title: bXL RNaseA Hi-C Biological Replicate 1

description:
bXL RNaseA Rep1
Processed data file: bXL_RA_allValidPairs.txt

data_processing:
library strategy: Hi-C-Seq
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.8.1. The sequenced reads were mapped to the hg19 human reference genome, and corrected for biases, including read depth2. There was a high correlation among all the Hi-C biological replicates (Fig. 1c, Supplementary Fig. 1a), indicating the high quality and reproducibility of the datasets.
Genome_build: hg19
Supplementary_files_format_and_content: Processed, iterative corrected sparse Hi-C matrix in the "Juicer" hic format (PMID:27467249)

source_name: bXL RNaseA Hi-C

growth_protocol:
K562 cells were obtained from (ATCC #CCL-243) and cultured in RPMI 1640 (Thermo Fisher #22400-105), 10% Fetal Bovine Serum (Thermo Fisher #26140-079), 1% L-Glutamine (Thermo Fisher #25030-164) and 1% Penicillin/Streptomycin (Thermo Fisher #15140-163) in a 37°C incubator.  The media was changed every 2 days, and when the cells’ density reached ~8x10^5 cells/mL, the culture was split to ~3x10^5 cells/mL with fresh, warm media.
Transcription inhibition was achieved by treating the cells with actinomycin D (5micrograms/mL) for 24 hours.

extract_protocol:
For the RNase A treatment before crosslinking (bXL) condition, ~10 x 10^6 K562 cells were aliquoted and spun down at 1000xg for 10 minutes at 4°C.  The supernatant was removed and the cell pellet was re-suspended with 1mL of cold PBS + 0.02% Tween-20 followed by incubation on ice for 10 minutes. Next, Either of 500μg RNase A (Qiagen #19101), or 30U of RNase Inhibitor (NEB, #M0314L) was added to the suspension, and incubated at 37°C for 30 mins in a thermomixer at 950rpm.  Next, the cells were spun down at 1000xg for 10 minutes at 4°C, washed once with 1mL cold PBS with protease inhibitor cocktail (Roche, #04693159001), and then re-suspended in 10mL 1X PBS at room temperature with protease inhibitor cocktail, followed by crosslinking of the cells with formaldehyde at 1% final concentration and quenching the formaldehyde with glycine. Then, the RNase A and RNase inhibitor treated samples were processed for downstream Hi-C experiments.
Hi-C libraries were generated with the in-situ ligation using the HindIII restriction enzyme (PMID: 28435001), Briefly, after crosslinking the cells with 1% formaldehyde for 10 minutes at room temperature, the nuclei were extracted by dounce homogenization. Next, the chromatin was digested with HindIII either in the presence of 500μg RNase A (Qiagen #19101), or 30U of RNase Inhibitor (NEB, #M0314L).  These samples that are treated after formaldehyde crosslinking (aXL) are referred as “aXL RNase A” and “aXL CTRL”, respectively. The bXL samples were processed according to the original protocol(PMID: 28435001). The digested chromatin was then end-labelled with biotin-14-dCTP (Thermo Fisher 19519016), and in-situ ligation was performed. Extraction of the DNA was performed by phenol-chloroform extraction, and the biotin was removed from unligated ends, followed by shearing of the DNA by using a Covaris S220 instrument to 100-500bp size range. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Hi-C libraries for each condition were generated in two biological replicates.

value: RNase A treatment before crosslinking


title: Patient 296

status: Public on Apr 01 2019

type: RNA

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

country: USA

institute: MGH

description:
Test
SAMPLE 296

data_processing: The study does not have the normalized Ct values. This is because raw CT values after applying a threshold (Ct<=22) was used.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: Plasma extracelular RNA

label_protocol: According to BioMark System protocol.

extract_protocol: RNA was extracted from plasma (331 patients, OMEGA-REMODEL trial) using miRCURY RNA Isolation Kit – Biofluids (Exiqon) and reverse transcribed using miScript II RT Kit (Qiagen, Fredrick, MD, USA). cDNA samples were pre-amplified with miScript Microfluidics PreAMP Kit (Qiagen, Fredrick, MD, USA) and RT-qPCR miRNA profiling analyses performed on the BioMark System (Fluidigm Corp. South San Francisco, CA) using miScript miRNA Assays (Qiagen, Fredrick, MD, USA) and Dynamic Array 96.96 (Fluidigm Corp. South San Francisco, CA). A Ct value of 23 was set as the cut-off point for detectable miRNA species.

tag: individual

value: patient who underwent a myocardial infarction

tag: tissue

value: plasma

tag: gender

value: Female

tag: race

value: Caucasian

tag: diabetes

tag: omega-3 fatty acid therapy

tag: age


title: bXL RNaseA Hi-C Biological Replicate 2

type: SRA

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
bXL RNaseA Rep2
Processed data file: bXL_RA_allValidPairs.txt

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: condition


title: aXL RNaseA Hi-C Biological Replicate 2

description:
aXL RNaseA Rep2
Processed data file: aXL_RA_allValidPairs.txt

source_name: aXL RNaseA Hi-C

value: RNase A treatment after crosslinking


title: bXL CTRL Hi-C Biological Replicate 1

description:
bXL CTRL Rep1
Processed data file: bXL_CTRL_allValidPairs.txt

source_name: bXL CTRL Hi-C

value: Rnase inhibitor treatment before crosslinking


title: Patient 283

description:
Test
SAMPLE 283

value: Male


title: Patient 282

description:
Test
SAMPLE 282


title: Patient 281

description:
Test
SAMPLE 281


title: aXL RNaseA Hi-C Biological Replicate 1

description:
aXL RNaseA Rep1
Processed data file: aXL_RA_allValidPairs.txt


title: aXL CTRL Hi-C Biological Replicate 2

description:
aXL CTRL Rep2
Processed data file: aXL_CTRL_allValidPairs.txt

source_name: aXL CTRL Hi-C

value: RNase inhibitor treatment after crosslinking


title: DDLPS_T2_H3K27ac

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: DDLPS_T2_H3K27ac_FCHNY2LBBXX_L3_wHAPPI076353-62_1

data_processing:
Raw fastq files were aligned to human gneome using bowtie and duplicates were removed using picard. Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01. Alignment and peak calling pipelines with hard-coded parameters are available at https://github.com/PoisonAlien/chiptk.
ChIP signals (Bedgraph) were simultaneously generated and input signal was subtracted with MACS2 bdgmp function. Bedgraphs were later converted to bigwig files with UCSC bedGraphTobigWig utility.
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million.

growth_protocol: LPS cells were  cultured in Roswell Park Memorial Institute medium 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
ChIP was performed by following a standard protocol. Briefly, cells were fixed with 1% formaldehyde for 10 min at room temperature, followed with 3 washes by cold PBS. Nuclei were extracted and re-suspended in SDS lysis buffer for 10 min on ice before sonication by Bioruptor (Diagenode). Optimal condition of sonication yielded genomic fragments around 200 to 500 bp. After sonication, cell debris was removed by centrifugation (13,000 rpm, 10 min). Supernatant was then pre-cleared and incubated with magnetic beads (Invitrogen Dynabeads) conjugated with specific antibodies (Supplementary Table 5).  After overnight incubation, magnetic beads were washed stepwise with cold low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer. Bound DNA was eluted, reverse-crosslinked, and purified by QIAquick PCR purification kit (Qiagen).
Standard Illumina library preparation protocol

tag: cell type

value: DDLPS primary tissue

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: Patient 289

description:
Test
SAMPLE 289


title: Patient 279

description:
Test
SAMPLE 279


title: Patient 280

description:
Test
SAMPLE 280


title: Patient 288

description:
Test
SAMPLE 288


title: LP6_H3K27ac

description: LP6 H3K27ac ChIP-seq

value: liposarcoma cells


title: DDLPS_T1_H3K27ac

description: DDLPS_T1_H3K27ac_FCHTL3HBBXX_L8_CHKPEI85218040359_1


title: aXL CTRL Hi-C Biological Replicate 1

description:
aXL CTRL Rep1
Processed data file: aXL_CTRL_allValidPairs.txt


title: Patient 278

description:
Test
SAMPLE 278


title: Patient 284

description:
Test
SAMPLE 284


title: Patient 276

description:
Test
SAMPLE 276


title: bXL CTRL Hi-C Biological Replicate 2

description:
bXL CTRL Rep2
Processed data file: bXL_CTRL_allValidPairs.txt


title: Patient 277

description:
Test
SAMPLE 277


title: LP6_Input

description: LP6 ChIP-seq Input


title: MLS1765_Input

description: MLS1765 ChIP-seq Input


title: MLS1765_H3K27ac

description: MLS1765 H3K27ac ChIP-seq

value: H3K27ac (Activemotif, #39133)


title: Patient 274

description:
Test
SAMPLE 274


title: Patient 273

description:
Test
SAMPLE 273


title: MLS402_RNAPol2

description: MLS402 RNAPol2 ChIP-seq

value: RNAPol2 (Santa Cruz, #sc-899X)


title: MLS402_DDIT3

description: MLS402 DDIT3 ChIP-seq

value: DDIT3 (Cell Signaling Technology, #2895)


title: Patient 275

description:
Test
SAMPLE 275


title: MLS402_H3K4me3

description: MLS402 H3K4me3 ChIP-seq

value: H3K4me3 (Emdmillipore, #04-745)


title: Patient 271

description:
Test
SAMPLE 271


title: Patient 269

description:
Test
SAMPLE 269


title: Patient 270

description:
Test
SAMPLE 270


title: Patient 272

description:
Test
SAMPLE 272


title: MLS402_H3K4me1

description: MLS402 H3K4me1 ChIP-seq

value: H3K4me1 (Abcam, #ab8895)


title: Patient 268

description:
Test
SAMPLE 268


title: LPS141_panRUNX

description: LPS141 panRUNX ChIP-seq

value: pan-RUNX (Abcam, #ab92336)


title: MLS402_Input

description: MLS402 ChIP-seq Input


title: Patient 267

description:
Test
SAMPLE 267

value: patient who underwent a myocardial infarction


title: LPS141_BRD4

description: LPS141 BRD4 ChIP-seq

value: BRD4 (Bethyl, #A301-985A, lot4)


title: Patient 266

description:
Test
SAMPLE 266

value: plasma


title: Patient 265

description:
Test
SAMPLE 265

value: Caucasian


title: Patient 264

description:
Test
SAMPLE 264


title: LPS141_BRD2

description: LPS141 BRD2 ChIP-seq

value: BRD2 (Proteintech, #22236-1-AP)


title: LPS141_RNAPol2

description: LPS141 RNAPol2 ChIP-seq


title: Patient 262

description:
Test
SAMPLE 262


title: LPS141_H3K27ac

description: LPS141 H3K27ac ChIP-seq


title: MLS402_H3K27ac

description: MLS402 H3K27ac ChIP-seq


title: Patient 258

description:
Test
SAMPLE 258


title: MLS402_ARV825_24h_rep2

description: MLS402 cells treated with ARV-825, replicate 2

library_source: transcriptomic

data_processing:
Paired-end reads were pseudo-aligned and quantified to Ensemble (hg19; version 88) transcripts using kallisto program. Kallisto results were imported into R bioconductor DESeq2 using tximport Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Expression values were calculated in terms of FPKM for every gene with DESeq2::fpkm function.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted by using RNeasy Kit (Qiagen).
Standard Illumina protocol

treatment_protocol: LPS cells were treated with DMSO or OTX015/ARV-825 using 200 nM for 24 hours.

