 1

description:
WAT_Msc_1
RNA_HumanPrimaryStromalCells.txt


title: endometrium PAEC-7

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

description: Gene Expression from PAEC subject 7

hyb_protocol: Hybridization of ST cDNA was performed on Affymetrix GeneChip HTA 2.0 Array as per the manufacturers protocol.

scan_protocol: Scanning was done as per the Affymetrix protocol.

data_processing:
Initial Data processign was done with Affymetrix Expression Command Console software. Background correction was done by composition based and normalisation was done by IterativeProbe Logarithmic Intensity Error Estimation (iterPLIER) summarization algorithm with Global Median method
Probe signal intenisty/ Hybridization signal.

label: Biotin

source_name: Endometrial biopsy

label_protocol: Fragmentation and Biotin labelling and target preparation of the ST cDNA  were performed using the NuGEN Encore Biotin Module.

growth_protocol: Endometrial biopsies are obtained from the women who displayed PAEC changes and no PAEC chnaegs with 3months of mifepristone treatment

extract_protocol: Snap froxen tissue was extracted for RNA using trizol in liquid nitrogen

treatment_protocol: three months of mifepristone treatment for leiomyoma

value: Endometrium


title: endometrium PAEC-6

description: Gene Expression from PAEC subject 6


title: endometrium PAEC-3

description: Gene Expression from PAEC subject 3


title: endometrium PAEC-1

description: Gene Expression from PAEC subject 1


title: endometrium PAEC-4

description: Gene Expression from PAEC subject 4


title: endometrium PAEC-2

description: Gene Expression from PAEC subject 2


title: endometrium NPAEC3

description: Gene Expression from NPAEC subject 3


title: endometrium PAEC-5

description: Gene Expression from PAEC subject 5


title: endometrium NPAEC4

description: Gene Expression from NPAEC subject 4


title: endometrium NPAEC1

description: Gene Expression from NPAEC subject 1


title: endometrium NPAEC2

description: Gene Expression from NPAEC subject 2


title: ATAC-seq, Primary stromal cells from BM undifferentiated donor a

description:
ATAC_HumanPrimaryStromalCells.bed
ATAC_HumanPrimaryStromalCells.txt

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
ATAC-seq reads were aligned to the hg19 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept.
Sequencing reads from donors of a tissue of origin were pooled to indentify regions enriched of open chromatin using HOMER. ATAC- regions for Human Primary Stromal Cells were merged using Homer with distance option -d given.
ATAC-seq signal was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -noadj. Normalization of sequencing reads was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Donors into the design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain genomic regions identified from ATAC-seq experiments in the immortalized cells and in human primary stromal cells. Peak column in bed files indicate with 1 if the peak was found in the specific samples, 0 indicates absence. Txt file contains non-adjusted gene expression values for eauch replicate and averaged normalized counts and standard deviation for each time point as well as FDR and Log2FC with respect to undifferentiated state for human primary stromal cells. Txt file contains non adjusted quantification of ATAC-seq libraries from human primary stromal cells for two individual donors, averaged normalized counts as well as standard deviations.

extract_protocol:
ATAC-seq: Cells were scrabed off from 6-well dishes in ice cold PBS, centrifuged and permeabilised. Nuclei were rinsed through a cell strainer (10 micro m) and counted. 5.000 nuclei were exposed to 1 micro l transposase as described originally (Buenrostro J D, et. al 2015. Current Protocols in Molecular Biology 109: 1-9).
ATAC-seq libraries were constructed according to the manufacturer's instructions (Illumina).


title: ATAC-seq, Primary stromal cells from MUS undifferentiated donor b


title: ATAC-seq, Primary stromal cells from BM undifferentiated donor b


title: ATAC-seq, Primary stromal cells from WAT undifferentiated donor b


title: CemSS - APoBEC3G #2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

description:
A3G.2
CemSS T cells stably transduced with control construct replicate 2

hyb_protocol: Microarray hybridization was performed using the Affymetrix Fluidics Station 450 with  program FS450_0001.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were preprocessed in the R v3.2.0 environment using Bioconductor package oligo v1.32.0; background correction, normalization and gene-level probeset summary were performed with the rma command using default parameter settings.

label_protocol: 100ng total RNA from each sample was processed with the WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

growth_protocol: Cells were cultured in RPMI medium containing 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

extract_protocol: RNA was extrated with Trizol reagent.

