title: Bone marrow sinusoidal endothelial cells, DT treated, biological rep 3

first: Daniel

middle: C

last: Link

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University in St Louis

description:
Normalized_count_data_FPKM.txt
DT 3

data_processing:
All data from RNA sequencing were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018 (Partek Inc., St. Louis, MO, USA).
Single reads from Illumina sequencing were aligned to the mm10 mouse reference genome by STAR (v. 2.5.3a).
Aligned reads were then quantified to annotation model (Partek E/M, mm10 Ensembl Transcripts release 88).
Gene counts were all added with 0.0001 and were then normalized to total counts.
Partek GSA algorithm was utilized for differential expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples

source_name: FACS sorted bone marrow SECS from DT-treated mice

growth_protocol: Mice were maintained under SPF conditions, and all experimental procedures were performed according to methods approved by the Animal Studies Committee at Washington University.

extract_protocol:
Sinusoidal endothelial cells were sorted using flow cytometry, gated as Lineage- (CD45, Ter119, Gr1, CD11b) CD31+ Sca1- cells, and the RNA from these cells was extracted using RNeasy micro Kit (74004, Qiagen).
Library preparation was performed with 1ng of total RNA, integrity was determined using an Agilent bioanalyzer. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles/burst 50, time 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 14 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

treatment_protocol: 200ng Diphtheria toxin (DT) in 100ul PBS or just 100ul PBS was injected into mice intraperitoneally, and the mice were harvested 1 day after treatment.

value: Sinusoidal endothelial cells

value: bone marrow

value: DT


title: NHLF Control siRNA  unstimulated 24 hours

status: Public on Aug 02 2018

type: RNA

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

country: Japan

institute: Saga Medical School

hyb_protocol: 0.6 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes and hybridized to Agilent Expression Arrays at 65°C for 17 hours using GE Hybridyzation kit  (Agilent). The hybridized arrays were washed with GE Wash Buffers Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: NHLF Control siRNA, 24hr, 0 ng/mL　of IL-13

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp labeling Kit, One-Color  (Agilent) according  to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NHLF  were maintained in DMEM supplied with 10% fetal bovine serum, 100 units/mL penicillin and 100 ug/mL streptomycin.

extract_protocol: RNA was prepared using RNAiso plus following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: NHLF cells were treated with SOX11 siRNA or control siRNA and then incubated with or without IL-13 for 24 hr in DMEM supplied with 10% fetal bovine serum.

tag: cell type

value: Normal human primary lung fibroblasts (NHLF)


title: NHLF SOX11 siRNA  stimulated 24 hours

source_name: NHLF SOX11 siRNA, 24hr, 50 ng/mL of IL-13


title: Bone marrow sinusoidal endothelial cells, PBS treated, biological rep 4

type: SRA

city: St. Louis

state: MO

country: USA

description:
Normalized_count_data_FPKM.txt
PBS 4

library_source: transcriptomic

organism: Mus musculus

source_name: FACS sorted bone marrow SECS from PBS-treated mice

tag: tissue

tag: treatment

value: PBS


title: bulk ATAC 54-1 Day 0 MeisKO guide 6

city: Seattle

first: Cole

last: Trapnell

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
Accessible genomic DNA
54_1_bulk_multi_cov_counts.txt.gz

library_source: genomic

data_processing:
BCL files were converted to fastq format with bcl2fastq v2.16.
Barcode sequences were corrected to expected barcodes with custom python script.
Reads were trimmed (for adapter read-through) with Trimmomatic v0.32.
Reads were mapped to hg19 with bowtie v2.2.3.
Reads not mapping to the assembled nuclear chromsomes, as well as reads with invalid cell barcodes, were filtered using samtools v1.1 and grep.
Duplicate reads from each cell were filtered out with a custom python script.
Filtered out barcodes with few reads using custom R script.
Called peaks using MACS2 v2.1.1
Overlapped reads with summits of accessibility using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: "counts.txt.gz": Gzipped multiple column tab-separated vector in sparse matrix format - Column 1 = location information for each hypersensitivity summit; Column 2 = barcode representing single cell; Column 3 = count of reads from that barcode overlapping that hypersensitivity summit
Supplementary_files_format_and_content: ".indextable.txt": 2 column tab-separated vector - Column 1 = list of valid barcode combinations included in experiment; Column2 = time of collection
Supplementary_files_format_and_content: "54_1_bulk_multi_cov_counts.txt.gz":  Multiple column tab-separated vector - Columns 1-3 = bed format genomic coordinates, Remaining Columns = count of reads overlapping the genomic coordinates from the named bulk ATAC seq library

molecule: genomic DNA

extract_protocol:
Nuclei were isolated (please see publication for more details).
Please see publication for details on library construction.

value: Immortalized skeletal muscle myoblasts

tag: crispr perturbation target

value: Meis1 knockout

tag: crispr guide

value: Meis1 knockout 6

tag: time

value: Day 0


title: Bone marrow sinusoidal endothelial cells, DT treated, biological rep 2

description:
Normalized_count_data_FPKM.txt
DT 2


title: Bone marrow sinusoidal endothelial cells, DT treated, biological rep 1

description:
Normalized_count_data_FPKM.txt
DT 1


title: Bone marrow sinusoidal endothelial cells, PBS treated, biological rep 3

description:
Normalized_count_data_FPKM.txt
PBS 3


title: 002 arthroscopic partial meniscectomy

first: Muhammad Farooq

last: Rai

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: Gene expression in APM cartilage

hyb_protocol: For hybridization, amplified RNA samples were suspended in Agilent 2X Gene Expression buffer, Agilent 10X blocking agent, and Kreablock. The hybridization solution was applied to human SurePrint G3 Human 8X60K microarrays (Catalog # G4851C, Agilent Technologies) and incubated with streptavidin-cyanine 5 at 65oC for 20h. Washing procedures were performed according to Agilent Gene Expression protocol.

scan_protocol: Slides were  scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence as per manufacturer’s specification.

data_processing: Gridding and analysis of images were performed using Feature Extraction software v. 11.5.1.1 (Agilent Technologies).

source_name: Knee cartilage

label_protocol: 20 ng of RNA transcripts were amplified with the use of Sigma-WTA2 kit (Sigma-Aldrich) and then complementary DNA (cDNA) was labelled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics). Briefly, 3 g of cDNA was mixed with Kreatech 10X labeling buffer and Kreatech cyanine 5/DY-ULS. The reaction mixture was incubated at 85oC for 15 min in the dark and then quenched on ice for 3 min. Labelled cDNA was purified with Qiagen purification columns according to the supplier’s protocol (Qiagen).

extract_protocol: RNA was isolated using a combination of TRIzol:Chloroform (5:1 ratio) method and Minispin columns (Qiagen).  The pulverized tissues were first dissolved in 1 ml of TRIzol reagent (Invitrogen) followed by addition of 0.2 ml of Chloroform. Sample were then vortexed and transferred to phase lock gel tubes. Tubes were centrifuged for 15 min at 4°C. The clear aqueous layer was transferred by decanting of pipetting and 1 volume of 70% RNase-free ethanol was added to precipitate RNA. Finally, RNA was collected using RNeasy spin columns (Qiagen). The quality of the RNA was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: A small segment of the healthy-appearing cartilage was harvested from femoral notch of 12 patients during arthroscopic partial meniscectomy and a location-matched segment was obtained from 12 patients during total knee arthroplasty. Tissues were homogenized prior to RNA isolation.

value: Knee cartilage

tag: age (years)

tag: Sex

value: Male

tag: bmi (kg/m2)


title: bulk ATAC 54-1 Day 0 NTC guide 1

value: Non template control

value: Non template control 1


title: Bone marrow sinusoidal endothelial cells, PBS treated, biological rep 2

description:
Normalized_count_data_FPKM.txt
PBS 2


title: Bone marrow sinusoidal endothelial cells, PBS treated, biological rep 1

description:
Normalized_count_data_FPKM.txt
PBS 1


title: bulk ATAC 54-1 Day 0 NTC guide 3

value: Non template control 3


title: bulk ATAC 54-1 Day 0 NTC guide 2

value: Non template control 2


title: mouse4

city: Cincinnati

first: C.

middle: Alexander

last: Valencia

state: OH

address: 3333 Burnet Ave

department: Division of Human Genetics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
BOWTIE2-BUILD
FASTQC
CUTADAPT
FASTQC
TOPHAT
COVERAGE
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: FPKM count file

source_name: +PID: targeted transgenic mouse carrying a conditionally activated PID allele at the Rosa26 locus

extract_protocol:
RNA isolation, (q)RT-PCR and RNA-Seq - Total RNA was isolated using Tri reagent (Sigma)  and digested by DNase I (Life Technology). First-Strand cDNA was synthesized using  SuperScript III reverse transcriptase (Life Technology) according to manufacture’s protocol and  standard PCR was performed afterwards. Quantitative Real-time PCR analysis was  accomplished using Fast SYBR Green master mix on a 7500 quantitative Real-time PCR  machine (Applied Biosystems). The relative amount of gene transcripts and pre-micro-RNA  (pre-miRNA) was normalized to GAPDH and U6, respectively.
350 to 900 ng of total RNA determined by Invitrogen Qbit high sensitivity spectrofluorometric measurement is poly A selected and reverse transcribed using Illumina’s TruSeq RNA library preparation kit V2. Each sample can be fitted with one of 24 adapters containing a different 6 base molecular barcode for high level multiplexing. After 12 cycles of PCR amplification, completed libraries are sequenced on an Illumina HiSeq2000 or HiSeq2500, generating around 20-50 million high quality 50 base long reads per sample.

