title: MCLR2

city: Hefei

first: Zhao

last: Sujuan

address: Meishan road 81

institute: Anhui Medical University

description:
Gene expression of zebrafish testes after 6 weeks in 20µg/L MCLR groups
20-2

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

organism: Danio rerio

source_name: zebrafish testes,20µg/L MCLR, replicate 2

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen life technologies) according to the manufacturer's protocol. RNA quantity was determined using a NanoDrop ND1000 (Nanodrop Technologies, Wilmington, DE, USA) and the integrity of RNA can be assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: Zebrafish were exposed to 0 and 20µg/L MCLR for 6 weeks and fresh testes from zebrafish were obtained for microarray assay.

value: testes

value: 4 months

tag: agent

value: MCLR


title: HET embryo_HET father_rep1

status: Public on Feb 09 2018

type: RNA

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

country: Australia

institute: Monash University

description: Gene expressin in stage matched heterozygous E8.5 embryo sired by heterozygous Eedl7Rn5-1989SB males

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was  fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x  Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression  hybridisation buffer was added and 40ul of sample hybridised for 17 hours at  65oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays  were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1  minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray  scanner using one color scan settings for 8x60k array slides; scan area  61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1  (Agilent) using default parameters (protocol GE1-1100_Jul11 and  Grid:028005_D_F_20120201) to obtain background subtracted and spatially  detrended Processed Signal intensities.

molecule: total RNA

organism: Mus musculus

source_name: 184-7_E8.5 embryo_HET father

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.2ug total RNA using the  One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012)  according to the manufacturer’s instructions, followed by RNeasy column  purification (Qiagen). Dye incorporation and cRNA yield were checked with the  NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the Genelute Mammalian total RNA miniprep kit (Sigma, RTN70-1KT), DNAse treated using TURBO DNA-free™ Kit (Ambion, AM1907) and purified from the DNAse reaction using Agencourt RNAClean XP (Beckman coulter, A63987).

treatment_protocol: Homozygous (HOM) and heterozygous (HET) Eedl7Rn5-1989SB C57bl6/129 male mice were time mated with C57bl6/129 wild-type mice. Embryos were collected 8.5 days after the female was plugged. Samples were stored at -80 °C until RNA extraction. RNA was extracted from accurately match samples of the same developmental time points.

tag: father's genotype

value: HET

tag: mothers's genotype

value: WT

tag: mouse strain and backgroud

tag: embryo's sex

value: F

tag: tissue

value: embryo


title: HET embryo_HET father_rep4

source_name: 237-1_E8.5 embryo_HET father

value: M


title: control 2

country: China

description:
Gene expression of zebrafish testes after 6 weeks in 0µg/L MCLR groups
0-2

source_name: zebrafish testes, control, replicate 2

tag: age

value: control


title: MCLR1

description:
Gene expression of zebrafish testes after 6 weeks in 20µg/L MCLR groups
20-1

source_name: zebrafish testes,20µg/L MCLR, replicate 1


title: WT embryo_HET father_rep3

description: Gene expressin in stage matched wild-type E8.5 embryo sired by heterozygous Eedl7Rn5-1989SB males

source_name: 246-2_E8.5 embryo_HET father

treatment_protocol: Heterozygous (HET) and wild-type (WT) Eedl7Rn5-1989SB C57bl6/129 male mice were time mated with C57bl6/129 wild-type female mice. Embryos were collected 8.5 days after the female was plugged. Samples were stored at -80 °C until RNA extraction. RNA was extracted from accurately match samples of the same developmental time points.

tag: mother's genotype

tag: mouse strain and background


title: WT embryo_WT father_rep4

description: Gene expressin in stage matched wild-type E8.5 embryo sired by wild-type Eedl7Rn5-1989SB males

source_name: 2.2-4_E8.5 embryo_WT father


title: WT embryo_HET father_rep4

source_name: 2.5-7_E8.5 embryo_HET father


title: Control

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

country: USA

institute: Mayo Clinic

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performedusing XRAY sofware (Boutique).
Probe signal intensities were normalized by scaling to a common median value.  A scaling factor was added to each value such that for each chip, the median probe value was equal to the probe median expression across all arrays. Background correction was performed by subtracting the median expression score of background probes with similar GC content.

label: Biotin

organism: Homo sapiens

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were cultured on collagen plated 35mm plates

extract_protocol: RNA was isolated using Trizol. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Cells were transfected with control or TUC338 LNA

tag: cell line

tag: transfection

value: Control


title: YAP-OE +DOX rep2

type: SRA

city: Vancouver

first: Pamela

last: Hoodless

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratories

country: Canada

institute: BC Cancer Agency

description: mRNA

library_source: transcriptomic

data_processing:
De-multiplexed read sequences were aligned to the UCSC mouse mm10 (GRCm38) reference sequence using TopHat2 splice junction mapper with Bowtie2.
Fragments per kilobase of exon per million reads (FPKM) were calculated using Cufflinks.
RNA-seq gene expression values were compared for significance using Cuffdiff2.
Genes were considered differentially expressed if expression was greater than or equal to 1 FPKM in -DOX or +DOX conditions, fold change greater than or equal to 2, and FDR less than 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.genes.fpkm_tracking: Tab-delimited text files include FPKM values for each gene.

source_name: Liver hepatocytes

extract_protocol:
Livers were perfused with a PBS and collagenase mixture through the inferior vena cava, minced with a razor blade, and passed through a 40 µm strainer. Hepatocytes were separated by low-speed centrifugation (50 g x 30 s) and washed with PBS. Total RNA from hepatocytes was extracted using RNeasy Mini Kit (Qiagen). RNA quality was assessed on the BioAnalyzer (Agilent Technologies).
Qualifying samples were prepared following the standard protocol for the TruSeq stranded mRNA library kit (Illumina) on the Illumina Neoprep automated nanofluidic library prep instrument. Triplicate libraries were sequenced on the Illumina NextSeq 500.

