title: ZT18_H3K9ac _ChIPseq_rep2

city: Wuhan

first: Yue

last: Lu

state: Hubei

address: No.1 Shizishan street

department: national key lab of crop genetic improvement

institute: Huazhong Agriculture University

description: ZT18_H3K9ac _ChIPseq

data_processing:
RNA-seq and ChIP-seq data were filtered by Trimmomatic (version 0.33) to remove contaminations and low-quality reads.
Tophat (version 2.0.14) and Cufflinks (version 2.2.1) were used to map RNA-seq clean reads to rice genome (MSU 7.0) and calculate differentially expressed genes.
ChIP-seq clean reads were mapped to the rice genome (MSU7.0) by Bowtie2 (version 2.2.5), allowing up to two mismatches.
Samtools (version 0.1.19) was used to remove potential PCR duplicates
MACS software (version 1.4.2) was used to call histone modification peaks by default parameters (bandwidth, 300 bp; model fold, 10, 30; P-value, 1.00e-5).
Genome_build: MSU7.0
Supplementary_files_format_and_content: For RNA-seq, xlsx files contain gene expression level in different samples; for ChIP-seq, *_1.xls and *_2.xls files contain peak information provided by MACS from two biological replicates.

organism: Oryza sativa Japonica Group

source_name: DongJin

growth_protocol: rice seeds were germinated and grown on the hormone-free, half-strength Murashige & Skoog (MS) medium under 16/8 hrs light/dark at 30/25°C.

extract_protocol:
Total RNA samples were isolated using TRIzol reagent (Invitrogen). Chromatin fragments were incubated with antibody-coated beads overnight, after extensive washing, immunoprecipitated chromatin was de-cross-linked and retrieved for qPCR or sequencing.
ChIP-seq libraries were constructed following the instructions of Illumina TruSeq ChIP Sample Prep Set A. RNA-seq libraries were constructed following the instructions of Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: For starvation treatment, seedlings were moved into dark culture at 10 DAG 6:00pm and treated for 48 hours. For submergence treatment, seedlings were submerged in distilled water at 12DAG 12:00am and treated for 6 hours. Seedling leaves from each group were harvested at 12DAG 6:00pm for chromatin and total RNA extraction.

value: leaf

value: 30 day

tag: cultivar

value: DongJin

tag: treatment

tag: time


title: BDH2-5-8F-rep2

status: Public on Sep 08 2018

type: RNA

city: Nanning

first: Bo

last: Li

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

country: China

institute: Guangxi Medical University

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: ectopic expression of BDH2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: All cells were incubated at 37℃ in a humidified atmosphere containing 5% CO2 and cultured in Modified Eagles Medium/High glucose (DMEM) medium supplemented with 10% fetal bovine serum (FBS) in the presence of streptomycin and penicillin.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: The pCMV6-vector or BDH2 plasmid was transferred into NPC cell line 5-8F by liposome transfection. After 3 weeks of selection in 4 μg/ml of G418 resistant cell clones were grown up and the transfection efficiency was validated for BDH2 expression by RT-qPCR.

tag: cell line

tag: tissue

value: Nasopharyngeal carcinoma


title: intestinal organoids_54week vs. 4week

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Mus musculus

source_name: 4w organoid

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

growth_protocol: Organoids were embedded in Matrigel on ice (growth factor-reduced, phenol red-free; BD Biosciences). The Matrigel was polymerized for 10 minutes at 37 °C, and overlaid with 250 μL/well basal culture medium (advanced Dulbecco’s modified Eagle medium/F12 supplemented with penicillin/streptomycin, 10 mmol/L HEPES, Glutamax, 1 × N2, 1 × B27 [all from Thermo Fisher Scientific], and 1 mmol/L N-acetylcysteine [Sigma-Aldrich]) containing the following optimized growth factor combinations:  EGF, noggin, Y-27632 and Rspo1 for intestinal epithelia

extract_protocol: Total RNA extracted using RNeasy® Plus Mini Kit and QIAshredder [QIAGEN] following manufacturer's instructions.

tag: passage

source_name: 54w organoid

tag: gender

value: female


title: prostate_cancer_biopsy_sample_pid_12611

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: GenomeDx

hyb_protocol: Following fragmentation, 3.5-7ug of cDNA were hybridized for 20 hr at 45C on GeneChip Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000Dx V.2

data_processing:
The data were analyzed with the Affymetrix Power Tools packages, probeset summarization and normalization were performed using the single channel array normalization (SCAN) algorithm.
Decipher, a 22-marker prognostic gene-expression score, was determine from the Decipher prostate cancer classifier assay.

source_name: FFPE prostate cancer

label_protocol: Fragmented and biotinylated cDNA were prepared according to the NuGen Encore Biotin Module from total RNA.

growth_protocol: Biopsy core cell tissue were preservated by being Formalin-Fixed Paraffin-Embedded

extract_protocol: Extraction of total RNA from FFPE tissue was performed using the QIAGEN RNeasy kit and QIAcube .

treatment_protocol: Cores were incubated in deparaffinization solution at 56C

tag: disesase state

value: prostate cancer

tag: institution

value: Cleveland Clinic

tag: age

tag: nccn

value: Favorable Intermediate

tag: tumor stage

tag: percent positive cores

tag: psa

tag: gleason score

tag: primary gleason grade

tag: secondary gleason grade

value: prostate cancer biopsy


title: prostate_cancer_biopsy_sample_pid_17259

value: Johns Hopkins


title: PCMV6-5-8F-rep2

source_name: control


title: PCMV6-5-8F-rep3


title: BDH2-5-8F-rep1


title: MDA-MB-231_siRNA_control_rep1

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: Gene expression after transfected with negative control siRNA

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: MDA-MB-231 cell, siRNA control

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: RNA was prepared and quantified using a NanoDrop-1000 spectrophotometer. Quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MDA-MB-231 cells were transfected with negative control siRNA or siRNAs against HSD3B1.

tag: genotype/variation

value: siRNA control


title: ZT18_H3K9ac _ChIPseq_rep1

type: SRA

description: ZT18_H3K9ac _ChIPseq

library_source: genomic

molecule: genomic DNA

tag: cultivar

tag: treatment

tag: chip antibody


title: prostate_cancer_biopsy_sample_pid_17255

tag: tissue


title: MDA-MB-231_siRNA_HSD3B1_rep1

source_name: MDA-MB-231 cell, siRNA HSD3B1

tag: cell line

value: siRNA HSD3B1


title: prostate_cancer_biopsy_sample_pid_17251


title: prostate_cancer_biopsy_sample_pid_17253

value: Low


title: prostate_cancer_biopsy_sample_pid_17249


title: ZT12_H3K9ac_ChIPseq_rep2

tag: time


title: prostate_cancer_biopsy_sample_pid_17247

tag: disesase state


title: ZT12_H3K9ac_ChIPseq_rep1


title: prostate_cancer_biopsy_sample_pid_17244

tag: institution


title: prostate_cancer_biopsy_sample_pid_17240

tag: age


title: prostate_cancer_biopsy_sample_pid_17238

tag: nccn


title: ZT6_H3K9ac_ChIPseq_rep2


title: prostate_cancer_biopsy_sample_pid_17237

tag: tumor stage


title: ZT6_H3K9ac_ChIPseq_rep1


title: ZT0_H3K9ac_ChIPseq_rep2


title: prostate_cancer_biopsy_sample_pid_14045

value: Spectrum Health

tag: percent positive cores


title: prostate_cancer_biopsy_sample_pid_14042

tag: psa


title: ZT18_RNAseq_rep2

description:
ZT18_RNAseq
ZT0_ZT18_diffgenes.xlsx

library_source: transcriptomic

molecule: polyA RNA


title: prostate_cancer_biopsy_sample_pid_14038

tag: gleason score


title: prostate_cancer_biopsy_sample_pid_14041

tag: primary gleason grade


title: ZT18_RNAseq_rep1

description:
ZT18_RNAseq
ZT0_ZT18_diffgenes.xlsx


title: prostate_cancer_biopsy_sample_pid_14022

tag: secondary gleason grade


title: prostate_cancer_biopsy_sample_pid_14023


title: prostate_cancer_biopsy_sample_pid_14049


title: prostate_cancer_biopsy_sample_pid_14048


title: prostate_cancer_biopsy_sample_pid_14047


title: ZT12_RNAseq_rep2

description:
ZT12_RNAseq
ZT12_ZT18_diffgenes.xlsx


title: prostate_cancer_biopsy_sample_pid_17241


title: ZT0_H3K9ac_ChIPseq_rep1


title: prostate_cancer_biopsy_sample_pid_14020


title: prostate_cancer_biopsy_sample_pid_14019


title: prostate_cancer_biopsy_sample_pid_14706


title: ZT6_RNAseq_rep2

description:
ZT6_RNAseq
ZT6_ZT12_diffgenes.xlsx
ZT6_ZT18_diffgenes.xlsx


title: ZT12_RNAseq_rep1

description:
ZT12_RNAseq
ZT12_ZT18_diffgenes.xlsx


title: prostate_cancer_biopsy_sample_pid_14018


title: ZT6_RNAseq_rep1


title: prostate_cancer_biopsy_sample_pid_14016


title: prostate_cancer_biopsy_sample_pid_17357


title: ZT0_RNAseq_rep2

description:
ZT0_RNAseq
ZT0_ZT6_diffgenes.xlsx
ZT0_ZT12_diffgenes.xlsx


title: prostate_cancer_biopsy_sample_pid_14043


title: prostate_cancer_biopsy_sample_pid_17311


title: prostate_cancer_biopsy_sample_pid_14044


title: prostate_cancer_biopsy_sample_pid_17291


title: ZT0_RNAseq_rep1


title: prostate_cancer_biopsy_sample_pid_17370


title: prostate_cancer_biopsy_sample_pid_17369


title: prostate_cancer_biopsy_sample_pid_17365


title: submergence_RNAseq_rep2

description:
submergence_RNAseq
submergence_diff_genes.xlsx

value: seedling leaves (no root or endosperm)

value: 12 day

value: submergence 6hrs


title: input


title: prostate_cancer_biopsy_sample_pid_17363


title: submergence_RNAseq_rep1


title: prostate_cancer_biopsy_sample_pid_17362


title: B16-F10-Flv-1

city: Cincinnati

first: Kakajan

last: Komurov

state: OH

address: 3333 Burnet Ave OH 45229

department: Division of Experimental Hematology & Cancer Biology

country: USA

institute: Cincinnati Children's Hospital

data_processing:
Normalized gene and isoform expression values (RPKM) of the mm10 transcriptome were obtained from fastq files using RSEM (v1.2.15) using the command rsem-calculate-expression and options  --bowtie2 --forward-prob 0
Genome_build: mm10

source_name: Skin

growth_protocol: cultured inDMEM) containing 10% FBS with 0.1% antibiotic and antimycotic (Gibco)

extract_protocol:
Total RNA was extracted from the cells using Tri reagent (Sigma). RNase-free DNase was used for removing all genomic DNA contamination. The RNA was precipitated by Isopropanol (Sigma), washed by ice cold 75% ethanol (Sigma), and air dried prior to resuspension in 20 µl of DEPC-treated water. Purity and concentration of RNA was measured by NanoDrops (Thermo Scientific). The 260/280 ratio was 1.90-2.00 and the 260/230 ratio was 2.00-2.20 for all RNA Samples.
Stranded polyA RNAseq was carried out using illumina dUTP protocol, 50bp single end

tag: disease

value: melanoma

tag: morphology

value: mixture of spindle-shaped and epithelial-like cells

value: B16/F10 cells pre-treated with flavopiridol (25nM) for one week


title: B16-F10-flv-2

tag: treatment


title: prostate_cancer_biopsy_sample_pid_17361


title: starvation_RNAseq_rep2

description:
starvation_RNAseq
starvation_diff_genes.xlsx

tag: cultivar

value: DongJin

value: continuous darkness 48hrs


title: prostate_cancer_biopsy_sample_pid_17360

value: prostate cancer

tag: tissue


title: B16-F10-2


title: prostate_cancer_biopsy_sample_pid_17359


title: B16-F10-1


title: control_RNAseq_rep2


title: control_RNAseq_rep1


title: submergence_Kcr_ChIPseq_rep2

tag: chip antibody

value: Kcr (PTM Biolabs, PTM-501, Lot#2D60GA08P0)