tag: treatment


title: Patient 256

description:
Test
SAMPLE 256


title: MLS402_ARV825_24h_rep1

description: MLS402 cells treated with ARV-825, replicate 1


title: Patient 257

description:
Test
SAMPLE 257


title: LPS141_FOSL2

description: LPS141 FOSL2 ChIP-seq

value: FOSL2 (Santa Cruz, #sc-604X)


title: LPS141_H3K4me1

description: LPS141 H3K4me1 ChIP-seq


title: MLS402_OTX015_24h_rep2

description: MLS402 cells treated with OTX015, replicate 2


title: Patient 261

description:
Test
SAMPLE 261

value: Female


title: Patient 260

description:
Test
SAMPLE 260

value: Male


title: MLS402_OTX015_24h_rep1

description: MLS402 cells treated with OTX015, replicate 1


title: Patient 254

description:
Test
SAMPLE 254


title: Patient 255

description:
Test
SAMPLE 255


title: LPS141_Input

description: LPS141 ChIP-seq Input


title: Patient 263

description:
Test
SAMPLE 263

value: African American


title: MLS402_DMSO_24h_rep2

description: MLS402 cells treated with DMSO, replicate 2

value: DMSO


title: Patient 253

description:
Test
SAMPLE 253

value: Hispanic


title: LPS141_ARV825_24h_rep2

description: LPS141 cells treated with ARV-825, replicate 2

value: liposarcoma cells


title: LPS141_BRD3

description: LPS141 BRD3 ChIP-seq


title: Patient 252

description:
Test
SAMPLE 252


title: MLS402_DMSO_24h_rep1

description: MLS402 cells treated with DMSO, replicate 1


title: LPS141_H3K4me3

description: LPS141 H3K4me3 ChIP-seq


title: Patient 251

description:
Test
SAMPLE 251


title: LPS141_OTX015_24h_rep2

description: LPS141 cells treated with OTX015, replicate 2


title: LPS141_ARV825_24h_rep1

description: LPS141 cells treated with ARV-825, replicate 1


title: Patient 259

description:
Test
SAMPLE 259


title: Patient 250

description:
Test
SAMPLE 250


title: LPS141_OTX015_24h_rep1

description: LPS141 cells treated with OTX015, replicate 1


title: Patient 249

description:
Test
SAMPLE 249


title: Patient 248

description:
Test
SAMPLE 248


title: Patient 247

description:
Test
SAMPLE 247


title: LPS141_DMSO_24h_rep1

description: LPS141 cells treated with DMSO, replicate 1


title: Patient 246

description:
Test
SAMPLE 246


title: LPS141_DMSO_24h_rep2

description: LPS141 cells treated with DMSO, replicate 2


title: Patient 242

description:
Test
SAMPLE 242


title: Patient 243

description:
Test
SAMPLE 243


title: Patient 245

description:
Test
SAMPLE 245


title: Patient 240

description:
Test
SAMPLE 240


title: Patient 241

description:
Test
SAMPLE 241


title: Patient 239

description:
Test
SAMPLE 239


title: Patient 237

description:
Test
SAMPLE 237


title: Patient 238

description:
Test
SAMPLE 238


title: Patient 236

description:
Test
SAMPLE 236


title: Patient 244

description:
Test
SAMPLE 244


title: Patient 233

description:
Test
SAMPLE 233


title: Patient 232

description:
Test
SAMPLE 232

value: Other


title: WT day6

city: Kyoto

first: Yukino

last: Hatazawa

address: 1-5 Hangi-cho, Shimogamo, Sakyo-ku

country: Japan

institute: Kyoto Prefectural University

description: WT day6

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Feature Number version) was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1-v5_95_Feb07 and Grid: 026655_D_F_20100123 to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

organism: Mus musculus

source_name: WT day6

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

extract_protocol: Satellite cells were isolated from the EDL of Dnmt3a-KO mice and age- and sex-matched WT littermates (8 weeks of age, male). After isolation, satellite cells were cultured in growth medium for 5 days, replated with cell number matching, and cultured in differentiation medium for 2, 4, 5, and 6 days. For microarray analysis, RNA was isolated from the satellite cells from wild-type control mice as well as Dnmt3a-KO mice using the RNeasy Mini kit (Qiagen, Hilden, Germany).

tag: genotype/variation

value: wild type

tag: gendar

value: male

value: skeletal muscle; extensor digitorum longus (EDL)

value: Satellite cells


title: WT day5

description: WT day5

source_name: WT day5


title: Dnmt3a-KO day5

description: KO day5

source_name: Dnmt3a-KO day5


title: Dnmt3a-KO day4

description: KO day4

source_name: Dnmt3a-KO day4


title: WT day4

description: WT day4

source_name: WT day4


title: Patient 230

description:
Test
SAMPLE 230

value: patient who underwent a myocardial infarction


title: Plaster cast_skeletal muscle

source_name: Immobilization plaster cast (11days)

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of control mice and plaster cast mice. RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany).

tag: strain

value: 9 weeks

tag: treated with

value: a plaster cast for 11 days

value: skeletal muscle


title: Denervation

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version) was used.

source_name: Denervation (14days)

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of control mice and denervated mice. RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany).


title: Dnmt3a-KO day2

description: KO day2

source_name: Dnmt3a-KO day2


title: Patient 229

description:
Test
SAMPLE 229

value: plasma

value: Caucasian


title: Control_skeletal muscle

source_name: Control


title: Sham_Control


title: Cables2 KO rep3

city: Tsukuba

first: Hiroyoshi

last: Iseki

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench Version 7.5.1 (Qiagen).
Sequences were mapped to mouse genome (mm10) and quantified for annotated genes.
Transcription expression values were estimated as reads per kilobase per million reads (RPKM) and analyzed by the Empirical analysis of DGE tool (Qiagen).
EdgeR (http://www.r-project.org/) was used to detect differential expression of genes (false discovery rate, FDR < 0.05).
Genome_build: mm10

source_name: EpiLCs

growth_protocol: Mouse ESCs were maintained on 0.1% gelatine-coated dishes in mouse ESC medium consisting of DMEM containing 20% KSR, 1% NEAA, 1% GlutaMAX, 0.1 mM 2-ME, and LIF-containing conditioned medium, supplemented with two chemical inhibitors, i.e., 3 μM CHIR99021 and 1 μM PD0325901.

extract_protocol:
Total RNAs were extracted from EpiLCs 2 days after induction using RNeasy Plus Mini Kit (Qiagen). RNA quality was evaluated using Agilent Bioanalyzer with RNA 6000 Pico kit (Agilent Technologies).
An amount of 500 ng total RNA was used for RNA-seq library preparation with NEB NEBNext rRNA Depletion Kit and ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs); 2 × 36 base paired-end sequencing was performed with NextSeq500 (Illumina) by Tsukuba i-Laboratory LLP.

treatment_protocol: EpiLCs were induced by plating 2.0 × 105 ESCs on human fibronectin-coated 6-well plates in N2B27-containing NDiff 227 medium supplemented with 20 ng/mL activin A, 12 ng/mL bFGF, and 1% KSR.

value: ESC-derived EpiLC

value: 2 days post-induction

tag: genotype


title: Dnmt3a-KO day6

description: KO day6

source_name: Dnmt3a-KO day6


title: Patient 231

description:
Test
SAMPLE 231

tag: individual

value: Female


title: Patient 235

description:
Test
SAMPLE 235

tag: tissue

value: Male


title: Patient 234

description:
Test
SAMPLE 234

tag: gender

value: African American


title: WT day2

description: WT day2

source_name: WT day2


title: Cables2 KO rep2


title: HDCGFP+/hiCD11b+Gr1lo.3

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

description: Gene expression of bone marrow derived  cells from HdcGFP mice sorted for  HdcGFP-CD11b+Gr1lo

hyb_protocol: Hybridization was performed on Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm

label: biotin

source_name: Bone marrow from the femur and tibia bones of HdcGFP mice(C57BL/6 background) sorted for HDCGFP+/hiCD11b+Gr1lo myeloid cells

label_protocol: 100 ng of total RNA was labeled with 3' IVT Express Kit (Affymetrix)

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: Extraction of total RNA was performed using Rneasy Micro Kit (Qiagen) according to the manufacturer's instructions.

value: female

value: HdcGFP mice (C57BL/6 background)

value: bone marrow

tag: marker

value: Hdc-GFP, CD11b, Gr1


title: Patient 226

description:
Test
SAMPLE 226

source_name: Plasma extracelular RNA

tag: race

tag: diabetes


title: HDCGFP+/hiCD11b+Gr1hi.1

description: Gene expression of bone marrow derived  cells from Hdc-GFP mice sorted for  HdcGFP+/hiCD11b+Gr1hi

source_name: Bone marrow from the femur and tibia bones of HDCGFP mice (C57BL/6 background) sorted for HDCGFP+/hiCD11b+Gr1hi myeloid cells

value: Hdc-GFP mice (C57BL/6 background)

tag: markers


title: HDC-GFP+/hiCD11b+Gr1hi.2

description: Gene expression of bone marrow derived  cells from HdcGFP mice sorted for  HDCGFP+/hiCD11b+Gr1hi .

source_name: Bone marrow from the femur and tibia bones of HDCGFP mice (C57BL/6 background) sorted for HDCGFP+CD11b+Gr1hi myeloid cells.

value: Hdc=-GFP mice (C57BL/6 background)

value: Hdc-GFPhi/+CD11b+Gr1hi myeloid cells


title: Cables2 KO rep1

tag: age


title: HDCGFP+/hiCD11b+Gr1hi.3

description: Gene expression of bone marrow derived  cells from Hdc-GFP mice sorted for  HDC-GFP+/hiCD11b+Gr1hi .

hyb_protocol: Hybridization was performed oo Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

source_name: Bone marrow from the femur and tibia bones of HDCGFP mice (C57BL/6 background) sorted for HDCGFP+CD11b+Gr1hi myeloid cells

value: Hdc-GFP, CD11b, Hi Gr1


title: HDCGFP+/hiCD11b+Gr1lo.2

description: Gene expression of bone marrow derived  cells from HdcGFP mice sorted for  HDCGFP+/hiCD11b+Gr1lo

source_name: Bone marrow from the femur and tibia bones of HdcGFP mice (C57BL/6 background) sorted for HdcGFP+/hiCD11b+Gr1lo myeloid cells.


title: Patient 228

description:
Test
SAMPLE 228

value: patient who underwent a myocardial infarction

tag: omega-3 fatty acid therapy


title: Patient 225

description:
Test
SAMPLE 225

value: Hispanic


title: Patient 290

description:
Test
SAMPLE 290

value: plasma


title: Patient 223

description:
Test
SAMPLE 223

value: Caucasian


title: Patient 222

description:
Test
SAMPLE 222


title: WT rep1

tag: cell type

value: ESC-derived EpiLC

value: wild type


title: Patient 224

description:
Test
SAMPLE 224


title: Patient 220

description:
Test
SAMPLE 220


title: Patient 221

description:
Test
SAMPLE 221


title: Patient 218

description:
Test
SAMPLE 218

value: Female


title: WT rep2

value: 2 days post-induction


title: CXCR5+_wt_IFNI_2

city: San Diego

first: John

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

description:
PolyA RNA
raw_counts.txt

data_processing:
Quality of raw RNA-sequencing reads was checked using FastQC version 0.11.3 (Barbaham Institute, Cambridge, UK; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Illumina’s bcl2fastq Conversion Software (version 2.17.1.14) was used to de-multiplex reads and convert BCL files generated by the Illumina NextSeq 500 to FASTQ.
Reads were mapped to the mouse genome (GRCm38 assembly with Ensembl v87 transcriptome annotations) and gene counts calculated using STAR version 2.5.2a (Dobin et al., 2013) using the following parameters: --quantMode GeneCounts –outSAMtype None –sjdbGTfile /Ensembl/Mus_musculus.GRCm38.87.gtf –sjdbOverhang 74
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.txt: Tab-delimited text file includes raw gene counts.