tag: group

value: control

tag: rin

tag: hybridization date

value: CemSS

tag: cell type

value: T cells


title: ATAC-seq, Primary stromal cells from MUS undifferentiated donor a


title: ATAC-seq, Primary stromal cells from WAT undifferentiated donor a


title: CemSS - APoBEC3G #3

description:
A3G.3
CemSS T cells stably transduced with control construct replicate 3


title: G206-12 prefrontal cortex

description: suicide victim G206-12 prefrontal cortex

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, normalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: prefrontal cortex of suicide victim

extract_protocol: After hippocampus, amygdala, thalamus and prefrontal cortex tissue was homogenized, total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies). Genomic DNA was removed using the RNeasy Plus kit (Qiagen).

value: suicide victim

tag: individual

tag: brain region

value: prefrontal cortex

tag: hybridiziation date


title: CemSS - APoBEC3G #1

description:
A3G.1
CemSS T cells stably transduced with control construct replicate 1


title: RNA-seq, AT-hMSC-TERT adipocyte diff 14d rep1

description:
RNA_14dAd_AT_rep1
GeneExpr_AT.txt

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
ChIP-seq and DNase-seq reads were aligned to the hg19 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept. RNA-seq reads were aligned to hg19 genome using STAR aligner and default settings. Only one read per position and read length was kept.
Regions enriched for open chromatin or MED1 recruitment were identified using the ENCODE IDR (LI Q H, et al. 2011. Annals of Applied Statistics, 5:1752-1779) pipeline and MACS2 peak caller (Zhang Y, et al. 2008. Genome Biology 9:R137). For ChIP-seq samples a pooled Inout control sample was used as control. Reproducible peaks between replicates for the single time points were merged using Homer with distance option -d given.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Replicates and Time Points into the design matrix, excluding genes which were not detected in both cell lines. Log 2 fold changes and FDR values were calculated with respect to undifferentiated MSC.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph and bigWig files were created using HOMER for visualization of enhancer features in genome browser. Bed files contain reproducible genomic regions from IDR analysis of DNase1-seq, MED1 ChIP-seq and their overlap with and without promoters. Txt file contains non-adjusted gene expression values for eauch replicate and averaged normalized counts and standard errors for each time point as well as FDR and Log2FC with respect to undifferentiated MSC for both BM-hMSC-TERT4 and AT-hMSC-TERT4 cells.

source_name: AT-hMSC-TERT osteAdlast diff 14d

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) or adipose tissue origin (AT-hMSC-TERT) were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
RNA was extracted from 6-well dishes using TRI Reagent (Sigma) follwed by chloroform extraction and purification of RNA using Econo Spin columns (Epoch Life Sciences).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 2 µg RNA for preparation of cDNA libraries.

treatment_protocol: Two days post confluency cells were induced to undergo osteoblast or adipocyte differentiation by switched to α-MEM supplemented with 10% FCS, 10 mM dexamethasone, 10 nM vitamin D, 10 mM β-glycerolphosphate, and 50 µg/ml ascorbic acid or to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine. Media was replaced on day 2, 4, 7, 9 and 11.

value: AT-hMSC-TERT


title: RNA-seq, AT-hMSC-TERT adipocyte diff 14d rep2

description:
RNA_14dAd_AT_rep2
GeneExpr_AT.txt


title: RNA-seq, AT-hMSC-TERT adipocyte diff 7d rep2

description:
RNA_7dAd_AT_rep2
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteAdlast diff 7d


title: CemSS + APoBEC3G #3

description:
pcMS28.3
CemSS T cells stably overexpressing APOBEC3G replicate 3

value: overexpression


title: CemSS + APoBEC3G #2

description:
pcMS28.2
CemSS T cells stably overexpressing APOBEC3G replicate 2


title: G192-12 thalamus

description: control person G192-12 thalamus

source_name: thalamus of control person

value: control person

value: thalamus


title: RNA-seq, AT-hMSC-TERT adipocyte diff 7d rep1

description:
RNA_7dAd_AT_rep1
GeneExpr_AT.txt


title: CemSS + APoBEC3G #1

description:
pcMS28.1
CemSS T cells stably overexpressing APOBEC3G replicate 1


title: RNA-seq, AT-hMSC-TERT adipocyte diff 3d rep2

description:
RNA_3dAd_AT_rep2
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteAdlast diff 3d


