title: LV-HF_LV3


title: prostate: PACB5 ATAC-seq

status: Public on Oct 05 2018

type: SRA

city: Los Angeles

first: Owen

middle: N

last: Witte

state: CA

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

country: USA

institute: UCLA

library_source: genomic

data_processing:
ENCODE processing pipeline (https://www.encodeproject.org/atac-seq/)
Genome_build: hg38 human genome
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: prostate

tag: tissue

value: prostate

tag: cell type

value: transformed prostate basal epithelial

tag: transplant

value: NSG mice


title: LV-HF_LV4

first: Christoph

middle: Daniel

last: Rau

state: United States

address: 675 Charles E Young Drive S

library_source: transcriptomic

data_processing:
Remove Adapters and low quality reads using Cutadapt
Reads mapped to genome using HISAT2 with standard parameters
Transcripts assembled using StringTie and merged together with gtfcompare to create unified mRNA expression profile
Differentially expressed mRNAs identified using Ballgown
Genome_build: hg38
Supplementary_files_format_and_content: CSV file with FPKMs and raw counts of each mapped gene

molecule: polyA RNA

source_name: Left Ventricle

extract_protocol:
Human ventricular myocardium was obtained from end-stage ischemic cardiomyopathic hearts explanted at the time of cardiac transplantation. Non-failing donor hearts that had been deemed unsuitable for transplantation were used as control. Prior to explant, hearts underwent intra-operative antegrade coronary perfusion with 4:1 blood cardioplegia solution. Following arrest, hearts were explanted and placed into cold Ca2+-free, modified Krebs-Henseleit solution as previously described (120). Samples were taken from mid-myocardial regions of the left ventricular free wall and the right ventricular free wall, in areas void of scar tissue. Tissue samples were rapidly frozen in liquid nitrogen and stored at -80°C until RNA isolation. Prospective written informed consent for research use of heart tissue was obtained from all transplant recipients or next of kin (non-failing donors). Patient consent, sample collection and preparation, and clinical data collection were performed according to a human subject research protocol approved by the Institutional Review Board of the Lewis Katz School of Medicine at Temple University (PI: Tsai).
Sequencing libraries were generated using a NEBNext Ultra™ RNA Library Prep Kit for Illumina  following the manufacturer’s recommendations

value: Left Ventricle

tag: condition

value: Left Ventricle Heart Failure


title: prostate: NCI-H660 ATAC-seq

value: small cell prostate cancer


title: lung: NCI-H524 ATAC-seq

source_name: lung

value: lung

value: small cell lung cancer


title: LV-HF_LV1


title: AR2754_04: Ex vivo Fibroblast of LS with compound rep2

type: RNA

city: Shimotsuke-shi

first: Akihiko

last: Miyauchi

state: Tochigi

address: 3311-1 Yakushiji

department: Pediatrics

country: Japan

institute: Jichi Medical University

description: Gene expression in compound-treated fibroblast of Leigh syndrome patient

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

source_name: Fibroblast of LS, 1uM compound, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Fibroblasts from Leigh syndrome patient were maintained in 1.0 g/L low-glucose DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from the fibroblasts using RNeasy Mini Kit (QIAGEN).

treatment_protocol: We treated the fibroblast of Leigh syndrome patient (LSND3) with or without compound. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: fibroblast

tag: age

tag: diagnosis

value: Leigh syndrome


title: NF_LV5

value: Not Failing


title: AR2754_01: Ex vivo Fibroblast of LS rep1

description: Gene expression in fibroblast of Leigh syndrome patient

source_name: Fibroblast of LS, replicate 1


title: BiV-HF_LV1

value: BiVentricular Heart Failure


title: LV-HF_LV2


title: C42B-MDV-resistant

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Affymetrix microarray gene expression profiling data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Genechip Human Genome U133 Plus 2 arrays using Affymetrix hybridization kit reagents. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol  FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.0 software.  Probe intensity values (CEL files) were background-corrected, summarized, and normalized using the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003).

label: biotin

source_name: LNCaP-C42B cultured for long-term in enzalutamide (MDV3100)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Rev3, Affymetrix).

growth_protocol: C4-2B parental cells were were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and 0.1 mg/ml streptomycin. The C4-2B MDVR (C4-2B enzalutamide resistant) and C4-2B AbiR (C4-2B abiraterone resistant) were maintained in medium containing 20 μM enzalutamide or 10 μM abiraterone acetate, respectively.

extract_protocol: Total RNA was isolated from each cell line using the using TRIzol reagent (Invitrogen).

treatment_protocol: C4-2B parental, C4-2B MDVR, and C4-2B AbiR cells were were cultured according the conditions described in the growth protocol above, and harvested for RNA isolation.

tag: cell line

value: human castration-resistant prostate carcinoma


title: NF_LV4


title: lung: NHBE4-PARCB2 ATAC-seq

value: transformed bronchial epithelial


title: lung: NHBE4-PARCB1 ATAC-seq


title: lung: NHBE1-PARCB1 ATAC-seq


title: NF_LV3


title: C42B-Abiraterone-resistant

source_name: LNCaP-C42B cultured for long-term in abiraterone


title: lung: NHBE5-PARCB ATAC-seq


title: NF_LV1


title: NF_LV2


title: lung: NHBE1-PARCB2 ATAC-seq


title: BiV-HF_RV5

source_name: Right Ventricle

value: Right Ventricle


title: BiV-HF_RV3


title: BiV-HF_RV2


title: BiV-HF_RV4


title: BiV-HF_RV1


title: lung: NHBE5 ATAC-seq

value: normal bronchial epithelial


title: lung: NHBE4 ATAC-seq


title: LV-HF_RV3


title: LV-HF_RV5


title: lung: NHBE1 ATAC-seq


title: prostate: Basal3 ATAC-seq

value: normal prostate basal epithelial


title: LV-HF_RV4


title: prostate: Basal2 ATAC-seq

value: prostate


title: LV-HF_RV2


title: prostate: Basal1 ATAC-seq


title: UN_2

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G at a resolution of 0.7 µm.

data_processing: Raw data (.CEL files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. The data were RMA normalized in R and Bioconductor, using the oligo package.

organism: Mus musculus

source_name: Spleen

label_protocol: 3 to 20 ng of total RNA from each sample was used to synthesize biotinylated probes, using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit, according to NuGEN recommendations, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted from sorted cells with the Qiagen RNeasy PLUS Micro Kit, according to the manufacturer protocol.

treatment_protocol: Mice were untreated or infected for 1.5 days with a salivary gland stock of the Smith strain of MCMV that was administered through intraperitoneal injection.

tag: phenotype

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high)

tag: mouse

value: WT CD45.2 pDC

tag: treatment

value: Uninfected


title: IN_CTR_MyD88_5p1_2

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD45.1(pos)

value: CD45.1 WT:CD45.2 MyD88-KO MBMC

value: WT CD45.1 pDC

value: d1.5 MCMV-infected


title: IN_TST_MyD88_5p2_2

value: Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), CD11c(low) CD317(high) CD45.2(pos)

value: MyD88-KO CD45.2 pDC


title: UN_1


title: IN_CTR_MyD88_5p2_1


title: IN_TST_MyD88_5p1_2


title: LV-HF_RV1

value: Left Ventricle Heart Failure


title: NF_RV5

value: Not Failing


title: IN_2


title: IN_TST_MyD88_5p2_1


title: IN_1


title: IN_CTR_MyD88_5p2_2


title: NF_RV4


title: NF_RV3


title: UN_TST_MyD88_5p2_2


title: IN_TST_MyD88_5p1_1


title: UN_TST_MyD88_5p2_1


title: IN_CTR_MyD88_5p1_1


title: UN_TST_MyD88_5p1_2


title: UN_CTR_MyD88_5p2_2


title: UN_CTR_MyD88_5p1_2


title: UN_TST_MyD88_5p1_1


title: UN_CTR_MyD88_5p2_1


title: UN_CTR_MyD88_5p1_1


title: IN_TST_IFNAR_5p1_2

value: CD45.1 WT:CD45.2 Ifnar1-KO MBMC


title: IN_CTR_IFNAR_5p1_2


title: IN_CTR_IFNAR_5p2_2


title: U58_5RNA

city: Stanford

first: Michael

last: Snyder

address: 300 Pasteur Drive

department: Department of Genetics

institute: Stanford University

description: mRNA profiling

data_processing:
Alignment with STAR v 2.3.0e
Sort with PICARD v1.80
Duplicate Read Removal with PICARD v1.80
FPKM Calling with Cufflinks v2.2.1
genome_build: hg19
processed_data_files_format_and_content: fpkm-tracking file from Cufflinks; column header: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMCs were isolated by standard Ficoll-based protocol, and genomic DNA and total RNA were extracted using the QIAGEN AllPrep DNA/RNA/Protein Mini Kit.
Methyl-Seq and RNA-Seq libraries were prepared using standard Illumina protocols.

value: Peripheral Blood Mononuclear Cells

tag: day number


title: IN_TST_IFNAR_5p2_2

value: Ifnar1-KO CD45.2 pDC


title: U60RNA

description: mRNA profiling


title: U58RNA

description: mRNA profiling


title: NF_RV1

value: Right Ventricle


title: U56RNA

description: mRNA profiling


title: U55RNA

description: mRNA profiling


title: U59RNA

description: mRNA profiling


title: NF_RV2


title: U54RNA

description: mRNA profiling


title: UN_CTR_IFNAR_5p1_2


title: IN_CTR_IFNAR_5p2_1


title: UN_TST_IFNAR_5p2_1


title: IN_TST_IFNAR_5p2_1


title: UN_CTR_IFNAR_5p2_2


title: IN_CTR_IFNAR_5p1_1


title: UN_TST_IFNAR_5p1_2


title: UN_TST_IFNAR_5p2_2


title: IN_TST_IFNAR_5p1_1


title: UN_CTR_IFNAR_5p1_1


title: U52RNA

description: mRNA profiling


title: LNCap shTRIM28 + TRIM24-2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 19