title: prostate_cancer_biopsy_sample_pid_17358


title: prostate_cancer_biopsy_sample_pid_17296

value: Favorable Intermediate


title: MSH2KO21B_B

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
TPM determined using Kallisto v0.43.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Files are given as TPM for each sample

source_name: Uterine cancer

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicate

tag: cell type

value: endometrial cancer cell line


title: MSH2KO21B_A


title: MECPK_B


title: prostate_cancer_biopsy_sample_pid_17352

tag: disesase state

tag: institution

value: Johns Hopkins

value: prostate cancer biopsy


title: prostate_cancer_biopsy_sample_pid_17353

tag: age

tag: nccn


title: submergence_Kcr_ChIPseq_rep1

tag: time


title: submergence_Kbu_ChIPseq_rep2

value: Kbu (PTM Biolabs, PTM-301, Lot#2419G222P5)


title: MECPK_A


title: prostate_cancer_biopsy_sample_pid_17351

tag: tumor stage

tag: percent positive cores

tag: psa


title: 291

data_processing:
Normalized gene and isoform level expression(RPKM) of the hg19 transcriptome were computed using RSEM using the command rsem-calculate-expression run with the options --paired-end --bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: excel; matrices with gene and isoform expression levels of all 12 samples

source_name: OCT embedded  kidney tumor tissue

extract_protocol:
RNA was isolated from 10-10μm thick sections of OCT embedded kidney tumor tissue using a Qiagen RNeasy Micro Kit. It was then quantified and its integrity tested on an Agilent 2200 TapeStation. All of the samples had RNA Integrity Number (RIN) values > 8.0.
PolyA+ unstranded RNA sequencing (2x100bp at 50M depth) was done at Beijing Genome Institute (BGI).

value: Renal Clear Cell Carcinoma


title: prostate_cancer_biopsy_sample_pid_17350

tag: gleason score

tag: primary gleason grade

tag: secondary gleason grade


title: starvation_RNAseq_rep1

tag: treatment


title: submergence_H3K9ac_ChIPseq_rep2

tag: cultivar


title: submergence_Kbu_ChIPseq_rep1

tag: tissue


title: prostate_cancer_biopsy_sample_pid_17328

value: Low


title: prostate_cancer_biopsy_sample_pid_17234


title: 283

tag: disease


title: starvation_Kcr_ChIPseq_rep2

value: seedling leaves (no root or endosperm)

tag: chip antibody


title: submergence_H3K9ac_ChIPseq_rep1

value: 12 day


title: 277


title: Fig 5 - 192 hrs -3

city: Carlsbad

first: Milos

last: Babic

state: CA

address: 5922 Farnsworth Court, Suite 102

institute: BioSpyder Technologies Inc.

description:
RatGeneCountsMaster.csv
F5-192-3

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: TempO-Seq is a targeted sequencing assay, and sequencing results are aligned to a pseudo-transcriptome formed from known probe sequences (see Yeakley et al., PLoS One. 2017, 12(5):e0178302). For each species, the entire pseudo-transcriptome used for alignment is present in the corresponding master gene count files (Probe_ID and Probe_Sequence columns).
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

organism: Rattus norvegicus

source_name: rat liver FFPE

growth_protocol: For experiments involving cell pellets, MCF7 and MDA-MB-231 cells were grown in RPMI supplemented with 10% FBS

extract_protocol:
For cells that were not prepared as FFPE, cells were washed once with PBS, then lysed using TempO-Seq Lysis Buffer
TempO-Seq targeted expression assay. Addition of adapters by amplification.

treatment_protocol: For preparing FFPE cell pellets, live cells were washed twice with 1X PBS, and then fixed with 1% formaldehyde in 1X PBS for 30 minutes at room temperature

value: liver

tag: sample preparation

value: rat tissue fixed for variable amounts of time before embedding

tag: input

value: 10 mm ^2, 5 micron thick


title: prostate_cancer_biopsy_sample_pid_17231

tag: disesase state

tag: institution


title: starvation_Kcr_ChIPseq_rep1

tag: age


title: 226


title: Fig 5 - 192 hrs -2

description:
RatGeneCountsMaster.csv
F5-192-2


title: Fig 5 - 192 hrs -1

description:
RatGeneCountsMaster.csv
F5-192-1


title: prostate_cancer_biopsy_sample_pid_17230

tag: nccn


title: 225


title: starvation_Kbu_ChIPseq_rep2

tag: time


title: starvation_Kbu_ChIPseq_rep1


title: prostate_cancer_biopsy_sample_pid_17229

tag: tumor stage

tag: percent positive cores


title: Fig 5 - 96 hrs -3

description:
RatGeneCountsMaster.csv
F5-96-3


title: 215


title: Fig 5 - 96 hrs -2

description:
RatGeneCountsMaster.csv
F5-96-2


title: 210


title: starvation_H3K9ac_ChIPseq_rep2


title: 287


title: starvation_H3K9ac_ChIPseq_rep1


title: prostate_cancer_biopsy_sample_pid_14010

value: Spectrum Health

tag: psa

tag: gleason score


title: 179


title: control_Kcr_ChIPseq_rep2

value: DongJin


title: Fig 5 - 96 hrs -1

description:
RatGeneCountsMaster.csv
F5-96-1


title: 110


title: prostate_cancer_biopsy_sample_pid_14009

tag: primary gleason grade

tag: secondary gleason grade


title: Fig 5 - 24 hrs -3

description:
RatGeneCountsMaster.csv
F5-24-3


title: 94


title: prostate_cancer_biopsy_sample_pid_17223


title: control_Kcr_ChIPseq_rep1

tag: cultivar

tag: treatment


title: control_Kbu_ChIPseq_rep2

tag: tissue


title: Fig 5 - 24 hrs -2

description:
RatGeneCountsMaster.csv
F5-24-2


title: Fig 5 - 24 hrs -1

description:
RatGeneCountsMaster.csv
F5-24-1


title: Fig 5 - 384 hrs -3

description:
RatGeneCountsMaster.csv
F5-384-3


title: control_Kbu_ChIPseq_rep1

tag: chip antibody


title: control_H3K9ac_ChIPseq_rep2


title: T47D_RNApol2-ser5

data_processing:
Chipseq reads were aligned to the human reference genome (hg19) using BWA-MEM (v0.7.12)
Samtools (v 0.1.1 9) is then used to exclude reads that were either unaligned, were not primary alignments, failed vendor QC, are PCR duplicates or have quality < 10 (option: -F 1084)
genebody, TSS and TES and 2000bp flanking regions is computed using ngs.plot (v 0.2.61). Briefly, reads from the BAM file are overlaid with regions of interest and coverage at single base resolution and the vector is normalized by length. Coverage vector is then fit to a spline and then 101 points are sampled at equal intervals and normalized by library size (per million reads).
Genome_build: hg19
Supplementary_files_format_and_content: excel file; matrices of RNA pol2 or RNApol2 Ser5 coverage across gernes generated using ngs.plot

source_name: Mammary gland:Breast: derived from metastatic site. pleural effusion

growth_protocol: cultured in RPMI 1640 (Gibco) containing 10% FBS with 0.1% antibiotic and antimycotic (Gibco)

extract_protocol:
Chromatin extrated cell cell lysate was sonicated and shered to 300bp to 1kb fragments using a Sonifier Cell Disruptor (Branson Ultrasonics #101-063-588). To 0.5ml sheared chromatin (after clarification of debrie), we added 150µl ChIP mix (440mM NaCl, 0.44% sodium deoxycholate, 4.4% Triton X-100) and antibody-coupled beads for immunoprecipitation overnight at 4C.
Precipitated DNA fragments were processed to ChIP-seq library using the ThruPLEX DNA-seq 12S kit (Takara #R400428) according to manufacturer’s instructions. 75bp single end 10M depth

tag: disease

value: Ductal Carcinoma

tag: morphology

value: epithelial

value: p-Ser5-RNAPII (Active Motif :61085)


title: 49


title: prostate_cancer_biopsy_sample_pid_17269

tag: disesase state

value: prostate cancer


title: prostate_cancer_biopsy_sample_pid_17226

tag: institution

value: Favorable Intermediate


title: control_H3K9ac_ChIPseq_rep1

tag: age


title: prostate_cancer_biopsy_sample_pid_14012

tag: nccn


title: prostate_cancer_biopsy_sample_pid_17266

value: Johns Hopkins


title: Fig 5 - 384 hrs -1

description:
RatGeneCountsMaster.csv
F5-384-1

tag: sample preparation

tag: input


title: T47D_RNApol2

value: RNAPII (Active Motif :39097)


title: prostate_cancer_biopsy_sample_pid_17267

tag: tumor stage

tag: percent positive cores

value: prostate cancer biopsy


title: prostate_cancer_biopsy_sample_pid_17373

tag: psa

tag: gleason score


title: Fig 5 - 384 hrs -2

description:
RatGeneCountsMaster.csv
F5-384-2


title: T47D_input


title: prostate_cancer_biopsy_sample_pid_14008

tag: primary gleason grade

tag: secondary gleason grade


title: Fig 2 liver replicate 3

description:
RatGeneCountsMaster.csv
F2liv3

value: rat FFPE tissue


title: UACC-812_RNApol2-ser5

source_name: Mammary gland:Breast

growth_protocol: cells were grown in Leibovitz’s L-15 (Gibco) medium with 2mM L-glutamine containing 20% fetal bovine serum (FBS) and 0.1% antibiotic and antimycotic (Gibco)


title: prostate_cancer_biopsy_sample_pid_14007

value: Low


title: UACC-812_RNApol2


title: Fig 2 liver replicate 2

description:
RatGeneCountsMaster.csv
F2liv2


title: 600YA (538 year-old tree) [miRNA-seq]

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

description: miRNA.readcount.txt

data_processing:
the NGS QC Toolkit v2.3.3 was used to filiter the reads with adapter sequences, reads with an N (unknown bases in a read＞5%) and low-quality reads (reads with a base quality ≤ 20).
Sequence alignments were performed using TopHat v2.0.12 with v2.2.3 for mapping to the reference genome (http://gigadb.org/dataset/90209, Guan et al.  2016).
The Cufflinks v2.1.1 Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from TopHat alignment results.
FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene
sRNA libraries were sequenced using the Illumina Genome Analyzer. Raw data of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze the expression and distribution on the reference.miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts.The mapped sRNA tags were also mapped to Rfam, RepeatMasker, to annotate the tags and remove those originating from proteincoding genes, repeat sequences, ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). The remaining unannotated tags were used to predict novel miRNAs by exploring secondary structures, Dicer cleavage sites, and minimum free energies using the miREvo and miRDeep2 software packages.
RNA fragments with a poly (A) tail were isolated from the total RNA of mixed samples. A series of steps, including ligation of 5' RNA adaptors, digestion, ligation of double-stranded DNA adaptor, purification, and amplification were conducted and sequencing was done on an Illumina HiSeq 2000. The raw sequencing reads were processed by Illumina's Pipeline v1.5 to obtain clean reads, which were then used to identify potentially cleaved targets.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/90209, Guan et al. 2016).
Supplementary_files_format_and_content: Text file includes gene.description (Gene_id chromosome strand start end length VC20A_fpkm VC20B_fpkm VC20C_fpkm VC200A_fpkm VC200B_fpkm VC200C_fpkm VC600A_fpkm VC600B_fpkm VC600C_fpkm) and miRNA.readcount (miRNA_name VC20A.readcount VC20B.readcount VC200A.readcount VC200B.readcount VC600A.readcount VC600B.readcount) and miRNA.targets （gene ID miRNA）

organism: Ginkgo biloba

source_name: cambium

growth_protocol: Cabium were obtained from healthy G. biloba trees of different ages growing under natural conditions in in two sites in Anlu of Hubei Province (31°40'N, 113°35'E; Anlu, China) and Pizhou of Jiangsu Province (34°53'N ,118°12'E; Pizhou, China)