treatment_protocol: tumor induction

value: +PID:targeted transgenic mouse carrying a conditionally activated PID allele at the Rosa26 locus


title: mouse3

source_name: Normal, untreated

value: untreated


title: mouse1


title: mouse7


title: WT cell line 18 3h Activin A

city: London

first: Vasso

last: Episkopou

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description: RNA sequencing and alignment performed by GATC Biotech

data_processing:
Data processing and bioinformatic analys was performed by GATC Biotech according to their InView Transcriptome Explore package.
Genome_build: Standard mouse genome (mm10)
Supplementary_files_format_and_content: Gene expression table including FPKM value (tsv)

source_name: Embryonic stem cells

growth_protocol: Cells were maintained in 2i medium + LIF on gelatin coated culture dishes with replacement of medium daily and passaging of cells every second day. The recipe for the 2i medium is as follows: 100 mL DMEM F12 (#21331-046, Gibco), 100 mL Neurobasal (#21103-049, Gibco), 1 mL N2 (#17502-048, Gibco), 2 mL B27 without Vit A (#12587-010, Gibco), 2 mL Glutamine   (#25030-024, Gibco), 200uL b-mercaptoethanol (#31350-010, Gibco), CHIRON - 3uM final concentration (#13122 from Cayman Chemical), PD03 - 1uM final concentration (#PZ0162 from Sigma), LIF - 1:500 (made in house)

extract_protocol:
Cells were harvested from dishes using the RNeasy Plus Mini Kit (#74134, Qiagen) Briefly, 600 ul Buffer RLT was added to each plate, cells were scraped and transfered to a microfuge tube (RNase free). Samples were homogenized using the Qiashredder (79654, Qiagen) and transfered to -80C. The following day, RNA extraction was performed according to manufacturers instructions. RNA integrity was checked using the bioanalyzer and 1ug total RNA in up to 50ul, RIN>8, dissolved in RNase-, DNase-, protease-free water was sent to GATC Biotech for sequencing. pSmad levels were checked in protein extracts using SDS-PAGE and Immunoblotting to confirm activin stimulation
RNA libraries were prepared by GATC Biotech for sequencing using standard Illumina protocols as part of their InView Transcriptome Explore package (https://www.eurofinsgenomics.eu/en/next-generation-sequencing/ngs-built-for-you/inview-transcriptome/inview-transcriptome-explore/). Briefly, mRNA is poly-(A) enriched and subsequently fragmented. cDNA synthesis is performed with random hexamer priming. 50 bp single reads with 30 million single reads guaranteed.

treatment_protocol: Prior to treatment, cells from each cell line were seeded into 3X10cm fibronectin coated (1:100 dilution, Millipore FC010, stock is 1ug/ul, 4 ml of diluted fibronectin added per dish = 40ug per dish) Corning Cellbind dishes at a concentration of 3X10^6 cells per dish for 24 hours in N2B27 medium to achieve a epiblast like state. 24 hours after changing medium to N2B27, all plates were incubated in N2B27 containing 10uM SB compound for 4 hours. At 4 hours, dishes were treated as follows: Dish 1 - Wash in ice cold PBS, remove PBS, harvest cells and transfer to the -80. Dish 2 and 3: Remove SB media, wash 2X in PBS, and replace with N2B27 containing 10 ng/ml Activin A. At 3 and 6 hours after adding AA to Dish 2 and 3, respectively, stop experiment by washing cells in ice cold PBS, harvest cells and transfer to the -80.

tag: strain

tag: genotype

value: Wild type


title: Ark -/- cell line 25 6h Activin A

value: Arkadia -/-


title: WT cell line 18 6h Activin A


title: WT cell line 26 6h Activin A


title: Ark -/- cell line 25 SB


title: Ark -/- cell line 39 SB


title: WT cell line 26 3h Activin A


title: WT cell line 26 SB


title: Ark -/- cell line 39 6h Activin A


title: Ark -/- cell line 25 3h Activin A


title: bulk ATAC HSMM to HSMMtube

description: Accessible genomic DNA

source_name: HSMM to HSMMtube

value: Skeletal Muscle Myoblasts/Myotubes


title: mouse26


title: Thymus 62016

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

description:
sci-ATAC-seq
Accessible genomic DNA

data_processing:
BCL files were converted to fastq format with bcl2fastq v2.16.
Barcode sequences were corrected to expected barcodes with custom python script.
Reads were trimmed (for adapter read-through) with Trimmomatic v0.32.
Reads were mapped to mm9 with bowtie v2.2.3.
Reads not mapping to the assembled nuclear chromosomes, as well as reads with invalid cell barcodes, were filtered using samtools v1.1 and grep.
Duplicate reads from each cell were filtered out with a custom python script.
Filtered out barcodes with few reads using custom R script.
Mapped reads to 5kb windows in the genome using custom python script.
After clustering cells, called peaks on clusters of cells using MACS2 v2.1.1.20160309.
Overlapped reads with peaks of accessibility using custom python script.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: ".5kbmatrix.txt.gz": Multiple column tab-separated vector - first 4 columns contain location information for each 5kb window, remaining columns include counts of reads overlapping that site assigned to each barcode.
Supplementary_files_format_and_content: ".peakmatrix.txt.gz": Multiple column tab-separated vector - first 4 columns contain location information for each hypersensitivity peak, remaining columns include counts of reads overlapping that site for each cell barcode.
Supplementary_files_format_and_content: ".indextable.txt": 2 column tab-separated vector - Column 1 = list of valid barcode combinations included in experiment; Column 2 = tissue and PCR plate that barcode represents.

source_name: Nuclei isolated from tissue

extract_protocol:
Tissues were dissected and nuclei were isolated via a tissue-specific protocol (please see associated publication for more details).
Please see associated publication for details on library construction.

tag: strain/background

value: Thymus

tag: gender

tag: age

value: 8 weeks


title: Whole Brain A 62816

description:
sci-ATAC-seq
Accessible genomic DNA

value: Whole Brain


title: MRC5 cells stimulated 24 hours

hyb_protocol: 0.6 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes and hybridized to Agilent Expression Arrays at 65°Cfor 17 hours using GE Hybridyzation kit  (Agilent). The hybridized arrays were washed with GE Wash Buffers Pack (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MRC-5, 24hr, 50 ng/mL of IL-13

growth_protocol: MRC5 cells were maintained in DMEM supplied with 10% fetal bovine serum, 100 units/mL penicillin and 100 ug/mL streptomycin.

treatment_protocol: MRC5 cells were treated with or without IL-13 for 24 hr in DMEM supplied with 10% fetal bovine serum.

value: Human normal lung fibroblast cells (MRC-5)


title: Whole Brain A 62216

description:
sci-ATAC-seq
Accessible genomic DNA


title: MRC5 cells unstimulated 24 hours

source_name: MRC-5, 24hr, 0 ng/mL　of IL-13


title: Glia_RNAseq_1

city: Stockholm

first: Jonas

last: Muhr

address: Biomedicum D5

department: CMB

country: Sweden

institute: Karolinska Institutet

description:
GPC_Glia_RNAseq.txt
Glia_sampleA

data_processing:
ChIPseq and RNAseq reads were aligned to the mouse genome assembly mm9 by star/2.3.1o (Dobin et al, 2013).
RNAseq data was after quality control processed by rpkmforgenes. Processed file contains RPKM and raw counts for each refseq transcript.
Mapped reads from ChIP-seq replicates were pooled for each factor and peak calling preformed on pooled files according to Lun et.al., 2014. The highest possible score for centrally enriched binding motifs for the specific factor decided which peak calling approach that finally were used for the processed files; For SOX3 ChIPseq, MACS14 (default settings), for SOX9 ChIPseq, MACS2 (default settings), for NFIA ChIPseq, SISSRS (FDR 10-7). For H3K27Ac ChIPseq, mapped reads were pooled from all three replicates and the pooled file was used directly as a processed file (through Seqminer software).
Genome_build: mm9
Supplementary_files_format_and_content: For RNAseq, tab-delimited text files include RPKM values and counts for each sample. For ChIPseq, bed files include summits of called peaks, expanded in both directions.

source_name: Glial cells

growth_protocol: ESCs were propagated in feeder-free conditions. Neural differentiation was induced in N2B27 medium by 0.1 μM all-trans RA (Sigma) on bovine fibronectin (Sigma) treated culture plastic. GPCs were isolated from differentiating cultures by magnetic sorting with A2B5 magnetic beads (Miltenyi Biotec, 130-093-388) according to the manufacturer’s instructions at d8 and propagated on fibronectin treated plastic in N2B27 media in the presence of EGF and FGF2 (10ng/ml, Life Technologies).

extract_protocol:
For ChIPseq, lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. For RNAseq, extraction kit for total RNA was used according to the manufacturer’s instructions (Qiagen).
ChIP libraries were prepared using TruSeq ChIP library preparation kit (Illumina) according to the manufacturer’s recommendations followed by sequencing on Illumina HiSeq 2000 giving 43bp reads, 7-20x106 reads per ChIP experiment. For RNAseq, TruSeq RNA Library Preparation Kit (Illumina) was used.

value: ESC-derived glial cells


title: Glia_RNAseq_2

description:
GPC_Glia_RNAseq.txt
Glia_sampleB


title: Glia_RNAseq_3

description:
GPC_Glia_RNAseq.txt
Glia_sampleC


title: GPC_RNAseq_4

description:
GPC_Glia_RNAseq.txt
GPC_sampleD

source_name: Glial progenitor cells

value: ESC-derived glial progenitor cells


title: mouse2


title: Ark -/- cell line 39 3h Activin A


title: WT cell line 18 SB


title: GPC_RNAseq_3

description:
GPC_Glia_RNAseq.txt
GPC_sampleC


title: GPC_RNAseq_2

description:
GPC_Glia_RNAseq.txt
GPC_sampleB


title: GPC_RNAseq_1

description:
GPC_Glia_RNAseq.txt
GPC_sampleA


title: H3K27Ac_ChIPseq_GPC_3

tag: chip antibody

value: H3K27Ac, Diagenode, C15410174


title: H3K27Ac_ChIPseq_GPC_1


title: Input_NFIA_ChIPseq_2

description: Input for ChIP-seq


title: Input_NFIA_ChIPseq_1

description: Input for ChIP-seq


title: Lung B 62216

description:
sci-ATAC-seq
Accessible genomic DNA

value: Lung

value: Male


title: Prefrontal Cortex 62216

description:
sci-ATAC-seq
Accessible genomic DNA

value: Prefrontal Cortex


title: H3K27Ac_ChIPseq_GPC_2


title: SOX9_ChIPseq_3

value: Sox9, Millipore, AB5535


title: Spleen 62016

description:
sci-ATAC-seq
Accessible genomic DNA

value: Spleen


title: Kidney 62016

description:
sci-ATAC-seq
Accessible genomic DNA

value: Kidney


title: Small Intestine 62816

description:
sci-ATAC-seq
Accessible genomic DNA

value: Small Intestine


title: Liver 62016

description:
sci-ATAC-seq
Accessible genomic DNA

value: Liver


title: NFIA_ChIPseq_2

value: NFIA, Sigma, HPA006111


title: NFIA_ChIPseq_1


title: SOX3_ChIPseq_2

value: Sox3, Muhr-lab


title: SOX9_ChIPseq_1


title: Lung A 62216

description:
sci-ATAC-seq
Accessible genomic DNA


title: SOX9_ChIPseq_2


title: SOX3_ChIPseq_1


title: Heart 62816

description:
sci-ATAC-seq
Accessible genomic DNA

value: Heart


title: Testes 62016

description:
sci-ATAC-seq
Accessible genomic DNA

value: Testes

value: 8 weeks


title: Large Intestine A 62816

description:
sci-ATAC-seq
Accessible genomic DNA

value: Large Intestine


title: Large Intestine B 62816

description:
sci-ATAC-seq
Accessible genomic DNA


title: Cerebellum 62216

description:
sci-ATAC-seq
Accessible genomic DNA

value: Cerebellum


title: Arabidopsis_pifq_R1

city: Durham

first: xing

last: zhang

address: FFSC Bldg., 124 Science Drive

institute: duke university

data_processing:
BWA, v0.7.7, default parameter
degeR, v3.20.1, default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: Gene, reads per Gene(Total:40890624), length, coverage, rpkm