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

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: Prostate cancer cell line

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

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

treatment_protocol: LNCaP infected with pLKO, shTRIM28 or shTRIM24 were hormone starved for 3 days before treatment with ethanol or 1nM R1881 for 48h. LNCaP cells were infected with lentivirus harboring pLKO, shTRIM24, shTRIM28, or shTRIM28 and TRIM24

value: LNCaP

tag: genotype

value: WT


title: UN_TST_IFNAR_5p1_1


title: U51RNA

description: mRNA profiling


title: U53RNA

description: mRNA profiling


title: LNCap shTRIM28 + TRIM24-1

description: SAMPLE 18

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


title: LNCap shTRIM28-3

description: SAMPLE 17

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


title: LNCap shTRIM24-3

description: SAMPLE 14


title: LNCap shTRIM28-1

description: SAMPLE 15


title: LNCap shTRIM24-1

description: SAMPLE 12


title: LNCap LKO-2

description: SAMPLE 10


title: LNCap LKO-3

description: SAMPLE 11


title: LNCap shTRIM24-2

description: SAMPLE 13


title: LNCap shTRIM28-2

description: SAMPLE 16


title: LNCap shTRIM28 + TRIM24-3

description: SAMPLE 20


title: U49RNA

description: mRNA profiling


title: LNCap LKO-1

description: SAMPLE 9


title: UN_CTR_IFNAR_5p2_1


title: U46RNA

description: mRNA profiling


title: U48RNA

description: mRNA profiling


title: U47RNA

description: mRNA profiling


title: LNCap shTRIM24 +R1881

description: SAMPLE 8


title: U42RNA

description: mRNA profiling


title: LNCap shTRIM24 +Ethl

description: SAMPLE 6


title: U41RNA

description: mRNA profiling


title: U50RNA

description: mRNA profiling


title: LNCap pLKO.1 +R1881

description: SAMPLE 7


title: U40RNA

description: mRNA profiling


title: LNCaP shTRIM28 + Ethl

description: SAMPLE 3


title: U38RNA

description: mRNA profiling


title: U45RNA

description: mRNA profiling


title: U39RNA

description: mRNA profiling


title: LNCaP pLKO.1 + R1881

description: SAMPLE 2


title: U37RNA

description: mRNA profiling


title: hNSC-Day20-rep1

first: Anil

last: Ori

state: Verenigde Staten van Amerika

address: 695 Charles E Young Drive South

department: Center for Neurobehavioral Genetics

institute: University of California, Los Angeles

hyb_protocol: Illumina’s HumanHT-12 v4 Expression BeadChip Kit according to manufacturer's guidelines

data_processing: Background corrected, variance-stabilization transformation, robust spline normalization

source_name: NSC differentiated day 20

growth_protocol: hNSC Expansion: WA09-derived hNSCs were grown as adherent culture on tissue culture plates coated with CELLstart CTSTM (Thermo Fisher Scientific) diluted (1:50) in DPBS with Ca2+ and Mg2+ and expanded in KnockOut™ DMEM⁄F-12 Basal Medium (Gibco) with 2% StemPro® Neural Supplement (Gibco), 2mM GlutaMax™-I Supplement (Gibco), FGF Basic and EGF Recombinant proteins (Gibco, both at 20 ng/ml), and 1x Pen Strep (Thermo Fisher Scientific). Cells were plated at 1.0x105 cells per 3.8 cm2, dissociated with preheated Stem Pro Accutase (Gibco) and subsequently passaged at ~90% confluency.

extract_protocol: Qiagen’s Allprep DNA/RNA/miRNA Universal Kit according to the manufacturer’s protocol

treatment_protocol: hNSC Differentiation: Low passage WA09/H9 hNSCs (< 4 passage rounds) were plated in 12-well plates coated with poly-D-lysine (0.1 mg/mL, VWR) and laminin (4.52ug/cm2, CorningTM) at 1.5x105 cells, which were equally distributed and subsequently cultured in expansion medium as described above. After 24h of proliferation, media was changed to neuronal differentiation medium consisting of Neurobasal® Medium (Gibco), 2% B-27® Serum-Free Supplement (Gibco), 2mM GlutaMax™-I Supplement, 0.05 mM β-mercaptoethanol (Gibco), and 1x Pen Strep. Media was changed every 2-3 days.

tag: gender

value: Female

tag: day

tag: replicate

tag: rin


title: LNCaP shTRIM28 + R1881

description: SAMPLE 4


title: hNSC-Day30-rep3

scan_protocol: Illumina’s HumanHT-12 v4 Expression BeadChip Kit according to manufacturer's guidelines

source_name: NSC differentiated day 30


title: hNSC-Day15-rep2

source_name: NSC differentiated day 15

label_protocol: Illumina’s HumanHT-12 v4 Expression BeadChip Kit according to manufacturer's guidelines


title: hNSC-Day2-rep2

source_name: NSC differentiated day 2


title: LNCap pLKO.1 + Ethl

description: SAMPLE 5


title: hNSC-Day5-rep1

source_name: NSC differentiated day 5


title: hNSC-Day5-rep2


title: U43RNA

description: mRNA profiling


title: LNCaP pLKO.1 + Ethl

description: SAMPLE 1


title: hNSC-Day30-rep1


title: hNSC-Day2-rep1


title: hNSC-Day0-rep2

source_name: NSC differentiated day 0


title: U33RNA

description: mRNA profiling


title: U31RNA

description: mRNA profiling


title: U32RNA

description: mRNA profiling


title: U34RNA

description: mRNA profiling


title: hNSC-Day10-rep2

source_name: NSC differentiated day 10


title: U35RNA

description: mRNA profiling


title: U28RNA

description: mRNA profiling


title: hNSC-Day30-rep4


title: hNSC-Day0-rep3


title: hNSC-Day0-rep1


title: U30RNA

description: mRNA profiling


title: hNSC-Day20-rep2


title: U23RNA

description: mRNA profiling


title: U29RNA

description: mRNA profiling


title: hNSC-Day5-rep3


title: SAFA-HSV-1 (HSV-1 study)

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

country: China

institute: Peking university health science center

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

source_name: macrophage

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

value: BMDMs

value: Safa-/-

tag: infection


title: U25RNA

description: mRNA profiling

tag: tissue


title: U36RNA

description: mRNA profiling


title: U24RNA

description: mRNA profiling


title: U27RNA

description: mRNA profiling


title: U60Met

description: methyl-Seq

data_processing:
Alignment with BSMAP v2.73
Sort with SAMtools v0.1.19
Duplicate Read Removal with PICARD v1.80
Methylation Ratios Calling with Python Script metratio.py in BSMAP v2.73
genome_build: hg19
processed_data_files_format_and_content: metratio file from bsmap; column header: chr pos enviroment CT_count_ref C_count_ref rc_GA_count_ref rc_G_count_ref | CT_count_ref C_count_alt rc_GA_count_alt rc_G_count_alt


title: hNSC-Day10-rep3


title: WT-HSV-1 (HSV-1 study)

tag: cell type

value: Wild-type


title: U26RNA

description: mRNA profiling


title: U54Met

description: methyl-Seq


title: hNSC-Day2-rep3


title: hNSC-Day10-rep1


title: hNSC-Day2-rep4


title: hNSC-Day30-rep2


title: WT-VSV (VSV study)

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

value: iBMDMs

value: wild-type

value: VSV


title: WT (HSV-1 study)

value: control


title: H2A.Z_ChIP-seq

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

data_processing:
Sequenced reads were aligned to the GRCm38 (mm10) assembly of mouse genome using Bowtie (1.1.2) using “-n 2 -l 65 -k 1 -M 5 --best” parameters. Redundant reads were removed using MACS2 (2.1.0) filterdup option with default parameters. Pileup tracks were generated using MACS2 callpeak module and ChIP/input fold enrichment pileups were further created with the MACS2 bdgcmp module using “-m FE” parameter. Conversion to bigwig files was performed using bedGraphToBigWig program (v4) from the UCSC utilities. Peaks were called with SICER (1.1) using “fragment size 150 bp, window size 200 bp, gap size 800 bp and FDR < 0.01” parameters.
Sequenced reads were aligned to the GRCm38 (mm10) assembly of mouse genome using Bowtie (1.1.2) using “-n 2 -l 65 -k 1 -M 5 --best” parameters. Redundant reads were removed using MACS2 (2.1.0) filterdup option with default parameters. Pileup tracks were generated using MACS2 callpeak module and ChIP/input fold enrichment pileups were further created with the MACS2 bdgcmp module using “-m FE” parameter. Conversion to bigwig files was performed using bedGraphToBigWig program (v4) from the UCSC utilities. Peaks were called with SICER (1.1) using “fragment size 150 bp, window size 200 bp, gap size 800 bp and FDR < 0.01” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain the ChIP/input fold enrichment scores across the genome generated by MACS2 bdgcmp module (2.1.0). Bed files contains the genomic positions of significant peaks called by SICER (1.1).

source_name: dermal fibroblast (DF)

growth_protocol: DFs were grown in DMEM with 10% FBS, 1% Penicillin/Streptomycin, 2.5 units/ml Amphotericin B, 2mM L-Glutamine and 6 mM CaCl2

extract_protocol:
nChIP was performed with 100ug of Mnase digested chromatin as previously described (Gaspar-Maia et al. 2013)
Total of 25ng MNase-ChIPed DNA was processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3Õ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the HiSeq 2000 illumina platform.

treatment_protocol: no treatment

tag: strain background

tag: Sex

value: female

value: primary neonatal dermal fibroblast

tag: passages

tag: genotype/variation

value: wild type

tag: treated with

tag: chip-antibody


title: U58Met

description: methyl-Seq


title: hNSC-Day20-rep3


title: U47Met

description: methyl-Seq


title: U50Met

description: methyl-Seq


title: U52Met

description: methyl-Seq


title: hNSC-Day15-rep1


title: U48Met

description: methyl-Seq


title: prostate: ARCB4 RNA-seq

data_processing:
TOIL processing pipeline (https://github.com/BD2KGenomics/toil-rnaseq)
RNA-Seq measurements expressed as upper quartile normalized counts, log2 transformed, filtered for coding genes using HUGO
Genome_build: hg38 human genome
Supplementary_files_format_and_content: RSEM and Kallisto outputs

source_name: prostate

extract_protocol: Library preparation performed by Techonology Center for Genomics & Bioinformatics (TCGB) at UCLA. Libraries for mRNA-Seq were prepared with KAPA Stranded RNA-Seq Kit.

value: prostate

value: transformed prostate basal epithelial

tag: transplant

value: NSG mice


title: Sm eggs-4

city: Liege

first: Benjamin

middle: G

last: Dewals

address: Avenue de Cureghem, 10

country: Belgium

institute: University of liege

description: Sm_vs_PBS_Gexon_KwGn_DESeq2-All_2.anntNM.xlsx

data_processing:
Quality control checks on raw sequencing data for each sample were performed using FastQC (Babraham Bioinformatics).  Reads were mapped to the mouse reference genome (mm10) using STAR (version 3.4.0). Subsequently the analysis was performed with R Bioconductor packages: Rsamtools (version 1.18.3) and GenomicAlignments (version 1.2.2) were used to count the reads by exons.
Supplementary_files_format_and_content: processed data file contains entrezid and read counts for PBS1, PBS2, PBS4, Smeggs2, Smeggs3, Smeggs4

source_name: Virtual memory CD8+ T cells

growth_protocol: ex vivo samples

extract_protocol:
Qiagen microRNA easy prep from 1.5-3 million sorted cells and bioanalyzer 2100
500 ng of total RNA was subjected to library synthesis using the TruSeq Stranded mRNA-Seq kit. Single-read (1*75, high output) sequencing was performed on a Illumina HiSeq2000.

treatment_protocol: Spleens were harvested from BALB/c mice and CD8+ T cells enriched using a depletion enrichment kit (Miltenyi). Cells were then stained with an antibody panel to detect thelevel of expression of CD44, CXCR3, CD44, CD62L, CD49d, CD8 and CD3 by flo cytometry and the cell population expressing CD49d-low CD62L-high CXCR3-high CD44-high CD8+ CD3+ were sorted to high purity (> 98%) using a FACS Aria IIIU. In total, about between 1.5 million to 3 million cells were sorted per mouse spleen.