tag: strain/background

value: Liver

value: 8-12 weeks

tag: overexpression

value: YAP


title: WT embryo_HET father_rep2

source_name: 236-1_E8.5 embryo_HET father


title: YAP-OE +DOX rep3

description: mRNA


title: YAP-OE -DOX rep2

description: mRNA


title: YAP-OE -DOX rep3

description: mRNA


title: TUC338 knockdown

value: TUC338 knockdown


title: YAP-OE -DOX rep1

description: mRNA


title: WT embryo_WT father_rep3

source_name: 2.2-2_E8.5 embryo_WT father


title: control 1

description:
Gene expression of zebrafish testes after 6 weeks in 0µg/L MCLR groups
0-1

source_name: zebrafish testes, control, replicate 1


title: WT embryo_WT father_rep1

source_name: 124-2_E8.5 embryo_WT father


title: WT embryo_HET father_rep1

source_name: 184-1_E8.5 embryo_HET father


title: Inguinal WAT, cold exposure, wild type mouse, replicate 5

status: Public on Feb 10 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

label: biotin

source_name: Inguinal white adipose tissue from a wild type mouse housed at cold (5 °C) for 10 days

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Three to four months old male wildtype and PPARα−/− mice that had been backcrossed on a pure C57Bl/6J background for more than 10 generations were acquired from Jackson Laboratories (no. 000664 and 008154, respectively). The mice were further bred at the animal facility of Wageningen University under specific pathogen free conditions to generate the number of mice necessary for the experiments.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Forty 3-4-month-old male wildtype and PPARα−/− mice were placed at thermo-neutral temperature (28 °C) for 5 weeks. Thereafter, 20 wildtype and 20 PPARα−/− mice were randomly distributed across 2 groups: half of the mice of each genotype were kept at thermo-neutral temperature and half of the mice of each genotype was placed at 21 °C for one week followed by a period of 10 days at in the cold (5 °C) (n = 10 per group). For cold exposure, mouse cages were placed in a cold cabinet that was kept at 5 °C (ELDG800, VDW Coolsystems, Geldermalsen). Mice had ad libitum access to chow feed and water.

tag: background strain

tag: genotype

value: wild type

tag: jackson laboratories mouse strain id

tag: housing temperature

value: cold (5 C) for 10 days

tag: Sex

value: male


title: WT embryo_WT father_rep2

source_name: 2.2-1_E8.5 embryo_WT father

tag: father's genotype


title: YAP-OE +DOX rep1

description: mRNA


title: PL043

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description:
Single cell RNA-seq
processed data file: All_WT_Gene_expression.txt

data_processing:
trimmomatic-0.35 was used for data trimming. Chop head 5bp of each read, slide the window with 4bp and trim the read with quality less than 20, the minimum length of read is 25bp and max length is 50bp.
tophat-2.0.13 was used for alignment with default parameter for pair-end sequencing.
cufflinks-2.2.1 was used with default parameter to get gene FPKM value.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: All_WT_Gene_expression.txt: Gene FPKM value for each sample are summarized in tab-delimited text file.

source_name: Luminal mammary cell

extract_protocol:
The sorted mammary basal or luminal cells re-suspended in FACS buffer (300-500 cells/µL) were mixed (3:2 ratio) with C1 Cell Suspension Reagent (Fluidigm) before loading onto a 5 to 10 or 10 to 17-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm). Each capture site was carefully examined and recorded under a ZEISS microscope in bright field channel for cell doublets. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (protocol 100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (protocol 100-7168 E1).

treatment_protocol: Three- to four-month-old female virgin or pregnant at day 12.5 FVB mice were sacrificed to isolate the fourth pair of mammary glands for single-cell preparation. In brief, the mammary glands were minced, washed in PBS and digested in DMEM/F12 containing 300 U/ml collagenase III (S4M7602S, Worthington, Lakewood, NJ), 100 U/ml hyaluronidase (H3506; Sigma-Aldrich), 5% FBS (Gibco), 5 µg/ml insulin (350-020; Biosource, Rockville, MD), 10 ng/ml EGF (13247-051, Invitrogen), and 500 ng/ml hydrocortisone (H0888; Sigma-Aldrich) for about 1 hour at 37℃, 5% CO2. The resultant organoid suspension was sequentially re-suspended in DMEM/F12 supplemented with 5 mg/ml dispase (825-001; Roche Diagnostics, Indianapolis, IN) and 0.1 mg/ml DNase I (58C10349; Worthington) for 5 min at 37℃, and then digested with 0.25% trypsin-EDTA for 1–2 min, and treated with RBC lysis buffer (00433-57; eBioscience, San Diego, CA) for 3 min to remove the red blood cells before filtration through a 40-µm cell strainer (352340, BD Falcon) to obtain single-cell suspension. Enrichment of Lin- epithelial cells was achieved through selective depletion of hematopoietic and endothelial cells by using the EasySeq mouse epithelial cell enrichment kit according to the manufacturer (19758; Stemcell). The enriched Lin- mouse mammary epithelial cells were stained at a concentration of 1x10^6 cells per 100 μl of FACS buffer (HBSS with 0.5% BSA and 2 mM EDTA). Antibodies against mouse CD24 (anti CD24-PE-Cy™7, BD), CD29 (anti CD29-APC, Bioligand) and CDH5 (also known as CD144, anti CD144-PE, BD) were used. DAPI (1 µg/ml) was also used as an indicator for cell viability. Antibody incubations were performed at 4℃ for 30 min. Then the cells were washed with PBS for twice before sorting by using FACSAria III Cell Sorter (Becton Dickinson). DAPI-CD24MidCD29Hi cells and DAPI-CD24HiCD29Lo cells were gated and sorted out as basal and luminal mammary epithelial cells, respectively.