title: RNA-seq, AT-hMSC-TERT adipocyte diff 3d rep1

description:
RNA_3dAd_AT_rep1
GeneExpr_AT.txt


title: RNA-seq, AT-hMSC-TERT adipocyte diff 1d rep2

description:
RNA_1dAd_AT_rep2
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteAdlast diff 1d


title: G190-12 prefrontal cortex

description: suicide victim G190-12 prefrontal cortex


title: RNA-seq, AT-hMSC-TERT adipocyte diff 1d rep1

description:
RNA_1dAd_AT_rep1
GeneExpr_AT.txt


title: G192-12 hippocampus

description: control person G192-12 hippocampus

source_name: hippocampus of control person

value: hippocampus


title: RNA-seq, AT-hMSC-TERT adipocyte diff 4h rep2

description:
RNA_4hAd_AT_rep2
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteAdlast diff 4h


title: G192-12 amygdala

description: control person G192-12 amygdala

source_name: amygdala of control person

value: amygdala


title: RNA-seq, AT-hMSC-TERT adipocyte diff 4h rep1

description:
RNA_4hAd_AT_rep1
GeneExpr_AT.txt


title: G138-12 thalamus

description: control person G138-12 thalamus


title: G44-13 thalamus

description: suicide victim G44-13 thalamus

source_name: thalamus of suicide victim


title: RNA-seq, AT-hMSC-TERT undifferentiated rep1

description:
RNA_Msc_AT_rep1
GeneExpr_AT.txt

source_name: AT-hMSC-TERT undifferentiated


title: RNA-seq, AT-hMSC-TERT undifferentiated rep2

description:
RNA_Msc_AT_rep2
GeneExpr_AT.txt


title: G192-12 prefrontal cortex

description: control person G192-12 prefrontal cortex

source_name: prefrontal cortex of control person


title: RNA-seq, AT-hMSC-TERT osteoblast diff 4h rep1

description:
RNA_4hOb_AT_rep1
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteoblast diff 4h

value: osteoblast


title: G41-12 thalamus

description: suicide victim G41-12 thalamus


title: RNA-seq, AT-hMSC-TERT osteoblast diff 4h rep2

description:
RNA_4hOb_AT_rep2
GeneExpr_AT.txt


title: G138-12 amygdala

description: control person G138-12 amygdala


title: G41-12 hippocampus

description: suicide victim G41-12 hippocampus

source_name: hippocampus of suicide victim


title: G138-12 hippocampus

description: control person G138-12 hippocampus


title: RNA-seq, AT-hMSC-TERT osteoblast diff 1d rep2

description:
RNA_1dOb_AT_rep2
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteoblast diff 1d


title: RNA-seq, AT-hMSC-TERT osteoblast diff 1d rep1

description:
RNA_1dOb_AT_rep1
GeneExpr_AT.txt


title: G138-12 prefrontal cortex

description: control person G138-12 prefrontal cortex


title: G109-12 thalamus

description: suicide victim G109-12 thalamus


title: RNA-seq, AT-hMSC-TERT osteoblast diff 3d rep2

description:
RNA_3dOb_AT_rep2
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteoblast diff 3d


title: G193-12 prefrontal cortex

description: control person G193-12 prefrontal cortex


title: RNA-seq, AT-hMSC-TERT osteoblast diff 3d rep1

description:
RNA_3dOb_AT_rep1
GeneExpr_AT.txt


title: RNA-seq, AT-hMSC-TERT osteoblast diff 7d rep1

description:
RNA_7dOb_AT_rep1
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteoblast diff 7d


title: RNA-seq, AT-hMSC-TERT osteoblast diff 14d rep2

description:
RNA_14dOb_AT_rep2
GeneExpr_AT.txt


title: G41-12 prefrontal cortex

description: suicide victim G41-12 prefrontal cortex

source_name: prefrontal cortex of suicide victim


title: G193-12 hippocampus

description: control person G193-12 hippocampus


title: RNA-seq, AT-hMSC-TERT osteoblast diff 14d rep1

description:
RNA_14dOb_AT_rep1
GeneExpr_AT.txt

source_name: AT-hMSC-TERT osteAdlast diff 14d


title: G41-12 amygdala

description: suicide victim G41-12 amygdala

source_name: amygdala of suicide victim


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 14d rep3

description:
RNA_14dAd_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteAdlast diff 14d