tag: tissue origin

value: spleen

tag: phenotype

value: CD49d-low CD62L-high CXCR3-high CD44-high CD8+ T cells

tag: strain

value: BALB/c

tag: treatment

value: Schistosoma mansoni eggs


title: WT (VSV study)

tag: genotype


title: SAFA (HSV-1 study)

value: BMDMs


title: prostate: ARCB6 RNA-seq


title: hNSC-Day0-rep4

tag: gender

value: Female

tag: day

tag: replicate


title: hNSC-Day15-rep3

tag: rin


title: U46Met

description: methyl-Seq

tag: tissue

value: Peripheral Blood Mononuclear Cells

tag: day number


title: U42Met

description: methyl-Seq


title: Sm eggs-2


title: prostate: ARCB5 RNA-seq

tag: cell type


title: PBS-2

value: PBS (control)


title: prostate: ARCB1 RNA-seq


title: U39Met

description: methyl-Seq


title: U38Met

description: methyl-Seq


title: U34Met

description: methyl-Seq


title: PBS-1


title: prostate: PACB4 RNA-seq


title: Pineal_Gland_Vehicle_Control

first: Joseph

middle: Charles

last: Mays

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU School of Medicine

description: Animals were given phosphate buffered sailine (PBS) vehicle alone

data_processing:
Base-calling was performed using Illumina RTA v1.18.64.
Sequenced reads were aligned to the Rnor6.0 genome using CellRanger v2.1.0 with default parameters, once with the Ensembl 6.0.90 annotation, and again with a custom (ExtendedRef) annotation.
Cell barcodes predicted not to be associated with a cell were filtered using CellRanger v2.1.0 with default parameters.
Transcript counts were normalized to 10,000 molecules per cell. Additional manual filtering was performed to remove barcodes thought to be associated with multiple cells.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimited text files in which each row is one gene, each column is one cell, and each entry is the library size-normalized transcript count value for a given gene in a given cell.

organism: Rattus norvegicus

source_name: Pineal Gland

extract_protocol:
Rat pineal glands were extracted following sacrifice and dissocated into a single-cell suspension using the Papain Dissociation System, following manufacturer's instructions. PolyA mRNA was extracted using the 10X Genomics Chromium 3' v2 kit and manufacturer's protocol.
cDNA libraries were constructed and prepared for Illumina sequencing from ployA mRNA using the 10X Genomics Chromium 3' v2 kit and manufacturer's protocol.

value: Vehicle Control

value: Sprague Dawley


title: Pineal_Gland_Isoproterenol

description: Animals were given isoproterenol dissolved in phosphate buffered saline (PBS)

value: Isoproterenol


title: prostate: ACB5 RNA-seq


title: Sm eggs-3


title: U36Met

description: methyl-Seq


title: prostate: PACB1 RNA-seq


title: prostate: ACB3 RNA-seq


title: prostate: ACB4 RNA-seq


title: prostate: ACB2 RNA-seq


title: PBS-4


title: U32Met

description: methyl-Seq


title: U29Met

description: methyl-Seq


title: prostate: PACB5 RNA-seq


title: U19Met

description: methyl-Seq


title: U16Met

description: methyl-Seq


title: prostate: PACB3 RNA-seq


title: U27Met

description: methyl-Seq


title: prostate: VCaP RNA-seq

value: prostate adenocarcinoma


title: U13Met

description: methyl-Seq


title: U11Met

description: methyl-Seq


title: U33Met

description: methyl-Seq


title: U08Met

description: methyl-Seq


title: U09Met

description: methyl-Seq


title: U26Met

description: methyl-Seq


title: U25Met

description: methyl-Seq


title: lung: NHBE5-PARCB RNA-seq

source_name: lung

value: lung

value: transformed bronchial epithelial


title: prostate: ACB1 RNA-seq

value: prostate


title: lung: NHBE4-PARCB2 RNA-seq


title: U03Met

description: methyl-Seq


title: lung: NHBE1-PARCB1 RNA-seq


title: U01Met

description: methyl-Seq


title: lung: NHBE1-PARCB2 RNA-seq


title: prostate: PARCB5 RNA-seq

value: transformed prostate basal epithelial


title: prostate: PARCB2 RNA-seq

value: NSG mice


title: U02Met

description: methyl-Seq


title: lung: NHBE4-PARCB1 RNA-seq


title: RAW264.7_AEPS_4hr_rep3

city: Hangzhou

first: Xiangfeng

last: Chen

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

description: RAW264.7 cells treated with AEPS (50 μg/mL) for 4 h

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3  8 × 60 k Mouse Gene Expression Microarray was used for the analysis.

scan_protocol: Hybridized microarrays were scanned with Agilent C scanner using Agilent’s Scan Control software, version A.8.4.1.

data_processing: The features were extracted with the Feature Extraction software. Data pre-processing and differential expression analysis were done in R software. Data were normalized between arrays using the quantile method (GENESPRING12.0).

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: RAW264.7 macrophages were purchased from ATCC (American Type Tissue Culture Collection), and maintained in a 5% CO2 atmosphere in DMEM medium supplemented with 10% FBS (Gibco), 100 μg/ml streptomycin, and 100 U/ml penicillin.

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: RAW264.7 macrophages were treated with or without AEPS (50 µg/mL) for 4 hours.

tag: cell line

value: macrophage cells

value: AEPS (50 µg/mL) for 4 hrs


title: RAW264.7_AEPS_4hr_rep2


title: lung: NHBE5 RNA-seq

value: normal bronchial epithelial


title: RAW264.7_AEPS_4hr_rep1


title: RAW264.7_Ctrl_rep2

description: RAW264.7 cells treated with DMEM for 4 h

value: none (DMEM medium)


title: lung: NHBE4 RNA-seq


title: RAW264.7_Ctrl_rep3


title: Sox11cKO versus wild-type control_keratinocyte_replicate 2

city: Houston

first: Hoang

last: Nguyen

state: TX

address: 1 Baylor Plaza

department: Center for Cell and Gene Therapy

institute: Baylor College of Medicine

description: Biological replicate 2 of 2

hyb_protocol: 300 ng of each labeled cRNA were fragmented. Approximately 480-ng total of each fragmented cRNA sample pair were loaded onto each of the Mouse G3 8x60K Expression arrays. The arrays were hybridized in an Agilent Hybridization Chamber for 17 hours at 65C with rotation at 10 rpm, and then washed using the Agilent Expression Wash Buffers One and Two, followed by acetonitrile.

scan_protocol: The slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.5.1.

data_processing: Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1. The microarray data were background corrected by ‘normexp’ method  and then normalized by global loess method using Bioconductor limma packages version 3.5.

source_name: Sox11cKO keratinocytes

label_protocol: 25 ng of total RNA, combined with RNA spike mix, were reverse transcribed using a T7 Primer Mix to produce cDNA. The cDNA product was transcribed using T7 RNA Polymerase, producing cyanine-3- and cyanine-5-labeled cRNA. The labeled cRNA was purified using a Qiagen RNeasy Mini Kit.

growth_protocol: Primary keratinocytes were isolated from newborn pups using dispase and trypsin method of cell dissociation. Cells were plated on J2 feeder cells. Keratinocytes were grown on the feeder cells for 3 passages and were off feeder cells at least 2 passages prior to being used in experiments.

extract_protocol: Total RNA extracted using Trizol and purifed using RiboPure kit following manufacturer's instructions

value: skin primary keratinocytes

source_name: wild-type  control keratinocytes


title: lung: NHBE1 RNA-seq


title: Sox11cKO versus wild-type control_keratinocyte_replicate 1

description: Biological replicate 1 of 2.


title: Sox4cKO versus wild-type control_keratinocyte_replicate 2

description: Biological replicate 2 of 2

source_name: Sox4cKO keratinocytes


title: RAW264.7_Ctrl_rep1


title: Sox4/11 dcKO versus wild-type control_keratinocyte_replicate 1

description: Biological replicate 1 of 2.

source_name: Sox4/11 dKO keratinocytes


title: Sox4/11 dcKO versus wild-type control_keratinocyte_replicate 2

description: Biological replicate 2 of 2


title: Sox4cKO versus wild-type control_keratinocyte_replicate 1

description: Biological replicate 1 of 2.


title: prostate: Basal1 RNA-seq

value: normal prostate basal epithelial


title: prostate: Basal2 RNA-seq


title: prostate: Basal3 RNA-seq


title: lung: NHBE5-PARCB Exome-seq

data_processing:
Library strategy: Whole Exome Seq
Mapping with GATK4 (https://software.broadinstitute.org/gatk/gatk4) and gnomAD germline reference
Annotation with ANNOVAR (http://annovar.openbioinformatics.org/en/latest/), avsnp database (https://www.ncbi.nlm.nih.gov/projects/SNP/), and COSMIC (https://cancer.sanger.ac.uk/cosmic)
Genome_build: hg38 human genome
Supplementary_files_format_and_content: tab-delimited text file

extract_protocol:
SeqCap EZ Human Exome Library v3.0
Low-Throughput Library Preparation Kit


title: lung: NHBE1-PARCB1 Exome-seq


title: Sox4/11 dcKO versus wild-type control_E16 epidermis_replicate 2

description: Biological replicate 2 of 2

data_processing: Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1. The microarray data were background corrected by ‘normexp’ method  and then normalized by global loess method using Bioconductor limma version 3.5 packages.

source_name: E16 Sox4/11 dKO epidermis

tag: age

source_name: E16 wild-type littermate control epidermis


title: Sox11cKO versus wild-type control_E16 epidermis_replicate 2

description: Biological replicate 2 of 2

source_name: E16 Sox11cKO epidermis


title: Sox11cKO versus wild-type control_E16 epidermis_replicate 1

description: Biological replicate 1 of 2.


title: lung: NHBE4-PARCB1 Exome-seq


title: Sox4/11 dcKO versus wild-type control_E16 epidermis_replicate 1

description: Biological replicate 1 of 2.


title: Sox4cKO versus wild-type control_E16 epidermis_replicate 1

description: Biological replicate 1 of 2.

source_name: E16 Sox4cKO epidermis


title: Fibroid [MP156F2]

type: genomic

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing:
Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking. Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating full lack of methylation and “1” full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.
The data tables do not include data for the following 59 RS IDs not found on the platform record. The normalized data for all data including these probes is available on the series record in the file normalized_data_allprobes.txt.
rs10033147
rs1019916
rs1040870
rs10457834
rs10796216
rs10882854
rs10936224
rs11034952
rs11249206
rs13369115
rs133860
rs1416770
rs1467387
rs1484127
rs1495031
rs1510189
rs1510480
rs1520670
rs1941955
rs1945975
rs2032088
rs2125573
rs213028
rs2208123
rs2235751
rs2385226
rs2468330
rs2521373
rs264581
rs2804694
rs2857639
rs2959823
rs348937
rs3936238
rs4331560
rs472920
rs4742386
rs5926356
rs5987737
rs6426327
rs6471533
rs654498
rs6546473
rs6626309
rs6982811
rs6991394
rs715359
rs739259
rs7660805
rs7746156
rs798149
rs845016
rs877309
rs9292570
rs9363764
rs939290
rs951295
rs966367
rs9839873

label: Cy5 and Cy3

source_name: Fibroid myometrium

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.  Array beadchips were scanned on the Illumina iScan platform.  DNA methylome was captured by HumanMethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) using the manufacturer’s standard protocol.