value: FVB

tag: cell type

value: Luminal mammary cell

tag: virgin/pregnancy status

value: pregnant day 12


title: PL037


title: PL049


title: PL042


title: PL044


title: PL045


title: PL047


title: PL040


title: PL041


title: PL048


title: PL046


title: PL039


title: PL036


title: PL035


title: PL033


title: PL028


title: PL034


title: PL027


title: PL026


title: PL029


title: PL032


title: PL022


title: PL021


title: PL024


title: PL031


title: PL023


title: PL020


title: PL038


title: PL019


title: PL013


title: PL017


title: PL015


title: PL030


title: PL025


title: PL010


title: PL006


title: PL012


title: PL011


title: PL007


title: PL009


title: PL018


title: PL016


title: PL008


title: PL004


title: PB100

source_name: Basal mammary cell

value: Basal mammary cell


title: PB099


title: PL005


title: PB097


title: PL001


title: PL002


title: PB098


title: PB101


title: PB096


title: PB102


title: PB094


title: PB095


title: PL014


title: PB093


title: PB092


title: PB091


title: PB085


title: PB084


title: PB086


title: PL003


title: PB088


title: PB090


title: PB089


title: PB083


title: PB081


title: PB079


title: PB076


title: PB073


title: PB074


title: PB077


title: PB078


title: PB072


title: PB075


title: PB080


title: PB068


title: PB066


title: PB071


title: PB069


title: PB070


title: PB065


title: PB067


title: PB087


title: PB064


title: PB063


title: PB061


title: PB058


title: PB082


title: PB059


title: PB062


title: PB057


title: PB060


title: PB055


title: PB054


title: PB053


title: PB052


title: PB051


title: PB049


title: PB050


title: PB047


title: PB045


title: PB046


title: PB048


title: PB040


title: PB039


title: PB043


title: PB038


title: PB037


title: PB036


title: PB041


title: PB034


title: PB032


title: PB031


title: PB035


title: PB056


title: PB029


title: PB030


title: PB044


title: PB027


title: PB033


title: PB028


title: PB026


title: PB042


title: PB024


title: PB021


title: PB020


title: PB019


title: PB018


title: PB013


title: PB016


title: PB015


title: PB012


title: PB017


title: PB011


title: PB010


title: PB009


title: PB008


title: PB007


title: PB006


title: PB004


title: PB022


title: PB005


title: VL053

value: virgin


title: PB003


title: PB025


title: PB023


title: PB001


title: PB014


title: VL050


title: VL051


title: VL052


title: VL046


title: VL047


title: PB002


title: VL048


title: VL042


title: VL044


title: VL041


title: VL040


title: VL045


title: VL038


title: VL039


title: VL054


title: VL036


title: VL035


title: VL033


title: VL034


title: VL031


title: VL032


title: VL049


title: VL028


title: VL027


title: VL030


title: VL029


title: VL026


title: VL043


title: VL025


title: VL022


title: VL023


title: VL024


title: VL021


title: NSM_IP_Replicate3

city: Cambridge

first: Steven

middle: Willem

last: Flavell

state: MA

address: 77 Massachusetts Ave, 46-4243

department: Brain and Cognitive Sciences

institute: MIT

data_processing:
Adaptors added during sample prep were removed from sequences using cutadapt
For Replicate 1, there were two rounds of sequencing on same sample. These were combined into one fastq file for subsequent data processing. Both raw files are available from SRA for these records as individual SRR.
Reads were aligned to genome using Tophat 2.0.11
INPUT vs IP samples were compared using Cufflinks 2.1.1
Genome_build: C. elegans Ensemble WS220
Supplementary_files_format_and_content: .DIFF files - Output of cuffdiff analysis

organism: Caenorhabditis elegans

source_name: NSM Ribotag RNA

growth_protocol: Growth on enriched peptone NGM plates

extract_protocol:
RNA was collected via Stratagene Absolutely RNA Nanoprep Kit
Clontech SMARTer Ultra Low RNA kit, then Illumina Nextera XT

treatment_protocol: Whole-animal samples were directly lysed, NSM ribotag samples were processed via HA-antibody ribotagging

tag: sample type

value: IP

tag: rna source

value: NSM enriched


title: NSM_IP_Replicate2


title: VL020


title: NSM_INPUT_Replicate3

source_name: C. elegans whole-animal RNA

value: INPUT

value: whole animal


title: VL019


title: NSM_INPUT_Replicate2


title: NSM_IP_Replicate1


title: VL037


title: VL018


title: ANIT3

city: 云南

first: Qi

last: Zhao

address: State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

data_processing:
Basecalls performed using Zebracall process version 0.5.0.13875
Adaptors were trimmed and low quality reads were filtered to get clean reads, then mapped to mm10 genome using hisat2.
featureCounts program was used for reads summarization and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Libraries were  prepared by BGI (Hongkong)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice with ANIT-induced cholestasis were protected with or without celastrol for five days