extract_protocol:
Samples were collected in late May 2014 and 2015. Total RNAs of cambium were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cambium

value: 538 year-old


title: Y (mix) [degradome seq]

description: miRNA.targets.txt

source_name: cambium_mix of different ages

value: mix of different ages


title: 600YB (553 year-old tree) [miRNA-seq]

description: miRNA.readcount.txt

value: 553 year-old


title: UACC-812_input


title: Fig 2 liver replicate 1

description:
RatGeneCountsMaster.csv
F2liv1

value: liver

value: 10 mm ^2, 5 micron thick


title: prostate_cancer_biopsy_sample_pid_14006

value: Spectrum Health


title: Fig 2 kidney replicate 3

description:
RatGeneCountsMaster.csv
F2kid3

source_name: rat kidney FFPE

value: kidney


title: Mixed RNA from four cultures

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Read trimming and adapter clipping: cutadapt 1.13
Read mapping: READemption 0.4.3 and segemehl 0.2.0
Coverage calculation: READemption 0.4.3
Genome_build: NC_013967.1 (CHR), NC_013968.1 (pHV1), NC_013965.1 (pHV2), NC_013964.1 (pHV3), NC_013966.1 (pHV4)
Supplementary_files_format_and_content: wiggle

organism: Haloferax volcanii

source_name: mixed RNA from four cultures

growth_protocol: 1) complex medium, 2.1 M salt,  to mid-exponential phase; 2) complex medium, low salt (0.9 M) to mid-exponential phase; 3) complex medium, 2.1 M salt,  to stationary phase; 4) synthetic medium, 2.1 M salt, to mid-exponential phase

extract_protocol:
5 x 10e8 cells were harvested and total RNA was isolated using the NucleoSpin miRNA Kit of Macherey-Nagel with an on-column Dnase digestion. Afte the first isolation, the sample was not totally DNA free, and the isolation with the NucleoSpin miRNA Kit of Macherey-Nagel with an on-column DNase digestion was reteated. The total absence of DNA was verified by PCR.
library construction and RNA-Seq was performed by StarSeq (Mainz, Germany)

tag: culture

value: mid-exponential growth phase


title: Fig 2 kidney replicate 2

description:
RatGeneCountsMaster.csv
F2kid2

tag: tissue


title: 200YA (193 year-old tree) [miRNA-seq]

description: miRNA.readcount.txt

value: 193 year-old


title: prostate_cancer_biopsy_sample_pid_14005

value: prostate cancer


title: replicate 2 of SK11

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

data_processing:
Demultiplexed fastq-files were analyzed using Transcriptor with default settings (Todt TJ, Derks M, Siezen RJ, van Hijum SAFT, submitted for publication). Read data were mapped against the reference genome sequence of SK11 using Bowtie2 (Langmead and Salzberg, 2012). Transcripts were determined by applying a segmentation algorithm to the alignment results (Todt et al., 2012). Segments with read coverage above a minimum read count threshold of five reads were identified and adjacent segments were joined. For each sample, transcripts were annotated by matching them with gene annotations provided by the selected reference genome.
Genome_build: NC_008527
Supplementary_files_format_and_content: Read counts were used to to identify differentially expressed genes across the different derivatives and the original SK11 strain using edgeR (Robinson et al., 2010). P-values were corrected for multiple testing using the Benjamini and Hochberg procedure provided by the edgeR package.

organism: Lactococcus lactis

source_name: total RNA

growth_protocol: SK11 and its robust derivatives A3, A5, B1, B2 and B7 were cultured in duplicate in 50 ml GM17 at 30°C.

extract_protocol:
RNA isolation was performed using routine procedures, as described previously (Bron et al., 2012) with minor adjustments. Aliquots of 5 ml of culture were centrifuged at 4000 × g for 3 minutes at 2°C and cells were resuspended in 0.5 ml cold TE buffer. To this suspension, 500 µl 1:1 phenol/chloroform, 30 µl 10% SDS, 30 µl 3M sodium acetate pH 5.2 and 500 mg 0.1 mm zirconia beads (Biospec Products, Inc., Bartlesville, USA) was added in a 2 ml screw-cap tube and samples were frozen in liquid nitrogen and stored at -80°C.
cDNA synthesis and sequencing with an Ion Proton system using an Ion PI-chip (Life Technologies) was performed by PrimBio Research Institute (Exton, USA).

treatment_protocol: In exponential phase of growth (OD 0.8-1.1) samples were taken for RNA isolation.

tag: strain

value: original strain SK11


title: prostate_cancer_biopsy_sample_pid_14004


title: replicate 2 of B7

value: robust derivative B7


title: prostate_cancer_biopsy_sample_pid_14692


title: 20YB (20 year-old tree) [miRNA-seq]

description: miRNA.readcount.txt

value: 20 year-old


title: 20YA (15 year-old tree) [miRNA-seq]

description: miRNA.readcount.txt

value: 15 year-old


title: Fig 2 brain replicate 3

description:
RatGeneCountsMaster.csv
F2bra3

source_name: rat brain FFPE

value: brain

value: rat FFPE tissue


title: prostate_cancer_biopsy_sample_pid_17342

value: Johns Hopkins

value: Low

value: prostate cancer biopsy


title: replicate 2 of B2

value: robust derivative B2


title: 600YC (667 year-old tree)

description: gene.description.txt

value: cambium

value: 667 year-old


title: prostate_cancer_biopsy_sample_pid_17341

value: Favorable Intermediate


title: replicate 2 of B1

value: robust derivative B1


title: Fig 2 brain replicate 2

description:
RatGeneCountsMaster.csv
F2bra2

value: 10 mm ^2, 5 micron thick


title: 200YB (211 year-old tree) [miRNA-seq]

description: miRNA.readcount.txt

value: 211 year-old


title: Fig 2 brain replicate 1

description:
RatGeneCountsMaster.csv
F2bra1


title: 600YA (538 year-old tree)

description: gene.description.txt

value: 538 year-old


title: prostate_cancer_biopsy_sample_pid_17340

value: prostate cancer


title: replicate 2 of A3

value: robust derivative A3


title: prostate_cancer_biopsy_sample_pid_17335


title: 200YB (211 year-old tree)

description: gene.description.txt


title: replicate 1 of B7

value: robust derivative B7


title: Fig 2 kidney replicate 1

description:
RatGeneCountsMaster.csv
F2kid1

value: kidney


title: replicate 1 of SK11

value: original strain SK11


title: 200YA (193 year-old tree)

description: gene.description.txt

value: 193 year-old


title: prostate_cancer_biopsy_sample_pid_17334

value: Johns Hopkins


title: prostate_cancer_biopsy_sample_pid_17333


title: replicate 1 of B2


title: 600YB (553 year-old tree)

description: gene.description.txt

value: 553 year-old


title: replicate 1 of B1


title: prostate_cancer_biopsy_sample_pid_14109

value: Cedars-Sinai

value: prostate cancer biopsy


title: replicate 2 of A5

value: robust derivative A5


title: 20YA (15 year-old tree)

description: gene.description.txt

value: cambium

value: 15 year-old


title: iPSC #5_1

city: Hennigsdorf

first: Martina

last: Schad

address: Neuendorfstrasse 16b

institute: OakLabs GmbH

hyb_protocol: 600 ng of each cRNA is hybridised (using Agilent Gene Expression Hybridisation Kit) on 8x60K microarrays at 65°C for 17 h in Agilent’s hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37°C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides.

data_processing: Agilent’s Feature Extraction software version 11 was used to read and process the TIFF files. Furthermore default parameters (protocol GE1_1105_Oct12 and Grid: 084124_D_F_20160608) were used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Sus scrofa

source_name: iPSC #5_1

label_protocol: For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate fluorescent cRNA (complementary RNA). For 1st strand synthesis, oligo-dT primer was used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed.

tag: group

value: b

tag: cell type

value: Porcine induced pluripotent stem cells (piPSCs)


title: prostate_cancer_biopsy_sample_pid_14547

source_name: FFPE prostate cancer

tag: disesase state

value: Low


title: prostate_cancer_biopsy_sample_pid_17337

tag: institution

value: Favorable Intermediate


title: iPSC #2_1

source_name: iPSC #2_1


title: 200YC (236 year-old tree)

description: gene.description.txt

tag: age

value: 236 year-old


title: iPSC #5_2

source_name: iPSC #5_2


title: replicate 1 of A3

value: robust derivative A3


title: prostate_cancer_biopsy_sample_pid_14108

value: prostate cancer

tag: nccn


title: iPSC #2_2

source_name: iPSC #2_2


title: 20YC (22 year-old tree)

description: gene.description.txt

value: 22 year-old


title: iPSC #7_1

source_name: iPSC #7_1


title: RELACS Input (4 replicates), 3 base UMI

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: 5 biological replicates of HepG2 cells with the indicated UMI strategy.

data_processing:
ChIP-seq reads were aligned to the mm10 and hs37d5 genome assembly using Bowtie2-2.2.8 with the following configuration: -X 1000 --local --fr --rg CN:mpi-ie_deep_sequencing_unit --rg PL:ILLUMINA
BigWig files were created with bamCoverage (deepTools 2.4.1) using `-e --normalizeTo1x -bs 50`
Genome_build: mouse: mm10, human: hs37d5
Supplementary_files_format_and_content: BigWig files contain coverage information generated from genomic alignments.

growth_protocol: HepG2 (ATCC, HB-8065TM) were culture in EMEM (Lonza, 06-174) supplemented with 10% FBS, 2 mM L-Glutamine, 1.8 mM CaCl2, 1mM sodium pyruvate and penicillin-streptomycin mixture (100 units/ml, Lonza), at 37 ˚C at 5% CO2. S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27°C. Mouse experiments were performed on 9 weeks-old wild-type (WT) FVB/NJ littermate male mice fed chow diet and maintained on a 12h light cycle (lights on at 7 am).

extract_protocol:
RELACS: nuclei have been extracted, permeabilized and barcoded following RELACS protocol. Nuclei labeled with distinct barcodes have been pooled and lysed to complete chromatin preparation. Traditional ChIP-seq: after nuclei extraction chromatin has been fragmented by sonication. Immunoprecipitation has been performed using the antibody of interest.
RELACS libraries: as described in the paper, using A-tailing strategy and ligation of adapters containing nuclear barcodes. After ChIP and DNA purification library preparation has been completed by PCR amplification using NEB workflow (NEBNext Ultra II DNA library preparation kit (E7645L, NEB)). Traditional ChIP-seq libraries: NEBNext Ultra II DNA library preparation kit (E7645L, NEB)

value: liver hepatocellular carcinoma

tag: provider/strain

value: ATCC, HB-8065

tag: chip antibody

value: CTCF (Abcam, ab70303)


title: Henle-407 infected with Shigella

city: Kalamazoo

first: Ben

middle: James

last: Koestler

state: MI

address: 1903 West Michigan Avenue, 3119 Wood Hall

department: Biological Sciences

institute: Western Michigan University

data_processing:
CLC Workbench version 9.5.1 used for mapping and analysis
Reads were pooled by sample
Mapping was performed to inter-genic regions and both strands, using a mismatch cost of 2, insertion cost of 3, deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8
We restricted the maximum number of hits per read to 1
RPKM was used for differential expression
Genome_build: S. flexneri 2457T genome (GenBank accession no. AE014073.1) and the pCP301 plasmid (GenBank accession no. AF386526.1)
Supplementary_files_format_and_content: .xlsx files contain Shigella reads that mapped to mock treatment, which were dropped from analysis, and differential gene expression between Shigella and Shigella with formate

organism:
Homo sapiens
Shigella flexneri 2a str. 2457T

source_name: Sf

growth_protocol: Shigella flexneri 2457T was grown in LB with DOC, then added to Henle-407 cells at an MOI of 20. After 60 minute incubation, Henle-407 cells were washed with PBS, and MEM+gentamycin was added to kill extracellular bacteria. Cells were incubated wih or without 20 mM formate for 2 hours prior to RNA extraction

extract_protocol:
RNABee was applied directly to infected cells for lysis, total RNA was extracted and DNAse treated.
RNA libraries were prepared for sequencing using standard Illumina protocols by the University of Texas at Austin GSAF, and RiboZero Gold was used to remove rRNA. Sequencing was performed twice, and reads were combined.