value: myometrium

tag: diagnosis

value: fibroid

tag: ethnicity

value: Caucasian


title: prostate: PARCB5 Exome-seq

tag: transplant


title: gtl1-2 flg22 Rep3

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequences reads were trimmed using Trimmomatic0.32 to remove adapters and low quality sequences.
Trimmed reads were again quality checked using FASTQC.
Trimmed reads were aligned to the TAIR10 geome using TOPHAT V2.1.1
FPKM for each samples and differential expression between samples were calculated using Cufflinks V.2.2.1 package.
GO annotation was performed using AgriGO V2.0, and heatmaps were calculated using TMeV.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values

organism: Arabidopsis thaliana

source_name: gtl1-2 flg22

growth_protocol: 14 days-old seedlings were grown under long-day conditions on sugar-free MS (Murashige and Skoog) plates at 23oC

extract_protocol:
The whole 14 days-old seedlings were used for total RNA extraction.
mRNA library generation followed by paired end sequencing (Hiseq4000)

treatment_protocol: 1µM flg22 treatment for 1 hour

tag: ecotype


title: Fibroid [NW166F1]

description: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.

value: African American


title: Fibroid [MP156F1]


title: SOX11 overexpression versus control_replicate 1

description: Biological replicate 1 of 2. Littermate pair.

hyb_protocol: Performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. 300 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA  were combined and hybridized overnight (17 hours, 65 °C) to microarrays using Agilent’s recommended hybridization chamber and oven. After hybridization, slides were washed sequential

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The microarray data were background corrected by ‘normexp’ method  and then normalized by global loess method using Bioconductor limma packages version 3.5.

source_name: K14-rtTA epidermis, Dox for 12 h

label_protocol: 100 ng of each total RNA sample was used for the linear T7-based amplification step. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

value: FVB/N

source_name: K14-rtTA;TRE-Sox11-FLAG epidermis, Dox for 12 h


title: prostate: PARCB3 Exome-seq


title: Fibroid [NW63F2]


title: Sox4cKO versus wild-type control_E16 epidermis_replicate 2

description: Biological replicate 2 of 2


title: Fibroid [MP168F]


title: Fibroid [NW1F]


title: gtl1-2 flg22 Rep2


title: Fibroid [MP136F1]


title: E13 vs P4 differential gene expression replicate 2

description: Biological replicate 2 of 2

source_name: P4 epidermal basal cells

source_name: E13 epidermal cells


title: prostate: PARCB2 Exome-seq

source_name: prostate


title: Fibroid [MP111F1]


title: Fibroid [MP140F2]


title: WT flg22 Rep3

source_name: WT flg22

value: wild type


title: Fibroid [MP153F]


title: E13 vs P4 differential gene expression replicate 1

description: Biological replicate 1 of 2.


title: Fibroid [GO535F1]


title: WT flg22 Rep2


title: Fibroid [MP136F2]


title: Fibroid [NW166F2]


title: Fibroid [GO537F1]


title: gtl1-2_6

value: control


title: WT flg22 Rep1


title: Fibroid [NWRAF]


title: Fibroid [NW206F2]


title: gtl1-2_4


title: WT_3

source_name: WT


title: WT_2


title: Fibroid [GO562F]


title: Fibroid [MP120F2]


title: Fibroid [MP111F2]


title: Fibroid [MP140F1]


title: gtl1-2 flg22 Rep1


title: HJ7_ML04-1_S154

status: Public on Oct 04 2018

city: Madison

first: Hongli

last: Jiao

state: WI

address: 1111 Highland Ave WIMR 5039

department: Department of Orthopedics and Rehabilitation

institute: University of Wisconsin-Madison

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter masked fastq files were generated.
Read alignment using Tophat 2.1.1 using GRCh38 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used Ensembl GRCh38 gtf file as guided annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: xls files for FPKM values for each sample

source_name: derived from iPSCs

extract_protocol:
Cells were lysed in Trizol and stored at -80C until RNA isolation. Total RNA was extracted using a Direct-zol™ RNA Kit (Zymo Research, cat#:R2051) according to the manufacturer’s instructions. The extracted RNAs were quantified and quality checked using a NanpDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and a BioAnalyzer RNA 6000 Nano Kit (Agilent Technologies).
The cDNA libraries were prepared using the NEXTflex™ Rapid Directional RNA Sequencing Kit and NEXTflex™ RNA-Seq Barcodes – 24 Kit (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Libraries were pooled equimorlarily, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

value: iPSC-MSCS


title: HJ8_ML04-2_S155


title: HJ6_ML02-3_S153

source_name: derived from SF-MSCs

value: iPSCs


title: HJ9_ML04-3_S156


title: Fibroid [MP100F]


title: SOX11 overexpression versus control_replicate 2

description: Biological replicate 2 of 2. Littermate pair.


title: HJ4_ML02-1_S151


title: HJ5_ML02-2_S152


title: HJ3_ML09-3_S150

source_name: primary cell

value: SF-MSCs


title: HJ2_ML09-2_S149


title: Fibroid [MP164F]


title: Patients with T cell mediated rejection S16

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: TCMR

data_processing:
GRCh37/hg19 genome with TopHat2 in very sensitive settings for Bowtie2 and GENCODE annotation release 19 (GRCh37.p13)
Gene expression was quantified by HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: Blood

growth_protocol: Kidney transplanted patients with stable graft function, antibody mediated rejection or t cell mediated rejection episodes

extract_protocol:
Total RNA (tRNA) was isolated from blood cells contained in PAXgene Blood RNA Tubes with the PAXgene blood miRNA Kit (PreAnalytix, Qiagen, Hilden, Germany) according to the manufacturers instruction. Total RNA concentration and quality of each sample were determined with the NanoDrop ND-Lite (peqlab, Erlangen, Germany) and Qubit fluorometer (ThermoFisher Scientific, Darmstadt, Germany). Dependent on quantity and quality of RNA, six samples from patients with ABMR, six samples from patients with SGF and 4 samples from patients with TCMR were chosen for high-throughput sequencing.
The “TruSeq Stranded Total RNA library PrepKit with Ribo-Zero” kit (Illumina, San Diego, CA, USA) was used to prepare cDNA libraries for small RNA sequencing from a minimum of 100ng of total RNA isolated from the whole blood of patients with Tx according to manufacturer’s instruction. RNA quality was assessed on a bioanalyzer using the RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and only RNA with a RIN >8 was considered for further processing.  After quality control (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany). The final cDNA libraries were quality checked (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany), quantified (Qubit dsDNA HS Assay Kit, Invitrogen, Darmstadt, Germany) and were paired-end (100 bp) sequenced on a HiSeq2500 Illumina Next Generation Sequencing Device (Illumina, San Diego, CA, USA).

tag: cells

value: Whole blood cells

tag: human origin

value: human

tag: organ

value: blood


title: Patients with stable graft function S9

description: SGF


title: Patients with stable graft function S10

description: SGF


title: Patients with stable graft function S7

description: SGF


title: Patients with stable graft function S11

description: SGF


title: Patients with T cell mediated rejection S13

description: TCMR


title: Patients with antibody mediated rejection S6

description: ABMR


title: Patients with T cell mediated rejection S14

description: TCMR


title: Patients with stable graft function S8

description: SGF


title: Patients with antibody mediated rejection S3

description: ABMR


title: Patients with antibody mediated rejection S2

description: ABMR


title: Patients with antibody mediated rejection S4

description: ABMR


title: Patients with T cell mediated rejection S15

description: TCMR


title: Fibroid [MP169F]


title: Patients with antibody mediated rejection S5

description: ABMR


title: Patients with antibody mediated rejection S1

description: ABMR


title: Normal [NW1N]

source_name: Normal myometrium

value: normal


title: HJ1_ML09-1_S148


title: D9 LCL RNA

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

description: Ribozero Total RNA

data_processing:
RNA-seq: HISAT (default settings) and STRINGTIE were used to aligned and assess FPKM for annotated (hg19 refseq) and non-annoated transcripts
Genome_build: hg19
Supplementary_files_format_and_content: GTF files

source_name: LCL

extract_protocol:
RNA was isolated from B cells and LCLs with Trizol.
Libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems)

treatment_protocol: B cells (CD19+) cells were isolated from fresh donor blood samples with Dyanbeads CD19 Pan B (Invitrogen). LCLs were derived from B cells by culturing with EBV. Isolated cells were immediately used for chromatin immunoprecipitation experiments or RNA experimetns

value: LCL

tag: ID

value: Donor 9

tag: antibody


title: D6 B cell RNA

description: Ribozero Total RNA

source_name: CD19 B cells

value: CD19 B cells

value: Donor 6


title: D6 LCL RNA

description: Ribozero Total RNA


title: D7 B cell RNA

description: Ribozero Total RNA

value: Donor 7


title: D7 LCL RNA

description: Ribozero Total RNA


title: D9 LCL Input

data_processing:
ChIP-seq: Raw data was aligned to the hg19 genome with bowtie and macs (with default settings) was used to find H3K4me3 peaks
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: BED format

value: input


title: D7 LCL Input


title: D9 LCL H3K4me3 IP

value: H3K4me3, ab8580 (Abcam)


title: D6 LCL Input


title: Patients with stable graft function S12

description: SGF


title: D9 B cell RNA

description: Ribozero Total RNA


title: D9 B cell Input


title: D6 LCL H3K4me3 IP


title: D9 B cell H3K4me3 IP


title: D7 LCL H3K4me3 IP


title: Normal [NW166N]

value: myometrium

value: African American


title: D7 B cell Input


title: Normal [MP140N]

value: Caucasian


title: D7 B cell H3K4me3 IP


title: D6 B cell Input


title: D6 B cell H3K4me3 IP


title: Normal [NW206N]


title: MDA-MB-231_ATRi+APH,9h_Input

city: Philadelphia

first: Nishita

last: Shastri

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

description:
processed data file:
ATRi_APH_9h.narrowPeak

data_processing:
For basecalling and demultiplexing, Illumina bcl2fastq v2.17.1.14 was used
BrITL reads were aligned to the hg19 genome assembly using STAR-2.5.2a with the following configurations: outFilterMultimapNmax 3, outFilterMultimapNmax 100, outReadsUnmapped Fastx
Alignment tracks were converted to bam and sorted using samtools-0.1.19. Unique, deduplicated, blacklist-regions-removed tracks were then derived from the sorted bams using samtools-0.1.19 view -bq 10 to get unique reads, ngsutils-0.5.7 bamutils filter -excluded to remove blacklisted regions according to the mm10 blacklisted track from ENCODE (https://sites.google.com/site/anshulkundaje/projects/blacklists), picard-tools-1.141 MarkDuplicates REMOVE_DUPLICATES=true to remove duplicates.
Conditions with at least two quality replicate peaks were called using IDR methodology (https://sites.google.com/site/anshulkundaje/projects/idr) with MACS2 version 2.1.0 with the following setting: -p 1e-3. Without replicates, MACS2 version 2.1.0 was used with -q 0.01.
Peaks that were within 2 kb were merged for each condition. Merged peaks were further selected by filtering for those that contained peaks with p-value <10-6, >4-fold signal enrichment value, and with peak width >500 bp. The final peak list was generated as a set intersection and subtraction from the DMSO-control peak list
Genome_build: hg19
Supplementary_files_format_and_content: peaks

growth_protocol: MDA-MB-231 cells were grown in 100 mm tissue-culture plates in DMEM containing high glucose 4.5gm/L and supplemented with 10% FBS, 2mM L-glutamine and Pen/Strep to obtain ~2 x 106 cells upon collection for BrITL.