tag: strain

tag: age

value: post natal day 21

tag: treated with

value: ANIT

tag: tissue


title: Celastrol3

institute: Kunming Institute of Botany, Chinese Academy of Sciences

value: ANIT+Celastrol

value: Liver


title: ANIT2


title: VL017


title: NSM_INPUT_Replicate1


title: ANIT1


title: Celastrol1


title: VL016


title: VL015


title: VL014


title: CHIP_DMC1_B6-TgYF_C

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

description:
DMC1 ChIP-seq of the B6-Tg(YF) mouse, replicate C
CHIP_DMC1_B6TgcastYF_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6TgcastYF_Rep0_RPM_sorted.bw

library_source: genomic

data_processing:
Base-calling was performed  using CASAVA
ChIPseq reads were aligned to the mm9 genome using  Bowtie2 (H3K4me3) or BWA and its modified algorithm proposed in Khil et al., 2012  (DMC1)
Reads that were unmapped, multi-mapped, unpaired, duplicated were filtered out in each experiment, unpaired reads were removed for paired-end experiments, and reads that  mapped with more than 1 mismatch were removed in all ChIPseq experiments.
Peaks were called using MACS2
IDR method was used to deal with replicates for H3K4me3 and DMC1 peaks. Final peaksets were built from merged replicates, according to the IDR method.
Genome_build: mm9
Supplementary_files_format_and_content: For H3K4me3 ChIPseq, bedfiles represent peaks called from  MACS2 for merged replicates after the filtering step of the IDR method. Bigwig (.bw) files represent the normalized signal calculated after merging replicates and subtracting input signal. For DMC1 ChIP-seq, bedgraph files represent peaks centered as described earlier (Brick et al., 2012) with the 4th column representing the normalized signal. Bigwig files represent the DMC1 ChIPseq signal along the genome calculated after merging aligned reads (ssDNA type 1) from replicates.

molecule: genomic DNA

source_name: testis

extract_protocol:
Cell suspension was prepared by filtering homogenized tissue, then lysed.Lysates were sonicated and chromatin complexes were isolated with appropriate antibody.
Standard library construction was performed with the Illumina Trueseq protocol (Illumina, IP-202-9001DOC). For DMC1 ChIP an additional step of kinetic enrichment was performed as described in Khil et al. 2012.
ChIP-seq for H3K4me3 CHIPseq experiment ; SSDS method described in Khil et al. 2012 for DMC1 ChIPseq

tag: strain/genotype

value: whole-testis

value: adult

tag: chip antibody

value: Santa Cruz, goat polyclonal anti-DMC1, C-20, lot #J1215


title: CHIP_DMC1_KO-TgWT_B

description:
DMC1 ChIP-seq of the KO-Tg(WT) mouse, replicate B
CHIP_DMC1_B6KOTgcastWT_B_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6KOTgcastWT_B_Rep0_RPM_sorted.bw

value: Santa Cruz, goat polyclonal anti-DMC1, C-20, lot #D2215


title: CHIP_DMC1_KO-TgYF_A

description:
DMC1 ChIP-seq of the KO-Tg(YF) mouse, replicate A
CHIP_DMC1_B6KOTgcastYF_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6KOTgcastYF_Rep0_RPM_sorted.bw


title: CHIP_DMC1_KO-TgYF_B

description:
DMC1 ChIP-seq of the KO-Tg(YF) mouse, replicate B
CHIP_DMC1_B6KOTgcastYF_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6KOTgcastYF_Rep0_RPM_sorted.bw


title: CHIP_DMC1_B6-TgYF_D

description:
DMC1 ChIP-seq of the B6-Tg(YF) mouse, replicate D
CHIP_DMC1_B6TgcastYF_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6TgcastYF_Rep0_RPM_sorted.bw


title: VL013

tag: strain/background

value: FVB


title: CHIP_DMC1_B6-TgWT_A

description:
DMC1 ChIP-seq of the B6-Tg(WT) mouse, replicate A
CHIP_DMC1_B6TgcastWT_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6TgcastWT_Rep0_RPM_sorted.bw


title: VL012

value: Luminal mammary cell


title: CHIP_K4_B6-TgYF_INPUT

description:
Input DNA of the B6-Tg(YF) mouse
CHIP_H3K4me3_B6TgcastYF_finalpeaks.bed
CHIP_H3K4me3_B6TgcastYF_subtractratio_bs10_s50_RPKM.bigwig

value: 13 days post-partum

value: Abcam, rabbit polyclonal antibody anti-H3K4me3, ab8580


title: CHIP_DMC1_B6-TgWT_B

description:
DMC1 ChIP-seq of the B6-Tg(WT) mouse, replicate B
CHIP_DMC1_B6TgcastWT_finalpeaks_nochrM.normStrength.bedgraph
CHIP_DMC1_B6TgcastWT_Rep0_RPM_sorted.bw


title: Celastrol2


title: CHIP_K4_B6-TgYF_B

description:
H3K4me3 ChIP-seq of the B6-Tg(YF) mouse, replicate B
CHIP_H3K4me3_B6TgcastYF_finalpeaks.bed
CHIP_H3K4me3_B6TgcastYF_subtractratio_bs10_s50_RPKM.bigwig


title: VL009

value: virgin


title: VL008


title: CHIP_K4_B6_INPUT

description:
Input DNA of the B6 mouse
CHIP_H3K4me3_B6_d12_finalpeaks.bed
CHIP_H3K4me3_B6_d12_subtractratio_bs10_s50_RPKM.bigwig


title: CHIP_K4_B6-TgWT_A

description:
H3K4me3 ChIP-seq of the B6-Tg(WT) mouse, replicate A
CHIP_H3K4me3_B6TgcastWT_finalpeaks.bed
CHIP_H3K4me3_B6TgcastWT_subtractratio_bs10_s50_RPKM.bigwig