treatment_protocol: 20 mM formate was added to tissue culture medium after Shigella invasion for 2 hours

tag: host cell line

value: Henle-407 cells

tag: host cell type

value: epithelial cell

tag: treatment

value: Shigella infection


title: iPSC #3_1.2

description: Tested twice as technical control.


title: replicate 1 of A5

value: robust derivative A5


title: 20YB (20 year-old tree)

description: gene.description.txt

value: cambium

value: 20 year-old


title: RELACS Input (4 replicates), 2 base UMI


title: RELACS Input (4 replicates), no UMI


title: Infected T cells as positive control [SupT1]

city: seattle

first: Serge

last: Barcy

state: WA

address: 1900 Ninth Avenue

department: SCRI

institute: Seattle Children's

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to alignment to the HHV-6B Z29 reference genome (Genbank accession number NC000898) using TopHat v2.0.12.  Counts were generated from TopHat or Bowtie alignments for each viral gene using the Python package HTSeq v0.6.1 ( http://www-huber.embl.de/users/anders/ HTSeq/doc/overview.html).
Genome_build: HHV-6B Z29 reference genome/NC_000898 (GCF_000846365.1)
Supplementary_files_format_and_content: viral read count values for each sample determined by Htseq; normalized viral read count values for each sample expressed in VPMM

organism:
Homo sapiens
Human betaherpesvirus 6B

source_name: cell pellet

extract_protocol:
Whole blood samples were collected and frozen in Paxgene tubes. Total RNA was isolated from PAXgene tubes (MagMAX Blood RNA kit, Ambion) according to the manufacturer’s instructions. The total RNA obtained was then further processed using the GLOBIN clear kit (Ambion) to strongly reduce the level of alpha and beta globin transcripts. Finally, RNA samples were further purified on “Clean and Concentrate” columns (Zymo research) according to the manufacturer’s instructions. Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences).
For cell pellet (SupT1 T cells), total mRNA was extracted in trizol and isolated column  (Directzol, Zymoresearch) according to manufacturer's directions
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit (Illumina, Inc.) and a Sciclone  NGSx Workstation (PerkinElmer).  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technology’s Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen).
RNA-Seq on polyA selected mRNA

tag: cell line

value: CD4 T cell line

tag: viral strain

value: HHV-6B Z29

tag: molecule subtype

value: globulin mRNA depleted, total mRNA


title: case 7 [UPN59974]

source_name: Whole blood in paxgene tube

tag: source subject status

value: hematopoietic transplant patient

tag: subject age

value: whole blood

value: HHV-6B wild type


title: pFF #5_1

value: a

value: porcine fetal fibroblasts (pFF)


title: RELACS Input (4 replicates), 4 base UMI

value: liver hepatocellular carcinoma


title: RD+Dox_rep 3

first: Yun-Ting

last: Hsieh

address: Rm. 521-1, 5F., No.1, Changde St., Zhongzheng Dist.

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Mouse Genome 430_2 GeneChip (Affymetrix). GeneChips were then washed, stained and read by Affymetrix GeneChip Scanner 3000 7G

scan_protocol: GeneChips were read by Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GeneSpring GX 14.8 (Sillicon Genetics) and GC-RMA was used as normalization method.

source_name: regular diet, lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Mice were kept feeding HFD diet until 8 weeks that body weight arise to 150%, and then start feeding doxycycline-contained diet for 7 weeks. To ensure the effect of doxycycline, each diet was replaced twice a week. Drinking water which contains 2mg/ml doxycycline(Sigma, #Cat D9891) with 1% sucrose was replaced once a week. and 1% L-glutamine.

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

treatment_protocol: Customized diets used in this study included 625 ppm doxycycline contained RD (TestDiet, Cat. #5TWN), HFD (Test Diet, Cat#58Y1, 34.9% fat, 23.1% protein, and 25.8% carbohydrates. Fat supplies 60% of energy), and 625 ppm doxycycline contained HFD (Test Diet, Cat#5W5W, 34.9% fat, 23.1% protein, and 25.8% carbohydrates. Fat supplies 60% of energy)

tag: diet treatment

value: regular diet+Dox

tag: tissue

value: lung

tag: mouse model

value: transgenic mouse with spontaneous lung cancer formation driven by mutant EGFR (by Doxycycline induction)


title: RELACS CTCF (4 replicates), 4 base UMI

tag: cell type

value: ATCC, HB-8065

value: CTCF (Abcam, ab70303)


title: case 3 [56244]


title: RELACS CTCF (4 replicates), 3 base UMI


title: RD+Dox_rep 2


title: RD+Dox_rep 1


title: case 2 [U3185134]


title: Henle-407 infected with Shigella, 20 mM formate

source_name: Sf Formate

value: Henle-407 cells

value: epithelial cell

value: Shigella infection with 20 mM formate


title: pFF #2_1

tag: group


title: case 1 [U3366944]


title: RELACS CTCF (4 replicates), 2 base UMI


title: HFD+Dox_rep 3

source_name: high-fat diet, lung

value: high-fat diet+Dox


title: pFF #7_1


title: HFD+Dox_rep 2


title: pFF #2_2


title: pFF #5_2


title: HFD+Dox_rep 1


title: pFF #3_1.1

description: Tested twice as technical control.


title: pFF #3_1.2

description: Tested twice as technical control.


title: 33315 RA-Diff HRT rep2

status: Public on Sep 07 2018

city: Stanford

first: Caitlin

last: Rodriguez

address: 450 Serra Mall

department: Department of Genetics

institute: Stanford University

data_processing:
Illumina Casava v1.8 was used for basecalls
Reads were trimmed of adapter sequences, and then by quality, then aligned to an rRNA sequence database to deplete the libraries of secondary sequence contaminants using Bowtie v1.2
Remaining reads were aligned to the Ensembl v78 genome and transcriptome using TopHat v2.0.10 with the following parameters: --bowtie1 --no-novel-juncs --library-type fr-unstranded --solexa-quals
Fragments per kilobase of exon per megabase of library size (FPKM) was calculated for each Ensembl v78 transcript using Cufflinks v2.0.0 with default parameters
Genome_build: GRCh38 (Ensembl v78)
Supplementary_files_format_and_content: Tab-delimited text files with transcript level measurements of FPKM for each sample

source_name: SH-SY5Y cells

growth_protocol: SH-SY5Y cells were grown in DMEM:F12 media (Invitrogen) supplemented with 10% FBS, .01mg mL-1Gentamicin and .25ug mL-1 Amphoreticin B. Cells were plated on 150mm plates that were either coated with .1mg/mL poly-D lysine (Millipore) for differentiation or uncoated. Cells were allowed to propagate to 80% confluency for 1-2 days prior to lysing for ribosome profiling or induction of differentiation.

extract_protocol:
Cells were washed with ice cold PBS with CHX at 100ug mL-1. Plates were immediately flash frozen in liquid nitrogen, moved to dry ice, and lysed (in the presence of CHX) to prevent ribosome loading and runoff. Additional lysates were processed in parallel for poly(A) mRNA purification  and  mRNA-sequencing  library  preparation.  Polysomes  were  isolated  from  the ribosome footprinting lysates on a 1M sucrose cushionwith high speed centrifugation using a 70.1Ti rotor (Beckman) at 55,000 r.p.m. for 4 hrs at 4°C. rRNA was eliminated prior to linker ligation using Ribo-Zero Gold rRNA Removal Kit (Illumina).
Ribosome profiling libraries were prepared as in Ingolia et al., 2010 and Ingolia et al., 2012.
Ribosome Profiling libraries were barcoded and multiplexed with2-4 libraries per lane, and sequenced on a HiSeq 2000 (Illumina) using 50 cycles of single end reads. mRNA libraries were multiplexed on a single lane. All sequencing was conducted at the University of Michigan DNA Sequencing Core.

treatment_protocol: SH-SY5Y cells were differentiated for 6 days in 10μM retinoic acid (all-trans, Sigma), with media changed every 24 hours.

value: RA-differentiated SH-SY5Y cells

tag: days treatment


title: 33314 RA-Diff HRT rep1


title: 33313 RA-Diff CHX rep2


title: 33312 RA-Diff CHX rep1


title: 33311 Non-Diff HRT rep2

value: Non-differentiated SH-SY5Y cells


title: iPSC #3_1.1

description: Tested twice as technical control.

value: b

value: Porcine induced pluripotent stem cells (piPSCs)


title: RELACS CTCF (4 replicates), no UMI


title: 33310 Non-Diff HRT rep1


title: 32874 RA-Diff mRNA


title: miR-CKO3

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
miR CKO3
Run00182_L6_BC1V41ACXX_TS16_CCGTCC

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that the molecule counting by unique molecule identifiers was omitted.
Sequence reads were aligned to the mouse genome using Bowtie1 allowing for up to 3 mismatches.
The data was further analyzed using Qlucore omics explorer.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Comma separated table of read counts normalized by kilobase transcript length and to a million per sample (RPKM)

growth_protocol: miR-183-96-182-flox/+ mice (Peng et al. (2017) Science 356, 1168-1171) were crossed with Wnt1-Cre-129/SvEv mice (Danielian et al. (1998) Current biology 8, 1323-1326) to obtain Wnt1-Cre; miR-183-96-182-flox/+ mice. These were in turn mated to obtain Wnt1-Cre; miR-183-96-182-flox/flox mice and Wnt1-Cre control mice.

extract_protocol:
Mouse lumber DRG tissue was dissected from E12.5 embryos.
Total RNA was isolated using Trizol Reagent (Invitrogen) and processed with TruSeq Stranded mRNA Sample Prep Kit (Illumina/USA) .

tag: strain background

value: mixed C57/Bl6 x 129/SvEv

tag: genotype/variation

value: miR conditional knockout

tag: developmental stage

value: lumbar dorsal root ganglia (DRG)


title: miR-CKO1

description:
miR CKO1
Run00182_L6_BC1V41ACXX_TS5_ACAGTG


title: miR-CKO2

description:
miR CKO2
Run00182_L6_BC1V41ACXX_TS6_GCCAAT


title: acd, biological rep2

city: Ankara

first: Ceren

last: Sucularli

address: Sihhiye

country: Turkey

institute: Hacettepe University

description: Gene expression data from acd mutant mouse embryo

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: RMA normalized and analyzed using BRB-Array tools version 4.4.0

source_name: acd mutant mouse embryo

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit according to manufacturer's instructions.  On-column DNA digestion was performed.

treatment_protocol: Whole embryos were isolated at E10.5 and placed in cold PBS prior to RNA extraction.