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 14d rep2

description:
RNA_14dAd_BM_rep2
GeneExpr_BM.txt


title: RNA-seq, AT-hMSC-TERT osteoblast diff 7d rep2

description:
RNA_7dOb_AT_rep2
GeneExpr_AT.txt


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 7d rep3

description:
RNA_7dAd_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteAdlast diff 7d


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 14d rep1

description:
RNA_14dAd_BM_rep1
GeneExpr_BM.txt


title: G123-12 hippocampus

description: suicide victim G123-12 hippocampus


title: G193-12 thalamus

description: control person G193-12 thalamus

source_name: thalamus of control person


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 7d rep2

description:
RNA_7dAd_BM_rep2
GeneExpr_BM.txt


title: G193-12 amygdala

description: control person G193-12 amygdala


title: G123-12 prefrontal cortex

description: suicide victim G123-12 prefrontal cortex


title: G44-13 amygdala

description: suicide victim G44-13 amygdala


title: G109-12 amygdala

description: suicide victim G109-12 amygdala


title: G51-12 hippocampus

description: control person G51-12 hippocampus

source_name: hippocampus of control person


title: G131-12 thalamus technical replicate

description: control person G131-12 thalamus technical replicate


title: G51-12 thalamus

description: control person G51-12 thalamus


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 3d rep3

description:
RNA_3dAd_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteAdlast diff 3d


title: G131-12 amygdala technical replicate

description: control person G131-12 amygdala technical replicate

source_name: amygdala of control person


title: G123-12 thalamus

description: suicide victim G123-12 thalamus

source_name: thalamus of suicide victim


title: G51-12 amygdala

description: control person G51-12 amygdala


title: G123-12 amygdala

description: suicide victim G123-12 amygdala


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 7d rep1

description:
RNA_7dAd_BM_rep1
GeneExpr_BM.txt


title: G131-12 hippocampus technical replicate

description: control person G131-12 hippocampus technical replicate


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 3d rep2

description:
RNA_3dAd_BM_rep2
GeneExpr_BM.txt


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 3d rep1

description:
RNA_3dAd_BM_rep1
GeneExpr_BM.txt


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 1d rep3

description:
RNA_1dAd_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteAdlast diff 1d


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 1d rep1

description:
RNA_1dAd_BM_rep1
GeneExpr_BM.txt


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 1d rep2

description:
RNA_1dAd_BM_rep2
GeneExpr_BM.txt


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 4h rep1

description:
RNA_4hAd_BM_rep1
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteAdlast diff 4h


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 4h rep2

description:
RNA_4hAd_BM_rep2
GeneExpr_BM.txt


title: G597-12 hippocampus

description: control person G597-12 hippocampus


title: G44-13 thalamus technical replicate

description: suicide victim G44-13 thalamus technical replicate


title: RNA-seq, BM-hMSC-TERT4 undifferentiated rep2

description:
RNA_Msc_BM_rep2
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 undifferentiated


title: RNA-seq, BM-hMSC-TERT4 undifferentiated rep1

description:
RNA_Msc_BM_rep1
GeneExpr_BM.txt


description: control person G131-12 prefrontal cortex technical replicate

source_name: prefrontal cortex of control person


title: RNA-seq, BM-hMSC-TERT4 undifferentiated rep3

description:
RNA_Msc_BM_rep3
GeneExpr_BM.txt


title: RNA-seq, BM-hMSC-TERT4 adipocyte diff 4h rep3

description:
RNA_4hAd_BM_rep3
GeneExpr_BM.txt


title: G44-13 hippocampus technical replicate

description: suicide victim G44-13 hippocampus technical replicate

source_name: hippocampus of suicide victim


title: G597-12 thalamus

description: control person G597-12 thalamus


title: G597-12 amygdala

description: control person G597-12 amygdala


title: G51-12 prefrontal cortex

description: control person G51-12 prefrontal cortex


title: G44-13 amygdala technical replicate

description: suicide victim G44-13 amygdala technical replicate


title: G597-12 prefrontal cortex

description: control person G597-12 prefrontal cortex


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 4h rep2

description:
RNA_4hOb_BM_rep2
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteoblast diff 4h