source_name: CD8+ T cells

extract_protocol:
Mouse spleens were processed into splenocytes, enriched for mouse T cells using a magnetic negative selection (STEMCELL Technologies), stained and T cells were isolated by flow cytometry. RNA isolation from sorted cells was performed using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA). RNA integrity was analyzed using Agilent RNA Nano Kit (Agilent, Santa Clara, CA).
Amplified cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA), sheared using Covaris tubes (Covaris, Woburn, MA) and Illumina libraries constructed using the NEBNext Ultra DNA Library Prep Kit (NEB, Ipswich, MA) and sequenced using the NextSeq 500 system (Illumina, San Diego, CA) at a depth of 20-25 million single-end 75 bp reads per sample.

treatment_protocol: Splenic CXCR5+ CD8+ and CXCR5- CD8+ T cells were purified by flow cytometry, plated at a concentration of 1 x 10^6 cell/ml and treated with growth medium (RPMI1640 containing 10% FBS, and supplemented with Non-essential amino acids, sodium pyruvate, HEPES, L-Glutamine, 2-Mercaptoethanol, Penicillin-Streptomycin (Gibco)) with or without recombinant IL-27 (20 ng/ml, R&D Systems, Minneapolis, MN) or recombinant IFN-β (1000 U/ml, carrier-free, PBL Assay Science) for 12 h at 37°C.

tag: infection

value: LCMV clone 13

value: CXCR5+ CD8+ T cells

tag: tcr specificity

value: undetermined

tag: donor mice

tag: flow cytometry population

value: IFN-I, 12 h


title: CXCR5-_wt_vehicle_1

description:
PolyA RNA
raw_counts.txt

tag: strain

value: CXCR5- CD8+ T cells

tag: treatment

value: medium only, 12 h


title: CXCR5+_Ifnar1ko_IL27_2

description:
PolyA RNA
raw_counts.txt


title: HDCGFP+/hiCD11b+Gr1lo.1

description: Gene expression of bone marrow derived  cells from HDCGFP mice sorted for  HdcGFP+/hiCD11b+Gr1lo .

source_name: Bone marrow from the femur and tibia bones of HdcGFP mice ((C57BL/6 background) sorted for HDCGFP+/hiCD11b+Gr1lo myeloid cells.

value: female

tag: genotype

value: HdcGFP mice (C57BL/6 background)

value: bone marrow

value: HdcGFP, CD11b, Low Gr1


title: Patient 227

description:
Test
SAMPLE 227

tag: individual

value: patient who underwent a myocardial infarction

value: Male


title: Patient 215

description:
Test
SAMPLE 215

tag: tissue

value: plasma

value: African American


title: CXCR5+_wt_IFNI_1

description:
PolyA RNA
raw_counts.txt


title: WT rep3

value: ESC-derived EpiLC

value: wild type


title: Patient 214

description:
Test
SAMPLE 214

tag: gender

value: Caucasian


title: CXCR5+_wt_IL27_1

description:
PolyA RNA
raw_counts.txt

value: LCMV clone 13


title: CXCR5+_wt_IL27_2

description:
PolyA RNA
raw_counts.txt

value: CXCR5+ CD8+ T cells


title: CXCR5-_wt_vehicle_2

description:
PolyA RNA
raw_counts.txt

value: undetermined


title: Patient 217

description:
Test
SAMPLE 217


title: CXCR5+_Ifnar1ko_vehicle_2

description:
PolyA RNA
raw_counts.txt


title: CXCR5+_Ifnar1ko_IL27_1

description:
PolyA RNA
raw_counts.txt


title: CXCR5+_Ifnar1ko_vehicle_1

description:
PolyA RNA
raw_counts.txt


title: Patient 216

description:
Test
SAMPLE 216

value: Female

value: Hispanic


title: Patient 219

description:
Test
SAMPLE 219


title: MLPS_T2_H3K27ac

description: MLPS_T2_H3K27ac_FCHNY2LBBXX_L3_wHAPPI076358-65_1

value: MLPS primary tissue

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: Patient 213

description:
Test
SAMPLE 213

tag: race


title: Patient 212

description:
Test
SAMPLE 212

tag: diabetes


title: Patient 210

description:
Test
SAMPLE 210


title: virus-specific_Il27rako_aIFNAR_continuous_3

description:
PolyA RNA
raw_counts.txt

value: CD8+ T cells

value: endogenous GP33-specific TCR

value: tetramer+ CD8+ B220-


title: Patient 211

description:
Test
SAMPLE 211

value: patient who underwent a myocardial infarction


title: CXCR5+_wt_vehicle_2

description:
PolyA RNA
raw_counts.txt

value: medium only, 12 h


title: Patient 208

description:
Test
SAMPLE 208

value: plasma

value: Male


title: virus-specific_Il27rako_aIFNAR_continuous_2

description:
PolyA RNA
raw_counts.txt


title: CXCR5+_wt_vehicle_1

description:
PolyA RNA
raw_counts.txt


title: Patient 209

description:
Test
SAMPLE 209


title: Patient 207

description:
Test
SAMPLE 207


title: virus-specific_wt_aIFNAR_continuous_2

description:
PolyA RNA
raw_counts.txt


title: Patient 206

description:
Test
SAMPLE 206


title: virus-specific_Il27rako_aIFNAR_continuous_1

description:
PolyA RNA
raw_counts.txt


title: Patient 205

description:
Test
SAMPLE 205


title: virus-specific_wt_aIFNAR_continuous_3

description:
PolyA RNA
raw_counts.txt


title: virus-specific_wt_aIFNAR_continuous_1

description:
PolyA RNA
raw_counts.txt


title: Patient 204

description:
Test
SAMPLE 204


title: virus-specific_Il27rako_Iso_2b

description:
PolyA RNA
raw_counts.txt


title: Patient 203

description:
Test
SAMPLE 203


title: virus-specific_Il27rako_Iso_3b

description:
PolyA RNA
raw_counts.txt


title: virus-specific_Il27rako_Iso_1b

description:
PolyA RNA
raw_counts.txt


title: Patient 201

description:
Test
SAMPLE 201


title: Patient 202

description:
Test
SAMPLE 202

value: African American


title: virus-specific_wt_Iso_3b

description:
PolyA RNA
raw_counts.txt


title: virus-specific_wt_Iso_2b

description:
PolyA RNA
raw_counts.txt


title: Patient 200

description:
Test
SAMPLE 200


title: Patient 199

description:
Test
SAMPLE 199


title: virus-specific_wt_Iso_1b

description:
PolyA RNA
raw_counts.txt


title: Patient 198

description:
Test
SAMPLE 198

value: Other


title: Hira null  day15 differentiated Cardiomyocytes rep2

city: London

first: Rasha

middle: Noureldin

last: Saleh

address: 30 Guilford street

country: United Kingdom

institute: University College London

description: deseq_Rasha_Day15_differentiated_CM_Hiranull_Differential_expression.deseq.res

data_processing:
Illumina Isis software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Deseq2 v 1.6.3 was used for differential expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: csv files include FPKM values for each Sample
Supplementary_files_format_and_content: csv files include log2 fold change for each gene in Hira-null vs WT in undifferentiated mESCs and Day15 differentiated CM

source_name: Clone104 Hira-null mESCs cell line

extract_protocol:
Cells were harvested,  and RNA was extracted using Trizol reagent.  Library preparation was performed using KAPA stranded mRNA-seq kit (KAPABIOSYSTEMS KK8421) and KAPA mRNA capture kit (KAPABIOSYSTEMS KK8441).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: day of differentiation

value: Hira-null


title: Hira null  day15 differentiated Cardiomyocytes rep1


title: Patient 196

description:
Test
SAMPLE 196

tag: age


title: Patient 194

description:
Test
SAMPLE 194

value: Caucasian

tag: omega-3 fatty acid therapy


title: WT day15 differentiated Cardiomyocytes rep2

source_name: W9.5 mESCs cell line

value: Wild type

tag: cell line


title: Hira-null undifferentiated mESCs rep2

description: deseq_Rasha_Undifferentiated_mESCs_Hiranull_Differential_expression.deseq.res

value: Day zero


title: Patient 191

description:
Test
SAMPLE 191


title: Patient 193

description:
Test
SAMPLE 193


title: WT day15 differentiated Cardiomyocytes rep1


title: Patient 190

description:
Test
SAMPLE 190


title: Patient 195

description:
Test
SAMPLE 195

value: Female


title: Patient 188

description:
Test
SAMPLE 188


title: Patient 187

description:
Test
SAMPLE 187

value: Hispanic


title: WT undifferentiated mESCs rep1


title: Patient 186

description:
Test
SAMPLE 186


title: WT undifferentiated mESCs rep2


title: Patient 192

description:
Test
SAMPLE 192


title: Patient 189

description:
Test
SAMPLE 189


title: Patient 185

description:
Test
SAMPLE 185


title: virus-specific_Il27rako_aIFNAR_3

data_processing:
Quality of raw RNA-sequencing reads was checked using FastQC version 0.11.3 (Barbaham Institute, Cambridge, UK; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Illumina’s bcl2fastq Conversion Software (version 2.17.1.14) was used to de-multiplex reads and convert BCL files generated by the Illumina NextSeq 500 to FASTQ.
Reads were mapped to the mouse genome (GRCm38 assembly with Ensembl v87 transcriptome annotations) and gene counts calculated using STAR version 2.5.2a (Dobin et al., 2013) using the following parameters: --quantMode GeneCounts –outSAMtype None –sjdbGTfile /Ensembl/Mus_musculus.GRCm38.87.gtf –sjdbOverhang 74
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts