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: pifq_etiolated seedlings except roots

growth_protocol: The air-dried seeds were placed on MS medium after surface-sterilization and kept at 4℃ for fully imbibition. Three days later, the samples were exposed to light for 3-6 hours in order to stimulate germination and then maintained in darkness at 22℃ for another 3 days before sample collection.

extract_protocol:
RNAeasy Kit
standard Illumina mRNA-seq protocol

treatment_protocol: No treatment

tag: ecotype background

tag: genotype/variation

value: pifq

value: etiolated seedlings except roots


title: Arabidopsis_ein3 eil1_R2

description: Clean_BN2-825_ein3 eil1_R2

source_name: ein3 eil1_etiolated seedlings except roots

value: ein3 eil1


title: Arabidopsis_ein3 eil1_R1

description: Clean_BN2-824_ein3 eil1_R1


title: Arabidopsis_pifq_R2


title: Bone Marrow 62216

description:
sci-ATAC-seq
Accessible genomic DNA

value: Bone Marrow

value: Male


title: Arabidopsis_pifq ein3 eil1_R1

description: Clean_BN2-820_pifq ein3 eil1_R1

source_name: pifq ein3 eil1_etiolated seedlings except roots

value: pifq ein3 eil1


title: Arabidopsis_hls1_R2

source_name: hls1_etiolated seedlings except roots


title: OHC_5

city: Omaha

first: David

middle: ZZ

last: He

state: Nebraska

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

description:
OHCs - 5_CBA_1m_OHC_3_AGGCAGAA-CTCTCTAT_L001
This biological replicate has paired-end sequencing and two associated raw reads files.

data_processing:
CLC Genomics Workbench software (CLC bio, Waltham, MA, USA) was used to map the reads to the  mouse genome (mm10, build name GRCm38) and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads (RPKM) values
Genome_build: mm10, build name GRCm38
Supplementary_files_format_and_content: Normalized RPKM gene expression values

source_name: Outer hair cells, organ of Corti

growth_protocol: Adult CBA/J mice (28 to 32 days old) were used for the study.

extract_protocol:
The basilar membrane together with the organ of Corti was isolated and transferred to a small Petri dish with an enzymatic digestion medium. After 5 min incubation at room temperature, the tissue was transferred to a small plastic chamber containing enzyme-free culture medium. Cells were separated after gentle trituration of the tissue with a small pipette. Morphologically distinct cells were individually collected with suction pipette technique. Approximately 1,000 cells of each type were separately suspended in RNALater (~100 µL in total volume) and total RNA, including small RNAs (> ~18 nucleotides), were extracted and purified using the Qiagen RNeasy mini plus Kit (Qiagen, Germantown, MD). On-column DNase digestion was performed to eliminate DNA contamination in the collected RNA.
Libraries were prepared using the SMARTer Low Input RNA kit (Clontech Laboratories, Mountain View, CA) to generate cDNA in combination with the Nextera Library preparation kit (Illumina, San Diego, CA). Library size and concentration were assessed using an Agilent 2100 Bioanalyzer and a Quibit fluorometer (Invitrogen, Thermo Fisher Scientific) to ensure the inserts were the appropriate size and determine concentration prior to sequencing. Transcriptome libraries were sequenced using the HiSeq 2500 Sequencing System (Illumina).

tag: strain/ age

value: CBA/J

value: adult; 28 to 32 days old

tag: sample size

value: ~1,000 isolated cells

tag: cell type

value: Outer hair cell


title: Arabidopsis_hls1_R1

tag: tissue


title: OHC_4

description:
OHCs - 5_CBA_1m_OHC_2_GGACTCCT-CTCTCTAT_L002
This biological replicate has paired-end sequencing and two associated raw reads files.


title: OHC_3

description:
OHCs - 5_CBA_1m_OHC_2_GGACTCCT-CTCTCTAT_L001
This biological replicate has paired-end sequencing and two associated raw reads files.


title: Bone Marrow 62016

description:
sci-ATAC-seq
Accessible genomic DNA


title: Arabidopsis_Col-0_R1

source_name: Col-0_etiolated seedlings except roots

value: wild type


title: Arabidopsis_Col-0_R2


title: OHC_1

description:
OHCs - 5_CBA_1m_OHC_1_TAAGGCGA-CTCTCTAT_L001
This biological replicate has paired-end sequencing and two associated raw reads files.


title: IHC_4

description:
IHCs - 6_CBA_1m_IHC_2_TAGGCATG-TATCCTCT_L002
This biological replicate has paired-end sequencing and two associated raw reads files.

source_name: Inner hair cells, organ of Corti

value: Inner hair cell


title: IHC_3

description:
IHCs - 6_CBA_1m_IHC_2_TAGGCATG-TATCCTCT_L001
This biological replicate has paired-end sequencing and two associated raw reads files.


title: OHC_2

description:
OHCs - 5_CBA_1m_OHC_1_TAAGGCGA-CTCTCTAT_L002
This biological replicate has paired-end sequencing and two associated raw reads files.


title: H37Rv_176VER_D0_rep4

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

data_processing:
Raw FASTQ read data processing was carried out using a custom processing pipeline that harnesses the Bowtie 2 utilities, which is available at https://github.com/sturkarslan/DuffyNGS, and https://github.com/sturkarslan/DuffyTools, as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Genome_build: MT_H37Rv_V3
Supplementary_files_format_and_content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: H37Rv Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen). Messenger RNA was enriched using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc.) according to manufacturer's instructions.
Libraries were prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions and using the AMPure XP reagent (Agencourt Bioscience Corporation) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries associated with each replicate and multiplexing up to 48 libraries per sequencing run. The prepared libraries were quantified using the Kapa qPCR quantification kit, and were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit (Illumina Inc).

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of verapamil (0μM, 176μM) (as indicated in each sample title).

tag: verapamil dose

tag: days post drug


title: At_miR1507OX_2

status: Public on Aug 03 2018

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA
miR1507 overexpression rep 2  in Arabidopsis

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Medicago Genome v3.5
Supplementary_files_format_and_content: tag count file

source_name: miR1507 overexpression

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Plant RNA reagent (Ambion, Life Technologies, USA) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001). PARE libraries were constructed according to the protocols by German et al., 2009 and Zhai et al., 2014.

tag: ecotype

value: leaves

value: miR1507 overexpression


title: IHC_2

description:
IHCs - 6_CBA_1m_IHC_1_CGTACTAG-TATCCTCT_L002
This biological replicate has paired-end sequencing and two associated raw reads files.


title: H37Rv_176VER_D1_rep3


title: H37Rv_176VER_D0_rep3


title: MEL2 5% O2_2

city: Melbourne

first: Jarmon

middle: Gerald

last: Lees

state: Victoria

address: Royal Parade

country: Australia

institute: University of Melbourne

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing was performed with 12 samples per lane, using 50 bp single-end reads. The quality of resultant raw FASTQ data files was assessed with FastQC
Processed using the following pipeline: FASTQ Groomer to convert raw Illumina FASTQ files to Sanger Quality score format, Trim Galore! to trim the 13 bp of Illumina standard adapters, RNA STAR to align reads to the UCSC GRCh37/hg19 human reference genome, featureCounts to measure gene expression, and DESeq2 to identify DEGs
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: .csv DESeq files comparing 5% and 20% oxygen treatments within cell lines, and Cell lines at each oxygen treatment.

source_name: embryonic stem cell

growth_protocol: hESC cultured in mTeSR1 medium on matrigel. Passaged with dispase using cell scrapers.

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). RNA Integrity Numbers (RIN) of 10 for all samples were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was analyzed on the Illumina HiSeq 2500 Sequencing System (Illumina) at the Australian Genome Research Facility (AGRF) using 1 µg of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Long term (over 5 passages) in 5% or 20% oxygen, controlled at the incubator.

tag: cell line

tag: oxygen

tag: passage


title: MEL2 5% O2_3


title: Arabidopsis_pifq ein3 eil1_R2

description: Clean_BN2-821_pifq ein3 eil1_R2


title: IHC_1

description:
IHCs - 6_CBA_1m_IHC_1_CGTACTAG-TATCCTCT_L001
This biological replicate has paired-end sequencing and two associated raw reads files.


title: MEL2 20% O2_3


title: H37Rv_176VER_D1_rep1


title: OHC_6

description:
OHCs - 5_CBA_1m_OHC_3_AGGCAGAA-CTCTCTAT_L002
This biological replicate has paired-end sequencing and two associated raw reads files.


title: H37Rv_176VER_D0_rep1


title: MEL2 20% O2_2


title: H37Rv_176VER_D1_rep4


title: mouse IgG mock

city: Los Angeles

first: Meng

last: Qu

state: California

address: 1002 West Childs Way

department: Keck Medical School

institute: University of Southern California

description:
ZT4 and ZT16 mix
HNF4A ChIP-seq

data_processing:
Illumina SE 75 bp reads produced by HNF4A ChIP-Seq on C57BL/6 mouse liver were mapped to the mouse mm9 genome using Bowtie2 with the following parameters: -N 1
Peak calling for HNF4A ChIP-seq was performed with PePr with the following parameters: --threshold 1e-2 --peaktype sharp.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using HOMER (v4.10) with default parameters.