description: suicide victim G44-13 prefrontal cortex technical replicate


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 4h rep3

description:
RNA_4hOb_BM_rep3
GeneExpr_BM.txt


title: G599-12 thalamus

description: suicide victim G599-12 thalamus


title: G44-12 thalamus

description: suicide victim G44-12 thalamus


title: G44-13 prefrontal cortex

description: suicide victim G44-13 prefrontal cortex


title: G109-12 prefrontal cortex

description: suicide victim G109-12 prefrontal cortex


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 4h rep1

description:
RNA_4hOb_BM_rep1
GeneExpr_BM.txt


title: G44-12 amygdala

description: suicide victim G44-12 amygdala


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 1d rep3

description:
RNA_1dOb_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteoblast diff 1d


title: G599-12 amygdala

description: suicide victim G599-12 amygdala


title: G599-12 hippocampus

description: suicide victim G599-12 hippocampus


title: G44-12 prefrontal cortex

description: suicide victim G44-12 prefrontal cortex

source_name: prefrontal cortex of suicide victim


title: G599-12 prefrontal cortex

description: suicide victim G599-12 prefrontal cortex


title: 35S::CLE41 stem rep 3

city: Durham

first: Peter

last: Etchells

address: South Road

department: Biosciences

country: United Kingdom

institute: Durham University

hyb_protocol: Hybridization protols was as described in https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets/LSG/manuals/expression_analysis_technical_manual.pdf&title=Manuals:%20Expression%20Analysis%20Technical%20Manual,%20with%20Specific%20Protocols%20for%20Use%20with%20the%20Hybridization,%20Wash,%20and%20Stain%20Kit  using the GeneChip Hybridzation Oven 645 and Fluidics protocol: EukGE-WS2

scan_protocol: GeneChip Scanner 3000 7G as detailed in the GeneChipTM Expression Wash, Stain and Scan User Manual, P/N 702731 (ThermoFisher)

data_processing: Technical quality control was performed with dChip (V2005; www.dchip.org), using the default settings. Background correction, quantile normalization, and gene expression analysis were performed using RMA in Bioconductor. Differential expression analysis was performed using Limma using the functions lmFit and eBayes.

source_name: 35S::CLE41_Inflorescence stem

label_protocol: Labelling protocol was the Two-cycle Target labelling protocol as described in https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets/LSG/manuals/expression_analysis_technical_manual.pdf&title=Manuals:%20Expression%20Analysis%20Technical%20Manual,%20with%20Specific%20Protocols%20for%20Use%20with%20the%20Hybridization,%20Wash,%20and%20Stain%20Kit

growth_protocol: long day growth conditions (16h light, 8 hours dark)

extract_protocol: RNA extractions were performed using Trizol according to the manufacturers instructions

treatment_protocol: 35S::CLE41 lines were generated in the Col background as described in Etchells and Turner (2010) Development 137:767-774.

tag: ecotype

value: Columbia

tag: age

value: 5 week old plants

tag: genotype/variation

value: lower third of inflorescence stem exluding 1 cm directly above the rosette


title: G44-12 hippocampus

description: suicide victim G44-12 hippocampus


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 1d rep1

description:
RNA_1dOb_BM_rep1
GeneExpr_BM.txt

tag: chip antibody


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 3d rep3

description:
RNA_3dOb_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteoblast diff 3d


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 1d rep2

description:
RNA_1dOb_BM_rep2
GeneExpr_BM.txt


title: WT stem rep 2

source_name: WT_Inflorescence stem

value: wild type

tag: tissue


title: G44-13 hippocampus

description: suicide victim G44-13 hippocampus


title: G131-12 hippocampus

description: control person G131-12 hippocampus


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 3d rep2

description:
RNA_3dOb_BM_rep2
GeneExpr_BM.txt

tag: cell line


title: 35S::CLE41 stem rep 1


title: G131-12 thalamus

description: control person G131-12 thalamus


title: G534-13 thalamus

description: suicide victim G534-13 thalamus


title: WT stem rep 3


title: WT stem rep 1


title: Pru rep5

city: Rochester

first: Felix

last: Yarovinsky

address: 601 Elmwood Ave, Box 609

department: Department of Microbiology and Immunology

institute: University of Rochester Medical Center

description:
PBMC stimulated by PRU
PBMC 5 PRU-5 media.txt

data_processing:
Within Galaxy platform sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat v2.1.0 (default parameters) followed by Cuffdiff v2.2.1(default parameters)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, logarithmic fold change (treated vs untreated), p-values and q-values for each Sample