tag: infection

value: LCMV clone 13

tag: cell type

value: endogenous GP33 and GP276-specific TCR


title: virus-specific_wt_aIFNAR_3

value: CD8+ T cells

tag: tcr specificity

tag: donor mice


title: virus-specific_Ifnar1ko_3

tag: strain

tag: flow cytometry population


title: virus-specific_Il27rako_aIFNAR_2


title: Patient 184

description:
Test
SAMPLE 184


title: virus-specific_Il27rako_aIFNAR_1


title: virus-specific_Ifnar1ko_2


title: virus-specific_Ifnar1ko_1


title: Patient 197

description:
Test
SAMPLE 197


title: virus-specific_wt_aIFNAR_2


title: Patient 183

description:
Test
SAMPLE 183


title: Patient 182

description:
Test
SAMPLE 182


title: Hira-null undifferentiated mESCs rep1

tag: genotype


title: Patient 181

description:
Test
SAMPLE 181

tag: individual


title: virus-specific_Il27rako_Iso_2


title: Patient 180

description:
Test
SAMPLE 180

tag: tissue


title: Patient 179

description:
Test
SAMPLE 179

tag: gender


title: virus-specific_Il27rako_Iso_1


title: Patient 178

description:
Test
SAMPLE 178


title: Patient 177

description:
Test
SAMPLE 177


title: virus-specific_wt_Iso_3


title: virus-specific_wt_Iso_1


title: Patient 174

description:
Test
SAMPLE 174


title: Patient 172

description:
Test
SAMPLE 172


title: Patient 176

description:
Test
SAMPLE 176


title: Patient 171

description:
Test
SAMPLE 171


title: Patient 167

description:
Test
SAMPLE 167


title: Patient 166

description:
Test
SAMPLE 166


title: Patient 163

description:
Test
SAMPLE 163


title: Patient 165

description:
Test
SAMPLE 165


title: Patient 169

description:
Test
SAMPLE 169


title: Patient 175

description:
Test
SAMPLE 175


title: Patient 168

description:
Test
SAMPLE 168


title: Patient 160

description:
Test
SAMPLE 160


title: Patient 162

description:
Test
SAMPLE 162


title: virus-specific_wt_aIFNAR_1


title: Patient 158

description:
Test
SAMPLE 158


title: Patient 173

description:
Test
SAMPLE 173


title: Patient 159

description:
Test
SAMPLE 159


title: Patient 157

description:
Test
SAMPLE 157


title: Patient 170

description:
Test
SAMPLE 170


title: Patient 161

description:
Test
SAMPLE 161


title: Patient 156

description:
Test
SAMPLE 156


title: Patient 154

description:
Test
SAMPLE 154


title: Patient 153

description:
Test
SAMPLE 153


title: Patient 151

description:
Test
SAMPLE 151


title: Patient 150

description:
Test
SAMPLE 150


title: Patient 149

description:
Test
SAMPLE 149


title: Patient 152

description:
Test
SAMPLE 152


title: Patient 155

description:
Test
SAMPLE 155


title: Patient 164

description:
Test
SAMPLE 164


title: Patient 147

description:
Test
SAMPLE 147


title: virus-specific_wt_Iso_2


title: Patient 144

description:
Test
SAMPLE 144


title: Patient 143

description:
Test
SAMPLE 143


title: Patient 148

description:
Test
SAMPLE 148


title: IgG

city: Rotterdam

first: Raymond

middle: A

last: Poot

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmu MC

description: ChIP against IgG in NS5 neural stem cells

data_processing:
Filtering against low complexity reads using prinseq-lite using options -lc_method dust and -lc_treshhold 7
mapping reads using bowtie 0.12.7 the options -n 2 -l 36 -e 70 -k 1 --best
Picard-tools-1.81 MarkDuplicates was used to remove the duplicates from the sam/bam file
MACS 1.4.2 was used for generating wig files using default settings. The corresponding IgG-mock was used as control input file and was scaled to the treatment file by MACS.
The .wig files from MACS were converted to .bw files using UCSC WigToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bw, bed files

source_name: NS5 Neural Stem Cell

growth_protocol: Mouse neural stem cell line NS-5 was grown on gelatin coated dishes. Cells were cultured in N2 medium (Euromed (Clontech) with 1x N2 supplement (Gibco/Life Technologies), 1mM glutamine, BSA (50ug/mL), Insulin (20ug/mL), EGF and FGF2 both at 10 ng/mL)

extract_protocol:
NS-5 cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde to cross-link chromatin. Chromatin was prepared for sonication with 20 mM Tris-HCl pH8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100. We used 15 cycles of 30 seconds ON, 30 seconds OFF on a Bioruptor Pico sonication device (Diagenode Cat# B01060001) to shear chromatin to 150-200bp fragments. The resulting chromatin extract was incubated overnight at 4°C with 100ul of Dynal Protein G magnetic beads that had been pre-incubated with approximately 10 μg of the appropriate antibody. Beads were washed 1X with the sonication buffer, 1X with 20 mM Tris-HCl pH8, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1%Triton X-100, 1X with 10 mM Tris-HCl pH8, 250 mM LiCl, 2 mM EDTA, 1% NP40 and 1X with TE containing 50 mM NaCl. Bound complexes were eluted from the beads (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) by heating at 65°C for 1 hr with occasional vortexing and crosslinking was reversed by overnight incubation at 65°C. Finally ,DNA was precipitated using phenol:chloroform:isoamyl alcohol (PCI).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: Untreated

tag: antibody

value: IgG (Normal Rabbit IgG:Santa Cruz #sc-2027)


title: 1A

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Base calling was done by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.17 (Illumina, Inc. San Diego, CA, USA).
Aligment of reads to the genome (GRCh38, release 7) was done using STAR v2.4.1b.
Gene abundance quantification was performed with featureCounts (Liao Y et.al, Bioinformatics (Oxford, England) 2014; 30: 923-930.)
Genome_build: RCh38
Supplementary_files_format_and_content: raw counts, gene level, TSV format

source_name: CD_UACL_Intestinal epithelium monlayer

extract_protocol:
Total RNA was extracted from LCM material, using RNeasy FFPE kit (Qiagen, Hilden, Germany, cat. no. 73504) according to the manufacturer's instructions. Integrity was assessed using Agilent RNA 6000 Pico Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA). The DV200 value (percentage of RNA fragments > 200 nucleotides) was used as a measure of RNA quality. The mean DV200 values for the samples were 72.0±12.6 %.
RNA sequencing libraries were generated using SENSE FFPE total RNA-Seq library prep kit (with RiboCop rRNA depletion) according to the manufacturer’s instructions (Lexogen GmbH, Vienna, Austria). Libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The size range of the DNA fragments were measured to be in the range of 180-400 bp and peaked at mean size of 241.1±11.6 bp. Libraries were normalized and pooled before denaturation, final concentration of the library was 2.7 pM for clustering on NextSeq 500 high output flowcells. Single read sequencing was performed for 75 cycles on a NextSeq 500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions.

treatment_protocol: FFPE biopsies were cut into 10 µm slices, mounted on glass slides and stained with AB/dPAS in order to identify UACL. The sections were treated in 100% EtOH and Xylene in order to remove all traces of H2O. Sections were then air-dried in a desiccator (30 minutes) before laser capture microdissection (LCM) (MMI CellCut on Olympus IX71, Eching, Germany).  UACL crypts, inflamed non-UACL epithelium (crypts and villi) from the same biopsies and epithelium from controls were isolated.

tag: subject status

value: active Crohn's disease (CD) patient

tag: uacl or non-uacl

value: UACL

tag: inflamed or noninflamed

value: inflamed

tag: source location

value: terminal ileum

value: Intestinal epithelium monlayer


title: 3A

value: neoterminal ileum


title: Patient 146

description:
Test
SAMPLE 146

value: patient who underwent a myocardial infarction

value: plasma

value: Male

tag: race

tag: diabetes

tag: omega-3 fatty acid therapy

tag: age


title: 3B

value: non-UACL

tag: cell type


title: 24B

source_name: healthy control_non-UACL_Intestinal epithelium monlayer

value: healthy control

value: noninflamed


title: Patient 140

description:
Test
SAMPLE 140

value: Caucasian


title: Patient 139

description:
Test
SAMPLE 139

value: Female


title: 16B


title: Carm1

description: ChIP against Carm1 in NS5 neural stem cells

value: Carm1 (Cell Signaling Technology #12495)


title: Jmjd1c

description: ChIP against Jmjd1c in NS5 neural stem cells

value: Jmjd1c (Merck Millipore #17-10262)


title: Med1

description: ChIP against Med1 in NS5 neural stem cells

value: Med1 (Behtyl Labs #A300-793A)


title: 5B

value: active Crohn's disease (CD) patient


title: 7B


title: virus-specific_Il27rako_Iso_3

tag: infection

value: LCMV clone 13

value: CD8+ T cells

tag: tcr specificity

value: endogenous GP33 and GP276-specific TCR

tag: donor mice

value: tetramer+ CD8+ B220-


title: Patient 135

description:
Test
SAMPLE 135


title: 15B

value: terminal ileum

value: Intestinal epithelium monlayer


title: Patient 136

description:
Test
SAMPLE 136

value: patient who underwent a myocardial infarction

value: plasma


title: Patient 137

description:
Test
SAMPLE 137

value: Male


title: Patient 145

description:
Test
SAMPLE 145


title: 20B

value: non-UACL


title: Patient 138

description:
Test
SAMPLE 138


title: Patient 134

description:
Test
SAMPLE 134


title: Patient 141

description:
Test
SAMPLE 141


title: Patient 142

description:
Test
SAMPLE 142


title: 2A

value: UACL

value: inflamed

value: neoterminal ileum


title: 2B


title: Patient 133

description:
Test
SAMPLE 133

value: Caucasian


title: Patient 132

description:
Test
SAMPLE 132


title: Patient 131

description:
Test
SAMPLE 131


title: 22B

value: noninflamed


title: Patient 130

description:
Test
SAMPLE 130

value: Other


title: 1B

value: active Crohn's disease (CD) patient


title: Patient 129

description:
Test
SAMPLE 129


title: 6A


title: 21B


title: Patient 128

description:
Test
SAMPLE 128


title: Patient 127

description:
Test
SAMPLE 127


title: 6B


title: 5A


title: Patient 126

description:
Test
SAMPLE 126

value: Female


title: 8B

value: healthy control


title: 25B


title: 23B


title: BICM120+AVC292-23

city: Mountain View

first: Afshin

last: Beheshti

address: Moffett Blvd

institute: NASA Ames Research Center

description: replicate 2

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.

source_name: Jurkat Cells

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

growth_protocol: Jurkat, HH, L428, L540 cells were authenticated (by ATCC STR profiling) and maintained under 5% CO2 and at 37OC in culture medium RPMI1640 (Corning, Manassas, VA) with 10% heat inactivated Fetal Bovine Serum (FBS) and antibiotic-antimycotic (200 I.U. Penicillin/Streptomycin, 25µg Amphotericin; Corning, Manassas, VA).

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)

treatment_protocol: Lymphoma cell lines and primary tumor cells, 2x104 cells/100uL were plated in a 96-well plate, treated with appropriate drug concentrations of ixazomib, belinostat, or ixazomib and belinostat combination for 72 hours followed by assessment of MTT based cell viability using Cell Titer Aqueous Non-Radioactive Cell Proliferation assay, (Promega, Madison, WI), as described before. IC50 and combination indices for these assays were determined using method of Chou and Talalay and Calcusyn (Biosoft, Ferguson, MO). For drug combination studies, drug dilutions were performed based on fixed 1:1 ratio of IC50 values for ixazomib and belinostat, and assessment MTT based cell viability at 72 hours. A combination index (CI) value <1 indicates synergism.

tag: drug treatment


title: BICM120+AVC292-22

description: replicate 1


title: BICM120+AVC292-24

description: replicate 3


title: Belinustat 250nM-18

description: replicate 3

value: 250nM Belinostat


title: AZD 165nM-15

description: replicate 3

value: 165nM AZD


title: BICM120 0.89nM-21

description: replicate 3


title: BICM120 0.89nM-19

description: replicate 1


title: AZD 165nM-14

description: replicate 2


title: 4A


title: Patient 124

description:
Test
SAMPLE 124

tag: individual


title: 18B

value: terminal ileum


title: BICM120 0.89nM-20

description: replicate 2


title: Total DNA from the ChvI-HA strain, replicate B

type: genomic

city: Stanford

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated DNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: Rm1021 with the chromosomal chvI replaced with chvI-HA

label_protocol: DNA was fragmented and biotinylated as described by Barnett et al. 2004, Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

growth_protocol: 500 OD-600 of bacterial cells (Rm1021 and ES147) were grown in LB to 1.6-2.0 OD-600/ml

extract_protocol: Cells were lysed by incubating in 36 ml lysis buffer (50 mM Tris-HCl pH 8, 100 mM NaCl, 20% glycerol, 1 mg/ml lysozyme, and protease inhibitors for Histidine-tagged proteins (Sigma) for 20 min on ice followed by the addition of 4 ml of 10% Triton X-100 and an additional incubation on ice for 10 min.  The lysates were sonicated on ice in ten 1 min pulses, giving an average DNA fragment size of ~500 bp.  Cell debris was pelleted and the supernatant was precleared by incubating with Protein A agarose (Pierce/ThermoFisher) for 40 min at 4 degrees C.  After removal of the Protein A agarose, 750 ul of the precleared supernatant was set aside to prepare the Total DNA samples, and 38 ml of the precleared supernatant was subjected to ChIP.  For the Total DNA samples, DNA was isolated using phenol/choroform extraction and ethanol precipitation, followed by additional cleanup using the standard protocol in the Qiagen PCR Purification kit.  For ChIP, the supernatant was incubated with anti-HA antibody (F7; Santa Cruz Biotechnology) and Protein A agarose overnight at 4 degrees C.  The beads were washed 5 times with cold IP buffer (50 mM Tris-HCl pH 8, 100 mM NaCl, 20% glycerol) and 2 times with TE.  Then, beads were resuspended in TE and incubated for 6 h at 65 degrees C to reverse crosslinks.  Beads were removed by centrifugation, and the ChIP DNA was amplified.