source_name: liver

extract_protocol:
~ 50 mg of blood perfused liver tissue were dissected from C57BL/6J mice, snap frozen in liquid nitrogen and stored at -80°C. Frozen liver tissues were minced in ice-cold PBS using razor blades into 1 mm cubed, and then homogenized by pushing through 1.5-inch 18G needle for 10 times and then 1.5-inch 21G needle for 20 times. Homogenized cells were immediately crosslinked with 1% formaldehyde for 10 min. The crosslink was quenched by adding glycine to a final concentration of 125 μM. After two washes with cold PBS, the nuclei were lysed in 150 μl nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) containing 1x EDTA-free protease inhibitor cocktail (Roche), by keeping on ice for 5 min. Immediately, to fragment the chromatin, the lysates were sonicated 17 times for 30 sec by using Bioruptor (Diagenode). After centrifuged at 17,000 rpm for 15 minutes at 4°C, the 150 μl fragmented chromatin was diluted 10-fold with IP dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 1 mM EDTA) supplemented with 1x EDTA-free protease inhibitor cocktail, and then incubated with 7 μg anti-HNF4A (abcam cat. ab41898) overnight at 4°C. 100 μl of Dynabeads Protein G (Invitrogen cat. #10004D) was added to the chromatin and incubated for another 3 h. Afterwards, the beads were washed once with low salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA) and once with high salt wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA). 200 μl of IP elution buffer (1% SDS, 100 mM NaHCO3) was applied to the bead pellet and incubated at 30°C for 15 min. The eluate was added with 5M NaCl to final conc. of 200 mM and reverse-crosslinked at 65°C overnight. To remove RNA and protein, RNase A and proteinase K were subsequently applied by incubating at 45°C for 1 h. Finally, we diluted the DNA with 5 volumes of Qiagen buffer PB (QIAquick PCR Purification Kit) and purified with QIAquick PCR Purification columns. We eventually resolved our DNA fragments in 30 μl Qiagen Buffer EB.
For library preparation, 2 ng of each sample was prepared using the NEB Ultra DNA Library Prep Kit for Illumina following manufacturer’s instructions. Each library was dual size selected with 0.55X and 0.14X Ampure beads followed by PCR amplification with Kappa HiFi 2x PCR mix (15 cycles). PCR product was then quantitated using the Qubit (Thermo Fisher) and BioAnalyzer (Agilent BioAnalyzer 2100) to determine library quantity. Libraries were then gel purified on a 2% agarose gel to remove secondary PCR amplification artifacts, quantitated on the Qubit and loaded onto a NextSeq500 flowcell for 1 x 76 base single-end sequencing to generate approximately 20M reads per sample.

value: IgG

tag: strain

value: liver

value: 8-week old


title: MEL1 20% O2_3


title: H37Rv_0VER_D1_rep3

value: 0 μM


title: H37Rv_0VER_D0_rep4


title: H37Rv_0VER_D1_rep4


title: ZT16 mouse3

description:
ZT16
HNF4A ChIP-seq


title: ZT16 mouse2

description:
ZT16
HNF4A ChIP-seq


title: MEL1 20% O2_1


title: MEL1 20% O2_2


title: H37Rv_0VER_D0_rep3


title: ZT16 mouse1

description:
ZT16
HNF4A ChIP-seq


title: H37Rv_0VER_D1_rep2


title: AgNPs 12h

city: beijing

first: songshan

last: Wang

address: baiwanzhuang 11#

country: China

institute: ASAG

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Chlamydomonas reinhardtii whole genome using Tophat2.0.10.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the cuffdiff command in cufflinks2.1.1
Genome_build: Chlamydomonas reinhardtii v5.5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Chlamydomonas reinhardtii

source_name: algal cell

growth_protocol: TAP medium, 25°C with constant agitation and 2000 lux illumination

extract_protocol:
Algal cell were collected after centrifuge at 4000g 4°C for 2 min, RNA was immediately harvested using Trizol reagent. Illumina mRNA-Seq Sample Preparation Kit (Cat# RS-930-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.5 mg/L AgNPs treated for 2h and 12h

tag: genotype

tag: time


title: MEL2 5% O2_1


title: MEL1 5% O2_3


title: AgNPs 2h

value: 2 h


title: MEL1 5% O2_2


title: H37Rv_0VER_D0_rep2


title: ZT4 mouse3

description:
ZT4
HNF4A ChIP-seq

tag: age


title: CK 12h


title: ZT4 mouse2

description:
ZT4
HNF4A ChIP-seq

tag: chip antibody


title: H37Rv_0VER_D1_rep1


title: MEL1 5% O2_1


title: H37Rv_0VER_D0_rep1


title: pAW_4

city: Turku

first: Jyrki

last: Heino

address: Vatselankatu 2

department: Biochemistry

country: Finland

institute: University of Turku

data_processing:
The reads obtained from the instrument were base called using the instrument manufacturer’s Bcl2fastq version 1.8.4 base calling software.
The read alignment was performed in two stages: first, the reads were aligned against the reference genome using TopHat version 2.1.0. Then the reads were associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.0). The following reference data was downloaded from Illumina iGenomes web site (originally derived from UCSC database): Genome: human hg38, gene annotation: RefSeq based annotation.
The gene-wise read counts were normalised using the TMM normalisation method of the edgeR R/Bioconductor package. The method takes the variable number of total reads across samples into account by calculating specific scaling factors between the samples. For statistical testing the data were further transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalised counts are represented as RPKM values (Reads Per Kilobase of exon per Million reads mapped) (Mortazavi et al., Nat Methods, 2008, 5:621–8) which make the expression values comparable also between genes by taking the variable gene lengths into account.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data files contain raw read counts (RawData_withAnnotations.txt) or normalized values as RPKM (NormalizedData_withAnnotations.txt) for each gene with RefSeq-based annotations. The samples are in separate columns.

source_name: DU145 prostate cancer cell line

growth_protocol: Spheroids of the DU145 derivatives were made in micro-molds according to the manufacturer’s instructions (3D Petri Dish, MicroTissues) with 280 000 cells in one mold (8 000 cells in one spheroid). Spheroids were grown in serum-free RPMI 1640 -medium (Lonza) in standard conditions (5 % CO2, +37 °C) for 72 hours.

extract_protocol:
Total RNA was extracted from the cells cultured in spheroids by using NucleoSpin RNA (Macherey-Nagel) kit according to the manufacturer’s instructions. The quality and quantity of the RNA was checked using Nanodrop ND-2000 spectrophotometer (Thermo Scientific).
Libraries were prepared for the sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit according the manufacturer's instructions

tag: alpha2 integrin gene

value: CRISPR-Cas9 knock-out

tag: transfected with

value: empty pawneo2 vector


title: H37Rv_176VER_D0_rep2


title: H37Rv_5.6SUT_D1_rep4

description: Expression.MTB.GeneData.SUT.csv

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of sutezolid (0μM, 5.6μM) (as indicated in each sample title).

tag: drug dose


title: ZT4 mouse1

description:
ZT4
HNF4A ChIP-seq


title: H37Rv_5.6SUT_D0_rep4

description: Expression.MTB.GeneData.SUT.csv


title: pAW_1


title: H37Rv_5.6SUT_D1_rep3

description: Expression.MTB.GeneData.SUT.csv


title: miRNA_NHLF_IL-13_24hr

first: Masafumi

last: Horie

address: 2011 Zonal Ave

description: miRNA expression at 24 hr after stimulation with IL-13 10 ng/ml

hyb_protocol: Hybridization was performed with Hybridization Control Kit (Affymetrix, Inc., cat.# 900454)  and Hybridization, Wash, and Stain Kit (Affymetrix, Inc., cat.# 900720) in GeneChip Hybridization Oven 645 (Affymetrix, Inc.) for 18 hr (60 rpm) at 48 degree celsius. Washing was performed using GeneChip Fluidics Station 450 (Affymetrix, Inc.).

scan_protocol: Slides were scanned using GeneChip® Scanner 3000 7G

data_processing: Images were digitized with Affymetrix® Expression Console™ Software. Normalization performed with RMA.

label: biotin

label_protocol: Biotin-labeled samples were prepared using FlashTagTM Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA Arrays (Affymetrix, Inc., cat.# 901911) .

growth_protocol: NHLF (Lonza, and Walkersville, MD) were cultured in DMEM + 10% FBS.

extract_protocol: miRNeasy mini kit (Qiagen) was used for total RNA extraction. Total RNA QC was performed by Agilent 2100 Bioanalyzer.

treatment_protocol: NHLF were treated with 10 ng/ml of IL-13 on 4 and 24 hr.

value: normal human lung fibrobast (NHLF)

tag: time (hour)


title: B2 tdTom- Ecs

first: Alessandro

last: Fantin

state: - None -

address: 11-43 Bath Street

department: UCL Institute of Ophthalmology

institute: University College London

data_processing:
Raw sequence data were pre-processed to trim poor quality base calls and adapter contamination using Trimmomatic v.0.36.4 (Bolger et al., 2014).
Alignment to the mouse mm10 genome was performed with STAR v.2.5.2b (Dobin et al., 2013).
Mapped reads were deduplicated to reduce PCR bias using Picard v2.7.1.1 software (http://broadinstitute.github.io/picard/).
Reads-per-transcript were  calculated using FeatureCount v1.4.6.p5 software (Liao et al., 2014).
Differential expression was performed using the BioConductor package DESeq2 via the SARTools wrapper v1.3.2.0 (Varet et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw and normalised count values for each Sample, fold changes and adjusted P values.

source_name: whole embryo

extract_protocol:
PECAM1+ CD45- CD11b- KIT- ECs were isolated from n = 3 E12.5 Csf1r-Cre;RosatdTom embryos and divided into tdTom+ and tdTom- populations with the Influx cell sorter before RNA was extracted with the RNeasy Micro Kit (QIAGEN).
cDNA was generated and amplified using the SMART-seq V4 ultra low input RNA kit (Clontech). 100 pg of amplified cDNA per sample was used to prepare a library with the Nextera XT kit (Illumina).