source_name: PBMC

extract_protocol:
Invitrogen PureLinkTM RNA Mini Kit was used for RNA isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: T. gondii strain  PRU, type II( nonvirulent)

value: PBMC


title: G534-13 hippocampus

description: suicide victim G534-13 hippocampus


title: G131-12 amygdala

description: control person G131-12 amygdala


title: Pru rep4

description:
PBMC stimulated by PRU
PBMC 4 PRU-4 media.txt


title: G131-12 prefrontal cortex

description: control person G131-12 prefrontal cortex


title: 35S::CLE41 stem rep 2


title: G190-12 thalamus

description: suicide victim G190-12 thalamus


title: Pru rep3

description:
PBMC stimulated by PRU
PBMC 3 PRU-3 media.txt


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 7d rep3

description:
RNA_7dOb_BM_rep3
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteoblast diff 7d

tag: differentiation status

tag: timepoint


title: Pru rep2

description:
PBMC stimulated by PRU
PBMC 2 PRU-2 media.txt


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 7d rep2

description:
RNA_7dOb_BM_rep2
GeneExpr_BM.txt


title: G534-13 amygdala

description: suicide victim G534-13 amygdala

source_name: amygdala of suicide victim


title: GROUND BRIC B PDFU-3 341 HSFA2 KO Rep2

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description: 11992_Ferl_GCB3.2_(ATH1-121501).mas5-Signal

hyb_protocol: Amplified and labeled cDNA (5 µg/sample) was fragmented and hybridized with rotation onto Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays for 16h at 45°C. Arrays were washed on a Fluidics Station 450 (Affymetrix) with the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004.

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: The MAS5 data was generated by using the Affymetrix Expression Console software using default analysis settings and global scaling as normalization method.

source_name: solid media plates; BRIC-17; OES chamber: BRIC-B PDFU-4

label_protocol: cDNA was synthesized using Ovation Pico WTA System (NuGEN Technologies Inc.) and cDNA was labeled using Encore Biotin Module (NuGEN Technologies Inc.)

growth_protocol: General biology operations   Three Arabidopsis thaliana Col-0 cell culture lines were used: Wild Type (WT), ARG1 KO SALK_024542C line (ARG1 T-DNA insertion knockout) and HSFA2 KO SALK_008978C (HSFA2 T-DNA insertion knockout), all cell cultures derived from hypocotyls. Tissue culture cells were plated on 60mm round, nutrient agar Petri plates cultured in a horizontal position until turnover and installation into the BRIC hardware.  All of the sub-culturing on the plates was conducted in the laboratory of the PIs and the University of Florida.  Plates were planted in a laminar flow hood and stored in sterile Biotransfer Boxes (BT). Plates with cells were kept in the dark and at ambient temperature.  Preparation of specialized plates and biology  Petri plates.   Because of their configuration within the BRIC flight hardware, sterility was maintained on all surfaces (interior and exterior) of the Petri plates. The media in the plates for BRIC had to be 5mm deep or less to accommodate the biology and the PDFU cover hardware. For a 60mm dish, this calculates out to 6.7 mLs. After pouring, the plates are allowed to solidify, and then transferred to a sterile Biotransporter (to maintain sterility of external surface) until planting.  Preparation of cell culture plates.  The liquid media from a sterile cell suspension was decanted, and the cells were washed once with fresh liquid media, and then decanted again. A sterile scoop was used to place about 1 gram of cells in the surface on the plate and disperse evenly across the surface. The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at room temperature. The same day plates were transported by car to the Kennedy Space Center, NASA for the same night (3:00 AM) Turn Over. The ground control plates were turned over 48 hours later.   BRIC Spaceflight Hardware  The hardware for this experiment was the NASA BRIC-LED (Biological Research In a Canister – Light Emitting Diode). The LED component of the hardware was disabled and all biology was held in the dark for the duration of the experiment. The BRIC-LED canisters hold six 60 mm diameter Petri plates in small sub-compartments called PDFUs (Petri Dish Fixation Units). The PDFUs allow an externally activated fixation step without manipulating the samples. We were allocated 10 PDFUs: 5 in BRIC A and 5 in BRIC B. The 2 replicate plates of WT cultured cells and the 3 replicate plates of ARG1 KO were distributed among the BRIC A canister. The 2 replicate plates of WT cultured cells and the 3 replicate plates of HSFA2 KO were distributed among the BRIC B canister. One of the PDFU slots in each BRIC was used to hold a HOBO™ data logger to record temperature. The HOBO temperature data collection begins immediately after the biology is sealed in the BRICs, 24 hours before launch.   An additional set of Petri plates within BRIC hardware, identical to that launched for Spaceflight, was prepared for the Ground Control. The Ground Control was housed in the OES (Orbital Environmental Simulator) chamber in the Spaceflight Life Sciences Laboratory (SLSL) at Kennedy Space Center (KSC). The Ground Control was initiated with a precise 24 hour delay to enable the OES environment to be programmed with the environmental profile taken from telemetry of the Space Shuttle. Nominally, the Ground Control BRIC hardware and samples experienced the same external environment profile as the hardware and samples on the Space Shuttle. Environmental parameters that are controlled on the OES and made identical to flight are cabin temperature, humidity and CO2 concentration.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: The BRIC-17 experiment was turned over to payload engineers in the SLSL at KSC 48 hours before the scheduled launch time. The payload launched on Dragon cargo spacecraft, SpaceX CRS-2 on March 1st, 2013, at 10:10 EST, and achieved orbit approximately twelve minutes later. Dragon berthed to the ISS on the March 3rd, 2013. The biology was in orbit 10 days before being fixed on orbit with RNAlater. The Dragon unmanned spacecraft unberthed the ISS and splashed into Pacific on the March 26th and the biology was returned to the Kennedy Space Center and handed to the PIs at SLSL on the April the 2nd.