treatment_protocol: Cells were diluted with LB to 1 OD-600/ml, and Sodium phosphate and formaldehyde were added to a final concentration of 10 mM and 1%, respectively.  After incubation for 3 min at room temperature, cells were harvested by centrifugation and washed one time in TY without CaCl2

tag: strain


title: Total DNA from the ChvI-HA strain, replicate C


title: AZD 165nM-13

description: replicate 1


title: 17B

value: Intestinal epithelium monlayer


title: MLN+Belinustat-11

description: replicate 2

value: 250nM Belinostat + 38nM Ixazomib


title: Patient 122

description:
Test
SAMPLE 122

value: patient who underwent a myocardial infarction

tag: tissue

value: plasma

tag: gender


title: Patient 125

description:
Test
SAMPLE 125

value: Male

value: African American


title: 19B

tag: subject status

value: non-UACL


title: Patient 121

description:
Test
SAMPLE 121


title: Total DNA from the ChvI-HA strain, replicate A


title: Belinustat 250nM-17

description: replicate 2


title: ChvI-untagged sample subjected to chIP with anti-HA antibody, replicate C


title: LNCaP_shTMEFF2_DHT+3

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: LNCaP cells transfected with shRNA targeting TMEFF2 and treated with DHT

data_processing:
Sequenced reads first undergo quality control with the FASTQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Sequences are aligned to a contaminant genome to filter out reads which align to human ribosomal RNA, poly-A, poly-C, phiX virus or mitochondrial DNA sequence.
The filtered reads are trimmed using Trimmomatic (PMID:24695404) to further exclude sequences contaminated with Illumina adapters, as well as read clipping based on quality over a sliding window, retaining reads with a minimum length of 15 bp
Trimmed, filtered reads were pseudoaligned to the human reference transcriptome (version GRCh38) using kallisto version 0.42.3 (PMID:27043002) with enabled bias correction and 50 bootstrapping rounds
Transcripts with an average of 5 CPM or less across all individuals are removed from further analysis. To perform differential expression analysis, CPM values were summarized at the gene level and normalized with the R packages tximport (PMID: 26925227) and DESeq2 (PMID: 25516281)
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file describes a gene-by-sample matrix of gene-level estimated counts scaled by length and library size. Each sample was split across two flow cells - read counts are summarized separately for each sample/flow cell pair.

source_name: LNCaP Cell line

growth_protocol: LNCaP cells, maintained in 10% FBS RPMI-1640, were transduced with lentiviral particles containing TMEFF2 targeted and Scramble control shRNA expressed from the U6 promoter of the pLKO.1-puro plasmid. After 1 week in 1ug/ml puromycin selection TMEFF2 knockdown was confirmed in cells expressing TMEFF2 targeted shRNA. DHT treatment and subsequent RNA extraction were carried out at approximately 2.5 weeks after initial viral transduction. 3 repeats in RNA-seq were 3 independent treatments and RNA extractions from 2 separate initial transductions.

extract_protocol:
RNA was extracted using the Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols. Raw 75bp paired-end sequences were generated from an Illumina NextSeq 500 sequencer

treatment_protocol: LNCaP cells expressing TMEFF2 targeted (shTMEFF2) and Scramble control (shScramble) shRNA were seeded in T25 flasks approximately 2.5 weeks after initial viral transduction with shRNA sxpressing plasmids. When cells were approximately 50-60% confluent, cells were washed with PBS and given 10% charcoal-stripped FBS (10% CSS) RPMI-1640 to deplete androgen levels. After 24 hours in 10% CSS RPMI-1640 cells were treated with 10 nM dihydrotestosterone (+DHT) or .0001% EtOH vehicle control (-DHT), and cells were grown in the presence and absense of DHT for 24 hours at which time RNA was extracted.

tag: shRNA

tag: dht


title: Patient 123

description:
Test
SAMPLE 123


title: MLN+AZD-9

description: replicate 3

value: 38nM Ixazomib + 165nM AZD


title: Patient 119

description:
Test
SAMPLE 119

value: Caucasian


title: MLN+AZD-8

description: replicate 2


title: MLN+Belinustat-12

description: replicate 3


title: MLN+Belinustat-10

description: replicate 1


title: Belinustat 250nM-16

description: replicate 1


title: LNCaP_shTMEFF2_DHT+2


title: LNCaP_shTMEFF2_DHT+1


title: Patient 118

description:
Test
SAMPLE 118


title: Patient 117

description:
Test
SAMPLE 117


title: Ctrl_E13.5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Sample excluded -- no processed data available for this sample.

scan_protocol: Standard Illumina scanning protocol (HiScan)

data_processing: Data processing with the GenomeStudioV2011.1 software. Detection Pvalues are available in the file with the non-normalized data.

label: Biotin

source_name: Excluded sample

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Midi Kit (Qiagen) using Trizol Reagent (Sigma)

treatment_protocol: No treatment


title: Ctrl_E12.5


title: ChvI-untagged sample subjected to chIP with anti-HA antibody, replicate A


title: Patient 120

description:
Test
SAMPLE 120


title: ChvI-HA sample subjected to chIP with anti-HA antibody, replicate B


title: Ctrl_E09.5


title: Patient 116

description:
Test
SAMPLE 116


title: LNCaP_shTMEFF2_DHT-2

description: LNCaP cells transfected with shRNA targeting TMEFF2


title: ChvI-HA sample subjected to chIP with anti-HA antibody, replicate C


title: ChvI-HA sample subjected to chIP with anti-HA antibody, replicate A


title: ChvI-untagged sample subjected to chIP with anti-HA antibody, replicate B


title: Aey69_E13.5


title: LNCaP_shTMEFF2_DHT-1


title: MLN 38nM-6

description: replicate 3

value: 38nM Ixazomib


title: MLN+AZD-7

description: replicate 1


title: MLN 38nM-4

description: replicate 1


title: MLN 38nM-5

description: replicate 2


title: Ctrl-3

description: replicate 3

value: Control


title: Patient 115

description:
Test
SAMPLE 115


title: Ctrl-1

description: replicate 1


title: LNCaP_shTMEFF2_DHT-3


title: Ctrl-2

description: replicate 2


title: Patient 114

description:
Test
SAMPLE 114


title: Patient 113

description:
Test
SAMPLE 113


title: LNCaP_shScramble_DHT+2

description: LNCaP cells transfected with scrambled shRNA and treated with DHT

value: shScramble


title: LNCaP_shScramble_DHT+3


title: LNCaP_shScramble_DHT+1


title: Patient 112

description:
Test
SAMPLE 112


title: Patient 111

description:
Test
SAMPLE 111


title: LNCaP_shScramble_DHT-2

description: LNCaP cells transfected with scrambled shRNA


title: Patient 110

description:
Test
SAMPLE 110


title: p65TA1&2_3

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

country: France

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

hyb_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization

data_processing: RMA

source_name: p65-knockout 3T3 fibroblasts reconstituted with p65TA1&2, 1hr after TNF-alpha treatment

growth_protocol: Subconfluent growth in cell culture

extract_protocol: Qiagen RNeasy

treatment_protocol: 5ng/ml mouse TNF-alpha for 1hr

tag: cell line

value: 3T3 fibroblasts

value: no

tag: treatment

value: TNF-alpha


title: Patient 108

description:
Test
SAMPLE 108

source_name: Plasma extracelular RNA

extract_protocol: RNA was extracted from plasma (331 patients, OMEGA-REMODEL trial) using miRCURY RNA Isolation Kit – Biofluids (Exiqon) and reverse transcribed using miScript II RT Kit (Qiagen, Fredrick, MD, USA). cDNA samples were pre-amplified with miScript Microfluidics PreAMP Kit (Qiagen, Fredrick, MD, USA) and RT-qPCR miRNA profiling analyses performed on the BioMark System (Fluidigm Corp. South San Francisco, CA) using miScript miRNA Assays (Qiagen, Fredrick, MD, USA) and Dynamic Array 96.96 (Fluidigm Corp. South San Francisco, CA). A Ct value of 23 was set as the cut-off point for detectable miRNA species.

tag: race

tag: diabetes


title: p65TA1&2_2

scan_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization


title: p65TA1&2_1

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization


title: Ctrl_E13.5_rep2

description: Gene expression data from embryo eye region from control mice, E12.5, biological replicate 2

source_name: Embryo eye region from control mice, E12.5, biological replicate 2

tag: genotype

value: wildtype

value: eye region

tag: age


title: p65TA3_shZbtb7a_3

source_name: p65-knockout 3T3 fibroblasts reconstituted with p65TA3, with Zbtb7a knock-down, 1hr after TNF-alpha treatment

value: yes


title: Ctrl_E13.5_rep3

description: Gene expression data from embryo eye region from control mice, E12.5, biological replicate 3

source_name: Embryo eye region from control mice, E12.5, biological replicate 3


title: Ctrl_E13.5_rep1

description: Gene expression data from embryo eye region from control mice, E12.5, biological replicate 1

source_name: Embryo eye region from control mice, E12.5, biological replicate 1


title: LNCaP_shScramble_DHT-3


title: Aey69_E13.5_rep3

description: Gene expression data from embryo eye from Aey69 mutant mice, E13.5, biological replicate 3

source_name: Embryo eye from Aey69 mutant mice, E13.5, biological replicate 3

value: Aey69 mutant


title: Patient 107

description:
Test
SAMPLE 107

value: patient who underwent a myocardial infarction

tag: omega-3 fatty acid therapy


title: H8_V2_C47

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

description: rawCounts.csv

data_processing:
Trimming: Trimmomatic version 0.33, trailing = 20, minlength = 60 and end = “PE
Alignment: STAR 2.4.0, Default parameters
Quantification: HTSEQ 0.6., -f bam, -r name, -a 4, -i gene_id, -m union
Genome_build: Human reference genome GRCh38.p7 version 25 from GenCode

source_name: human ESC

growth_protocol: human ESC line (CRX-GFP) was expanded in mTeSR™1 (StemCell Technologies) at 37°C and 5% CO2 on 6 well plates pre-coated with Low Growth Factor Matrigel (Corning) as described in our previous publication (Collin et al. 2015, , Collin et al.Stem Cells. 2016 Feb;34:311-21) ). Differentiation to retinal organoids was performed as described in Mellough et al. 2015 (Stem Cells. 2015 Aug;33(8):2416-30) with minor modifications which included addition of 10µM Y27632 dihydrochloride for the first 48 hours of differentiation.

extract_protocol: Full length cDNA libraries were prepared using the Illumina Nextera XT DNA library preparation kit (Illumina). External RNA Control Consortium (ERCC) RNA spike-in Mix  (Ambion) was added to each cell sample prior to sequencing. Libraries were multiplexed as 24-48 libraries per lane and 75 bp single end reads were sequenced on the Ilumina HiSeq 2500.