value: whole embryo

value: embryonic day 12.5

value: tdTomato-


title: A3 tdTom+ Ecs

value: tdTomato+


title: H37Rv_5.6SUT_D0_rep3

description: Expression.MTB.GeneData.SUT.csv


title: a2_4

value: α2 integrin cDNA in pawneo2 expression vector


title: H37Rv_5.6SUT_D1_rep2

description: Expression.MTB.GeneData.SUT.csv


title: a2_3


title: miRNA_NHLF_IL-13_4hr

description: miRNA expression at 4 hr after stimulation with IL-13 10 ng/ml

tag: cell type


title: pAW_2


title: A2 tdTom+ Ecs

tag: tissue


title: A1 tdTom+ Ecs


title: miRNA_NHLF_IL-13_0hr

description: miRNA expression at 0 hr after stimulation with IL-13 10 ng/ml


title: H37Rv_5.6SUT_D0_rep2

description: Expression.MTB.GeneData.SUT.csv


title: B3 tdTom- Ecs


title: pAW_3


title: CK 2h

value: wild type


title: 16506_Mouse430A_2

city: New York

first: Jeffrey

middle: A

last: Knauf

state: NY

address: 1275 York Ave

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Affymetrix protocol, Mouse 430A 2.0

scan_protocol: Affymetrix protocol

data_processing: Partek Genomics Suite, RMA, Quantile normalization, Log base 2

source_name: thyroid tumor

label_protocol: Affymetrix protocol

extract_protocol: RNA extraction with PrepEase RNA Spin Kit, USB corp

value: recurrent tumor


title: H37Rv_5.6SUT_D1_rep1

description: Expression.MTB.GeneData.SUT.csv


title: 13494_Mouse430A_2


title: B1 tdTom- Ecs


title: H37Rv_0SUT_D1_rep4

description: Expression.MTB.GeneData.SUT.csv


title: 12559_Mouse430A_2


title: CRISPR_4


title: CRISPR_3


title: a2_2


title: H37Rv_5.6SUT_D0_rep1

description: Expression.MTB.GeneData.SUT.csv


title: H37Rv_0SUT_D0_rep4

description: Expression.MTB.GeneData.SUT.csv


title: 12556_Mouse430A_2


title: CRISPR_2


title: H37Rv_0SUT_D1_rep3

description: Expression.MTB.GeneData.SUT.csv


title: JK7_B14113_Mouse430A_2


title: CRISPR_1


title: H37Rv_0SUT_D0_rep3

description: Expression.MTB.GeneData.SUT.csv


title: FIB rep 2

city: Vienna

first: Paulina

middle: Anna

last: Latos

address: Schwarzspanierstraße 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
Basecalling performed using RTA 1.18.64.0
First 12 nucleotides of each read were trimmed.
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v2.1.1) against the Homo sapiens genome (hg38). Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC, 2015_01, hg38).
The aligned reads were counted with HTSeq (0.6.1p1; intersection-nonempty).
The genes were subjected to differential expression analysis with DESeq2 (v1.12.4).
Genome_build: hg38
Supplementary_files_format_and_content: Htseq-count standard output (tab-delimited text); DESeq2 standard output plus gene annotation (tab-delimited text)

source_name: placental fibroblasts

growth_protocol: Placental tissue was minced and digested using 0.125% trypsin and 1.25 mg/ml DNase I, filtered through a 100 µm cell strainer, further purified using a Percoll gradient and plated in (DMEM/Ham’s F-12, 10% FBS, 0.05 mg/ml gentamicin, 0.5 µg/ml fungizone) allowing for adherence of stromal cells within 45 min. Supernatant containing non-adherent CTBs was removed and replaced with fresh medium. Cells were passaged at least twice to gain pure fibroblast populations

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) with the DNaseI (Qiagen) digest performed on the column according to manufacturer's protocol
Libraries were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), according to manufacturer's protocol and multiplexed.

value: placental fibroblasts


title: H37Rv_0SUT_D1_rep2

description: Expression.MTB.GeneData.SUT.csv


title: JK6_B16286_Mouse430A_2


title: FIB rep 1


title: 13472_Mouse430A_2


title: a2_1


title: STB rep 3

source_name: in vitro differentiated syncytiotrophoblast

growth_protocol: To obtain syncytiotrophoblast in vitro (STB), isolated vCTBs were seeded onto fibronectin-coated dishes and cultured (DMEM/Ham’s F-12, 10% FBS, 0.05 mg/ml gentamicin, 0.5 µg/ml fungizone) for 72 hours


title: STB rep 2

value: in vitro differentiated syncytiotrophoblast


title: H37Rv_0SUT_D1_rep1

description: Expression.MTB.GeneData.SUT.csv


title: JK5_B11155_Mouse430A_2


title: 18836_Mouse430A_2

value: ATC


title: 18834_Mouse430A_2


title: H37Rv_0SUT_D0_rep1

description: Expression.MTB.GeneData.SUT.csv


title: H37Rv_0.09DEL_D0_rep4

description: Expression.MTB.GeneData.DEL.csv

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of delamanid (0μM, 0.09μM) (as indicated in each sample title).


title: H37Rv_0.09DEL_D1_rep4

description: Expression.MTB.GeneData.DEL.csv


title: CTB-ORG rep 4

source_name: cytotrophoblast organoids

growth_protocol: Cytotrophoblast organoids (CTB-ORG) were established by embedding the isolated vCTBs in 60% Matrigel in the presence of organoid media (advanced DMEM/F12, 10 mM Hepes, 1xB27, 1x N2 and 20mM Glutamine (all Gibco) supplemented with 1 µM R-Spondin, 1 µM A83-01, 100 ng/ml recombinant human epidermal growth factor, 50 ng/ml recombinant murine hepatocyte growth factor, 2.5 µM prostaglandin E2, 3 µM CHIR99021 and 100 ng/ml Noggin.

value: cytotrophoblast organoids


title: STB rep 1


title: CTB-ORG rep 3


title: 18238_Mouse430A_2


title: H37Rv_0.09DEL_D1_rep3

description: Expression.MTB.GeneData.DEL.csv


title: JK21_B17189_Mouse430A_2

value: PTC


title: JK3_B14108_Mouse430A_2


title: 11158_Mouse430A_2


title: CTB-ORG rep 2


title: H37Rv_0.09DEL_D0_rep3

description: Expression.MTB.GeneData.DEL.csv


title: JK20_B18280_Mouse430A_2


title: vCTB rep 3

source_name: villous cytotrophoblast

growth_protocol: Villous cytotrophoblast (vCTBs) cells were isolated from first trimester placentae using three consecutive digestion steps followed by Percoll density gradient centrifugation. vCTBs were collected between 35 and 50% of Percoll layers

value: villous cytotrophoblast


title: H37Rv_0.09DEL_D1_rep2

description: Expression.MTB.GeneData.DEL.csv


title: JK18_B17688_Mouse430A_2


title: H37Rv_0SUT_D0_rep2

description: Expression.MTB.GeneData.SUT.csv

value: 0 μM


title: H37Rv_0.09DEL_D0_rep2

description: Expression.MTB.GeneData.DEL.csv


title: vCTB rep 2


title: vCTB rep 1


title: 04379_24_Cre_Pool 1_Mouse430A_2

source_name: Normal thyroid

value: Pool of normal thyroid glands


title: Plasma_normal control_10

city: Sapporo

first: Masaki

last: Ito

address: North 15 West 7

department: Neurosurgery

institute: Hokkaido University

hyb_protocol: After column purification, samples were completely dried using a vacuum concentrator (Savant DNA 110 SpeedVac® Concentrator, Thermo Fisher, Waltham, MA) on the medium heat setting for about 1 hour. The dried samples were re-suspended in DNase/RNase-free ultrapure water with the Hyb Spike-In solution (microRNA Spike-In Kit, Agilent), and assembled with the hybridization reaction mixture as well as the array slide. The assembled array-slides were placed in a hybridization oven (set to rotate at 20 rpm), then the fluorescently-labeled microRNAs were hybridized to SurePrint® G3 Human miRNA microarray (Release 21.0, Agilent) at 55 °C for 20 hours. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent), and washed 5 minutes with 37 °C GE Wash buffer 2 (Agilent). After minimizing droplets on the slides, slides were put in slide holder for scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan® Microarray Scanner (G2600D) and Agilent Microarray Scan Control software, using the following scan setting: Dye Channel, Green; Scan Region, FullAgilentAlide; Resolution, 3 um high sensitivity; Tiff Dynamic Range, 20 bit; Red PMT Sensitivity, 100%; and Green PMT Sensitivity, 100%.

data_processing: The scanned images were analyzed with Feature Extraction® software (version 11.0.1.1, Agilent), using default parameters (protocol: miRNA_1100_Jul11; Read Only, and Grid: SG13034277_257015610176_S001_grid; from grid_file) to obtain feature intensities, flag calls for outlier pixels and detection, and summarized probe signals with corresponding miRNA annotations based on miRBase Rel 21.0. All the evaluation metrics for miRNA array experiment process, including Labeling and Hybridization were reported as Excellent or Good. All the 21 raw data files were loaded into GeneSpring® software (version 12.6.1). Only detected probes were filtered by flag calls, while entities present in at least one sample of the twins were retained. Raw probe signal values were normalized by quantile shift and log2 transformed as normalized intensities. No baseline transformation was performed.

source_name: peripheral blood plasma

label_protocol: Cyanine 3-pCp-labeled microRNA was prepared from 2-uL of total RNA isolated from 200-uL of plasma, using Agilent’s miRNA Complete Labeling and Hyb Kit (part number 5190-0456). Mean concentration of the total RNA was 205 ± 24 pg/ul (n=21, mean ± standard error of mean) measured by Agilent's Bioanalyzer (RNA 6000 Pico Kit for total RNA) without quantification accuracy. The Labeling Spike-In solution (microRNA Spike-In Kit, Agilent) was spiked into the labeling reaction mixture. The samples were dephosphorylated by incubating the reaction mixture at 37 °C for 30 minutes. Dephosphorylated samples were incubated with 100% DMSO and heated at 100 °C for 5 to 10 minutes, then assembled with the labeling reaction mixture at 16 °C for 2 hours. Cyanine 3-pCp-labeled microRNA, containing DMSO and free Cyanine 3-pCp was purified using MicroBioSpin 6 Columns (BioRad, Hercules, CA).

growth_protocol: not applicable

extract_protocol: Whole blood samples were collected into disodium ethylenediaminotetraacetate tubes, centrifuged (4 °C, 3000 rpm, 30 minutes) immediately, after which plasma samples were stored at -80 °C until further analysis. Total RNA was isolated from 200 uL of the pooled plasma using miRNeasy Serum/Plasma Kit (QIAGEN, Hilden, Germany) according to the manufacturer's protocol. RNA quality was confirmed using the RNA 6000 Pico Kit for total RNA (Agilent, Santa Clara, CA) and the Agilent 2100 Bioanalyzer. Since the Agilent RNA 6000 Pico Kit for total RNA does not guarantee quantitation accuracy, we could not prepare exactly same amount of total RNA input with accurate quantitation for the following array experiment. Therefore, we used a volume of 2-uL of total RNA out of a total volume of 14-uL isolated from 200-uL plasma in the array experiments.

treatment_protocol: not applicable

value: whole blood

tag: disease type

value: healthy-no cerebrovascular disease

tag: gender

value: female

tag: age at blood sampling

tag: age at disease onset

value: not applicable

tag: duration (years) between the latest onset of transient ischemic attack and blood sampling

tag: duration (years) between the latest bypass surgery and blood sampling

tag: comorbidity

tag: familial occurrence of mmd

value: No

tag: angiographical disease stage (mra)

value: no imaging study (no score)

tag: parenchymal brain lesion on mri

value: no imaging study

value: G/G


title: H37Rv_0.09DEL_D0_rep1

institute: University of Washington

description: Expression.MTB.GeneData.DEL.csv

tag: days post drug


title: H37Rv_0.09DEL_D1_rep1

description: Expression.MTB.GeneData.DEL.csv


title: Plasma_normal control_9

value: male


title: CTB-ORG rep 1


title: Plasma_normal control_7

data_processing: The scanned images were analyzed with Feature Extraction® software (version 11.0.1.1, Agilent), using default parameters (protocol: miRNA_1100_Jul11; Read Only, and Grid: SG13034277_257015610176_S001_grid; from grid_file) to obtain feature intensities, flag calls for outlier pixels and detection, and summarized probe signals with corresponding miRNA annotations based on miRBase Rel 21.0. All the evaluation metrics for miRNA array experiment process, including Labeling and Hybridization were reported as Excellent or Good. All the 19 raw data files were loaded into GeneSpring® software (version 12.6.1). Only detected probes were filtered by flag calls, while entities present in at least one sample were retained. Raw probe signal values were normalized by quantile shift and log2 transformed as normalized intensities. No baseline transformation was performed.