title: CHIP_K4_B6_B

description:
H3K4me3 ChIP-seq of the B6 mouse, replicate B
CHIP_H3K4me3_B6_d12_finalpeaks.bed
CHIP_H3K4me3_B6_d12_subtractratio_bs10_s50_RPKM.bigwig


title: VL007


title: VL004


title: VL005


title: VL002


title: VL003


title: VL011


title: VL006


title: VL010


title: CHIP_K4_B6-TgWT_INPUT

description:
Input DNA of the B6-Tg(WT) mouse
CHIP_H3K4me3_B6TgcastWT_finalpeaks.bed
CHIP_H3K4me3_B6TgcastWT_subtractratio_bs10_s50_RPKM.bigwig


title: VL001


title: CHIP_K4_B6_A

description:
H3K4me3 ChIP-seq of the B6 mouse, replicate A
CHIP_H3K4me3_B6_d12_finalpeaks.bed
CHIP_H3K4me3_B6_d12_subtractratio_bs10_s50_RPKM.bigwig


title: VB030

value: Basal mammary cell


title: VB031


title: VB034


title: VB032


title: CHIP_K4_B6-TgYF_A

description:
H3K4me3 ChIP-seq of the B6-Tg(YF) mouse, replicate A
CHIP_H3K4me3_B6TgcastYF_finalpeaks.bed
CHIP_H3K4me3_B6TgcastYF_subtractratio_bs10_s50_RPKM.bigwig


title: VB033


title: CHIP_K4_B6-TgWT_B

description:
H3K4me3 ChIP-seq of the B6-Tg(WT) mouse, replicate B
CHIP_H3K4me3_B6TgcastWT_finalpeaks.bed
CHIP_H3K4me3_B6TgcastWT_subtractratio_bs10_s50_RPKM.bigwig


title: VB029

description:
Single cell RNA-seq
processed data file: All_WT_Gene_expression.txt


title: VB027


title: VB026


title: VB025


title: VB023


title: VB028


title: VB021


title: VB022


title: SU-DHL-1

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

source_name: SU-DHL-1 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

tag: cell line

tag: cell line type

value: ALCL, ALK+

value: Lymphoma


title: L82

source_name: L82 cell line


title: VL51

source_name: VL51 cell line

value: SMZL (MZL)


title: amiCOX17-1/cox17-2 vs WT Rep1

city: Santa Fe

first: Agustin

middle: Lucas

last: Arce

state: Santa Fe

address: Ciudad Universitaria

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

description:
cox17vsWT_Rep1
Biological replicate 1

hyb_protocol: Agilent GE2 v6.5 protocol.

scan_protocol: Scanned on an Agilent G2505B-C scanner using Agilent Feature Extraction Software (10.7.31).

data_processing: Median intensity signals were processed in the R statistical programming environment using the limma package. Probes were filtered to exclude those with log2-background intensities above 7.2. Intensities were then background corrected employing the ‘normexp’ method with an offset of 16. Next, arrays were normalized using the locally weighted scatter plot smoothing (LOESS) procedure.

organism: Arabidopsis thaliana

label_protocol: 200 ng total RNA per sample were used to generate cRNA with labelling protocol version GE2 v6.5 for Cy3 and Cy5.

growth_protocol: Arabidopsis seeds from control and silenced plants were grown on MS during 10 days under long day (16-h/8-h dark) and then transferred to soil. Plant were grown on soil during 20 days under long-day photoperiod, 23°C and 100 µM.m-1.s-1 of light intensity.

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

treatment_protocol: Plants grown on 0.5x MS for 10 days.

tag: ecotype

tag: genotype/variation

value: shoot (leaves)

value: 30 days

source_name: WT

value: WT


title: amiCOX17-1/cox17-2 vs WT Rep2

description:
cox17vsWT_Rep2
Biological replicate 2


title: TMD8

source_name: TMD8 cell line

value: DLBCL-ABC


title: MAC-1

source_name: MAC-1 cell line

value: cALCL, ALK-


title: HBL-1

source_name: HBL-1 cell line


title: WSU-DLCL2

source_name: WSU-DLCL2 cell line

value: DLBCL-GCB


title: SSK41

source_name: SSK41 cell line


title: Karpas-422

source_name: Karpas-422 cell line


title: Granta 519

source_name: Granta 519 cell line

value: Granta 519

value: MCL


title: JB6

source_name: JB6 cell line


title: OCI-Ly8

source_name: OCI-Ly8 cell line


title: TS

source_name: TS cell line

value: TS


title: JVM-2

source_name: JVM-2 cell line


title: SUPM2

source_name: SUPM2 cell line


title: Karpas-299

source_name: Karpas-299 cell line


title: DoHH2

source_name: DoHH2 cell line


title: FE-PD

source_name: FE-PD cell line

value: FE-PD

value: PTCL-NOS


title: DB

source_name: DB cell line

value: DB


title: OCI-Ly10

source_name: OCI-Ly10 cell line


title: JeKo-1

source_name: JeKo-1 cell line


title: VB020

source_name: Basal mammary cell

value: FVB

value: virgin


title: VB019

value: Basal mammary cell


title: VB017


title: VB018


title: VB015


title: VB016


title: VB013


title: VB014


title: OCI-Ly1

source_name: OCI-Ly1 cell line

value: Lymphoma


title: OCI-Ly7

source_name: OCI-Ly7 cell line


title: MEC-1

source_name: MEC-1 cell line

value: CLL


title: OCI-Ly3

source_name: OCI-Ly3 cell line


title: Karpas-1718

source_name: Karpas-1718 cell line

value: SMZL (MZL)