extract_protocol:
Cells were permeabilized, biotin end-labeld, and lysed. Genomic DNA was extracted and sonicated to 0.2-2 kb size fragments prior to pull-down of biotin-labeled fragments with streptaviding-coated Dynabeads.
Libraries were prepared according to the NEBNext kit. Briefly, DNA was sonicated to ~200 bp. DNA was end-repaired using a combination of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA fragments of ~200 bp (insert plus adaptor) were band isolated from a 2% agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: 0.5 uM VE-822 + 0.2 uM aphidicolin for 9hrs

value: Human epithelial breast cancer cells; passage-immortalized

tag: treated with

tag: pull-down reagents

value: Biotin-16-ddUTP (Enzo Life Sciences, ENZ-42813); Dynabeads KilobaseBinder kit (Life Technologies, 601-01)


title: Normal [MP126N]


title: Normal [NW63N]


title: Normal [MP162N]


title: MDA-MB-231_ATRi+APH,9h_BrITL rep1

value: 0.5 uM VE-822 + 0.2 uM aphidicolin for 9hrs


title: MDA-MB-231_DMSO,9h_Input

description:
processed data file:
DMSO_9h.narrowPeak

treatment_protocol: DMSO treatment for 9hrs

value: DMSO for 9hrs


title: MDA-MB-231_DMSO,9h_BrITL rep1

description:
processed data file:
DMSO_9h.narrowPeak


title: IGTB677_unstim_Exp7

city: Cambridge

first: Jenny

address: 16 Divinity Ave

institute: Harvard

data_processing:
Tophat v1.4.1 (--mate-inner-dist 300 --mate-std-dev 500) was used to align reads to hg19.
StringTie v1.2.2 was used with default parameters for de novo reconstruction of transcriptomes.
kallisto v0.42.5 was used to quantify abundances of reconstructed transcripts.
Genome_build: hg19, de novo reconstructed transcriptome
Supplementary_files_format_and_content: *abundance.txt: Tab-delimited text files of transcript ID, length, effective length, estimated counts, and TPM.
Supplementary_files_format_and_content: dcRNASeq.denovo_transcriptome.bed

source_name: monocyte-derived dendritic cells, baseline

extract_protocol:
35-50 mL of peripheral blood from fasting subjects was collected and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Paque (GE Healthcare Life Sciences) centrifugation. Monocytes were isolated from PBMCs by negative selection using the Dynabeads Untouched Human Monocytes kit (Life Technologies) modified to increase throughput and optimize recovery and purity of CD14+ CD16lo monocytes. The remaining monocytes were cultured for seven days in RPMI (Life Technologies) supplemented with 10% FBS, 100 ng/mL GM-CSF (R&D Systems) and 40 ng/mL IL-4 (R&D Systems) to differentiate into monocyte-derived dendritic cells (MoDCs).
Total RNA was isolated from MoDCs using the RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: donor id

tag: disease state

value: healthy

value: monocyte-derived dendritic cells

tag: condition

value: baseline


title: 0713V020311_FLU

source_name: monocyte-derived dendritic cells, influenza stimulated

tag: cell type

value: influenza stimulated


title: IGTB1206_unstim_Exp1


title: IGTB885_unstim_Exp1


title: IGTB1273_unstim_Exp1


title: 1442V100411_baseline


title: 0010V052510_IFN

source_name: monocyte-derived dendritic cells, IFN-beta stimulated

value: IFN-beta stimulated


title: IGTB1197_unstim_Exp7


title: MDA-MB-231_ATRi+APH,9h_BrITL rep2

tag: cell line


title: MDA-MB-231_DMSO,9h_BrITL rep2

description:
processed data file:
DMSO_9h.narrowPeak


title: 1369V071211_baseline


title: 1448V081711_baseline


title: 1046V082411_baseline


title: IGTB843_unstim_Exp7


title: IGTB917_unstim_Exp7


title: 1242V110311_IFN


title: Normal [MP111N]

tag: tissue

value: normal


title: 1698V022812_baseline


title: 0570V062211_FLU


title: Fibroid [MP99F]

source_name: Fibroid myometrium

tag: diagnosis

value: fibroid


title: Normal [MP164N]

tag: ethnicity


title: 1123V030811_FLU


title: 1421V091311_baseline


title: 1202V051711_IFN


title: 1446V062811_IFN


title: 0885V060110_FLU


title: 0176V081611_IFN


title: 0412V021511_baseline


title: 0621V012611_FLU


title: 1674V011812_IFN


title: 1145V051811_FLU


title: 1133V021511_FLU


title: 1440V101211_IFN


title: 0351V081711_FLU


title: 1133V021511_baseline


title: 1250V083011_IFN


title: 1275V060811_IFN


title: 0678V081811_baseline


title: 1417V092911_baseline


title: 0517V062211_FLU


title: 0351V081711_IFN


title: 1432V092111_FLU


title: 0496V080411_FLU


title: 1394V082511_baseline


title: 1372V062911_FLU


title: 0638V121311_FLU


title: 1449V092711_FLU


title: 1448V081711_IFN


title: 1133V021511_IFN


title: 1446V062811_baseline


title: 1217V080411_IFN


title: 1193V042111_IFN


title: 1448V081711_FLU


title: 0575V081111_baseline


title: 1442V100411_FLU


title: 0665V011812_IFN


title: 1324V060111_IFN


title: 1324V060111_baseline


title: 0178V031011_baseline


title: 1440V101211_FLU


title: IGTB1211_unstim_Exp1


title: 0876V030211_IFN


title: 1393V060711_baseline


title: 1467V121411_IFN


title: 0178V031011_IFN


title: 0274V052610_FLU


title: 0136V033111_IFN


title: 1650V011012_IFN


title: 0930V062911_IFN


title: 1223V051911_baseline


title: 0064V080311_FLU


title: 1434V081811_baseline


title: 1415V091311_FLU


title: 1601V112211_baseline


title: 1421V091311_IFN


title: 0920V011911_IFN


title: 1162V040711_IFN


title: 0899V030811_baseline


title: 1639V011812_FLU


title: 1432V092111_IFN


title: 1138V031711_IFN


title: 1114V042011_baseline


title: 0802V063011_FLU


title: 0621V012611_IFN


title: 1229V062811_IFN


title: 1222V062311_IFN


title: 0876V030211_baseline


title: 1434V081811_IFN


title: 1245V082311_baseline


title: 1415V091311_IFN


title: IGTB621_unstim_Exp7


title: 0661V031711_IFN


title: 0876V030211_FLU


title: 1223V051911_FLU


title: 1217V080411_FLU


title: 1415V091311_baseline


title: 1037V090711_baseline


title: 1011V091311_FLU


title: 1344V062811_FLU


title: 1308V011912_FLU


title: 1046V082411_IFN


title: 1393V060711_FLU


title: 0496V080411_IFN


title: Normal [MP100N]


title: 1418V080911_baseline


title: 0536V081011_FLU


title: 1195V110311_IFN


title: 0843V021711_IFN


title: 0867V012011_IFN


title: 1369V071211_FLU


title: 1479V092911_IFN


title: 1577V111711_IFN


title: 0917V031711_FLU


title: 1227V051211_IFN


title: 1479V092911_baseline


title: 1394V082511_IFN


title: 0373V021711_IFN


title: 0945V051911_IFN


title: 1369V071211_IFN


title: 1421V091311_FLU


title: 1193V042111_FLU


title: 1396V022212_IFN


title: 1344V062811_baseline


title: 0010V052510_FLU


title: 0713V020311_IFN


title: 0661V031711_baseline


title: 0533V033011_IFN


title: 0843V021711_FLU


title: 1302V101911_IFN


title: 0678V081811_FLU


title: 0350V081811_IFN


title: 1308V011912_IFN


title: 0836V030311_FLU


title: 1200V041311_FLU


title: 1088V060911_baseline


title: 1417V092911_FLU


title: 1345V092811_IFN


title: 0661V031711_FLU


title: 1200V041311_baseline


title: 0930V062911_FLU


title: 1275V060811_baseline


title: 0469V072811_baseline


title: 0802V063011_IFN


title: 1324V060111_FLU


title: 1279V060911_FLU


title: 0863V113011_IFN


title: 1165V041211_IFN


title: 1312V011812_IFN


title: 1442V100411_IFN


title: 1483V092811_FLU


title: 1305V053111_baseline


title: 1242V110311_baseline


title: 1439V092111_IFN


title: 0330V121511_IFN


title: 1222V062311_FLU


title: 1046V082411_FLU


title: 1479V092911_FLU


title: 0506V080911_baseline


title: 1223V051911_IFN


title: 1396V022212_FLU


title: 0190V030911_FLU


title: 0412V021511_IFN


title: 0940V030211_baseline


title: 1466V011812_FLU


title: 1088V060911_IFN


title: 1145V051811_IFN


title: 0695V060711_FLU


title: 1446V062811_FLU


title: 1255V111711_IFN


title: 1372V062911_baseline


title: 0836V030311_IFN


title: 0176V081611_baseline


title: 0638V121311_IFN


title: 0612V021611_baseline


title: 0809V082411_FLU


title: 0910V021711_FLU


title: 1305V053111_FLU


title: 0945V051911_FLU


title: 0350V081811_FLU


title: 1136V081011_FLU


title: 1698V022812_IFN


title: 0498V013112_FLU


title: 1365V071211_FLU


title: 1335V060111_FLU


title: 0533V033011_FLU


title: 1418V080911_FLU


title: 1483V092811_baseline


title: 0256V071211_IFN


title: 1088V060911_FLU


title: 1385V072011_FLU


title: 1424V081811_baseline


title: 1575V120711_IFN


title: 0940V030211_IFN


title: 0945V051911_baseline


title: 0707V030911_FLU


title: 1439V092111_FLU


title: 0565V030111_IFN


title: 1265V022212_IFN


title: 1205V111511_IFN


title: 14mig_2_RNAseq

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
featureCounts_migration.txt
MIG14R

data_processing:
Read quality was confirmed with FastQC v0.11.4
Reads were aligned to hg38 and gencode annotations v27 using STAR v2.5.3a with default settings
FeatureCounts v1.5.2 was used to quantify the reads with gencode annotations v27
Differentially expressed genes were identified at FDR<0.05 using DEseq2 v1.16.1 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: FeatureCounts matrix of raw counts for each gene in each sample

source_name: Myeloid leukaemia

growth_protocol: A seed-lot store was generated of cells at 4 passages. Cells were grown in suspension in RPMI 1640 (ThermoFisher, 11875119) with 10% FBS (medi’Ray, MG-FBS0820-500ML-GEN), 1% pen/strep (ThermoFisher, 15140122), and 1% GlutaMAXTM (ThermoFisher, 35050061). Cells were differentiated into a granulocytic phenotype with 1µm all trans retinoic acid (ATRA)(Sigma Aldrich, R2625-50MG) for four days.