label_protocol: Cyanine 3-pCp-labeled microRNA was prepared from 2-uL of total RNA isolated from 200-uL of plasma, using Agilent’s miRNA Complete Labeling and Hyb Kit (part number 5190-0456). Mean concentration of the total RNA was 209 ± 22 pg/ul (n=19, mean ± standard error of mean) measured by Agilent's Bioanalyzer (RNA 6000 Pico Kit for total RNA) without quantification accuracy. The Labeling Spike-In solution (microRNA Spike-In Kit, Agilent) was spiked into the labeling reaction mixture. The samples were dephosphorylated by incubating the reaction mixture at 37 °C for 30 minutes. Dephosphorylated samples were incubated with 100% DMSO and heated at 100 °C for 5 to 10 minutes, then assembled with the labeling reaction mixture at 16 °C for 2 hours. Cyanine 3-pCp-labeled microRNA, containing DMSO and free Cyanine 3-pCp was purified using MicroBioSpin 6 Columns (BioRad, Hercules, CA).


title: Plasma_normal control_8


title: 04379_25_Cre_Pool 2_Mouse430A_2


title: Plasma_normal control_6


title: H37Rv_0DEL_D1_rep4

description: Expression.MTB.GeneData.DEL.csv


title: H37Rv_0DEL_D0_rep4

description: Expression.MTB.GeneData.DEL.csv


title: JK14_WT_P3_Mouse430A_2


title: H37Rv_0DEL_D1_rep3

description: Expression.MTB.GeneData.DEL.csv


title: Plasma_normal control_5


title: JK17_B17180_Mouse430A_2


title: H37Rv_0DEL_D0_rep3

description: Expression.MTB.GeneData.DEL.csv


title: Plasma_normal control_4


title: Plasma_normal control_3


title: JK13_WT_P2_Mouse430A_2


title: H37Rv_0DEL_D1_rep2

description: Expression.MTB.GeneData.DEL.csv


title: H37Rv_0DEL_D0_rep2

description: Expression.MTB.GeneData.DEL.csv


title: JK12_WT_P1_Mouse430A_2


title: 1_JK16_WT_P5_Mouse430A_2


title: Plasma_normal control_2


title: Plasma_normal control_1


title: JK2_B14107_Mouse430A_2


title: H37Rv_0DEL_D0_rep1

description: Expression.MTB.GeneData.DEL.csv


title: H37Rv_0DEL_D1_rep1

description: Expression.MTB.GeneData.DEL.csv


title: Plasma_MMD case_9

value: Moyamoya diease-Transient ischemic attack

value: Yes

value: A/G


title: Model_rep3

city: Shanghai

first: Qilong

last: Chen

address: 1200, Cailun Road

institute: TCM center

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent, Santa Clara, CA, USA).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm.

source_name: Untreated mouse tumor,replicate 3

label_protocol: The total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: Hepa1-6 cell was cultured in DMEM medium, supplemented with 10% fetal bovine serum, 100 U/ml penicillin-streptomycin mixed antibiotics at 37 °C in a humidified 5% CO2 incubator. The mice of were inoculated in the right flank, which with 0.1 ml of logarithmic phase Hepa1-6 cells.

extract_protocol: The total RNA were extracted using TRIzol reagent (Invitrogen, Grand Island, NY, USA) and quality evaluations were performed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: According to the conversion of the human clinical dosage and the mouse body surface area, the drug dose of mouse was calculated. The conversion coefficient of human and mouse was 9.1 (the human body weight was defined as 60 kg), and the total GLE dose of a 10 g mouse for one day was 0.023 g . The model group mice were treated with 0.9% NaCl, 0.2 ml per mouse, and once a day for 28 consecutive days.

value: tumor

tag: age

tag: strain/genotype

value: Hepa1-6-bearing C57 BL/6 mouse model

tag: treatment

value: untreated

tag: disease state

value: HCC


title: Model_rep1

source_name: Untreated mouse tumor,replicate 1


title: GLE_treated_rep3

source_name: GLE treated mouse tumor, replicate 3

value: Hepa1-6-bearing C57 BL/6 mouse

value: Ganoderma lucidum extract (GLE)


title: GLE_treated_rep2

source_name: GLE treated mouse tumor, replicate 2


title: Model_rep2

source_name: Untreated mouse tumor,replicate 2


title: Plasma_MMD case_8

value: whole blood


title: GLE_treated_rep1

source_name: GLE treated mouse tumor, replicate 1


title: Plasma_MMD case_7

value: female


title: Plasma_MMD case_6

value: hypertension


title: Kc167_scs_Rep2

city: Baton Rouge

first: Craig

middle: M.

last: Hart

state: Louisiana

address: 202 Life Science Building, LSU Campus

department: Biological Sciences

institute: Louisiana State University

data_processing:
Library strategy: 4C-seq
Viewpoint sequences at the 5’ and 3’ ends were trimmed using Btrim . The remaining sequences were aligned to the Drosophila Release 6.01 genome using bowtie2 The resulting sam files were converted to bam files, filtering out sequences with Q-scores < 30, for use in the fourSig analysis suite . Reads from both ends of viewpoints were combined for 4C analysis.
In fourSig, bamToReTab.pl converted bam files to tab files, which are tables of reads mapped to restriction fragments generated by the first 4C restriction enzyme. The tab files were used by fourSig.R to calculate significant cis- and trans-interaction intervals. Additional information required for the script to run are: chromosomal location of the viewpoint, sliding window size, and FDR cutoff value. Significance thresholds for calculating FDR values were generated using 1000 random shuffling steps. We excluded ±2 kb from the viewpoint while calculating significant interactions. Sliding window sizes of 5 and 20 were used for cis- and trans-interactions, respectively, with an FDR value of 0.001 and an FDR probability value of 0.01.
Genome_build: Dmel R6.01
Supplementary_files_format_and_content: Viewpoint interactions BED format

organism: Drosophila melanogaster

source_name: cultured cells

growth_protocol: Drosophila Kc cells (Drosophila Genomics Resource Center Kc167) were grown at 25°C in Shields and Sang M3 medium (Sigma) with 1x Pen-Strep (Gibco) and 5% fetal bovine serum (Gibco).

extract_protocol:
Cells (500 ml at ~9x106 cells/ml) were spun down (400g, 4°C, 10 minutes) two times and resuspended in 30 ml PBS both times. Protein-DNA complexes were cross-linked by adding 37% formaldehyde (final concentration 1%) to the cells and incubating at room temperature for 10 minutes. Formaldehyde was quenched by adding 1.25 M glycine (final concentration 125 mM). The cells were washed with 30 ml PBS, resuspended in 10 ml lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP40), and incubated on ice for 15 minutes. The cells were dounced 15 times on ice with a B pestle, incubated on ice for another 15 minutes, then dounced 15 times again. The nuclei were pelleted at 2000g at 4°C for 5 minutes.
Depending on the viewpoint, 5x108 nuclei were resuspended in 500 µl DpnII (scs’, hts, snf) or NlaIII (RpS6) restriction enzyme buffer and distributed into 50 µl aliquots in 10 tubes. Nuclei were lysed by adding 10% SDS (final concentration: 0.3%) and shaking at 37°C overnight. SDS was diluted to 0.1% with DpnII or NlaIII restriction enzyme buffer, and the SDS was quenched by adding 20% Triton X-100 (final concentration 1.1%) and shaking at 37°C overnight. The following day 22.5 units of DpnII or 15 units of NlaIII (New England Biolabs) was added to each of the appropriate 10 tubes and shaken at 37°C overnight. The same amount of restriction enzyme was added the next day and shaken again at 37°C overnight. Restriction digestion efficiency was determined by isolating DNA from 5% of the digested samples to determine the DNA concentration and perform PCR using primers spanning viewpoint restriction sites (S1 Table), as described [34], and found to be approximately 90% cut. Restriction digestions were stopped by adding SDS to 1.6% and heating at 65°C for 30 minutes. Samples cut with the same restriction enzyme were pooled, 30 µg was diluted to 2 ng/µl with ligation buffer, and 20% Triton X-100 was added to a final concentration of 1.1%. Samples were incubated at 37°C for 4 hours, then 6000 units T4 DNA ligase (New England Biolabs) was added and incubated at 4°C for 72 hours. After ligation, Proteinase-K was added to 0.1 mg/ml and incubated overnight at 65°C. Next samples were treated with 0.22 ng/ml RNAse A at 37°C for one hour, and DNA was extracted using phenol chloroform and ethanol precipitated. The DNA pellet was resuspended in 100 µl TE buffer and quantified by Qubit (Thermo-Fisher). We then set up second restriction digestions, using 3 µg per viewpoint. For DNA first cut with DpnII, we used CviQI (scs’) or NlaIII (snf and hts); for DNA first cut with NlaIII we used DpnII (RpS6). After the second digestion samples were phenol chloroform extracted, ethanol precipitated, resuspended, and 1 µg was ligated at 0.8 ng/µl at 16°C overnight. The final ligated DNA was again extracted, precipitated and quantified by Qubit. This DNA was the input for making 4C libraries. The four 4C libraries were made by inverse PCR using Phusion polymerase (New England Biolabs) and primers with Ion Torrent PGM barcodes and adapters incorporated into the primer sequences (S1 Table). Two libraries were made for each of the four viewpoints, one for each end of a viewpoint. PCR products were size selected on a 2% agarose gel (100 – 500 bp). DNA from the gel was extracted with a Wizard PCR clean-up kit (Promega) and submitted to the LSU Genomics Facility for Ion Torrent sequencing.