value: Whole embryo

tag: genotype

value: Acdacd/acd

tag: age


title: double, biological rep2

description: Gene expression data from acd and p53 mutant mouse embryo

source_name: acd and p53 mutant mouse embryo

value: Acdacd/acd, p53-/-


title: double, biological rep3


title: 32873 Non-Diff mRNA


title: Control3-Wnt-Cre

description:
Control 3
Run00182_L6_BC1V41ACXX_TS19_GTGAAA

value: control


title: acd, biological rep1


title: Control1-Wnt-Cre

description:
Control 1
Run00182_L6_BC1V41ACXX_TS4_TGACCA


title: double, biological rep1


title: p53, biological rep1

description: Gene expression data from p53 mutant mouse embryo

source_name: p53 mutant mouse embryo


title: 34080 Non-Diff CHX rep1


title: p53, biological rep2


title: 34081 Non-Diff CHX rep2


title: Control2-WT

description:
Control 2
Run00182_L6_BC1V41ACXX_TS14_AGTTCC


title: wt, biological rep2

description: Gene expression data from wt mouse embryo

source_name: wt mouse embryo

value: wt


title: human spleen NK cells from donor 3

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

description: Sample 3h

data_processing:
Cell Ranger software (v1.3.1)
Reads were first simultaneously aligned with the mm10 and GRch38 genomes, with CellRanger software (v1.3.1), for their assignment as murine or human sequences. Species assignments were improved by  individual alignment with the mm10 and GRch38 sequences, resulting in two clusters, one for each species. Finally, we took the intersection between the corresponding clusters of the two alignments and we removed cells identified as doublets (within a range of 1.5 to 3.8%).
Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed, and cells expressing more than 2500 genes.
Cells with more than 0.05% of mitochondrial-associated genes among their expressed genes were also removed.
Genome_build: GRch38 and mm10
Supplementary_files_format_and_content: csv files (gene/cell matrix)

source_name: Normal spleen human NK cells

extract_protocol:
10x Genomics Chromium Single-Cell 3’ v2 protocol
Single-cell RNAseq

value: spleen

value: NK cells


title: human spleen NK cells from donor 2

description: Sample 2h


title: human blood NK cells from donor 1

description: Sample 4h

source_name: Normal blood human NK cells

value: blood


title: human blood NK cells from donor 3

description: Sample 6h


title: wt, biological rep3


title: human spleen NK cells from donor 1

description: Sample 1h


title: p53, biological rep3


title: Vehicle-8 [HI.3147.001.BioO_6.K]

city: Cambridge

first: Hualin

last: Xi

state: MA

address: 1 portland st

institute: Pfizer

data_processing:
Sequenced by Illumina HiSeq 2500 at the McGill Innovation Centre.
RNA-seq reads were alligned to mm10 using Star v2.4.0
Read counts were summarized to gene-level by the feature count module of Subread package (version 1.4.6).
All samples passed quality control based on post-alignment metrics using RSeQC (version 2.6.1).
Genes that had raw counts = 0 and/or cpm<1 across all 227 samples were excluded from the final results.
Normalization was performed using limma/EdgeR package (version 3.10.5). Briefly, two levels of normalization were performed to adjust for: 1) library size; 2) mean-variance heteroscedasticity. The trimmed mean of M-values (TMM) method was used to calculate a weighted trimmed mean across all samples.
Mean-variance relationship was estimated by the voom module. Principle component analysis (PCA) was calculated to check for systemic bias across samples. The top 4 principle components were removed, and the resultant residuals were used for subsequent analysis. Robust z-scores were calculated for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: count and rpkm

source_name: Cerebral Cortex

growth_protocol: Briefly, dissociated cerebral cortices from embryonic day 16.5 filial 1 progeny of a FVB/N x C3B6F1 were cultured in Neurobasal medium containing B27 supplement (2%), GlutaMAX (2%), 100 I.U./mL penicillin, and 100 μg/mL streptomycin. Cultures were grown in 6-well plates at a density of one million cells per well.

extract_protocol:
RNA was isolated from cortical cultures using the NucleoSpin RNA kit (Macherey-Nagel). Purity and concentration of total RNA was tested by Nanodrop analysis while the RNA integrity number (RIN) of each total RNA sample was determined using the Agilent RNA 6000 nano kit and the Agilent 2100 Bioanalyzer.
Complementary DNA (cDNA) libraries were created using the KAPA Biosystems Stranded mRNA-Seq kit from high-quality RNA samples (RIN≥8). Chemical fragmentation was performed per kit specifications to generate an average fragment size 200-300bps (confirmed by Agilent DNA 1000 kit). NEXTflex™ RNA-Seq barcode adapters were ligated onto fragmented RNA samples and adapter ligated libraries were amplified by polymerase chain reaction (PCR) for 10 cycles.

treatment_protocol: Briefly, cerebrocortical cultures (DIV21) in 6-well plates were treated for 8 hours with vehicle (0.2% DMSO) or one of the 218 BBB-penetrant drugs used for the screen. Drug concentrations are provided as part of the Neuron Screen Database.

value: Primary Cerebrocortical Cultures

tag: days in vitro

tag: strain

value: F1 embryo FVBN(F)xC3B6F1(M)

tag: agent

value: Vehicle


title: Vehicle-6 [HI.3083.002.BioO_1.I]


title: Vehicle-9 [HI.3147.007.BioO_6.M]


title: Vehicle-5 [HI.3078.007.BioO_1.H]


title: Vehicle-7 [HI.3083.006.BioO_4.J]


title: wt, biological rep1


title: Vehicle-4 [HI.3145.001.BioO_1.F]


title: RA patient 2 RA3A

city: Guangzhou

first: Yaoyao

last: Zou

state: Guangdong

address: No. 58 Zhongshan Road 2

institute: The First Affiliated Hospital, Sun Yat-sen University

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0  at 65°C for 17 hours.

scan_protocol: After hibridaztion and washing, the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: FLS from rheumatoid arthritis patient 2

label_protocol: One ug of total RNA was labelled with Cy3 and specific activity of the labeled cRNAs  were measured by NanoDrop ND-1000

growth_protocol: Synovial tissues were cut into small pieces and digested with 1 mg/ml collagenase for 3 h at 37°C to isolate synoviocytes. All cells were cultured in DMEM/F12 with 10% FBS at 5% CO2 and 37℃.

extract_protocol: Total RNA was isolated with Trizol（Sigma）according to manufacturer’s instructions and quantified by the NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: synovial tissue


title: RA patient 3 RA3fo5

source_name: FLS from rheumatoid arthritis patient 3


title: ChIP-seq-Elf5-V5-L1-rep1

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
The ChIP-seq analysis worklow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed by the application of bowtie aligner (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Homer software (Heinz et al., Mol. Cell, 2010) was applied  for the generation of bedGraph files.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of ChIP-seq

source_name: Mammary gland

growth_protocol: Mouse mammary  tissues were harvested at day one of lactation (L1).

extract_protocol: Libraries for sequencing were prepared using standard Illumina protocols.

tag: Sex

value: female

tag: Stage

value: Lactation day 1

value: Mammary gland

tag: chip-antibody

value: V5 (ThermoFisher Scientific, R960-25)


title: Vehicle-3 [HI.3146.008.BioO_1.E]


title: Vehicle-1 [HI.3122.001.BioO_1.A]


title: Vehicle-2 [HI.3146.002.BioO_1.C]


title: human blood NK cells from donor 2

description: Sample 5h


title: PF-05019702-00 [HI.3147.001.BioO_4.262]


title: CE-326597 [HI.3147.001.BioO_3.261]


title: acd, biological rep3


title: ChIP-seq-Elf5-V5-L1-rep2


title: CE-210666 [HI.3147.001.BioO_2.260]


title: RA patient 1 RA2zhongshan1

source_name: FLS from rheumatoid arthritis patient 1


title: Trauma patient 3 N3A

source_name: FLS from trauma patient 3


title: CP-945598 [HI.3140.004.BioO_6.258]


title: CP-610927-01 [HI.3140.004.BioO_1.259]


title: PF-05416266-00 [HI.3139.003.BioO_4.254]


title: Ciprofibrate [HI.3140.003.BioO_2.251]

value: Ciprofibrate


title: CP-448187 [HI.3140.003.BioO_3.252]


title: PF-04995274-00 [HI.3139.003.BioO_5.257]


title: PF-04191834-00 [HI.3139.003.BioO_3.253]


title: Levetiracetam [HI.3140.002.BioO_5.204]

value: Levetiracetam


title: SD-7300 [HI.3140.004.BioO_4.255]


title: WAY-202041 [HI.3140.004.BioO_5.256]


title: Bezafibrate [HI.3140.003.BioO_6.249]

value: Bezafibrate


title: Ethosuximide [HI.3140.001.BioO_1.200]

value: Ethosuximide


title: Acetazolamide [HI.3140.001.BioO_5.198]

value: Acetazolamide


title: Methsuximide [HI.3140.002.BioO_2.201]

value: Methsuximide


title: Mefenamic Acid [HI.3140.001.BioO_6.199]

value: Mefenamic Acid


title: Diflunisal [HI.3140.002.BioO_4.203]

value: Diflunisal


title: Oxtriphylline [HI.3140.002.BioO_3.202]

value: Oxtriphylline


title: Trauma patient 1 N33

source_name: FLS from trauma patient 1


title: Trauma patient 2 N34

source_name: FLS from trauma patient 2


title: Deferasirox [HI.3083.008.BioO_3.196]

value: Primary Cerebrocortical Cultures

value: Deferasirox


title: Apigenin [HI.3083.008.BioO_2.195]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Apigenin


title: Luteolin [HI.3139.002.BioO_2.194]

value: Luteolin


title: Quercetin [HI.3083.008.BioO_1.193]

value: Quercetin


title: Daidzein [HI.3140.001.BioO_4.197]

value: Daidzein


title: Benzbromarone [HI.3139.002.BioO_1.192]

value: Benzbromarone


title: Kaempferol [HI.3083.008.BioO_6.191]

value: Kaempferol


title: Genistein [HI.3083.007.BioO_5.190]

value: Genistein


title: Vigabatrin [HI.3083.007.BioO_4.189]

value: Vigabatrin


title: Clofibrate [HI.3140.003.BioO_1.250]

value: Clofibrate


title: Valganciclovir·HCl [HI.3083.007.BioO_3.188]

value: Valganciclovir·HCl


title: Methocarbamol [HI.3078.006.BioO_4.180]

value: Methocarbamol


title: Sulfamethoxazole [HI.3083.006.BioO_6.185]

value: Sulfamethoxazole


title: Probenecid [HI.3078.006.BioO_6.182]

value: Probenecid


title: Topiramate [HI.3083.007.BioO_2.187]

value: Topiramate


title: Rufinamide [HI.3083.006.BioO_5.184]

value: Primary Cerebrocortical Cultures

value: Rufinamide


title: Theophylline [HI.3083.006.BioO_1.186]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Theophylline


title: Lacosamide [HI.3083.005.BioO_5.177]

value: Lacosamide


title: Etodolac [HI.3083.005.BioO_1.175]

value: Etodolac


title: Primidone [HI.3078.006.BioO_5.181]

value: Primidone


title: Chlorpropamide [HI.3083.004.BioO_6.174]

value: Chlorpropamide


title: Levocarnitine [HI.3146.001.BioO_5.178]

value: Levocarnitine


title: Methazolamide [HI.3146.001.BioO_6.179]

value: Methazolamide


title: Ziprasidone  [HI.3083.004.BioO_5.173]

value: Ziprasidone


title: Trimipramine Maleate [HI.3083.004.BioO_3.169]

value: Trimipramine Maleate


title: Hydroxyurea [HI.3083.005.BioO_4.176]

value: Hydroxyurea


title: Voriconazole [HI.3139.002.BioO_6.172]

value: Voriconazole


title: Trihexyphenidyl·HCl [HI.3083.003.BioO_2.168]

value: Trihexyphenidyl·HCl


title: Ursodiol [HI.3083.004.BioO_4.170]

value: Ursodiol


title: Varenicline Tartrate [HI.3139.002.BioO_5.171]

value: Varenicline Tartrate


title: Triazolam [HI.3083.003.BioO_1.167]

value: Primary Cerebrocortical Cultures

value: Triazolam


title: Triamterene [HI.3083.005.BioO_3.166]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Triamterene


title: Trazodone·HCl [HI.3083.003.BioO_6.165]

value: Trazodone·HCl


title: Trandolapril [HI.3083.003.BioO_5.164]

value: Trandolapril


title: Tolterodine Tartrate [HI.3083.002.BioO_4.163]

value: Tolterodine Tartrate


title: Tetrabenazine [HI.3083.002.BioO_3.162]

value: Tetrabenazine


title: 24h_10 kJ/m2_+SS_5

city: Ottawa

first: Sami

middle: Shaker

last: Qutob

state: Ontario

address: 775 Brookfiled Rd.

department: Consumer and Clinical Radiation Protection Bureau

institute: Health Canada

hyb_protocol: Samples were hybridized on Illumina human-12 v3 RNA BeadChips.

scan_protocol: BeadChips were imaged and quantified with the Illumina iScan scanner.

data_processing: Data pre-processing was carried out within GenomeStudio v2010.2.2 where the intensities were averaged per probe/gene. Normalization of dataset was conducted in GeneSpring (version GX 11.5).

source_name: HEKn_24h_10 kJ/m2_+SS

label_protocol: cRNA was labeled using biotin following protocols  in Genome Expression Profiling Assay Guide (11317302 Rev. A).