tag: cultivar

tag: genotype

value: HSFA2 KO

tag: material type

value: Tissue culture cells

tag: tissue source

value: derived from hypocotyls of SALK_008978C plants (HSFA2 T-DNA insertion knockout plants)

value: 14 days old

tag: biosource type

value: RNAlater fixed_sample


title: GROUND BRIC B PDFU-5 343 HSFA2 KO Rep2

description: 11994_Ferl_GCB5.2_(ATH1-121501).mas5-Signal

source_name: solid media plates; BRIC-17; OES chamber: BRIC-B PDFU-5


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 3d rep1

description:
RNA_3dOb_BM_rep1
GeneExpr_BM.txt


title: G534-13 prefrontal cortex

description: suicide victim G534-13 prefrontal cortex

tag: group

value: suicide victim

tag: individual

value: prefrontal cortex

tag: rin


title: G206-12 thalamus

description: suicide victim G206-12 thalamus

source_name: thalamus of suicide victim

tag: brain region

value: thalamus

tag: hybridiziation date


title: RH rep5

description:
PBMC stimulated by RH
PBMC 5 RH-5 media.txt

value: T. gondii strain RH, type I( virulent)


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 7d rep1

description:
RNA_7dOb_BM_rep1
GeneExpr_BM.txt


title: G190-12 hippocampus

description: suicide victim G190-12 hippocampus

value: hippocampus


title: media rep4

description:
PBMC no stimulation
PBMC 4 RH-4 media.txt;PBMC 4 PRU-4 media.txt

value: no parasite added


title: RH rep4

description:
PBMC stimulated by RH
PBMC 4 RH-4 media.txt


title: G206-12 hippocampus

description: suicide victim G206-12 hippocampus


title: RH rep3

description:
PBMC stimulated by RH
PBMC 3 RH-3 media.txt


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 14d rep2

description:
RNA_14dOb_BM_rep2
GeneExpr_BM.txt

source_name: BM-hMSC-TERT4 osteAdlast diff 14d

value: osteoblast


title: media rep5

description:
PBMC no stimulation
PBMC 5 RH-5 media.txt;PBMC 5 PRU-5 media.txt


title: GROUND BRIC B PDFU-3 341 HSFA2 KO Rep1

description: 11911_Ferl_GCB3_(ATH1-121501).mas5-Signal

source_name: solid media plates; BRIC-17; OES chamber: BRIC-B PDFU-3

tag: age


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 14d rep3

description:
RNA_14dOb_BM_rep3
GeneExpr_BM.txt

tag: chip antibody


title: media rep3

description:
PBMC no stimulation
PBMC 3 RH-3 media.txt;PBMC 3 PRU-3 media.txt

tag: tissue


title: Input for ChIP-seq, BM-hMSC-TERT4 pooled time points

source_name: BM-hMSC-TERT4 pooled time points

extract_protocol:
Chromatin was prepared from 150 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279). Chromatin used for ChIP-seq of MED1 was also cross-linked in 2 mM disuccinimidyl glutarate (DSG) for 20 minutes at RT prior to cross-linking with formaldehyde.
DNase-seq and ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

tag: cell line


title: media rep1

description:
PBMC no stimulation
PBMC 1 RH-1 media.txt;PBMC 1 PRU-1 media.txt