title: VB010


title: OCI-Ly19

source_name: OCI-Ly19 cell line


title: VB011


title: MAVER-1

source_name: MAVER-1 cell line


title: VB012


title: KI-JK

source_name: KI-JK cell line

value: KI-JK

value: ALCL, ALK+


title: U-2932

source_name: U-2932 cell line

value: DLBCL-ABC


title: VB009


title: VB008


title: SU-DHL-4

source_name: SU-DHL-4 cell line


title: OCI-Ly2

source_name: OCI-Ly2 cell line


title: OCI-Ly18

source_name: OCI-Ly18 cell line


title: VB007


title: SU-DHL-8

source_name: SU-DHL-8 cell line


title: RIVA

source_name: RIVA cell line

value: RIVA


title: VAL

source_name: VAL cell line

value: VAL

value: DLBCL-GCB


title: SU-DHL-2

source_name: SU-DHL-2 cell line


title: SU-DHL-7

source_name: SU-DHL-7 cell line


title: VB006

source_name: Basal mammary cell


title: SU-DHL-10

source_name: SU-DHL-10 cell line


title: VB005


title: Rec-1

source_name: Rec-1 cell line

value: MCL


title: VB024


title: SUDHL6

source_name: SUDHL6 cell line


title: HH

source_name: HH cell line

value: HH

value: Cutaneus T-NHL


title: HuT78

source_name: HuT78 cell line


title: VB003


title: Toledo

source_name: Toledo cell line

value: Toledo


title: RCK8

source_name: RCK8 cell line


title: H9

source_name: H9 cell line


title: SP-49

source_name: SP-49 cell line


title: VB002


title: Karpas-1106

source_name: Karpas-1106 cell line

value: PMBCL


title: VB001

value: FVB


title: VB004

value: virgin


title: HC-1

source_name: HC-1 cell line

value: HCL (MZL)


title: Farage

source_name: Farage cell line

value: Farage

value: Lymphoma


title: HAIR-M

source_name: HAIR-M cell line

value: HAIR-M


title: SP-53

source_name: SP-53 cell line


title: Pfeiffer

source_name: Pfeiffer cell line

value: Pfeiffer

value: DLBCL type3


title: ESKOL

source_name: ESKOL cell line

value: ESKOL


title: KMM1

source_name: KMM1 cell line

value: MM


title: OPM2

source_name: OPM2 cell line


title: UPN1

source_name: UPN1 cell line


title: SU-DHL-5

source_name: SU-DHL-5 cell line


title: RPMI-8226

source_name: RPMI-8226 cell line


title: Mino

source_name: Mino cell line

value: Mino


title: 8d_T_60_8217

city: Ulm

first: Jens-Uwe

last: Werner

address: Albert-Einstein-Allee 23

country: Germany

institute: Ulm University Hospital

description:
Gene expression data from obese trauma mouse 8d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

hyb_protocol: Hybridization was performed following Chapter 3 of GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: We evaluated the CEL files in R using RStudio with the following packages: questionr 0.6.1, affy 1.52.0, mogene10sttranscriptcluster.db 8.5.0, org.Mm.eg.db 3.4.0, AnnotationDbi 1.36.0, Iranges 2.8.1, S4Vectors 0.12.0, Biobase 2.34.0, BiocGenerics 0.20.0, preprocessCore 1.36.0, calibrate 1.7.2, MASS 7.3-45, gtools 3.5.0, missMDA 1.10, pvclust 2.0-0, FactoMineR 1.33, gplots 3.0.1, doParallel 1.0.10, iterators 1.0.8, foreach 1.4.3, dtplyr 0.0.1, plyr 1.8.4, dplyr 0.5.0, psych 1.6.9, data.table 1.9.6, tictoc 1.0 and openxlsx 3.0.0. We RMA-normalized control versus injured animals for time and diet, respectively. P-values were determined using the pval-function. Up-/down-regulation was assessed without considering significance or expression levels in order to generate an unbiased time lapse. Basal level of controls by this method equals ±1. Significance of p ≤ 0.05 was set to determine significant changes.

source_name: 8d; trauma; 60% kcal fat diet; ID

label_protocol: Labeling was performed following Chapter 2 of GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays

growth_protocol: 16-week-old male and female C57BL/6J used for breeding, kept in a pathogen free open cage facility in 12 hour light/dark cycle at 22.5 ±1°C with access to food and water ad libitum. Parental animals received a normal (10% kcal fat; D12450J; Research Diets Inc.) or high fat diet (60% kcal fat; D12492; Research Diets Inc.) one week prior to breeding to influence prenatal development. Litter received corresponding parent diet.

extract_protocol: Total RNA was isolated by using the RNeasy Mini Kit from Qiagen and following their protocol

treatment_protocol: 16 ±1 week old female normal weight and obese C57BL/6J mice anesthetized with 2.5 vol% sevoflurane mixed with 97.5 vol% oxygen. Analgesic treatment with s.c. injection of buprenorphine. The area around the muscle was shaved and marked. Control animals did not receive any injury. Induction of injury to extensor iliotibialis anticus muscle was as follows: The left hind limb was positioned under a mechanical drop tower device and fixed onto a scaffold. A wedge with a flat surface was placed onto the muscle, allowing a weight of 40 g being dropped to generate an indirect but controlled force input. Effective drop height is 104 cm. A removable spacer (3 mm) on top of a crossbar was used to limit the total depth of penetration. Muscle was isolated 1h, 6h, 24h, 3d and 8d post-injury.