growth_protocol: Cells were maintained in a humidified incubator (37oC, 5% CO2/95% air) in 75 cm2 tissue culture flasks (Costar, Cambridge, MA, USA). The cells were grown to confluence for 2-3 days in Royal Park Medical Institute-1640 (RPMI-1640) (Invitrogen Canada, Burlington, ON Canada) medium, containing 10% fetal bovine serum (FBS) (Sigma-Aldrich Canada, Oakville, ON, Canada).  A total of 1.0x106 cells were seeded into 5 mL of culture media containing 100 units/mL of penicillin and 100 µg/mL of streptomycin (Invitrogen Canada Inc.).

extract_protocol: The pelleted cells were resuspended in 350 µL of Buffer RLT containing 1% β-Mercaptoethanol (Qiagen’s RNeasy Mini kit; Qiagen Inc, Mississauga, ON) then frozen at -80oC until processed.   Frozen THP-1 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 and RNA quality were determined using both an Agilent 2100 Bioanalyzer and RNA Nanochips (Agilent Technologies Canada Inc., Mississauga, ON) and spectrophotometrically using an Ultrospec 2100 (Fisher Scientific) (OD ratio of A260:A280). All extracted RNA samples were determined to be of good quality (RNA Integrity Number=10) with minimal degradation and stored at -80oC until further analysis.  The pelleted cells were resuspended in 350 µL of Buffer RLT containing 1% β-Mercaptoethanol (Qiagen’s RNeasy Mini kit; Qiagen Inc, Mississauga, ON) then frozen at -80oC until processed.   Frozen THP-1 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 and RNA quality were determined using both an Agilent 2100 Bioanalyzer and RNA Nanochips (Agilent Technologies Canada Inc., Mississauga, ON) and spectrophotometrically using an Ultrospec 2100 (Fisher Scientific) (OD ratio of A260:A280). All extracted RNA samples were determined to be of good quality (RNA Integrity Number=10) with minimal degradation and stored at -80oC until further analysis.

treatment_protocol: The cells were exposed to α-particle radiation at doses ranging from 0.0 (control) to 1.5 Gy, using 241Americium (241Am) electroplated discs (Eckert and Ziegler Isotope Products Ltd, Valencia, CA, USA) having an activity level of 66.0 kBq ± 3% (dose rate of 0.98 ± 0.01 Gy/h, LET of 127.4±0.4 keV/m).

value: Human Epidermal Keratinocytes, neonatal (HEKn)

tag: treatment  (m = minus sunscreen; p = plus sunscreen)

value: p

tag: dose (gy)

tag: post-exposure time point (h)


title: 24h_0 kJ/m2_-SS_6

source_name: HEKn_24h_0 kJ/m2_-SS

tag: cell type

value: m


title: 24h_10 kJ/m2_+SS_6


title: 24h_0 kJ/m2_-SS_4


title: 24h_10 kJ/m2_+SS_4


title: 24h_0 kJ/m2_-SS_5


title: Pyrazinamide [HI.3139.003.BioO_6.183]

value: Pyrazinamide


title: Tadalafil [HI.3083.001.BioO_6.160]

value: Tadalafil


title: Sertraline·HCl [HI.3083.001.BioO_3.157]

value: Sertraline·HCl


title: Sitagliptin Phosphate [HI.3083.001.BioO_4.158]

value: Sitagliptin Phosphate


title: Tacrolimus [HI.3083.001.BioO_5.159]

value: Tacrolimus


title: Rizatriptan Benzoate [HI.3078.008.BioO_6.154]

value: Rizatriptan Benzoate


title: Ropinirole·HCl [HI.3078.008.BioO_1.155]

value: Primary Cerebrocortical Cultures

value: Ropinirole·HCl


title: Selegiline·HCl [HI.3078.008.BioO_2.156]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Selegiline·HCl


title: Rifabutin [HI.3078.008.BioO_5.153]

value: Rifabutin


title: Repaglinide [HI.3078.007.BioO_4.152]

value: Repaglinide


title: Temazepam [HI.3083.002.BioO_2.161]

value: Temazepam


title: Rasagiline Mesylate [HI.3078.007.BioO_3.151]

value: Rasagiline Mesylate


title: 24h_10 kJ/m2_+SS_3

value: Human Epidermal Keratinocytes, neonatal (HEKn)


title: 24h_0 kJ/m2_-SS_2


title: 6h_150 kJ/m2_-SS_6

source_name: HEKn_6h_150 kJ/m2_-SS


title: 24h_0 kJ/m2_+SS_6

source_name: HEKn_24h_0 kJ/m2_+SS

value: p


title: 24h_10 kJ/m2_+SS_2


title: 24h_0 kJ/m2_-SS_1

value: m


title: Raltegravir [HI.3078.007.BioO_2.150]

value: Raltegravir


title: 24h_0 kJ/m2_+SS_5


title: Rabeprazole·Na [HI.3078.006.BioO_3.149]

value: Rabeprazole·Na


title: Quinidine·HCl·H2O [HI.3078.005.BioO_2.148]


title: 6h_150 kJ/m2_-SS_5


title: Prasugrel [HI.3078.004.BioO_4.144]

value: Prasugrel


title: Protriptyline·HCl [HI.3078.005.BioO_6.146]

value: Protriptyline·HCl


title: Pregabalin [HI.3078.005.BioO_5.145]

value: Pregabalin


title: Posaconazole [HI.3078.004.BioO_3.143]

value: Posaconazole


title: 24h_0 kJ/m2_+SS_4


title: 6h_150 kJ/m2_-SS_4


title: 24h_10 kJ/m2_+SS_1


title: 24h_0 kJ/m2_+SS_2


title: 6h_150 kJ/m2_-SS_3


title: 6h_150 kJ/m2_-SS_2


title: 24h_0 kJ/m2_+SS_3


title: 24h_0 kJ/m2_+SS_1


title: 6h_0 kJ/m2_-SS_6

source_name: HEKn_6h_0 kJ/m2_-SS


title: Phenelzine Sulfate [HI.3078.004.BioO_2.142]

value: Primary Cerebrocortical Cultures

value: Phenelzine Sulfate


title: 6h_0 kJ/m2_+SS_5

source_name: HEKn_6h_0 kJ/m2_+SS


title: Pyridostigmine Bromide [HI.3078.005.BioO_1.147]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Pyridostigmine Bromide


title: 6h_0 kJ/m2_+SS_6


title: Perindopril Erbumine [HI.3078.004.BioO_1.141]

value: Perindopril Erbumine


title: Palonosetron·HCl [HI.3078.003.BioO_6.140]

value: Palonosetron·HCl


title: Oxybutynin Chloride [HI.3078.003.BioO_5.139]

value: Oxybutynin Chloride


title: Oxazepam [HI.3078.003.BioO_4.138]

value: Oxazepam


title: Oxaprozin [HI.3078.003.BioO_3.137]

value: Oxaprozin


title: Orlistat [HI.3078.002.BioO_2.136]

value: Orlistat


title: 6h_0 kJ/m2_-SS_5

value: Human Epidermal Keratinocytes, neonatal (HEKn)

value: m


title: 6h_150 kJ/m2_-SS_1


title: 6h_0 kJ/m2_+SS_4

value: p


title: 6h_0 kJ/m2_-SS_4


title: Nortriptyline·HCl [HI.3078.002.BioO_1.135]

value: Nortriptyline·HCl


title: 24h_0 kJ/m2_-SS_3


title: Nilotinib [HI.3078.002.BioO_5.133]

value: Nilotinib


title: Nitrofurantoin [HI.3078.002.BioO_6.134]

value: Nitrofurantoin


title: Nevirapine [HI.3078.001.BioO_4.132]

value: Nevirapine


title: 6h_0 kJ/m2_+SS_3


title: 6h_0 kJ/m2_-SS_2


title: 6h_0 kJ/m2_-SS_3


title: 6h_0 kJ/m2_+SS_2


title: Mirtazapine [HI.3145.008.BioO_5.127]

value: Primary Cerebrocortical Cultures

value: Mirtazapine


title: Naratriptan·HCl [HI.3078.001.BioO_2.130]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Naratriptan·HCl


title: Modafinil [HI.3145.008.BioO_6.128]

value: Modafinil


title: Nadolol [HI.3078.001.BioO_1.129]

value: Nadolol


title: 6h_0 kJ/m2_+SS_1


title: 6h_0 kJ/m2_-SS_1


title: Maraviroc [HI.3139.001.BioO_3.125]

value: Maraviroc


title: Lorazepam [HI.3139.001.BioO_1.123]

value: Lorazepam


title: Nebivolol·HCl [HI.3078.001.BioO_3.131]

value: Nebivolol·HCl


title: Loxapine Succinate [HI.3139.001.BioO_2.124]

value: Loxapine Succinate


title: Mexiletine·HCl [HI.3139.001.BioO_4.126]

value: Mexiletine·HCl


title: Liothyronine·Na [HI.3145.008.BioO_4.122]

value: Liothyronine·Na


title: 6h_150 kJ/m2_+SS_6

source_name: HEKn_6h_150 kJ/m2_+SS

value: Human Epidermal Keratinocytes, neonatal (HEKn)

value: p


title: 6h_150 kJ/m2_+SS_4


title: Levothyroxine·Na [HI.3145.008.BioO_3.121]

value: Levothyroxine·Na


title: 6h_150 kJ/m2_+SS_5


title: 6h_20 kJ/m2_-SS_5

source_name: HEKn_6h_20 kJ/m2_-SS

value: m


title: 6h_150 kJ/m2_+SS_3


title: 6h_20 kJ/m2_-SS_1


title: 6h_150 kJ/m2_+SS_1


title: 6h_20 kJ/m2_-SS_2


title: 6h_20 kJ/m2_-SS_4


title: 6h_20 kJ/m2_-SS_6


title: 6h_20 kJ/m2_-SS_3


title: Leucovorin Calcium Pentahydrate [HI.3145.007.BioO_2.120]

value: Leucovorin Calcium Pentahydrate


title: 6h_150 kJ/m2_+SS_2


title: Lansoprazole [HI.3145.007.BioO_1.119]

value: Primary Cerebrocortical Cultures

value: Lansoprazole


title: Lamivudine [HI.3145.007.BioO_6.118]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Lamivudine


title: Isosorbide Dinitrate [HI.3145.006.BioO_3.115]

value: Isosorbide Dinitrate


title: Isotretinoin [HI.3145.006.BioO_4.116]

value: Isotretinoin


title: Formoterol [HI.3145.005.BioO_6.112]

value: Formoterol


title: Hydroxyzine Dihydrochloride [HI.3145.006.BioO_1.113]

value: Hydroxyzine Dihydrochloride


title: Irbesartan [HI.3145.006.BioO_2.114]

value: Irbesartan


title: 6h_10 kJ/m2_-SS_6

source_name: HEKn_6h_10 kJ/m2_-SS


title: 6h_10 kJ/m2_+SS_4

source_name: HEKn_6h_10 kJ/m2_+SS


title: 6h_10 kJ/m2_+SS_6


title: 6h_10 kJ/m2_-SS_5


title: 6h_10 kJ/m2_-SS_3


title: 6h_10 kJ/m2_-SS_2


title: Fexofenadine·HCl [HI.3145.005.BioO_3.109]

source_name: Cerebral Cortex

value: Fexofenadine·HCl


title: 6h_10 kJ/m2_+SS_5


title: 6h_10 kJ/m2_+SS_2


title: Febuxostat [HI.3139.005.BioO_6.108]

value: Febuxostat


title: Everolimus [HI.3139.005.BioO_5.107]

value: Everolimus


title: Labetalol·HCl [HI.3145.007.BioO_5.117]

value: Labetalol·HCl


title: Fingolimod [HI.3145.005.BioO_4.110]

value: Fingolimod


title: Doxepin·HCl [HI.3145.004.BioO_2.105]

value: Doxepin·HCl


title: Dicyclomine·HCl [HI.3145.004.BioO_6.103]

value: Dicyclomine·HCl


title: Fluvoxamine Maleate [HI.3145.005.BioO_5.111]