treatment_protocol: Retinal organoids at day 90 of differentiation were disassociated to single cells using the embryoid body disassociation kit (Miltenyi Biotech) following the manufacturer’s instructions. CRX-GFP+ cells were sorted using a FACS-ARIA flow cytometric activated cell sorter (BD Biosciences). Single cells were loaded onto the C1 Single-Cell Auto Prep fluidic circuit (Fluidigm). Cell capture efficiency was assessed using the Zeiss Axiovert imaging system and empty sites, or sites with more than one cell were excluded from further analysis. Cell lysis, reverse transcription, cDNA amplification were performed using the SMARTer PCR cDNA synthesis kit (Clontech).

tag: condition

value: day 90 of retinal organoid differentiation

tag: cell type

value: human ESC (CRX-GFP line)


title: Patient 109

description:
Test
SAMPLE 109

data_processing: The study does not have the normalized Ct values. This is because raw CT values after applying a threshold (Ct<=22) was used.

value: plasma

value: Male


title: H7_V2_C46

description: rawCounts.csv


title: Patient 106

description:
Test
SAMPLE 106


title: p65TA3_3

source_name: p65-knockout 3T3 fibroblasts reconstituted with p65TA3, 1hr after TNF-alpha treatment


title: Aey69_E13.5_rep2

description: Gene expression data from embryo eye from Aey69 mutant mice, E13.5, biological replicate 2

source_name: Embryo eye from Aey69 mutant mice, E13.5, biological replicate 2


title: Ctrl_E12.5_rep2


title: p65TA3_shZbtb7a_2


title: p65TA3_2


title: H6_V2_C91

description: rawCounts.csv


title: Patient 105

description:
Test
SAMPLE 105

value: Hispanic


title: Patient 104

description:
Test
SAMPLE 104

value: Female

value: Other


title: p65_shZbtb7a_3

source_name: p65-knockout 3T3 fibroblasts reconstituted with p65, with Zbtb7a knock-down, 1hr after TNF-alpha treatment


title: p65TA3_shZbtb7a_1


title: Ctrl_E12.5_rep1


title: Aey69_E12.5_rep4

description: Gene expression data from embryo eye region from Aey69 mutant mice, E12.5, biological replicate 4

source_name: Embryo eye region from Aey69 mutant mice, E12.5, biological replicate 4


title: H5_V2_C92

description: rawCounts.csv


title: Aey69_E13.5_rep1

description: Gene expression data from embryo eye from Aey69 mutant mice, E13.5, biological replicate 1

source_name: Embryo eye from Aey69 mutant mice, E13.5, biological replicate 1


title: Patient 103

description:
Test
SAMPLE 103

value: Caucasian


title: H4_V2_C93

description: rawCounts.csv


title: H3_V1_C94

description: rawCounts.csv


title: p65TA3_1


title: Patient 102

description:
Test
SAMPLE 102


title: p65_shZbtb7a_2


title: Patient 101

description:
Test
SAMPLE 101


title: p65_3

source_name: p65-knockout 3T3 fibroblasts reconstituted with p65, 1hr after TNF-alpha treatment


title: Aey69_E12.5_rep3

description: Gene expression data from embryo eye region from Aey69 mutant mice, E12.5, biological replicate 3

source_name: Embryo eye region from Aey69 mutant mice, E12.5, biological replicate 3


title: Aey69_E12.5_rep2

description: Gene expression data from embryo eye region from Aey69 mutant mice, E12.5, biological replicate 2

source_name: Embryo eye region from Aey69 mutant mice, E12.5, biological replicate 2


title: H1_V2_C43

description: rawCounts.csv


title: Patient 100

description:
Test
SAMPLE 100


title: H12_V2_C94

description: rawCounts.csv


title: Patient 98

description:
Test
SAMPLE 98


title: H11_V2_C95

description: rawCounts.csv


title: Ctrl_E11.5_rep3

description: Gene expression data from embryo head from control mice, E11.5, biological replicate 3

source_name: Embryo head from control mice, E11.5, biological replicate 3

value: head


title: Patient 99

description:
Test
SAMPLE 99


title: H9_V2_C48

description: rawCounts.csv


title: Ctrl_E11.5_rep2

description: Gene expression data from embryo head from control mice, E11.5, biological replicate 2

source_name: Embryo head from control mice, E11.5, biological replicate 2


title: p65ko_2

source_name: p65-knockout 3T3 fibroblasts, 1hr after TNF-alpha treatment

value: 3T3 fibroblasts


title: p65ko_3

value: no


title: Patient 97

description:
Test
SAMPLE 97

source_name: Plasma extracelular RNA


title: H10_V2_C96

description: rawCounts.csv


title: p65_1

value: TNF-alpha


title: Ctrl_E11.5_rep4

description: Gene expression data from embryo head from control mice, E11.5, biological replicate 4

source_name: Embryo head from control mice, E11.5, biological replicate 4

value: wildtype


title: p65ko_1


title: Aey69_E12.5_rep1

description: Gene expression data from embryo eye region from Aey69 mutant mice, E12.5, biological replicate 1

source_name: Embryo eye region from Aey69 mutant mice, E12.5, biological replicate 1

value: eye region


title: Ctrl_E12.5_rep3

source_name: Embryo eye region from control mice, E12.5, biological replicate 3


title: H2_V2_C44

description: rawCounts.csv


title: p65_2


title: G9_V1_C77

description: rawCounts.csv


title: Aey69_E11.5_rep3

description: Gene expression data from embryo head from Aey69 mutant mice, E11.5, biological replicate 3

source_name: Embryo head from Aey69 mutant mice, E11.5, biological replicate 3


title: G8_V1_C28

description: rawCounts.csv

source_name: human ESC


title: Aey69_E11.5_rep4

description: Gene expression data from embryo head from Aey69 mutant mice, E11.5, biological replicate 4

source_name: Embryo head from Aey69 mutant mice, E11.5, biological replicate 4


title: p65_shZbtb7a_1

value: yes


title: Aey69_E11.5_rep2

description: Gene expression data from embryo head from Aey69 mutant mice, E11.5, biological replicate 2

source_name: Embryo head from Aey69 mutant mice, E11.5, biological replicate 2

value: Aey69 mutant


title: Patient 95

description:
Test
SAMPLE 95

value: patient who underwent a myocardial infarction

value: African American


title: Patient 94

description:
Test
SAMPLE 94


title: G7_V2_C40

description: rawCounts.csv

value: day 90 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: Ctrl_E11.5_rep1

description: Gene expression data from embryo head from control mice, E11.5, biological replicate 1

source_name: Embryo head from control mice, E11.5, biological replicate 1


title: G6_V1_C70

description: rawCounts.csv


title: Aey69_E11.5_rep1

description: Gene expression data from embryo head from Aey69 mutant mice, E11.5, biological replicate 1

source_name: Embryo head from Aey69 mutant mice, E11.5, biological replicate 1


title: Patient 96

description:
Test
SAMPLE 96

value: plasma

value: Male


title: Patient 92

description:
Test
SAMPLE 92


title: Patient 91

description:
Test
SAMPLE 91

value: Hispanic


title: G5_V2_C86

description: rawCounts.csv


title: G4_V2_C87

description: rawCounts.csv


title: G3_V2_C39

description: rawCounts.csv


title: Patient 90

description:
Test
SAMPLE 90


title: Patient 89

description:
Test
SAMPLE 89


title: G2_V2_C38

description: rawCounts.csv


title: LNCaP_shScramble_DHT-1

description: LNCaP cells transfected with scrambled shRNA

source_name: LNCaP Cell line

value: shScramble


title: G1_V2_C37

description: rawCounts.csv


title: Patient 93

description:
Test
SAMPLE 93


title: Ctrl_E10.5_rep2

description: Gene expression data from embryo head from control mice, E10.5, biological replicate 2

source_name: Embryo head from control mice, E10.5, biological replicate 2


title: Ctrl_E10.5_rep4

description: Gene expression data from embryo head from control mice, E10.5, biological replicate 4

source_name: Embryo head from control mice, E10.5, biological replicate 4


title: Patient 88

description:
Test
SAMPLE 88

value: Caucasian


title: Ctrl_E10.5_rep3

description: Gene expression data from embryo head from control mice, E10.5, biological replicate 3

source_name: Embryo head from control mice, E10.5, biological replicate 3

value: head


title: Ctrl_E10.5_rep1

description: Gene expression data from embryo head from control mice, E10.5, biological replicate 1

source_name: Embryo head from control mice, E10.5, biological replicate 1


title: Mouse frontal cortex 184 days old

city: Ankara

first: Babür

last: Erdem

state: Çankaya

address: ODTÜ, Biyoloji Böl., Lab 205

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

description: Gene expression data from frontal cortex of a 184 days old sacrificed mouse individual

hyb_protocol: Hybridization to Affymetrix Mouse Gene 1.0ST arrays was carried out following standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. We used the R Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation.

source_name: Dissected sacrificed mouse frontal cortex

label_protocol: Biotinylated cRNA were prepared from 1 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: Mouse brain samples were obtained from 12 C57BL/6 mice, housed and fed under standard conditions in the MPI-EVA Animal Facility (Leipzig, Germany). The mice were sacrificed for reasons independent of this study, their tissues were harvested and frozen immediately, and stored at -80°C.

value: 184 days after birth

tag: Sex

value: male

value: frontal cortex of the brain


title: Mouse frontal cortex 122 days old

description: Gene expression data from frontal cortex of a 122 days old sacrificed mouse individual

value: 122 days after birth


title: Mouse frontal cortex 365 days old

description: Gene expression data from frontal cortex of a 365 days old sacrificed mouse individual

value: 365 days after birth


title: Mouse frontal cortex 904 days old

description: Gene expression data from frontal cortex of a 904 days old sacrificed mouse individual

value: 904 days after birth


title: G12_V1_C37

description: rawCounts.csv


title: Mouse frontal cortex 649 days old

description: Gene expression data from frontal cortex of a 649 days old sacrificed mouse individual

value: 649 days after birth


title: Mouse frontal cortex 61 days old

description: Gene expression data from frontal cortex of a 61 days old sacrificed mouse individual

value: 61 days after birth


title: Aey69_E10.5_rep3

description: Gene expression data from embryo head from Aey69 mutant mice, E10.5, biological replicate 3

source_name: Embryo head from Aey69 mutant mice, E10.5, biological replicate 3

value: Aey69 mutant


title: Aey69_E10.5_rep4

description: Gene expression data from embryo head from Aey69 mutant mice, E10.5, biological replicate 4

source_name: Embryo head from Aey69 mutant mice, E10.5, biological replicate 4


title: Mouse frontal cortex 20 days old

description: Gene expression data from frontal cortex of a 20 days old sacrificed mouse individual

value: 20 days after birth


title: Mouse frontal cortex 32 days old

description: Gene expression data from frontal cortex of a 32 days old sacrificed mouse individual

value: 32 days after birth


title: Mouse frontal cortex 11 days old

description: Gene expression data from frontal cortex of a 11 days old sacrificed mouse individual

value: 11 days after birth


title: Aey69_E10.5_rep2

description: Gene expression data from embryo head from Aey69 mutant mice, E10.5, biological replicate 2

source_name: Embryo head from Aey69 mutant mice, E10.5, biological replicate 2


title: Patient 87

city: Boston

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

description:
Test
SAMPLE 87

source_name: Plasma extracelular RNA

tag: individual

value: patient who underwent a myocardial infarction

value: plasma

value: Male


title: Patient 86

description:
Test
SAMPLE 86

value: Caucasian


title: Mouse frontal cortex 5 days old

description: Gene expression data from frontal cortex of a 5 days old sacrificed mouse individual