value: extensor iliotibialis anticus

tag: gender

value: female


title: 8d_T_10_8256

description:
Gene expression data from normal weight trauma mouse 8d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 8d; trauma; 10% kcal fat diet; ID


title: 8d_T_10_8467


title: WT CTL, biological repl 1

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerwein-Str. 2

institute: Institute of Medical Microbiology

description: Gene expression array from CD8+ T cells cultured for 2 days under CTL-polarising conditions

hyb_protocol: 5 µg of fragmented and labeled cDNA were hybrized to the GeneChip Mouse gene 1.0 ST Array.

scan_protocol: GeneChips were scanned using 7G Scanner

data_processing: RMA normalization incorporates (separately for each RNA type data set) background correction, quantile normalization and probe-level summarization.

source_name: CTL differentiated for 2 days

label_protocol: Single-stranded cDNA was fragmented and labeled with biotin allonamide triphosphate using the GeneChip WT terminal labeling kit.

growth_protocol: For the generation of CTL and Tc17 cells, mice were sacrificed by cervical dislocation. Spleen and lymph nodes were removed and T cells were isolated by magentic negative selection.

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufaturer's specifications. Using the Ambion WT expression kit, two cycles of cDNA synthesis were performed.

treatment_protocol: CTL cell cultures were set up in RPMI supplemented with 10% FCS in the presence of IL-2,and anti-IFN-g. Tc17 cell cultures were set up in RPMI supplemented with 10% FCS in the presence of IL-2, IL6, TGF-b and anti-IFN-g

value: spleen and lymph node

value: CTL


title: WT CTL, biological repl 2


title: 8d_C_60_8218

description:
Gene expression data from obese control mouse 8d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 8d; control; 60% kcal fat diet; ID


title: 8d_T_60_8097


title: WT TC17, biological repl 1

description: Gene expression array from CD8+ T cells cultured for 2 days under TC17-polarising conditions

source_name: TC17 differentiated for 2 days


title: 8d_T_60_8277


title: 8d_C_10_8257

description:
Gene expression data from normal weight control mouse 8d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 8d; control; 10% kcal fat diet; ID


title: 8d_T_10_8116


title: 6h_T_60_7562

description:
Gene expression data from obese trauma mouse 6h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 6h; trauma; 60% kcal fat diet; ID


title: 6h_T_60_7564


title: 8d_C_60_8216


title: 8d_C_60_8214


title: 8d_C_10_8442


title: WT TC17, biological repl 2


title: 8d_C_10_8255


title: 6h_T_60_7413


title: MSCs, Control group C04

city: beijing

first: yu

middle: qian

last: zhuang

state: beijing

address: Peking Union Medical College Hospital, 1 Shuai Fu Yuan

department: Orthopedics

institute: Peking Union Medical College Hospital

description: LncRNA expression data of MSCs from Healthy donors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Expression console software 1.4 using Affymetrix default analysis settings and global scaling. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mesenchymal stem cells from Healthy donors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mononuclear cells were separated by Ficoll gradient centrifugation (density 1.077 g/cm3) and depleted of hematopoietic cells using MACS CD45, GlyA, and CD34 micromagnetic beads (Miltenyi Biotec, Inc., Auburn, CA, USA) [33,34]. The cells were washed twice and plated in T-75 tissue culture flasks at a density of 16106/ml. Expansion medium contained 57% DMEM/F-12 (Gibco Life Technologies, Paisley, UK), 40% MCDB-201 (Sigma, St.Louis, MO, USA), 2% fetal calf serum (FCS; Gibco), 16insulin transferrin selenium (ITS; Gibco), 1028 M dexamethasone (Sigma), 1024 M ascorbic acid 2-phosphate (Sigma), 10 ng/ml epidermal growth factor (EGF; Sigma), 10 ng/ml platelet-derived growth factor BB (PDGF-BB; Sigma), 100 U/ml penicillin, and 100 mg/ml streptomycin (Gibco). Once adherent cells were more than 70% confluent, they were detached with 0.125% trypsin and 0.01% EDTA, and replated at a 1:3 dilution under the same culture conditions. Confluent cells (approximately 26106) at the third passage were used for the experiments.

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

treatment_protocol: For immunophenotype analysis of BM-MSCs, the cells were detached and washed with phosphate buffered saline (PBS) containing 0.5% bovine serum albumin (BSA; Sigma), and incubated with primary antibodies for 30 min at 4uC. Working concentrations for primary antibodies against human CD29, CD31, CD34, CD44, CD45, CD73, and CD105, (BD Biosciences) were 10 ng/ml. We used same-species, same-isotype irrelevant antibody as the negative control. After washing with PBS containing 0.5% BSA, the cells were incubated with fluorescein isothiocyanate (FITC)-conjugated secondary antibodies for 30 min at 4uC. After three washes, cells were resuspended in PBS and analyzed by flow cytometry with a FACSCalibur flow cytometer. Each measurement contained 10000 events.To identify the MSC capacity for multilineage differentiation, MSCs were cultured under differentiation conditions. The culture-expanded cells at a density of 26104/cm2 were induced in the following osteogenic medium for 2–3 weeks: Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FCS, 10 mmol/L b-glycerophosphate, 1028 mol/L dexamethasone, and 0.2 mmol/L ascorbic acid (all from Sigma). Cells were then stained with the alkaline phosphatase (ALP) staining kit (Beyotime, China) to reveal osteogenic differentiation. To test the adipogenic differentiation ability, the cultureexpanded cells at a density of 26104/cm2 were induced for 3 weeks in DMEM supplemented with 10% FCS, 0.5 mmol/L hydrocortisone, 0.5 mmmol/L isobutylmethylxanthine, and 50 mg/ml indomethacin (all from Sigma). At the end of the culture, the cells were fixed in 10% formalin for 10 min and stained with fresh Oil red-O solution (Sigma) to show lipid droplets in induced cells.