extract_protocol:
Cells were lysed in TRiZOL LS and phase separated with chloroform. RNA was extracted with the Qiagen RNeasy micro kit (Qiagen, 74004).
libraries were prepared by Annoroad using ribosomal RNA depletion with RiboZero Magnetic Gold Kit (Human/Mouse/Rat) (MRZG12324)

tag: differentiation

value: neutrophil-like (4 days all-trans retinoic acid)

tag: passages

tag: migration pore size

value: 14 micrometer diameter


title: 1114V042011_IFN


title: 0517V062211_IFN


title: 1008V101911_FLU


title: 14mig_1_RNAseq

description:
featureCounts_migration.txt
MIG14Q


title: 5mig_2_RNAseq

description:
featureCounts_migration.txt
MIG5H

value: 5 micrometer diameter


title: 0695V060711_IFN


title: 0581V030111_IFN


title: ctrl_2_RNAseq

description:
featureCounts_migration.txt
NOMIGB


title: 1556V112311_FLU


title: 0373V021711_baseline


title: 1265V022212_FLU


title: 0565V030111_FLU


title: 14mig_3_RNAseq

description:
featureCounts_migration.txt
MIG14S


title: 1572V112311_FLU


title: ctrl_1_RNAseq

description:
featureCounts_migration.txt
NOMIGA


title: MHCCLM3_cell_RNC_seq

city: Guangzhou

first: Li

last: Dehua

state: Guangdong

address: Huangpu avenue west NO.601

institute: Jinan University

data_processing:
library strategy: translatome sequencing (RNC-seq)
Illumina Casava1.7 software used for basecalling.
Hela_RNC reads were aligned to the Human_refseq_mrna.fasta and 97H_RNC reads and LM3_RNC reads were aligned to the Human_refseq_mrna.fasta using FANSe3 with  configurations: 1.-L50 --all --rename -E3(Hela_RNC reads). 2.-L150 --all --rename -E7(97H_RNC reads and LM3_RNC reads)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The 97HRNC and LM3RNC mutation sites had been cover more than 10 reads and had pass the chi square test.
Supplementary_files_format_and_content: The *-rpkm-SVmerge.txt files contain  RPKM data. The *mutation.txt are the sites lists of single amion acid polymorphisms. For this example:ENST00000411463 185:R::K 347:V::M 403:L::R , there is two column were separated with tab, so the first column is ENST00000411463 which is a transcript's name.  And then the second column is 185:R::K 347:V::M 403:L::R , it indicates that ENST00000411463 has three sites of single amion acid polymorphisms. The three sites are 185,347 and 403, and the three amino acid substitution events are R is replaced with K, V is replaced with M, L is replaced with R. The different single amion acid polymorphisms sites are separated by blank.

source_name: MHCCLM3 cell lines

growth_protocol: Hela and MHCCLM3 and MHCC97H cells were cultured in 75 cm2 culture flasks in the complete medium DMEM (Life Technologies, Carlsbad, CA, USA) supplemented with 10% FBS (Life Technologies, Carlsbad, CA, USA), 100U/mL penicillin/ 0.1mg/mL streptomycin (GBCBIO Technologies Inc, Guangzhou, China), and 10 μg/mL ciprofloxacin. All cells were cultured in a 5% CO2 incubator at 37 ℃ and were negative for mycoplasma detection by PCR analysis.

extract_protocol:
Hela and MHCCLM3 and MHCC97H cells were washed by pre-chilled phosphate buffered saline twice and addition of 2 ml cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer) [20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200mM KCl, 100 mg/ml cycloheximide and 2mM dithiothreitol]. After 30-min ice-bath, cell lysates were scraped and transferred to pre-chilled 1.5 ml tubes. Cell debris was removed by centrifuging at 16 200 g for 10 min at 4C. Supernatants were transferred on the surface of 20 ml of sucrose buffer (30% sucrose in RB buffer). RNCs were pelleted after ultra-centrifugation at 185000 g for 5h at 4C. Then RNC-RNA were isolated by using TRIzol RNA extraction reagent (Ambion, Austin, TX), following the manufacturer’s instructions.
The Hela RNC-mRNA libraries were prepared according to BGI-MGIEasy's instructions accompanying the MGIEasy mRNA Library Prep Kit V2 (Part# 85-05536-01). The polyA+ mRNA was selected using NEB Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The mRNA libraries were constructed using the MGIEasy mRNA Library Prep Kit V2 for MGI (BGISEQ, Shen Zhen, China) following the manufacturer’s protocol. The MHCC97H RNC-mRNA  libraries were prepared according to VAHTS mRNA-seq V3 Library Prep Kit (Part# NR611-01/02). The polyA+ mRNA was selected using NEB Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The mRNA libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme, Nanjing, China) following the manufacturer’s protocol.
RNA-Seq (Hela cell RNC-mRNA sequencing were performed on a BGISEQ-500 sequencer for single-end 50, and the MHCC97H RNC-mRNA sequencing were performed on an Illumina HiSeq X Ten sequencer for paired-end 150.

treatment_protocol: Hela and MHCCLM3 and MHCC97H cells were cultured in culture flasks after growth to 80-90% confluence, then were pre-treated with 100 mg/ml cycloheximide for 15 min.

value: Hepatoma carcinoma cell

tag: state

value: steady


title: 1111V031511_IFN


title: ctrl_3_RNAseq

description:
featureCounts_migration.txt
NOMIGC


title: 1603V120711_IFN


title: 5mig_3_RNAseq

description:
featureCounts_migration.txt
MIG5I


title: MHCC97H_cell_RNC_seq

source_name: MHCC97H cell lines


title: 1312V011812_FLU


title: 1197V041211_FLU


title: 5mig_1_RNAseq

description:
featureCounts_migration.txt
MIG5G


title: 1255V111711_FLU


title: 0506V080911_IFN


title: 1327V102011_IFN


title: 1227V051211_FLU


title: 1305V053111_IFN


title: 1037V090711_IFN


title: 0178V031011_FLU


title: 0256V071211_FLU


title: 1192V051811_IFN


title: 1136V081011_IFN


title: 1202V051711_FLU


title: eggs-3

first: Vivien

last: Firtzlaff

address: Haderslebener Str. 9

department: Applied Zoology/Animal Ecology

institute: Freie Universität Berlin

description:
Gene expression in leaves after 'treatment'
6d eggs 20°C

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Hybridization was performed in a Agilent hybridization oven at standard conditions as recommended by the manufacturer. Subsequently, microarrays were washed 1 minute with GE Wash Buffer 1 (Agilent) at 23°C and 1 minute with GE Wash buffer 2 (Agilent) at 37°C.

scan_protocol: Microarrays were scanned immediately after washing with an Agilent High-Resolution Scanner (G2600D) using default settings.

data_processing: The images were processed with the Agilent Feature Extraction software 10.1 using default settings  (protocol GE1_1105_Oct12 (Read Only) and Grid_Name 049286_D_F_20130524). The resulting processed signals of all individual hybridizations were normalized and log2-converted as described in Firtzlaff V, Oberländer J, Geiselhardt S, Hilker M and Kunze R, 2015, .

label_protocol: Cy3-labeled cRNA was synthesized with the Agilent Quick Amp Labeling Kit one-cCy3-labeled cRNA was synthesized with the Quick Amp Labeling Kit, one-color (Agilent Technologies catalog number 5190-0442) according to the manufacturer's instructions.

growth_protocol: Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions at 20°C for seven weeks (6 weeks: 10 h/14 h light/dark + 1 week: 8 h/ 16 h light/dark). Seven week old plants were (i) deposited with eggs (one egg cluster with about 40 eggs was deposited onto the lower surface of a rosette leaf within position 14-17) or were (ii) left untreated. Six days after egg deposition, leaf tissue was harvested from egg-deposited and untreated plants. The tissue was harvested from a leaf region proximal to the egg deposition site.

extract_protocol: Total RNA was extracted from frozen and ground tissue according to Oñate-Sánchez & Vicente-Carbajosa (2008; BMC Research Notes 1:93.). RNA was photometrically quantified with a NanoPhotometer (Implen, München, Germany) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: ecotype

tag: genotype/variation

value: wild type

tag: treatment

value: 6d eggs 20C

tag: accession

value: rosette leaf 14-17


title: 0619V011812_IFN


title: eggs-1


title: untreated control-3

description:
Gene expression in leaves after 'treatment'
6d 20°C

source_name: untreated control-3


title: eggs-2


title: untreated control-1

source_name: untreated control-1


title: 0627V101311_FLU


title: 1577V111711_FLU


title: untreated control-2

source_name: untreated control-2


title: 1242V110311_FLU


title: Eggs+Feeding-3

description:
Gene expression in leaves after 'treatment'
PT-3

source_name: Eggs+Feeding

growth_protocol: Arabidopsis thaliana Col-0 wild type plants were grown on soil under short day conditions at 20°C for seven weeks (6 weeks: 10 h/14 h light/dark + 1 week: 8 h/ 16 h light/dark). Seven week old plants were (i) deposited with eggs (one egg cluster with about 40 eggs was deposited onto the lower surface of a rosette leaf within position 14-17) or were (ii) left untreated. For larval feeding, P. brassicae larvae were transferred to leaves of untreated and oviposition-treated plants and allowed to gregariously feed for two days.

value: 6d Eggs 20°C + 2d larval feeding


title: Eggs+Feeding-2

description:
Gene expression in leaves after 'treatment'
PT-2


title: Eggs+Feeding-1

description:
Gene expression in leaves after 'treatment'
PT-1


title: Feeding-3

description:
Gene expression in leaves after 'treatment'
T-3

source_name: Feeding

value: 6d 20°C + 2d larval feeding


title: 1274V102611_FLU

value: healthy


title: Feeding-2

description:
Gene expression in leaves after 'treatment'
T-2


title: 1406V111511_IFN

value: monocyte-derived dendritic cells


title: 0575V081111_FLU


title: Feeding-4

description:
Gene expression in leaves after 'treatment'
T-4


title: Control-5

description:
Gene expression in leaves after 'treatment'
C-5

source_name: Control

value: 8d 20°C


title: Control-2

description:
Gene expression in leaves after 'treatment'
C-2


title: Control-4

description:
Gene expression in leaves after 'treatment'
C-4


title: Control-3

description:
Gene expression in leaves after 'treatment'
C-3


title: 1502V120811_IFN


title: 0917V031711_IFN


title: 0176V081611_FLU

value: influenza stimulated


title: 1245V082311_IFN

value: IFN-beta stimulated


title: 1335V060111_IFN


title: 0494V031011_FLU


title: 1483V092811_IFN


title: 1489V101211_FLU


title: Feeding-1

description:
Gene expression in leaves after 'treatment'
T-1


title: 0619V011812_FLU


title: 0731V012412_FLU


title: RAW_Scramble_Ctrl_rep1

description: RAW264.7 cells treated with DMEM for 4 h

source_name: RAW264.7 mouse macrophage cells transfected with Scramble knockdown vectors

growth_protocol: RAW264.7 macrophages were purchased from ATCC (American Type Tissue Culture Collection), and maintained in a 5% CO2 atmosphere in DMEM medium supplemented with 10% FBS（Gibco）, 100 μg/ml streptomycin, and 100 U/ml penicillin.