value: 5 days after birth


title: Aey69_E10.5_rep1

description: Gene expression data from embryo head from Aey69 mutant mice, E10.5, biological replicate 1

source_name: Embryo head from Aey69 mutant mice, E10.5, biological replicate 1

value: head

tag: strain


title: Mouse frontal cortex 2 days old, rep2

description: Gene expression data from frontal cortex of a 2 days old sacrificed mouse individual

value: 2 days after birth

value: male

tag: tissue


title: G11_V2_C89

description: rawCounts.csv

value: day 90 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: G10_V2_C90

description: rawCounts.csv


title: Patient 85

description:
Test
SAMPLE 85

tag: gender


title: Mouse frontal cortex 2 days old, rep1

value: frontal cortex of the brain


title: Ctrl_E9.5_rep3

description: Gene expression data from whole embryo from control mice, E9.5, biological replicate 3

source_name: Whole embryo from control mice, E9.5, biological replicate 3

value: wildtype

value: whole embryo


title: Patient 84

description:
Test
SAMPLE 84


title: Patient 83

description:
Test
SAMPLE 83

value: Female


title: F8_V2_C35

description: rawCounts.csv

source_name: human ESC


title: F9_V2_C36

description: rawCounts.csv


title: F7_V2_C34

description: rawCounts.csv


title: Ctrl_E9.5_rep2

description: Gene expression data from whole embryo from control mice, E9.5, biological replicate 2

source_name: Whole embryo from control mice, E9.5, biological replicate 2


title: Patient 82

description:
Test
SAMPLE 82

value: Hispanic


title: Patient 80

description:
Test
SAMPLE 80


title: F6_V2_C79

description: rawCounts.csv


title: Patient 79

description:
Test
SAMPLE 79

value: Other


title: Rhesus macaque testis 22 years and 74 days old

description: Gene expression data from post-mortem testis of a 22.2 years old rhesus macaque individual

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0ST arrays was carried out following standard Affymetrix protocols.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches to the macaque genome, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the rheMac2 genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched the rhesus macaque genome perfectly and at a single location. Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >70% of individuals

organism: Macaca mulatta

source_name: Dissected rhesus macaque post-mortem testis

extract_protocol: Trisol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: Post-mortem testis samples from 12 rhesus macaques were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The individuals were housed under standard conditions, were healthy, and died of causes with no relation to the tissue used, and of reasons unrelated to this study. Whole testis samples were stored at -80°C.

value: 8104 days after birth

value: testis

tag: testis weight


title: Rhesus macaque testis 6 years and 165 days old

description: Gene expression data from post-mortem testis of a 6.5 years old rhesus macaque individual

value: 2355 days after birth


title: Ctrl_E9.5_rep1

description: Gene expression data from whole embryo from control mice, E9.5, biological replicate 1

source_name: Whole embryo from control mice, E9.5, biological replicate 1


title: F5_V2_C80

description: rawCounts.csv


title: F4_V2_C81

description: rawCounts.csv


title: Rhesus macaque testis 26 years and 28 days old

description: Gene expression data from post-mortem testis of a 26.1 years old rhesus macaque individual

value: 9518 days after birth


title: Rhesus macaque testis 7 years and 15 days old

description: Gene expression data from post-mortem testis of a 7 years old rhesus macaque individual

value: 2570 days after birth


title: F3_V2_C33

description: rawCounts.csv


title: alpha MHC/mir-143/145 transgenic mice line 19

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization and washing were performed following the protocol provided by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. After normalization, backgrounds were subtracted from log2 of processed Green signal/processed Red signal data.

label_protocol: cDNA and Amino Allyl aRNA were synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed following the protocol provided by TORAY Industries, Inc..

extract_protocol: Total RNAs were extracted using Trizol following manufacturer's instructions.

value: wild type

value: alpha MHC/mir-143/145


title: Patient 78

description:
Test
SAMPLE 78

value: patient who underwent a myocardial infarction

value: plasma

value: Male


title: Rhesus macaque testis 4 years and 27 days old

description: Gene expression data from post-mortem testis of a 4.1 years old rhesus macaque individual

value: 1487 days after birth

value: male


title: Aey69_E9.5_rep1

description: Gene expression data from whole embryo from Aey69 mutant mice, E9.5, biological replicate 1

source_name: Whole embryo from Aey69 mutant mice, E9.5, biological replicate 1

value: Aey69 mutant


title: Aey69_E9.5_rep4

description: Gene expression data from whole embryo from Aey69 mutant mice, E9.5, biological replicate 4

source_name: Whole embryo from Aey69 mutant mice, E9.5, biological replicate 4

value: whole embryo


title: Rhesus macaque testis 3 years and 110 days old

description: Gene expression data from post-mortem testis of a 3.3 years old rhesus macaque individual

value: 1205 days after birth


title: Aey69_E9.5_rep3

description: Gene expression data from whole embryo from Aey69 mutant mice, E9.5, biological replicate 3

source_name: Whole embryo from Aey69 mutant mice, E9.5, biological replicate 3


title: F2_V2_C32

description: rawCounts.csv

value: day 90 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: Patient 77

description:
Test
SAMPLE 77

value: Caucasian


title: alpha MHC/mir-143/145 transgenic mice line 9


title: Patient 81

description:
Test
SAMPLE 81


title: Aey69_E9.5_rep2

description: Gene expression data from whole embryo from Aey69 mutant mice, E9.5, biological replicate 2

source_name: Whole embryo from Aey69 mutant mice, E9.5, biological replicate 2


title: Rhesus macaque testis 3 years and 40 days old

description: Gene expression data from post-mortem testis of a 3.1 years old rhesus macaque individual

value: 1135 days after birth

value: testis


title: Baurle_562-18_bru1_52h_Rep3_ATH1

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

description: bru1 52h Rep3

hyb_protocol: Standard NASC hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content.

organism: Arabidopsis thaliana

label_protocol: Total RNA was labelled according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: Arabidopsis thaliana plants were grown in GM medium (1% [w/v] glucose) at 23°C/ 21°C in 16-h-light/8-h-dark cycles unless otherwise indicated. ago1-25 were obtained from N. Baumberger.

extract_protocol: For microarray analysis, RNA from three biological replicates per genotype and treatment (4 h after acclimation, 52 h after acclimation and 4 h non-treated control) was purified over an RNeasy Plant RNA extraction column (Qiagen) and processed for hybridization of Affymetrix ATH1 GeneChips (NASC microarray facility).

treatment_protocol: HS treatments were performed in a water bath or incubator. For the priming HS (ACC), 4-d-old seedlings were subjected to a heat regime of 1 h, 37°C; 1.5 h, 23°C; and 45 min, 44°C. All priming treatments were started 6 h after dawn to ensure comparability and minimize diurnal effects.

tag: genotype/variation

value: 4-d-old seedlings

tag: time point

value: 52 h after acclimation


title: F1_V2_C31

description: rawCounts.csv


title: Patient 76

description:
Test
SAMPLE 76


title: Rhesus macaque testis 2 years and 9 days old

description: Gene expression data from post-mortem testis of a 2 years old rhesus macaque individual

value: 739 days after birth


title: Baurle_562-16_bru1_52h_Rep1_ATH1

description: bru1 52h Rep1


title: Patient 75

description:
Test
SAMPLE 75


title: Patient 74

description:
Test
SAMPLE 74


title: F12_V2_C82

description: rawCounts.csv


title: F11_V1_C17

description: rawCounts.csv


title: Baurle_562-17_bru1_52h_Rep2_ATH1

description: bru1 52h Rep2


title: Baurle_562-15_bru1_4h_Rep3_ATH1

description: bru1 4h Rep3

value: 4 h after acclimation


title: F10_V1_C46

description: rawCounts.csv


title: Rhesus macaque testis 215 days old

description: Gene expression data from post-mortem testis of a 0.6 years old rhesus macaque individual

value: 215 days after birth


title: Rhesus macaque testis 1 year and 106 days old

description: Gene expression data from post-mortem testis of a 1.3 years old rhesus macaque individual

value: 471 days after birth


title: Patient 73

description:
Test
SAMPLE 73

value: patient who underwent a myocardial infarction

value: plasma

value: Male


title: Patient 72

description:
Test
SAMPLE 72

value: Hispanic


title: E9_V2_C30

description: rawCounts.csv


title: E8_V2_C29

description: rawCounts.csv


title: Patient 70

description:
Test
SAMPLE 70

value: Female


title: Patient 71

description:
Test
SAMPLE 71


title: E7_V2_C28

description: rawCounts.csv


title: Patient 69

description:
Test
SAMPLE 69


title: Rhesus macaque testis 16 days old

description: Gene expression data from post-mortem testis of a >0.1 years old rhesus macaque individual

value: 16 days after birth

value: male


title: E5_V2_C74

description: rawCounts.csv

value: day 90 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: Patient 68

description:
Test
SAMPLE 68

value: Other


title: Baurle_562-14_bru1_4h_Rep2_ATH1

description: bru1 4h Rep2


title: Patient 67

description:
Test
SAMPLE 67

value: Caucasian


title: E4_V2_C75

description: rawCounts.csv


title: E3_V2_C27

description: rawCounts.csv


title: Patient 66

description:
Test
SAMPLE 66


title: Baurle_562-11_bru1_contr_Rep2_ATH1

description: bru1 contr Rep2

value: 4-d-old seedlings

value: 4 h non-treated control


title: Baurle_562-13_bru1_4h_Rep1_ATH1

description: bru1 4h Rep1


title: Patient 65

description:
Test
SAMPLE 65


title: Baurle_562-12_bru1_contr_Rep3_ATH1

description: bru1 contr Rep3


title: E2_V2_C26

description: rawCounts.csv


title: Rhesus macaque testis 20 days old

description: Gene expression data from post-mortem testis of a 0.1 years old rhesus macaque individual

value: 20 days after birth

value: testis


title: E1_V2_C25

description: rawCounts.csv


title: Patient 64

description:
Test
SAMPLE 64


title: E12_V2_C76

description: rawCounts.csv


title: 6AM3HUA

city: Palo Alto

first: Ngan

last: Huang

address: 3801 Miranda Avenue

department: Cardiothoracic Surgery

data_processing:
The raw data were checked for quality with FastQC (Version 0.11.7) and results were aggregated with MultiQC and were aligned to the mouse genome (GRCm38) using STAR (Version 2.5.3a) with ENCODE options for long RNA-seq pipeline.
The alignment results were assessed using Samtools and aggregated with MultiQC (Version 1.5) and the differential gene expression analysis of the uniquely mapped reads/raw counts was performed using the DESeq2 package (Version 1.20.0).
Each DE analysis was composed of a pairwise comparison between an experimental group and the control group. Differentially expressed genes were identified after false discovery rate (FDR = 0.05) correction.
Genome_build: mouse genome (GRCm38)
Supplementary_files_format_and_content: txt files contain DE comparison analysis as described above

source_name: muscle cells

growth_protocol: Mouse myoblasts (C2C12, ATCC) were expanded in a high serum DMEM with 20% FBS. Human microvascular ECs (Center for Disease Control) were expanded in 10% FBS and 1% penicillin/streptomycin in DMEM. All cell culture was performed with 1% penicillin/streptomycin at 37°C and 5% CO2. Where indicated, mouse myoblasts were lentivirally transduced to express GFP under the control of ubiquitin promoter.  For in vitro studies, four conditions were assessed: 1) randomly-oriented scaffold seeded with myoblasts; 2) randomly-oriented scaffolds seeded with myoblasts + ECs; 3) aligned scaffold seeded with myoblasts only; 4) aligned scaffold seeded with myoblasts + ECs. Collagen scaffold strips (25mm x 1mm) were sterilized with 70% ethanol and rehydrated with 3 washes with 1X PBS.  Mouse myoblasts (5x105) were seeded into each scaffold and cultured in a high serum DMEM with 20% FBS.  After 24 hours (Day 0), the growth medium was switched to DMEM containing 2% horse serum to induce differentiation and fusion of myoblasts. After 5 days of differentiation (Day 5) during which myoblasts have fused to form myotubes, ECs were cocultured into the myoblast-seeded scaffolds (5x105 cells/scaffold). For conditions with myoblasts only, no ECs were added. For all conditions, media was switched to a maintenance medium (DMEM supplemented with 2% horse serum and 3% FBS), and constructs were culture for an additional 4 days (Day 9).