tag: agent


title: FLIGHT BRIC B PDFU-5 330 HSFA2 KO

description: 11908_Ferl_FB5_(ATH1-121501).mas5-Signal

source_name: solid media plates; BRIC-17; Dragon,ISS; BRIC-B PDFU-5

value: RNAlater in-flight fixed_sample


title: media rep2

description:
PBMC no stimulation
PBMC 2 RH-2 media.txt;PBMC 2 PRU-2 media.txt


title: Pru rep1

description:
PBMC stimulated by PRU
PBMC 1 PRU-1 media.txt


title: RH rep1

description:
PBMC stimulated by RH
PBMC 1 RH-1 media.txt


title: G190-12 amygdala

description: suicide victim G190-12 amygdala

value: amygdala


title: LHX9-V5_shKRAS_ChIPseq

city: Boston

first: Seav Huong

last: Ly

state: MA

address: 450 Brookline Avenue Dana 1511

institute: Harvard University

data_processing:
Reads mapping and peaks calling were performed using ChiLin pipeline (Qin et al. 2016)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file

source_name: colon

growth_protocol: RPMI-1640 media supplemented with 10% FBS and 1% pennicilin and streptinomycin

extract_protocol:
Chromatin immunoprecipitation was performed using SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling #9003). Monoclonal antibody against V5 tag was obtained from Invitrogen (V5 #46-0705) and used at 1:100 dilution
Libraries were prepared by Molecular Biology Core Facilities at Dana Farber Cancer Institute according to Illumina's instruction

treatment_protocol: Cells were treated with media or 1ug/mL of doxycycline to induce expression of shKRAS

value: colon

tag: disease

value: colorectal carcinoma

tag: genetic perturbation

value: Expressing LHX9-V5 open reading frame and shKRAS

value: V5 (Invitrogen #46-0705)


title: RNA-seq, BM-hMSC-TERT4 osteoblast diff 14d rep1

description:
RNA_14dOb_BM_rep1
GeneExpr_BM.txt

tag: differentiation status

tag: timepoint


title: FLIGHT BRIC B PDFU-4 329 HSFA2 KO

description: 11907_Ferl_FB4_(ATH1-121501).mas5-Signal

source_name: solid media plates; BRIC-17; Dragon,ISS; BRIC-B PDFU-4

tag: cultivar

tag: genotype

value: HSFA2 KO

tag: material type

value: Tissue culture cells


title: G206-12 amygdala

description: suicide victim G206-12 amygdala

tag: group


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 14d rep2

description:
H3K27ac_14dAd_BM_rep2
H3K27ac_14dAd_BM.bedGraph.gz
H3K27ac_14dAd_BM.bigWig

value: adipocyte

value: H3K27ac (ab4729, Abcam)


title: LHX9-V5_ChIPseq

value: Expressing LHX9-V5 open reading frame


title: RH rep2

description:
PBMC stimulated by RH
PBMC 2 RH-2 media.txt

value: PBMC


title: FLIGHT BRIC B PDFU-3 328 HSFA2 KO Rep2

description: 11991_Ferl_FB3.2_(ATH1-121501).mas5-Signal

source_name: solid media plates; BRIC-17; Dragon,ISS; BRIC-B PDFU-3

tag: tissue source

value: derived from hypocotyls of SALK_008978C plants (HSFA2 T-DNA insertion knockout plants)

value: 14 days old

tag: biosource type