value: Fluvoxamine Maleate


title: Cortisone Acetate [HI.3139.005.BioO_3.101]

value: Primary Cerebrocortical Cultures

value: Cortisone Acetate


title: 6h_10 kJ/m2_+SS_1

value: Human Epidermal Keratinocytes, neonatal (HEKn)

value: p


title: Darifenacin·HBr [HI.3145.004.BioO_5.102]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Darifenacin·HBr


title: 6h_10 kJ/m2_-SS_1

value: m


title: Bupropion  [HI.3145.003.BioO_3.99]

value: Bupropion


title: Brompheniramine Maleate [HI.3145.003.BioO_2.98]

value: Brompheniramine Maleate


title: Bisoprolol Fumarate [HI.3145.003.BioO_1.97]

value: Bisoprolol Fumarate


title: 24h_10 kJ/m2_-SS_6

source_name: HEKn_24h_10 kJ/m2_-SS


title: 24h_150 kJ/m2_+SS_5


title: 6h_10 kJ/m2_+SS_3


title: Biperiden·HCl [HI.3145.002.BioO_6.96]

value: Biperiden·HCl


title: 24h_10 kJ/m2_-SS_5


title: 24h_150 kJ/m2_+SS_6


title: 24h_150 kJ/m2_+SS_4


title: Benztropine Mesylate [HI.3145.002.BioO_5.95]

value: Benztropine Mesylate


title: 24h_10 kJ/m2_-SS_3


title: Clonazepam [HI.3145.003.BioO_4.100]

value: Clonazepam


title: 24h_150 kJ/m2_+SS_2


title: 24h_150 kJ/m2_+SS_3


title: 24h_10 kJ/m2_-SS_4


title: 24h_150 kJ/m2_+SS_1


title: 24h_150 kJ/m2_-SS_6


title: 24h_10 kJ/m2_-SS_1


title: 6h_10 kJ/m2_-SS_4


title: Ambrisentan [HI.3145.002.BioO_4.94]

value: Ambrisentan


title: Almotriptan [HI.3145.002.BioO_3.93]

value: Almotriptan


title: Acebutolol·HCl [HI.3139.004.BioO_2.91]

value: Acebutolol·HCl


title: Acetylcysteine [HI.3145.001.BioO_2.92]

value: Acetylcysteine


title: Cyproheptadine·HCl Sesquihydrate [HI.3145.001.BioO_6.89]

value: Primary Cerebrocortical Cultures

value: Cyproheptadine·HCl Sesquihydrate


title: BPR6

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

data_processing:
Sequenced reads were performed quality assessment using FastQC.
Adapters were trimmed using Bbmap toolkit.
Sequenced reads were then aligend to galgal5 reference mature miRNA sequences using ArrayStar.
Raw read counts then obtained from ArrayStar were then analyzed using JMP Genomics.
Genome_build: Gallus gallus 5
Supplementary_files_format_and_content: normalized read counts and expression data.

organism: Gallus gallus

source_name: Barred Plymouth Rock chicken_breast muscle

extract_protocol:
Breast muscles were removed, flash flozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
Illumina TruSeq small Library Prep Kit was used for construction of sequencing libraries.

tag: breed

value: Barred Plymouth Rock chicken

value: 8 weeks

tag: tissue

value: Breast muscle

tag: molecule subtype

value: Small RNA


title: BPR7


title: BPR4


title: Aprepitant [HI.3145.001.BioO_5.88]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Aprepitant


title: BPR3


title: Misoprostol [HI.3146.008.BioO_4.87]

value: Misoprostol


title: Ondansetron [HI.3139.004.BioO_6.86]

value: Ondansetron


title: BPR2


title: 24h_150 kJ/m2_-SS_4

value: Human Epidermal Keratinocytes, neonatal (HEKn)

value: m


title: 24h_20 kJ/m2_-SS_4

source_name: HEKn_24h_20 kJ/m2_-SS


title: 24h_150 kJ/m2_-SS_5


title: 24h_20 kJ/m2_-SS_6


title: Fluoxetine·HCl [HI.3139.004.BioO_5.85]

value: Fluoxetine·HCl


title: Acarbose [HI.3139.004.BioO_1.90]

value: Acarbose


title: BPR1


title: 24h_20 kJ/m2_-SS_2


title: Naloxone·HCl [HI.3147.008.BioO_4.84]

value: Naloxone·HCl


title: PeM16

source_name: pedigree male broiler_breast muscle

value: pedigree male broiler


title: 24h_150 kJ/m2_-SS_3


title: 24h_20 kJ/m2_-SS_3


title: 24h_150 kJ/m2_-SS_2


title: Ketotifen Fumarate [HI.3146.008.BioO_2.83]

value: Ketotifen Fumarate


title: TGF_2h_3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: processed data file: HSCs_vehicle_PDGF_TGF_raw.tsv

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
Genome_build: GRCh37
Supplementary_files_format_and_content: tsv format containing raw counts for samples

source_name: hepatic stellate cells

growth_protocol: Primary human HSCs (ScienCell Research Laboratories, #5300) were grown in DMEM (Life Technologies, #11965092) containing 10% fetal bovine serum FBS (Sigma-Aldrich #F4135) and 1% penicillin/streptomycin (Life Technologies, #15140122).All cell lines were maintained under standard tissue culture conditions (37 °C, 5% CO2 incubator).

extract_protocol:
The RNeasy kit (Qiagen) was used to extract total RNA from cells according to the manufacturer’s instructions
TruSeq

treatment_protocol: Cells were treated with TGF-β (R&D Systems #240-B) (10 ng/mL) or vehicle for 48h, and recombinant PDGF-BB (Sigma-Aldrich #P3201) (20 ng/mL), TGF-β (R&D Systems #240-B) (10 ng/mL) or vehicle for 2h.

value: hepatic stellate cells

tag: passages

tag: treatment

value: TGF-beta 10 ng/ml 2h


title: PDGF_2h_3

value: recombinant PDGF-BB 20 ng/mL for 2h


title: PeM10

value: 8 weeks


title: Terazosin·HCl [HI.3147.008.BioO_3.82]

value: Primary Cerebrocortical Cultures

value: Terazosin·HCl


title: 24h_20 kJ/m2_-SS_5


title: 24h_20 kJ/m2_-SS_1


title: PDGF_2h_2


title: PeM8

value: Breast muscle

value: Small RNA


title: Tamsulosin·HCl [HI.3254.001.BioO_6.80]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Tamsulosin·HCl


title: Telmisartan [HI.3147.008.BioO_2.81]

value: Telmisartan


title: 24h_150 kJ/m2_-SS_1

value: Human Epidermal Keratinocytes, neonatal (HEKn)

value: m


title: TGF_2h_2


title: TFEB-GFP, biological replicate2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Gene expression data from hela stable clone overexpressing TFEB-GFP

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 .

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: The hela stable clones overexpressing TFEB-GFP and hela WT were grown in standard conditions.

extract_protocol: Total RNAs from either WT and TFEB-GFP hela cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

tag: cell line

value: HeLa


title: TFEB-GFP, biological replicate3

source_name: hela stable clone overexpressing TFEB-GFP

treatment_protocol: The hela stable clones overexpressing TFEB-GFP and hela WT were grown in standard conditions.


title: PeM5

tag: age


title: Vehicle_2h_3

value: vehicle 2h


title: TGF_2h_1


title: PeM4

value: pedigree male broiler


title: TFEB-GFP, biological replicate1


title: Propranolol·HCl [HI.3147.008.BioO_1.78]

tag: days in vitro

value: Propranolol·HCl


title: Hela WT, biological replicate 3

description: Gene expression data from hela WT cells

source_name: hela WT cells


title: Hela WT, biological replicate 2

description: Gene expression data from hela WT cells


title: PDGF_2h_1

value: hepatic stellate cells


title: PeM1


title: Vehicle_2h_2


title: testis_rep2

city: Vienna

first: Andrea

last: Pauli

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
genes_fpkm_testis_ovary_oocyte.txt
Testis_2

data_processing:
Libraries were sequenced on a HiSeq 2000 (paired end 76 bp reads).
Reads were aligned to GRCz10, using the Ensembl transcriptome release 88. A custom file was generated by adding bouncer based on its position coordinates (tracking-ID: bouncer; exon = Chr18:50858259-50858859 (- strand); CDS = chr18:50858285-50858663  (- strand)).
The following command was used to map each sample: ‘tophat - o <output directory> -p 16 --library-type fr-firststrand –no-novel-juncs –g 1 –G <Custom_gene_table> <Bowtie2_genome_index> <fastq_reads>”.
Quantification of transcript levels (FPKM) was determined using cuffnorm with the following command “cuffnorm -p 22 --library-type=fr-firststrand -L < labels > -o <output_directory> <Custom_gene_table> <aligned_reads.bam file>.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delimited text file containing FPKMs

organism: Danio rerio

source_name: whole wildtype zebrafish testis (dissected from male)

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle) until point of sample collection.

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol, and genomic DNA was removed by TURBO-DNase treatment followed by phenol/chloroform extraction.
Libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2
Strand-specific libraries for 76-bp paired-end sequencing were prepared from cDNA by the Broad Institute Sequencing Platform.

value: testis

tag: genotype

value: wild type

tag: strain

value: TLAB


title: Spironolactone [HI.3254.001.BioO_5.79]

value: Primary Cerebrocortical Cultures

tag: agent

value: Spironolactone


title: Paroxetine·HCl [HI.3147.007.BioO_4.76]

value: Paroxetine·HCl


title: Ramipril [HI.3147.007.BioO_5.77]

value: Ramipril


title: testis_rep1

description:
genes_fpkm_testis_ovary_oocyte.txt
Testis_1


title: Pantoprazole [HI.3147.007.BioO_3.75]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Pantoprazole


title: Oxcarbazepine [HI.3147.006.BioO_2.74]

value: Oxcarbazepine


title: TGFβ_48h_2

description: processed data file: HSCs_Control_and_TGFb_raw.tsv

value: TGF-beta 10 ng/ml 48h


title: TGFβ_48h_3


title: oocyte_rep2

description:
genes_fpkm_testis_ovary_oocyte.txt
Oocyte_2

source_name: mature oocytes (obtained by squeezing)

value: oocyte


title: TGFβ_48h_1


title: oocyte_rep1

description:
genes_fpkm_testis_ovary_oocyte.txt
Oocyte_1


title: Nabumetone [HI.3147.006.BioO_6.72]

value: Nabumetone


title: ovary_rep1

description:
genes_fpkm_testis_ovary_oocyte.txt
Ovary_1

source_name: whole wildtype zebrafish ovary (dissected from female)

value: ovary


title: Vehicle_2h_1

value: vehicle 2h


title: Hela WT, biological replicate 1

description: Gene expression data from hela WT cells

value: HeLa


title: Control_48h_1

value: hepatic stellate cells

value: control 48h


title: Mitoxantrone·HCl [HI.3254.002.BioO_6.71]

value: Mitoxantrone·HCl


title: Metoprolol Tartrate [HI.3254.002.BioO_5.70]

value: Metoprolol Tartrate


title: Duloxetine·HCl [HI.3139.005.BioO_4.106]

value: Primary Cerebrocortical Cultures

value: Duloxetine·HCl


title: Medroxyprogesterone Acetate [HI.3254.002.BioO_4.69]

value: Medroxyprogesterone Acetate


title: Mebendazole [HI.3254.002.BioO_3.68]

value: Mebendazole


title: Losartan Potassium [HI.3254.001.BioO_2.67]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Losartan Potassium


title: Control_48h_3


title: ovary_rep2

description:
genes_fpkm_testis_ovary_oocyte.txt
Ovary_2

value: wild type

value: TLAB


title: Loratadine [HI.3254.001.BioO_1.66]

value: Loratadine


title: Omeprazole [HI.3147.006.BioO_1.73]

value: Omeprazole


title: GSF1670_Tennessen_C3

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

data_processing:
Samples were demultiplexed with bcl2fastq v2.20.0.422
Adapters and low quality sequences were removed with cutadapt v1.12 using the options "-m 30 -q 30"
Read pairs for which either read had fewer than 30 high quality bases were excluded from further analysis
Reads were mapped against dmel r6.19 using hisat2 version 2.1.0 with the parameters "--no-unal --no-mixed"
Mapped reads were assigned to genes using the FlyBase dmel annotation 6.19 with htseq-count 0.9.0
Genome_build: dmel r6.19
Supplementary_files_format_and_content: tab-delimited text files including gence counts for each sample

organism: Drosophila melanogaster

source_name: control_mid-L3 larvae

growth_protocol: Drosophila larvae were raised on molasses egg caps with yeast paste at 25ºC for 96 hours.