treatment_protocol: RAW264.7 macrophages transfected with pcDNATM6.2-GW/EmGFP-miR expression vector based Linc-AAM knockdown plasmids were selected for stable integrants with blasticidin (6 μg/mL) as bulk cultures and then were treated with or without AEPS (50 µg/mL) for 4 hours.

value: Scramble

value: DMEM


title: RAW_Linc-AAM KD_AEPS_rep1

description: RAW264.7 cells treated with AEPS (50 μg/mL) for 4 h

source_name: RAW264.7 mouse macrophage cells transfected with Linc-AAM knockdown vectors

value: Linc-AAM knockdown

value: AEPS


title: RAW_Linc-AAM KD_Ctrl_rep1


title: Control-1

description:
Gene expression in leaves after 'treatment'
C-1


title: 1639V011812_IFN


title: 1475V013112_IFN


title: 1424V081811_FLU


title: 1380V101911_FLU


title: 1198V042011_IFN


title: 1424V081811_IFN


title: 1327V102011_FLU


title: 0329V101311_FLU


title: RAW_Scramble_AEPS_rep1


title: 0469V072811_FLU


title: 0536V081011_baseline

value: baseline


title: 0612V021611_FLU


title: 1320V060211_IFN


title: 0373V021711_FLU


title: 0498V013112_IFN


title: 1650V011012_FLU


title: 0231V060711_IFN


title: 1300V090711_FLU


title: 1250V083011_FLU


title: 1293V101911_FLU


title: 1475V013112_FLU


title: 1603V120711_FLU


title: 1335V060111_baseline


title: 0707V030911_IFN


title: 0231V060711_FLU


title: 0930V062911_baseline


title: 1200V041311_IFN


title: 1192V051811_FLU


title: 1245V082311_FLU


title: 1138V031711_FLU


title: 1434V081811_FLU


title: 1148V090811_baseline


title: 0627V101311_IFN


title: 1417V092911_IFN


title: 1597V120611_IFN


title: 0536V081011_IFN


title: 1466V011812_IFN


title: 1523V113011_FLU


title: 1488V121411_FLU


title: 1197V041211_IFN


title: 1565V022812_IFN


title: 1488V121411_IFN


title: 1502V120811_FLU


title: 0775V121511_FLU


title: 1140V033011_IFN


title: 1370V101311_FLU


title: 1393V060711_IFN


title: 1148V090811_FLU


title: 1505V121511_IFN


title: 1198V042011_FLU


title: 1435V120111_IFN


title: 0668V062311_IFN


title: 1274V102611_IFN


title: 1698V022812_FLU


title: 1205V111511_FLU


title: 1317V091311_IFN


title: 1523V113011_IFN


title: 1156V061511_baseline


title: 1344V062811_IFN


title: 1523V113011_baseline


title: 1293V101911_IFN


title: 1487V121411_FLU


title: 1162V040711_FLU


title: 1674V011812_FLU


title: 1372V062911_IFN


title: 1406V111511_FLU


title: 0529V031011_IFN


title: 0612V021611_IFN


title: 1565V022812_FLU


title: 1130V011911_IFN


title: 1008V101911_IFN


title: 0940V030211_FLU


title: 1601V112211_FLU


title: 1140V033011_FLU


title: 0920V011911_FLU


title: 1418V080911_IFN


title: 1203V042011_IFN


title: 1193V042111_baseline


title: 1320V060211_FLU


title: 1156V061511_IFN


title: 1385V072011_baseline


title: 1248V121311_IFN


title: 0668V062311_FLU


title: 0863V113011_FLU


title: 1587V011712_IFN


title: 1586V112211_FLU


title: 1302V101911_FLU


title: 0641V101811_IFN


title: 1433V080211_FLU


title: 1195V110311_FLU


title: 1438V081111_IFN


title: 0775V121511_IFN


title: 1166V041211_IFN


title: 1394V082511_FLU


title: 0529V031011_FLU


title: 1317V091311_FLU


title: 0506V080911_FLU


title: 1166V041211_baseline


title: MEFs_ATRi+APH,18h_BrITL rep2

description:
processed data file:
ATRi_APH_18h.narrowPeak

data_processing:
For basecalling and demultiplexing, Illumina bcl2fastq v2.17.1.14 was used
BrITL reads were aligned to the mm10 genome assembly using STAR-2.5.2a with the following configurations: outFilterMultimapNmax 3, outFilterMultimapNmax 100, outReadsUnmapped Fastx
Alignment tracks were converted to bam and sorted using samtools-0.1.19. Unique, deduplicated, blacklist-regions-removed tracks were then derived from the sorted bams using samtools-0.1.19 view -bq 10 to get unique reads, ngsutils-0.5.7 bamutils filter -excluded to remove blacklisted regions according to the mm10 blacklisted track from ENCODE (https://sites.google.com/site/anshulkundaje/projects/blacklists), picard-tools-1.141 MarkDuplicates REMOVE_DUPLICATES=true to remove duplicates.
Conditions with at least two quality replicate peaks were called using IDR methodology (https://sites.google.com/site/anshulkundaje/projects/idr) with MACS2 version 2.1.0 with the following setting: -p 1e-3. Without replicates, MACS2 version 2.1.0 was used with -q 0.01.
Peaks that were within 5 kb were merged for each condition. Merged peaks were further selected by filtering for those that contained peaks with p-value <10-8 and >4-fold signal enrichment value. The final peak list was generated as a set intersection and subtraction from the DMSO-control peak list
Genome_build: mm10
Supplementary_files_format_and_content: peaks

growth_protocol: MEFs were grown in 100 mm tissue-culture plates in DMEM containing high glucose 4.5gm/L and supplemented with 10% FBS, 2mM L-glutamine and Pen/Strep to obtain ~2 x 106 cells upon collection for BrITL.

treatment_protocol: 1 uM ATR-45 inhibitor + 0.2 uM aphidicolin for 18hrs

value: Mouse embryonic fibroblasts; passage-immortalized

value: ATR+/- MEFs, Bcl-xL-expressing

tag: treated with

tag: pull-down reagents

value: Biotin-16-ddUTP (Enzo Life Sciences, ENZ-42813); Dynabeads KilobaseBinder kit (Life Technologies, 601-01)


title: Blastocysts_day7_rep1

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicate 1 of 3

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

organism: Bos taurus

source_name: Blastocyst

label_protocol: The labelling aRNA was done using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.  This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: production

value: in-vitro

tag: collected

value: Day 7 post-fertilization


title: Blastocysts_day7_rep3

description: Biological replicate 3 of 3

data_processing: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)


title: Blastocysts_day7+1_rep2

description: Biological replicate 2 of 3

value: Day 7+1 post-fertilization


title: Blastocysts_day7+1_rep3

description: Biological replicate 3 of 3


title: Blastocysts_day7+1_rep1

description: Biological replicate 1 of 3


title: Blastocysts_day7_rep2

description: Biological replicate 2 of 3


title: MEFs_ATRi+APH,18h_Input

tag: cell type

value: 1 uM ATR-45 inhibitor + 0.2 uM aphidicolin for 18hrs


title: Blastocysts_day6+1_rep2

description: Biological replicate 2 of 3

value: Day 6+1 post-fertilization


title: 1505V121511_FLU

tag: donor id

tag: disease state

value: healthy

value: monocyte-derived dendritic cells

tag: condition


title: Blastocysts_day6+1_rep3

description: Biological replicate 3 of 3


title: 1447V100611_FLU

value: influenza stimulated


title: MEFs_DMSO,18h_BrITL rep2

description:
processed data file:
DMSO_18h.narrowPeak

treatment_protocol: DMSO treatment for 18hrs

value: DMSO for 18hrs


title: 1165V041211_FLU


title: 1575V120711_FLU


title: 0697V120611_FLU


title: 1294V121411_FLU


title: GRO-Seq in primary B cells – ZMYND8-F/F Cd19-Cre/+ rep 1

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Reads were aligned to the National Center for Biotechnology Information mouse genome data (July 2007; NCBI37/mm9) by using the alignment software Bowtie with the following options: -S –m 1 –p [num_of_thread] -a --best --starta –n 2 –l [read_length] –trim5 2. These options report reads that align uniquely to the best stratum and allowing up to 2 mismatches after trimming 2 nucleotides from the 5’ end. For visualization, stranded density tracks were generated by using bedtools genomecov program with a normalizing scale factor to calculate rpm seperately for each strand. Rpkm value was calculated for comparative analysis and one sample t.test in R packge was used for the p-values.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Primary B cells

growth_protocol: The GRO-Seq analysis was performed on splenocytes 24 h after stimulation with LPS and IL-4 as it follows.

extract_protocol:
Global run-on and library preparation for sequencing was performed on nuclei from 10-15 million cells. After run-on reaction, the RNA was extracted with TRIzol LS Reagent (Invitrogen). RNA was treated with TURBO DNase (Invitrogen), fragmented using RNA Fragmentation Reagents (Invitrogen) and purified by running through BioSpin P-30 Gel Columns (Bio-Rad). The 3′ end of the fragmented RNA was dephosphorylated with T4 Polynucleotide Kinase (NEB) followed by heat-inactivation. Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz Biotech) and precipitated overnight. Poly(A)-tailing and cDNA synthesis were performed the next day. For reverse transcription, an oligo allowing custom barcoding during final amplification was used (RT-primer). After cDNA synthesis, Exonuclease I (NEB) was used to catalyze the removal of excess oligo. The DNA–RNA hybrid was purified using ChIP DNA Clean & Concentrator Kit (Zymo Research Corporation), RNase H (Thermo Scientific) treated and circularized. Circularized cDNAs were relinearized using APE1 (NEB) and were amplified for 12–14 cycles with primers oNTI201 and oNTI200. The final product was ran on a gel, purified and cleaned up as above.
DNA libraries were sequenced on a Hi-Seq 2500 for 50 cycle, single end run and the standard pipeline (1.8.2) was used for image analysis and base calling.

value: Splenocytes

tag: genotype

value: Cd19-Cre/+ ZMYND8-F/F


title: 1292V060211_IFN

value: IFN-beta stimulated


title: MEFs_DMSO,18h_BrITL rep1


title: Blastocysts_day6+1_rep1

description: Biological replicate 1 of 3


title: 1380V101911_IFN


title: GRO-Seq in primary B cells – ZMYND8-F/F Cd19-Cre/+ rep 2

description: nascent RNA


title: 1156V061511_FLU


title: GRO-Seq in primary B cells – ZMYND8-F/F

description: nascent RNA


title: Inf_plus_CTX_rep2

city: Buffalo

first: Elizabeth

last: Wohlfert

address: 955 Main Street

institute: University at Buffalo

description: T. gondii infected hindlimb skeletal muscle injured with cardiotoxin (28 days post-infection, 4 days post-injury), pooled n=3 mice, experiment 2

data_processing:
Fastq files were generated using 10X Genomics CellRanger v2.02 analysis package.
Each sample was analyzed using cellranger count function, aligning and quantifying each sample against the prebuilt 10x references for the mm10 genome
Resulting alignments were reviewed for quality using the 10x Cell Loupe Browser software
Genome_build: mm10
Supplementary_files_format_and_content: tsv files with barcodes and gene ids, matrix with count data

source_name: Hindlimb muscle

extract_protocol:
Mice were euthanized and injected muscles (or uninjected controls) were carefully harvested. Muscle was minced in digestion media containing Collagenase II, DNase I, and dispase for 55 minutes and subsequently filtered over a 70μm filter. Cells were purified using a 37.5% Percoll gradient to generate single cell suspensions. Cells were stained and sorted on the basis of 7AAD-CD45+CD64+MerTK+ cells on an BD Aria I. Bulk sorted cells were prepared for single-cell capture using a 10X Genomics Chromium platform.
cDNA was prepared on a BioRad T1000 overnight and double stranded DNA libraries were prepared. After a final Ampure XP (Beckman Coulter) bead cleanup, libraries were quantified using Qubit fluorescence and assessed using the Advanced Analytics Fragment Analyzer using standard reagents. Absolute concentration of libraries was achieved using the Kapa Biosystems Universal qPCR protocol according to the manufacturer. Following qPCR, libraries were diluted and denatured to 8 pM for loading onto a HiSeq2500 in RAPID mode with 26 x 98 paired end run parameters.