tag: cell type


title: Plasma_MMD case_5

tag: tissue


title: Scx siRNA rep3

city: Blacksburg

first: Linda A

last: Dahlgren

state: Virginia

address: Phase II Duck Pond Drive

department: Large Animal Clinical Sciences

institute: Virginia Tech

description:
Sample 6
processed data file: scram_v_scxsirna_out.txt

data_processing:
Basecalls performed using Real Time Analysis v1.18.54.
Base call to FASTQ conversion and demultiplexing using bcl2fastq v1.8.4.
Raw sequence reads were evaluated for quality using FastQC v0.11.3 and mapped to the reference genome (EquCab2) using HISAT2 v2.0.3 and default parameters.
Reads were mapped to known features (Ensembl EquCab2 version 90) using HTSeqv0.6.1.post1 in union mode.
Differential gene expression between scramble control and Scx knockdown samples was determined using DESEQ2 v1.12.4.
Genome_build: EquCab2
Supplementary_files_format_and_content: scram_v_scxsirna_out.txt: Tab-delimited text file containing matrix table of the mean normalized count for all samples, log2 fold change, adj p-value, and normalized counts for each sample.

organism: Equus caballus

source_name: Superficial digital flexor tendon

growth_protocol: Tenocytes were isolated by overnight collagenase digest, strained, pelleted, and plated at 6,000/cm2 in growth medium (Dulbecco’s modified Eagle’s medium [DMEM; 4.5 g/L glucose], 10% FBS, 2 mM L-glutamine, 50μg/mL ascorbic acid, 25mM HEPES, 100 units/mL penicillin, and 100 µg/mL streptomycin). Growth medium was exchanged every 3 days and cells were passaged upon reaching 70% confluence using 0.25% trypsin-EDTA.

extract_protocol:
Thirty minutes after completion of the final strain cycle, cells were collected into guanidine isothiocyanate-phenol solution (TRIzol® Reagent, Invitrogen, Carlsbad, CA) for RNA isolation by column purification according to manufacturer instructions (Direct-zol Microprep, Zymo Research, Irvine, VA). RNA was evaluated both spectrophotometrically for quantity (NanoDrop, Thermo Scientific, Waltham, MA) and by electrophoresis for RNA integrity (Bioanalyzer, Agilent, Santa Clara, CA).
1 ug of total RNA per sample was enriched for polyA RNA (PrepX PolyA mRNA isolation kit, Wafergen, Fremont, CA) and converted to cDNA libraries (PrepX RNA-seq for Illumina Library Kit, Wafergen). Libraries underwent 13 rounds of PCR to generate the final cDNA libraries for sequencing.

treatment_protocol: Tenocytes were transfected (Nucleofector™ system, Lonza, Cologne, Germany) with a siRNA targeting the equine Scx mRNA (Sense: 5’-AGAGAAAGUUGAGCAAGGAtt-3’, Antisense: 5’-UCCUUGCUCAACUUUCUCUgg-3’, GenBank ref. NM_001105150.1; Silencer™ Select, Ambion, Life Technologies) or a non-targeting scramble siRNA control (Silencer™ Select Negative Control No. 1, Catalog #4390843, Life Technologies). Cells were resuspended at 1x10^6/100 µL in Nucleofector™ Cell Line Solution V (Lonza) containing 10 nmol siRNA or scramble control, transferred to cuvettes, and nucleofected using the T20 program. Cells were recovered in growth medium for 15 minutes at 37°C before plating at 200,000 cells/well in UniFlex® culture plates (Collagen type I coated; Flexcell International, Hillsborough, NC). Cells were allowed to adhere for 24 hours before being synchronized in culture medium containing 1% FBS. After 18 hours, cells were exposed to cyclic uniaxial strain (1%, 0.5 Hz, 2 hours/day) every 24 hours for 3 days.

value: SDFT derived tenocytes

tag: passage

tag: cyclic strain

value: FlexCell Uniflex, collagen I coated, 1%, 0.5 Hz, 2 hours/day for 3 days

tag: sirna exposure

value: Scx siRNA


title: Plasma_MMD case_4

tag: disease type

tag: gender

tag: age at blood sampling

tag: age at disease onset

value: No


title: Kc167_snf_Rep2


title: Plasma_MMD case_3

value: male

tag: duration (years) between the latest onset of transient ischemic attack and blood sampling

tag: duration (years) between the latest bypass surgery and blood sampling

tag: comorbidity

tag: familial occurrence of mmd


title: Kc167_hts_Rep2


title: Kc167_snf_Rep1


title: Sulfisoxazole (SFX) treated MDA-MB231 (24 h treatment)_rep3

city: Daegu

first: Moon-Chang

last: Baek

address: Gukchebosang-ro 680

country: South Korea

institute: Kyungpook National University

description: Gene expression data from DMSO sulfisoxazole-treated MDA-MB231

hyb_protocol: 5.5μg of labeled DNA target was hybridized to the Affmetrix GeneChip Clariom S Human Array at 45 °C for 16hours. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450

scan_protocol: Hybridized arrays were scanned on a GCS3000 Scanner (Affymetrix)

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix Power Tools (APT).

label_protocol: The sense cDNA was fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using  the GeneChip WT Terminal labeling kit

growth_protocol: SKMEL28 cells were grown under following condition: Eagle's Minimum Essential Medium (EMEM) with 10 % fetal bovine serum (FBS) and 1% antibiotic and antimycotic agent. MDA-MB231 cells were grown under following condition: Dulbecco Modified Eagle Medium (DMEM) with 10 % fetal bovine serum (FBS) and 1% antibiotic and antimycotic agent.

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

treatment_protocol: Cells were treated 100μM of SFX for 24 hours under serum-free condition.

tag: cell line

value: mammary gland/breast

value: epithelial

tag: disease

value: adenocarcinoma/derived from metastatic site


title: Scx siRNA rep2

description:
Sample 5
processed data file: scram_v_scxsirna_out.txt


title: Scx siRNA rep1

description:
Sample 4
processed data file: scram_v_scxsirna_out.txt


title: Plasma_MMD case_2

value: Moyamoya diease-Transient ischemic attack

value: Yes

tag: angiographical disease stage (mra)

tag: parenchymal brain lesion on mri

value: A/G


title: Scramble control rep3

description:
Sample 3
processed data file: scram_v_scxsirna_out.txt

tag: cell type

value: Scramble control siRNA


title: Sulfisoxazole (SFX) treated MDA-MB231 (24 h treatment)_rep1

tag: tissue


title: DMSO treated MDA-MB231 (24 h treatment)_rep1

description: Gene expression data from DMSO (vehicle)-treated MDA-MB231


title: Kc167_rps6_Rep2


title: Plasma_MMD case_1


title: Sulfisoxazole (SFX) treated MDA-MB231 (24 h treatment)_rep2


title: Kc167_rps6_Rep1


title: Kc167_scs_Rep1


title: DMSO treated MDA-MB231 (24 h treatment)_rep2


title: DMSO treated MDA-MB231 (24 h treatment)_rep3


title: Plasma_non-affected MMD-discordant MZ twins

value: healthy-no cerebrovascular disease

value: not applicable

value: normal (no score)


title: Sulfisoxazole (SFX) treated SKMEL28 (24 h treatment)_rep3

description: Gene expression data from sulfisoxazole-treated SKMEL28

value: skin

value: melanoma

value: malignant melanoma


title: Scramble control rep2

description:
Sample 2
processed data file: scram_v_scxsirna_out.txt

value: SDFT derived tenocytes

tag: passage

value: FlexCell Uniflex, collagen I coated, 1%, 0.5 Hz, 2 hours/day for 3 days


title: Sulfisoxazole (SFX) treated SKMEL28 (24 h treatment)_rep2


title: Sulfisoxazole (SFX) treated SKMEL28 (24 h treatment)_rep1


title: Scramble control rep1

description:
Sample 1
processed data file: scram_v_scxsirna_out.txt

tag: cyclic strain


title: Kc167_hts_Rep1


title: Plasma_affected MMD-discordant MZ twins

value: whole blood

value: female


title: DMSO treated SKMEL28 (24 h treatment)_rep2

description: Gene expression data from DMSO (vehicle)-treated SKMEL28


title: DMSO treated SKMEL28 (24 h treatment)_rep3


title: Rhodobacter_Li_KPDS

status: Public on Aug 01 2018

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: G4-seq protocol

data_processing:
library strategy: Other (G4-Seq2: modified DNA-Seq)
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: Genome sources;
Homo sapiens (hg19) from http://hgdownload.cse.ucsc.edu/downloads.html/
Mus Musculus (mm10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Danio Rerio (danRer10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Drosophila Melanogaster (dm6) from http://hgdownload.cse.ucsc.edu/downloads.html/
Caenorhabditis elegans (ce10) from http://www.wormbase.org/species/c_elegans/
Saccharomyces cerevisiae (sacCer3) from http://hgdownload.cse.ucsc.edu/downloads.html/
Leishmania major (LmjF_v6.1_all_20131105) from www.genedb.org/Homepage/Lmajor
Trypanosoma Brucei (TriTrypDB-9.0_TbruceiTREU927) from http://www.genedb.org/Homepage/Tbruceibrucei927
Plasmodium falciparum (PlasmoDB-28_Pfalciparum3D7) from http://plasmodb.org/
Arabidopsis thaliana (Arabidopsis_thaliana.TAIR10.31.dna.genome) from https://www.arabidopsis.org/
Escherichia coli (Ecoli_K12) from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/
Rhodobacter sphaeroides from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/. Annotation files sources: Arabidopsis thaliana (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release%2FTAIR10_gff3)
Caenorhabditis elegans (ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/)
Drosophila Melanogaster (ftp://ftp.ensembl.org/pub/release-87/gff3/drosophila_melanogaster/)
E. coli (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/gff3/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/)
Homo sapiens (USCS annotation for genes:  http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html
Gencode annotation for non-coding RNAs: https://www.gencodegenes.org/releases/19.html)
Leishmania major( ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Mus musculus (ftp://ftp.ensembl.org/pub/release-87/gff3/mus_musculus/)
Plasmodium falciparum (http://plasmodb.org/common/downloads/release-28/Pfalciparum3D7/gff/data/)
Rhodobacter sphaeroides (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/gff3/bacteria_0_collection/rhodobacter_sphaeroides_2_4_1/)
Saccharomyces cerevisiae (ftp://ftp.ensembl.org/pub/release-87/gff3/saccharomyces_cerevisiae/)
Trypanosoma brucei (ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Danio rerio (ftp://ftp.ensembl.org/pub/release-87/gff3/danio_rerio/).
Supplementary_files_format_and_content: bedgraphs for coverage and mismatch levels; bed files for scoring G-quadruplexes (separated by strand)

organism: Cereibacter sphaeroides

source_name: whole cell

growth_protocol: Organisms were cultured in standard conditions, withouth any treatment.

extract_protocol:
DNA was extracted with standard phenol/chloroform extraction as previously described in Chambers et. al 2015 (doi: 10.1038/nbt.3295), except for samples where DNA was purchased from companies (see source and characteristics field).
Genomic DNA samples were  sonicated and the library prepared, as in Chambers et al. 2015 (doi: 10.1038/nbt.3295). Libraries were prepared using the TruSeq Nano DNA LT Library Prep Kit (Nano in each sample file name), or with PCR-Free Library Prep Kit (PCRFree or not specified in each sample file name).