extract_protocol:
Larvae were collected as described in Li, H., Tennessen, J. M. Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry (GC-MS)-based Metabolomics. J. Vis. Exp. (136), e57847, doi:10.3791/57847 (2018). RNA was extracted using a Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: developmental stage

value: mid-L3 larvae


title: GSF1670_Tennessen_S3

source_name: Sea mutant_mid-L3 larvae


title: GSF1670_Tennessen_S2


title: GSF1670_Tennessen_S1


title: Lisinopril·2H2O [HI.3146.005.BioO_4.65]


title: Control_48h_2


title: snf[148] 2 input

city: Boston

first: Mitzi

middle: I

last: Kuroda

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing:
Sequences were aligned to the Drosophila genome (UCSC dm6) using bowtie2 (2.2.6)
Duplicate reads were removed with samtools (1.3)
peaks were called with MACS (2.1.20150731) using the broadpeak option with all others set to default
Differential peak analysis was performed with DiffBind (2.4.8)
Genome_build: UCSC dm6
Supplementary_files_format_and_content: bedgraph files were generated using MACS (2.1.20150731)

growth_protocol: Flies were grown on standard growth media at 25 degrees Celcius for wild type and snf[148] and at 29 degrees Celcius for setdb1 GLKD

extract_protocol:
Lysates were prepared from whole dissected ovaries
Libraries were generated using the Rubicon Genomics Library Prep Kit

tag: full genotype

value: 3-5 days

value: ovaries

tag: chip antibody


title: snf[148] 2 H3K9me3

value: H3K9me3 (abcam 8898)


title: GSF1670_Tennessen_C1


title: wt.naive.r2

city: London

first: Richard

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description: replicate 2

hyb_protocol: For each sample, 300 ng of total RNA was amplified using the Total prep RNA amplification kit (Illumina), quantified using the Qubit and analysed by Agilent 2100 Bioanalyzer.  Amplified cDNA (1500 ng) samples were hybridized to microarray slides at 58 °C for 14–20 h with Illumina MOUSE WG-6 V2.0 Beadarrays according to the manufacturer’s protocols at the High Throughput Screening facility of the Francis Crick institute

scan_protocol: iScan system, Illumina

data_processing: Detection pvalues were calculated from the idat files using Limma's detectionPvalues function within R.  Data were subsequently background corrected and quantile normalized using Limma's neqc function with default settings.

source_name: C57BL/6 wildtype mouse, untreated

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

growth_protocol: Female C57BL/6 wildtype and IFNA Receptor knock-out (Muller et al 1992 Science, 264 1918) mice aged 6–10 weeks, obtained from the Biological Research Facility, Mill Hill, Francis Crick Institute, were housed conventionally with sterile bedding, food and irradiated water, with a 12 h light/dark cycle, and injected with 105 Plasmodium berghei ANKA infected red blood cells intraperitoneally. Parasitemia was monitored daily by Giemsa-stained thin blood films. Neurological complications typical of ECM, including ruffled fur, hunching, loss of equilibrium, partial paralysis, coma, loss of body weight and drop of temperature.   Methods are described in detail in described in Capuccini et al 2016, Scientific Reports, 6:39258

extract_protocol: Total RNA from approximately 10e5 sorted microglia cells was isolated using Ribopure (Ambion). RNA concentration was determined by Qubit fluorometric quantitation with  HS assay kit (ThermoFisher Scientific). The quality of RNA analysed on the Agilent 2100 Bioanalyzer; only samples with a RIN score above 8.50 were used for microarray analysis.

treatment_protocol: Brains were isolated in cold HBSS buffer (without Ca++ and Mg++), and enzymatically digested using a Neural Tissue Dissociation Kit (P) (Milteny Biotec) according to the manual. Digested brain samples were re-suspended in 4.5 ml of Percoll (GE Healthcare) 75% (in PBS) in a 15ml tube, on which 9.5ml of Percoll (37% in HBSS) was overlayed. After centrifugation at 800 g for 20 minutes at 4 °C without brake, the ring on the top of the upper layer containing myelin and debris was removed, and the ring between the phases 70% and 37% containing brain cells was collected and washed with PBS. Isolated microglia were incubated with Fc Receptor block (BD) for 15 minutes followed by 1h staining at 4 °C with Zombie, UV™ Fixable Viability kit (Biolegend) and combinations of fluorophore conjugated antibodies: APC-conjugated anti-CD11b, PE-conjugated-CD45, APCCy7- conjugated-Ly6C, pacific blue-cojugated-H-2Kb (Biolegend). Cells were then washed and resuspended in PBS containing 2% FCS. Cells sorting was performed on MoFlo XDP (Beckman coulter).Ghe purified microglia were collectd directly into TRIreagent (Ambion) and stored at −80 °C.  To access the purity of microglia, 50,000 to 100,000 cells were acquired on a BD LSR-Fortessa X-20 flow cytometer and analysed using FlowJoX (Treestar)

value: Wild type

tag: Sex

value: female

tag: background strain

value: brain

value: microglia

value: Untreated


title: snf[148] 1 input


title: Dimenhydrinate [HI.3145.004.BioO_1.104]

tag: cell type

value: Primary Cerebrocortical Cultures

value: Dimenhydrinate


title: Glimepiride [HI.3146.005.BioO_2.63]

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Glimepiride


title: wt.naive.r1

description: replicate 1

tag: tissue


title: wt.naive.r5

description: replicate 5


title: wt.naive.r4

description: replicate 4


title: wt.naive.r3

description: replicate 3


title: GSF1670_Tennessen_C2


title: Gemfibrozil [HI.3146.005.BioO_1.62]

value: Gemfibrozil


title: snf[148] 1 H3K9me3


title: wt.infected.r4

description: replicate 4

source_name: C57BL/6 wildtype mouse injected with 105 Plasmodium berghei ANKA infected red blood cells

value: Intraperitoneal injection with 105 Plasmodium berghei ANKA infected red blood cells


title: wt.infected.r6

description: replicate 6


title: setdb1 GLKD 2 input

source_name: setdb1 GLKD_ovaries_input


title: Indapamide [HI.3146.005.BioO_3.64]

value: Indapamide


title: Fenofibrate [HI.3147.006.BioO_5.60]

value: Fenofibrate


title: setdb1 GLKD 2 H3K9me3

source_name: setdb1 GLKD_ovaries_H3K9me3


title: setdb1 GLKD 1 input


title: Famciclovir [HI.3146.004.BioO_5.59]

source_name: Cerebral Cortex

value: Famciclovir


title: 24h_10 kJ/m2_-SS_2

source_name: HEKn_24h_10 kJ/m2_-SS

value: Human Epidermal Keratinocytes, neonatal (HEKn)

tag: treatment  (m = minus sunscreen; p = plus sunscreen)

value: m

tag: dose (gy)

tag: post-exposure time point (h)


title: setdb1 GLKD 1 H3K9me3

value: 3-5 days

value: ovaries

value: H3K9me3 (abcam 8898)


title: Finasteride [HI.3146.004.BioO_6.61]

value: Finasteride


title: Enalapril [HI.3146.004.BioO_4.58]

value: Enalapril


title: Corneal epithelia cells-2_3

city: Luoyang

first: Xueyi

last: Yang

address: 6# Jiqing road

institute: Luoyang normal university

description: Gene expression in corneal epithelia cells

organism: Ovis aries

source_name: Corneal epithelia cells, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit. One‐Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Epidermal stem cells and corneal epithelia cells were isolated and cultured used the methods previously reported (X Yang et al. 2007, 2008 and JC Jones 2011).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 1.5×106 adherent cells were digested with 0.25% trypsin and then neutralize by fetal calf serum. The cell suspension was then centrifuged at 1000rpm for 5min. The cell pellet was collected for RNA extraction.

value: cornea


title: wild type 2 input

source_name: wild type_ovaries_input

value: yw

value: 0-24 hours


title: gcn2∆_exponential_growth_3AT_treated_mRNA_decay_profile_time30

city: Berkeley

first: Leon

last: Chan

state: California

address: 628 Barker Hall UC Berkeley

department: Molecular Cell Biology

institute: UC Berkeley

data_processing:
reads aligned with Tophat
reads assembled and quantified with Cufflinks
Genome_build: W303_ALAV00000000_2012_SGD
Supplementary_files_format_and_content: fpkm_tracking files generated with Cufflinks

organism: Saccharomyces cerevisiae

source_name: gcn2∆ cells

growth_protocol: cells grown overnight and backdiluted and grown at least two doublings and never over OD = 0.7

extract_protocol:
hot phenol extraction followed by another phenol extraction followed by a chloroform extraction
BioO NEXTflex® Rapid Directional RNA-Seq Library Prep Kit

treatment_protocol: 4-thiouracil labeling, see associated publication

tag: growth phase

value: exponential growth

tag: time point


title: Corneal epithelia cells-2_2

source_name: Corneal epithelia cells, replicate 2


title: Corneal epithelia cells-2_1

source_name: Corneal epithelia cells, replicate 1


title: wt.infected.r3

description: replicate 3

value: Wild type

value: female

value: brain

value: microglia

tag: treatment


title: Doxycycline Monohydrate [HI.3146.004.BioO_3.57]

value: Primary Cerebrocortical Cultures

tag: days in vitro

value: F1 embryo FVBN(F)xC3B6F1(M)

value: Doxycycline Monohydrate


title: Skin epidermal stem cells-1_3

description: Gene expression in skin epidermal stem cells

source_name: Skin epidermal stem cells,  replicate 3

value: skin


title: wt.infected.r2

description: replicate 2

tag: genotype

value: Intraperitoneal injection with 105 Plasmodium berghei ANKA infected red blood cells


title: wt.infected.r5

description: replicate 5


title: Skin epidermal stem cells-1_2

source_name: Skin epidermal stem cells,  replicate 2


title: wild type 2 H3K9me3

source_name: wild type_ovaries_H3K9me3

tag: age

value: ovaries


title: Skin epidermal stem cells-1_1

source_name: Skin epidermal stem cells,  replicate 1


title: wt.infected.r1

description: replicate 1


title: Diclofenac·Na Salt [HI.3147.005.BioO_4.56]

tag: strain

tag: agent

value: Diclofenac·Na Salt


title: gcn2∆_exponential_growth_3AT_treated_mRNA_decay_profile_time15

tag: genotype/variation


title: Dextromethorphan [HI.3147.005.BioO_3.55]

value: Dextromethorphan


title: ko.naive.r3

description: replicate 3

source_name: IFNA Receptor knock-out mouse, untreated

value: IFNA Receptor knock-out

value: Untreated


title: wild type 1 input

tag: full genotype

value: yw

tag: chip antibody


title: wild type 1 H3K9me3

value: 0-24 hours

value: H3K9me3 (abcam 8898)


title: ko.naive.r5

description: replicate 5

tag: Sex

tag: background strain


title: gcn2∆_exponential_growth_3AT_treated_mRNA_decay_profile_time10

value: exponential growth


title: ko.naive.r2

description: replicate 2

value: female

tag: tissue

tag: cell type


title: ko.naive.r4

description: replicate 4

value: brain


title: gcn2∆_exponential_growth_3AT_treated_mRNA_decay_profile_time05


title: Citalopram·HBr [HI.3146.003.BioO_2.54]

value: Citalopram·HBr


title: Thalidomide [HI.3147.005.BioO_2.53]

value: Primary Cerebrocortical Cultures

value: Thalidomide


title: ko.naive.r1

description: replicate 1

value: microglia


title: gcn2∆_exponential_growth_3AT_treated_mRNA_decay_profile_time20