treatment_protocol:
For infection groups, mice were orally gavaged with 5 ME49 T. gondii cysts and tissues were harvested at 28 days-post infection.
For CTX injection, infected groups were injured at 24-days post infection with 0.03ng/ml Cardiotoxin naja pallida in 30ul/muscle of sterile PBS via intramuscular injection of hindlimb muscles on one-side of the mouse. Contralateral side was left uninjured. Age-matched uninfected mice were injected using the same protocol. Muscles were harvested 4 days-post injury

tag: strain

tag: tissue

value: skeletal muscle

value: macrophage

tag: cell markers

tag: ctx-injury day

value: 4 days post-CTX

tag: infection status

value: T. gondii infected


title: MEFs_DMSO,18h_Input

value: Mouse embryonic fibroblasts; passage-immortalized

tag: genotype/variation

value: ATR+/- MEFs, Bcl-xL-expressing

value: Biotin-16-ddUTP (Enzo Life Sciences, ENZ-42813); Dynabeads KilobaseBinder kit (Life Technologies, 601-01)


title: 1467V121411_FLU

source_name: monocyte-derived dendritic cells, influenza stimulated


title: Inf_plus_CTX_rep1

description: T. gondii infected hindlimb skeletal muscle injured with cardiotoxin (28 days post-infection, 4 days post-injury), pooled n=3 mice, experiment 1


title: 0119V052510_FLU


title: 0670V081111_FLU


title: N_plus_CTX_rep1

description: Naïve hindlimb skeletal muscle injured with cardiotoxin (4 days post-injury), pooled n = 3 mice, experiment 1

value: not infected


title: 1111V031511_FLU


title: 0330V121511_FLU


title: MEFs_ATRi+APH,18h_BrITL rep1

value: 1 uM ATR-45 inhibitor + 0.2 uM aphidicolin for 18hrs


title: N_plus_CTX_rep2

description: Naïve hindlimb skeletal muscle injured with cardiotoxin (4 days post-injury), pooled n = 3 mice, experiment 2


title: 1130V011911_FLU


title: Inf_rep2

description: T. gondii infected hindlimb (28 days post-infection), pooled n=3 mice, experiment 2

value: No CTX


title: 1489V101211_IFN

source_name: monocyte-derived dendritic cells, IFN-beta stimulated

value: healthy


title: 1375V071211_FLU

value: monocyte-derived dendritic cells


title: 0277V102511_baseline

source_name: monocyte-derived dendritic cells, baseline

value: baseline


title: 0866V012611_FLU

value: influenza stimulated


title: 0190V030911_IFN


title: 0119V052510_IFN


title: 1135V072711_FLU


title: 1265V022212_baseline


title: Inf_rep1

description: T. gondii infected hindlimb (28 days post-infection), pooled n=3 mice, experiment 1


title: 0670V081111_IFN


title: 1275V060811_FLU


title: 1319V120611_IFN


title: 0187V080211_FLU


title: 1345V092811_FLU


title: 1148V090811_IFN


title: 1037V090711_FLU


title: 0899V030811_FLU


title: 1319V120611_FLU


title: 1164V120111_IFN


title: 1597V120611_FLU


title: 1292V060211_FLU


title: 1521V011112_IFN


title: LD6rep3

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

data_processing:
Illumina bcl2fastq 2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then aligned with STAR v 2.5 with parameter --clip5pNbases 10 and --quantMode TranscriptomeSAM GeneCounts.
Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups.
Genome_build: GRCh38 v84
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each Sample

source_name: lens epithelial

growth_protocol: The cell-line was grown to confluence for 2-3 days in Eagle's minimum essential medium (EMEM) (ATCC, Burlington, ON, Canada) containing 20% fetal bovine serum (FBS) (Sigma-Aldrich Canada, Oakville, ON, Canada).

extract_protocol:
Twenty hours post-exposure to X-ray radiation or negative control conditions, 2 mL of trypsinzed cell culture were transferred to 15 mL Falcon centrifuge tubes (Invitrogen, Canada) and centrifuged at 200 x g for 5 min to pellet the cells. The supernatants were analyzed for oxidative stress markers (Bahia et al., 2018). A portion of the pelleted cells were resuspended in 350 µL of Buffer RLT containing 1% ?-Mercaptoethanol (Qiagen's RNeasy Mini kit; Qiagen Inc, Mississauga, ON) then frozen at -80oC until processing.  Frozen HLE cells were thawed on ice and mixed well by pipetting. The lysate was transferred directly onto a QIAshredder spin column (Qiagen Inc), placed in a 2 mL collection tube and centrifuged for 2 min at ~12,000 g. A volume of 350 µL of 70% ethanol was added. Total RNA was then extracted using the RNeasy Mini kit according to the manufacturer's instructions (Qiagen Inc), with the addition of Qiagen's On-Column RNase-free DNase (Qiagen Inc) to eliminate any remaining DNA contamination. All total RNA sample concentrations were determined spectrophotometrically using a Nanodrop (Fisher Scientific, Ottawa, ON) (OD ratio of A260:A280).
Total RNA (1 µg) was ribodepleted using Ribo-Zero Gold reagent (Illumina, San Diego, CA). Next-Generation Sequencing (NGS) libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) according to the manufacturer's protocols.

treatment_protocol: Irradiation was performed using a cabinet X-ray machine (X-RAD 320, Precision X-Ray Inc., North Branford, CT, USA) at 120 kVp and 12.5 mA using a 2-mm Al filter. Samples were exposed to 0, 0.01, 0.05, 0.25, 0.5, 2, and 5 Gy of X-rays at 37oC.  The cell-line was either exposed at a low dose rate (LDR) of 1.62 cGy/min by placing samples 72 cm from the point source, or at a high dose rate (HDR) of 38.2 cGy/min by placing samples 50 cm from the point source. The dose-rates were measured using a Radcal 9010 ion chamber (Radcal, Monrovia, CA) calibrated at the National Research Council, Ottawa, ON.  Following irradiation, the samples were placed in a humidified incubator at 37oC for 20 h, this time-point allowed for  sufficient cell recovery from .  The control treatment group was maintained under the same exposure conditions as the exposed group with the exception of being irradiated. Replicate (n=5) radiation exposure experiments were performed.

tag: stress

value: X-ray radiation

tag: dose

value: 5 Gy

tag: dose rate

value: low

value: HLE cells


title: LD6rep5


title: LD6rep4


title: 1587V011712_FLU


title: 1166V041211_FLU


title: 0412V021511_FLU


title: LD6rep2


title: 1361V062311_IFN

value: IFN-beta stimulated


title: 1438V081111_FLU


title: 0195V011212_FLU


title: 1114V042011_FLU


title: LD6rep1


title: LD5rep2

value: 2 Gy


title: LD5rep4


title: LD5rep5


title: 1365V071211_IFN


title: 1592V113011_FLU


title: 0888V111511_FLU


title: LD4rep5


title: LD4rep4


title: LD4rep3


title: 1203V042011_FLU


title: LD4rep2


title: 0277V102511_FLU


title: 1361V062311_FLU


title: LD4rep1


title: LD5rep3


title: LD3rep5


title: LD5rep1


title: LD3rep3


title: LD3rep4


title: 1361V062311_baseline


title: 1553V011212_FLU


title: 0568V112911_FLU


title: 0374V121311_IFN


title: LD3rep1


title: 1248V121311_FLU


title: 0888V111511_IFN


title: LD2rep3


title: 1229V062811_FLU


title: LD2rep5


title: LD3rep2


title: 1592V113011_IFN


title: LD2rep4


title: 0469V072811_IFN


title: 1222V062311_baseline


title: LD2rep2


title: 1294V121411_IFN


title: LD2rep1


title: LD1rep5


title: LD1rep4


title: LD1rep3


title: 1652V011912_IFN


title: LD1rep2


title: LD1rep1


title: 0374V121311_FLU


title: 0731V012412_IFN


title: 1105V111511_FLU


title: 1366V102611_IFN


title: 0641V101811_FLU


title: 0678V081811_IFN


title: 1360V102011_baseline


title: 1531V111611_FLU


title: 0697V120611_IFN


title: LCrep3

value: control


title: 1399V111011_baseline


title: HD6rep5

value: high


title: LCrep5


title: LCrep2


title: 0899V030811_IFN


title: 1553V011212_IFN


title: HD6rep1


title: 1652V011912_FLU


title: LCrep1


title: HD6rep3


title: 1366V102611_FLU


title: LCrep4


title: HD6rep2


title: 0501V120811_FLU


title: HD6rep4


title: 1399V111011_IFN


title: HD5rep4


title: 0490V111011_IFN


title: HD5rep3


title: HD5rep1


title: 1021V071911_IFN


title: 0839V112211_FLU


title: HD4rep3


title: HD5rep2


title: 0797V071411_FLU


title: HD4rep2


title: 1297V120711_IFN


title: 1297V120711_FLU


title: HD5rep5


title: HD4rep4


title: 0797V071411_IFN


title: HD3rep3


title: HD4rep5


title: HD3rep5


title: HD3rep4


title: 1021V071911_FLU


title: 1360V102011_IFN


title: 1290V120611_IFN


title: HD4rep1


title: HD3rep2


title: 1385V072011_IFN


title: 1399V111011_FLU


title: HD3rep1


title: 1164V120111_FLU


title: 0490V111011_FLU


title: 1290V120611_FLU


title: HD2rep2


title: 1531V111611_IFN


title: HD2rep5


title: 1360V102011_FLU


title: HD1rep3


title: HD2rep1


title: 1566V112311_FLU


title: 1671V011712_FLU


title: HD1rep4


title: HD1rep5


title: 1671V011712_IFN


title: 1547V110111_IFN


title: HD2rep3


title: HD1rep1


title: 1231V110211_FLU


title: 1231V110211_IFN


title: HD1rep2


title: HCrep4


title: 1355V060711_FLU


title: 0874V121411_FLU


title: 1355V060711_baseline


title: 0312V011012_FLU


title: 1547V110111_FLU


title: HCrep3


title: HD2rep4


title: HCrep1


title: HCrep5


title: 1355V060711_IFN


title: 0277V102511_IFN


title: HCrep2