treatment_protocol: All samples were untreated, wild type organisms.

value: whole cell


title: Rhodobacter_Li_K

description: G4-seq protocol


title: DMSO treated SKMEL28 (24 h treatment)_rep1


title: C5-C6

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Raw FASTQ files from the sequencing were processed in Illumina BaseSpace to filter reads with a q score < 30
Alignment was performed to version mm10 of the mouse genome and annotated to RefSeq (5-2-17) using the Bowtie2 algorithm
BAM files were downloaded into Partek Flow (Partek, Inc., St Louis, MO) for data summarization, quantification, and normalization of RNA counts into total reads per kilobase of gene model per million reads (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: separate csv matrix files include raw counts and RPKM values for each sample

source_name: Kidney cortex

extract_protocol:
Kidney cortex was removed from mice placed in RNA Later, and RNA extracted using Trizol reagent followed by RNeasy (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
Stranded mRNA-seq

tag: strain

value: kidney

tag: Sex

value: male

tag: age

value: adult

tag: disease state

value: control

tag: treatment

value: Water


title: W5-W6

value: glomerulonephritis (GN+)


title: H3-H4

value: Captopril


title: H5-H6


title: H1-H2


title: S5-S6


title: W1-W2


title: W3-W4


title: C1-C2


title: S3-S4


title: DRG RNA-seq cipn model [cipn input biosample8]

city: Richardson

first: Theodore

middle: John

last: Price

state: TX

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

institute: The University of Texas at Dallas

description:
DRG_CIPN_input8_TPM
3' sequencing assay : Quantseq assay (Lexogen)

data_processing:
Sequence files generated by the Illumina NextSeq500 sequencer were downloaded from BaseSpace. An  Initial quality check using FastQC 0.11.5 (Babraham Bioinformatics) was done on the sequencing files and then  trimming was performed on the server with the FASTQ Toolkit. Sequences were trimmed with optimized  parameters (13 bases from 3’-end, 17 bases from 5’-end, and any poly-adenine longer than 2 bases from the 3’  side). Trimming parameters were optimized based on FastQC results and mapping rate, as well as manually  checking high reads or abundant chromosomal regions with IGV 2.3.80. The trimmed sequencing samples were  then processed using TopHat 2.1.1 (with Bowtie 2.2.9) and mapped to the mouse reference genome (NCBI  reference assembly GRCm38.p4) and reference transcriptome (Gencode vM10) generating files in .bam format.
We filtered reads such that uniquely mapped reads were processed for further analysis (Supplementary Table 6).  Processed .bam files were then quantified for each gene using Cufflinks 2.2.1 with gencode.vM10 genome  annotation. Since reads only mapped to the 3’UTR of the gene, read counts were not normalized by length by  the using the Cufflinks option -- no–length–correction. Relative abundance for the ith gene was determined by  calculating transcripts per million (TPM) by constraining Cufflinks reported RPKMs to sum to a million for all coding genes in each sample to provide TPMs.
Two samples were pooled in silico to create biosample 7 (biosample7_subsample1 and biosample_subsample2) : the way this was done was to take a weighted average of TPMs based on the number of mapped reads for each sample.
Finally, TPM values were normalized to upper decile for each biological replicate and udTPM  (upper decile TPM) were used for analysis, to provide uniform processing for samples with varying sequencing  depth and because of varying number of genes in the transcriptome and translatome
Details about post processing steps can be found at : https://www.utdallas.edu/bbs/painneurosciencelab/sensoryomics/cipntrap/
Genome_build: GRCm38.p4 (reference annotation GENCODE vM10)
Supplementary_files_format_and_content: Zipped (gzip 1.3.12), tab separated text file (text encoding : Unicode UTF-8 with Unicode Byte Order Mark, end of line : \n) with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes

source_name: Dorsal root ganglia (DRG)

growth_protocol: Rosa26fsTRAP mice were generated (P. Zhou et al, Proc Natl Acad Sci U S A 110, 15395 (Sep 17, 2013)) and purchased from Jackson Laboratory (Stock number: 022367). Transgenic mice expressing Cre recombinase under the control of the Scn10a (Nav1.8) promoter were obtained initially from Professor John Wood (University College London) but are commercially available from Infrafrontier (EMMA ID: 04582). The initial characterization of these mice demonstrated that the introduction of the Cre recombinase in heterozygous animals does not affect pain behavior, and their DRG neurons have normal electrophysiological properties (2). Nav1.8cre mice on a C57BL/6J genetic background were maintained and bred at the University of Texas at Dallas. Upon arrival, Rosa26fstrap mice were crossed to Nav1.8cre to generate the Nav1.8-trap mice that express a fused EGFP-L10a protein in Nav1.8 expressing neurons. All experiments were carried out using male and female littermates aged 8 to 12 weeks old. Mice were group housed (4 maximum) in non-environmentally enriched cages with food and water ad libitum in a 12h light-dark cycle. Room temperature was maintained at 21 ± 2°C.

extract_protocol:
Nav1.8-trap male and female mice were decapitated and dorsal root ganglia (DRG) rapidly dissected in ice-cold dissection buffer (1X HBSS (Invitrogen 14065006), 2.5 mM HEPES, 35 mM Glucose, 4 mM NaHCO3, 100 μg/ml cycloheximide, 0.001V 2 mg/ml emetine). DRGs were transferred to ice-cold polysome buffer (20 mM HEPES, 12 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 100 μg/ml cyclohexamide, 20 μg/ml emetine, 40U/ml SUPERase IN (Promega), 1 μl DNAse and protease inhibitor and homogenized using a dounce homogenizer.  Samples were centrifuged at 3,000 x g for 10 min to prepare post-nuclear fraction (S1). Then, 1% NP-40 and 30 mM DHPC were added to the S1 fraction and then centrifuged at 15,000 x g for 15 min to generate a post-mitochnodrial fraction (S20). A 200 μl sample of S20 was removed for use as Input, and 800 μl of S20 was incubated with protein G-coated Dynabeads (Life Technologies) bound to 50 μg of anti-GFP antibodies (HtzGFP-19F7 and HtzGFP-19C8, Memorial Sloan Kettering Centre) for 3 hrs at 4°C with end-over-end mixing. Anti-GFP beads were washed with high salt buffer (20 mM HEPES, 5 mM MgCl2, 350 mM KCl, 1% NP-40, 0.5 mM DTT and 100 μg/ml cyclohexamide) and RNA was eluted from all samples using a Direct-zol kit (Zymo Research) according to the manufacturer’s instructions. RNA yield was quantified using a Nanodrop system (ThermoFisher Scientific) and RNA quality was determined by a fragment analyzer (Advanced Analytical Technologies Inc.) For RNA-seq, the pulldown step was not performed.
Libraries were generated from 100 ng to 1 ug of total RNA using Quantseq 3ʹ mRNA-Seq library kit (Lexogen) with RiboCop rRNA depletion kit (Lexogen) treatment according to the manufacturer’s protocols. The endpoint PCR amplification cycle number for each sample was determined by quantitative PCR (qPCR) assay with PCR Add-on kit for Illumina (Lexogen). The cycle number was selected when the fluorescence value reached 33% of the maximum for each sample. Purified libraries were quantified by Qubit (Invitrogen) and the average size was determined by fragment analyzer (Advanced Analytical Technologies Inc.) with high sensitivity NGS fragment analysis kit. Libraries were then sequenced on an Illumina NextSeq500 sequencer using 50-bp single-end reads. [library construction protocol]

treatment_protocol: Mice were treated with paclitaxel (4mg/kg in cremaphor vehicle) by intraperitoneal injection every other day for 8 days. They received a total of 4 injections for a cumulative dose of 16 mg/kg.  Vehicle treated animals were dosed in exactly the same way but without paclitaxel.

value: DRG

value: Paclitaxel treated

value: Nav1.8cre mice on C57BL/6J  background

tag: fraction

value: rRNA depleted RNA


title: DRG trap cipn model [cipn trap biosample5]

description:
DRG_CIPN_TRAP5_TPM
3' sequencing assay : Quantseq assay (Lexogen)

value: DRG / Scn10a +ve cells

value: rRNA depleted RNA associated with L10a + eGFP pulldown


title: DRG trap cipn model [cipn trap biosample7 subsample2]

description:
DRG_CIPN_TRAP7_subsample2_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG trap cipn model [cipn trap biosample7 subsample1]

description:
DRG_CIPN_TRAP7_subsample1_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG trap cipn model [cipn trap biosample8]

description:
DRG_CIPN_TRAP8_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq cipn model [cipn input biosample7 subsample1]

description:
DRG_CIPN_input7_subsample1_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq cipn model [cipn input biosample7 subsample2]

description:
DRG_CIPN_input7_subsample2_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq cipn model [cipn input biosample5]

description:
DRG_CIPN_input5_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq cipn model [cipn input biosample6]

description:
DRG_CIPN_input6_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG trap normal [normal trap biosample3]

description:
DRG_normal_TRAP3_TPM
3' sequencing assay : Quantseq assay (Lexogen)

value: Normal


title: DRG trap normal [normal trap biosample4]

description:
DRG_normal_TRAP4_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: C3-C4


title: DRG trap normal [normal trap biosample1]

description:
DRG_normal_TRAP1 _TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG trap cipn model [cipn trap biosample6]

description:
DRG_CIPN_TRAP6_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq normal [normal input biosample4]

description:
DRG_normal_input4_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq normal [normal input biosample3]

description:
DRG_normal_input3_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: DRG RNA-seq normal [normal input biosample2]

description:
DRG_normal_input2_TPM
3' sequencing assay : Quantseq assay (Lexogen)


title: S1-S2


title: MEL2 20% O2_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing was performed with 12 samples per lane, using 50 bp single-end reads. The quality of resultant raw FASTQ data files was assessed with FastQC
Processed using the following pipeline: FASTQ Groomer to convert raw Illumina FASTQ files to Sanger Quality score format, Trim Galore! to trim the 13 bp of Illumina standard adapters, RNA STAR to align reads to the UCSC GRCh37/hg19 human reference genome, featureCounts to measure gene expression, and DESeq2 to identify DEGs
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: .csv DESeq files comparing 5% and 20% oxygen treatments within cell lines, and Cell lines at each oxygen treatment.

source_name: embryonic stem cell

tag: oxygen


title: DRG RNA-seq normal [normal input biosample1]

description:
DRG_normal_input1_TPM
3' sequencing assay : Quantseq assay (Lexogen)