extract_protocol:
RNA was isolated from cell lysates from engineered muscle and endothelialized engineering muscle on randomly-oriented or aligned scaffolds (n=3) according to the manufacture’s protocol (GeneJet RNA Purification Kit, Thermo Fisher). At least 1000ng of total RNA was pelleted per sample.
Library preparation and RNA Sequencing was performed by Novogene Corporation using the NovaSeq 6000 (Illumina) sequencing platform, and 150-bp paired-end reads were generated (20-30 million reads per sample). Briefly, RNA integrity was assessed (RNA Nano 6000 Assay Kit, Bioanalyzer 2100, Aligent Technologies, CA) and 3ug RNA per sample was used to generate sequencing libraries (NEBNext Ultra RNA Library Prep Kit for Illumina) according to manufacturer’s recommendations. Library fragments were purified (AMPure XP system, Beckman Coulter, Beverly) to select cDNA fragments (150-200 bp in length). PCR was performed with Phusion High-Fidelity DNA polymerase, and purified by the AMPure XP system and assessed for quality on the Agilent Bioanalyzer 2100 system.

value: C2C12 mouse myoblasts

tag: passages


title: 5AM2HUA


title: E6_V2_C73

description: rawCounts.csv


title: 4AM1HUA


title: E11_V2_C77

description: rawCounts.csv


title: Patient 62

description:
Test
SAMPLE 62


title: Baurle_562-10_bru1_contr_Rep1_ATH1

description: bru1 contr Rep1


title: KG1a_48hr_Li8Gy_BAP_rep2

city: Delhi

first: Gangenahalli

middle: Ugraiah

last: Gurudutta

state: Delhi

address: Lucknow Road, Timarpur

department: Division of Stem Cell & Gene Therapy

country: India

institute: Institute of Nuclear Medicine and Allied Sciences (INMAS)

description: Gene expression after 48hr upon LiCl and BAP treatment in 8Gy irradiated KG1a cells

hyb_protocol: Hybridized to Human Whole Genome Arrary Chip (Human 8x60K Array AMAID: 039494/ GPL17077).

scan_protocol: Images were scanned and signaled data was acquired using feature extraction software (V/0.5 Agilent Tech). The images were manually verified and found to be devoid of uneven hybridization, strikes, blobs, and other artifacts.

data_processing: Inta-Array normalization was done using GeneSpring GX 12.1 software. The gProcessed signal (dye normalized background subtracted signal intensity) was log transformed and then for each of the array the 75th percentile value was calculated. In each sample the log transformed intensity values for each probe was subtracted by the calculated 75th percentile value of the respective array and expression values were obtained.

source_name: KG1a, 48hr, LiCl, 8Gy, BAP, replicate 2

label_protocol: Following reverse transcription of RNA into cDNA, Cy3 labelled cRNA was produced by in vitro transcription.

growth_protocol: KG1a cells were grown in IMDM medium containing 20% fetal bovine serum and antibiotic and antimycotic solution, in 5% CO2 atmosphere at 37°C.

extract_protocol: RNA isolated using RNeasy Minikit (Qiagn, #74104) and quantified in Nanodrop spectrophotometer. RNA sample purity ratio was more than 1.9 for 260/280 nm, and RIN values were greater than 9.0 as evaluated on Bioanalyzer (Agilent Tech).

treatment_protocol: For irradiation of cells, Bhabhatron Teletherapy unit (Co60 as radiation source) was used.

value: bone marrow

tag: disease

value: acute myelogenous leukemia

value: promyeloblast, Macrophage


title: KG1a_48hr_Li8Gy_BAP_rep1

source_name: KG1a, 48hr, LiCl, 8Gy, BAP, replicate 1


title: KG1a_48hr_Li8Gy_BAP_rep3

source_name: KG1a, 48hr, LiCl, 8Gy, BAP, replicate 3


title: KG1a_48hr_Li4Gy_BAP_rep1

description: Gene expression after 48hr upon LiCl and BAP treatment in 4Gy irradiated KG1a cells

source_name: KG1a, 48hr, LiCl, 4Gy, BAP, replicate 1


title: KG1a_48hr_Li4Gy_BAP_rep3

source_name: KG1a, 48hr, LiCl, 4Gy, BAP, replicate 3


title: E10_V2_C78

description: rawCounts.csv


title: 3RM3HUA


title: Patient 61

description:
Test
SAMPLE 61

source_name: Plasma extracelular RNA

value: patient who underwent a myocardial infarction

value: plasma

tag: race


title: 2RM2HUA


title: Patient 59

description:
Test
SAMPLE 59

value: Female

value: African American

tag: diabetes


title: Patient 60

description:
Test
SAMPLE 60

value: Male


title: Patient 58

description:
Test
SAMPLE 58


title: D8_V1_C92

description: rawCounts.csv

value: day 90 of retinal organoid differentiation


title: D9_V2_C22

description: rawCounts.csv

value: human ESC (CRX-GFP line)


title: D6_V1_C51

description: rawCounts.csv


title: Patient 63

description:
Test
SAMPLE 63


title: TNFa#3

city: Durham

first: Hiroaki

last: Katsura

address: 353 Nanaline Duke Bldg

institute: Duke University

description:
count data.csv
TNF1_3

data_processing:
Paired-end sequencing (150 bp for each read) was performed using HiSeq X with the depth of 24 million reads for each sample. Quality of sequenced reads were assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). PolyA/T tails were trimmed using PRINSEQ (Schmieder and Edwards, 2011). Adaptor sequences were trimmed and shorter reads than 24 bp were dropped using Trimmomatic (Bolger et al., 2014). Reads were mapped to the mouse reference genome (mm10) using Hisat2 (Kim et al., 2015) with default setting. Duplicate reads were removed using the markdup option of SAMtools (Li et al., 2009). Fragments numbers were counted using the featureCounts option of SUBREAD (Liao et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: csv, counted fragment numbers using featureCounts

source_name: Alveolar type II cells_TNFa

growth_protocol: FACS sorted cells were resuspended in Basic medium containing 10% FBS and Insulin-Transferrin-Selenium and mixed with equal amount of growth factor-reduced Matrigel (BD Biosciences #356230). Basic medium:Matrigel (100 ml) containing 2-5×10^3 AEC2s (SFTPC-tdTomato cells) and 5×10^4 stromal cells was seeded in 24-well 0.4 mm Transwell inserts (Falcon). Medium was changed every other day. ROCK inhibitor (10 mM, Y-27632; Sigma-Aldrich) was added for first 48 hrs and TGF-b inhibitor (10 mM SB431542; Abcam) was added for 7 days.

extract_protocol:
Total RNA was isolated from FACS-sorted cells using TRIzol (Thermo Fisher Scientific) and Direct-zol RNA MicroPrep (Zymo Research).
Messenger RNA was enriched from 200 ng of isolated total RNA of each sample using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: mouse recombinant IL-1b or TNFa were added to the culture at 10ng/ml

tag: genotype

value: Sftpc-CreERT2/+; R26-tdTomato/+

value: 12 week old

value: Alveolar type II cells


title: TNFa #2

description:
count data.csv
TNF1_2

tag: age


title: Patient 57

description:
Test
SAMPLE 57

tag: omega-3 fatty acid therapy


title: Patient 56

description:
Test
SAMPLE 56

value: Caucasian


title: Patient 55

description:
Test
SAMPLE 55


title: D5_V2_C68

description: rawCounts.csv

tag: condition


title: TNFa #1

description:
count data.csv
TNF1_1

tag: cell type


title: KG1a_48hr_Li4Gy_BAP_rep2

source_name: KG1a, 48hr, LiCl, 4Gy, BAP, replicate 2


title: IL-1b #3

description:
count data.csv
IL1b_3

source_name: Alveolar type II cells_IL-1b


title: Patient 54

description:
Test
SAMPLE 54


title: D3_V1_C36

description: rawCounts.csv

source_name: human ESC


title: IL-1b #2

description:
count data.csv
IL1b_2


title: IL-1b #1

description:
count data.csv
IL1b_1


title: Patient 53

description:
Test
SAMPLE 53


title: D2_V2_C20

description: rawCounts.csv


title: D4_V2_C67

description: rawCounts.csv


title: Patient 52

description:
Test
SAMPLE 52


title: D1_V2_C21

description: rawCounts.csv


title: Control #3

description:
count data.csv
SB_3

source_name: Alveolar type II cells_saline_control


title: 1RM1HUA


title: D7_V2_C24

description: rawCounts.csv


title: D12_V2_C72

description: rawCounts.csv


title: D11_V2_C71

description: rawCounts.csv


title: Control #2

description:
count data.csv
SB_2


title: Control #1

description:
count data.csv
SB_1


title: Patient 51

description:
Test
SAMPLE 51

value: Hispanic


title: Patient 50

description:
Test
SAMPLE 50


title: Wild typeCytoplasmic RNA

city: Birmingham

first: Anand

middle: Kumar

last: Singh

state: West Midlands

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

description: FCHKJ7YBBXX_L3_CHKPEI85217080039_indexCGGCTATG_1CC

data_processing:
For RNA-seq data, the BAM files were converted to bedgraph files. This was carried out with the genomeCoverageBed command and options -bga and -ibam from the Bedtools v2.26.0 suite.
Custom Perl scripts were then used to filter the Dm6 annotations either for genes separated by a minimum distance to avoid overlapping signals or RNA-seq expression levels.
Further custom scripts were used to extract the signal from the bedgraph files for each entry in the filtered gene list.
Each dataset was normalized by the total mapped sequencing reads in that dataset
Cross-referencing between different datasets was done based on the ‘name’ field, after filtering the annotations for multiple entries with identical name.
Genome_build: Dm6

organism: Drosophila melanogaster

source_name: S2_WT_cytoplasmic RNA

growth_protocol: Drosophila Embryonic S2 cells were cultured in Insect–XPRESS media (Lonza) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin-Glutamine mix (P/S/G) (Invitrogen) at 27°C

extract_protocol:
Nascent RNA were isolated following Khodor et al, 2011 using NUN buffer.
All RNA libraries prepared using a NEBNext Ultra Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S), using provided protocols.

treatment_protocol: For RNAi, dsRNA Specific for UPF1 transcripts were used

tag: cell line

tag: cell origin

value: Embryonic cell line

tag: molecule subtype

value: Poly(A) Cytoplasmic RNA


title: Patient 48

description:
Test
SAMPLE 48

tag: individual

tag: tissue


title: Patient 47

description:
Test
SAMPLE 47

tag: gender


title: C8_V2_C17

description: rawCounts.csv


title: C9_V2_C16

description: rawCounts.csv


title: C7_V2_C18

description: rawCounts.csv


title: Wild type Nascent RNA 1

description: FCHKJ7YBBXX_L3_CHKPEI85217080039_indexATTACTCG_1_CN1

source_name: S2_WT_nascent RNA

value: Nascent RNA


title: Patient 46

description:
Test
SAMPLE 46