value: mesenchymal stem cells

value: Donors age less than 18

tag: disease state

value: healthy


title: 6h_T_10_7594

description:
Gene expression data from normal weight trauma mouse 6h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 6h; trauma; 10% kcal fat diet; ID


title: 6h_T_10_7591


title: 6h_C_10_7398

description:
Gene expression data from normal weight control mouse 6h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 6h; control; 10% kcal fat diet; ID


title: 6h_C_10_7590


title: MSCs, Control group C05


title: 6h_C_60_7563

description:
Gene expression data from obese control mouse 6h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 6h; control; 60% kcal fat diet; ID


title: MSCs, Control group C02


title: MSCs, AIS group A12

description: LncRNA expression data of MSCs from AIS patients

source_name: mesenchymal stem cells from AIS patient

value: Patients age less than 18

value: AIS


title: MSCs, Control group C01


title: 3d_T_60_8188

description:
Gene expression data from obese trauma mouse 3d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 3d; trauma; 60% kcal fat diet; ID


title: MSCs, Control group C03


title: 6h_T_10_7400


title: 6h_C_10_8158


title: 3d_T_60_8185


title: 3d_T_10_7780

description:
Gene expression data from normal weight trauma mouse 3d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 3d; trauma; 10% kcal fat diet; ID


title: 3d_T_60_8080


title: 3d_T_10_8224


title: 3d_C_60_8272

description:
Gene expression data from obese control mouse 3d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 3d; control; 60% kcal fat diet; ID


title: 6h_C_60_7411


title: MSCs, AIS group A11


title: 3d_C_10_8441

description:
Gene expression data from normal weight control mouse 3d post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 3d; control; 10% kcal fat diet; ID


title: MSCs, AIS group A09


title: MSCs, AIS group A07


title: ionXpressRNA008

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

data_processing:
Assembly by Velvet v1.2.10 (https:// www.ebi.ac.uk/~zerbino/velvet/)
Calculation of expression values (read counts by Htseq)
Differential expression with EdgeR and DESeq2
Genome_build: performed novel assembly. FASTA file available on series record. Annotation files included.
Supplementary_files_format_and_content: output files from EdgeR and DESeq2.

organism: Acinetobacter baumannii

extract_protocol:
LB broth, Dnase-treated RNA (Ab-2_clon_2010 untreated versus Ab-2_clon_2010CHLX treated with CLHX) was isolated from stationary-phase cultures (OD=1.0-1.5) with the High Pure RNA Isolation Kit (Roche, Germany). The samples were treated with the Ribo-Zero rRNA Removal kit (Illumina, San Diego, California) in order to eliminate the ribosomal RNA (23S, 16S and 5S). The quality of the RNA samples was examined in a 2100 Bioanalyzer system (Agilent Technologies, Palo Alto, California).
Transcriptome libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion XpressTM RNa-Seq Barcode 01-16 kit (Thermo Fisher Scientific, Waltham Massachusetts) according to the manufacturer's instructions. The libraries were quantified in the 2100 Bioanalyzer system.
The mix reaction was carried out in automated Ion Chef systems (Thermo Fisher Scientific, Waltham Massachusetts): Ion PITM Hi-QTM Chef and Ion PITM chips v3 kits (Thermo Fisher Scientific, Waltham Massachusetts). The resulting readings (all >80 million) were used to generate FASTQ files with the FileExporter 4.6.0.0 plugin (19).

tag: treatment

value: control


title: IonXpressRNA006

value: clorhexidine


title: 3d_C_60_8186


title: IonXpressRNA007


title: 3d_C_60_8189


title: 3d_T_10_8223


title: 6h_C_60_8454


title: IonXpressRNA004


title: IonXpressRNA005


title: MSCs, AIS group A08


title: 3d_C_10_8221


title: 24h_C_60_8229

description:
Gene expression data from obese control mouse 24h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 24h; control; 60% kcal fat diet; ID


title: MSCs, AIS group A10


title: 24h_T_60_8102

description:
Gene expression data from obese trauma mouse 24h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 24h; trauma; 60% kcal fat diet; ID


title: MSCs, AIS group A05


title: Z-138

source_name: Z-138 cell line

value: MCL

tag: cell type

value: Lymphoma


title: MSCs, AIS group A06


title: 24h_T_10_7941

description:
Gene expression data from normal weight trauma mouse 24h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 24h; trauma; 10% kcal fat diet; ID


title: 24h_T_60_8101


title: MSCs, AIS group A04


title: 24h_C_60_8350


title: 24h_C_60_8352


title: IonXpressRNA002


title: 24h_T_10_7965


title: 3d_C_10_8222


title: 24h_T_60_8098


title: IonXpressRNA003


title: 24h_T_10_7718


title: IonXpressRNA001


title: MSCs, AIS group A01


title: 24h_C_10_8434

description:
Gene expression data from normal weight control mouse 24h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 24h; control; 10% kcal fat diet; ID


title: 1h_T_60_7425

description:
Gene expression data from obese trauma mouse 1h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 1h; trauma; 60% kcal fat diet; ID


title: MSCs, AIS group A02


title: 24h_C_10_8202


title: ΔDAL81-YPD-3

city: Dublin

first: Geraldine

last: Butler

address: Belfield, Dublin 4

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute

description: delta-CPAR2_800890 YPD sample 3

data_processing:
Raw Illumina reads for samples 1-12 were provided by BGI (http://www.genomics.cn/en/index)
Raw Illumina reads for samples 13-24 were obtained in-house using an Illumina NextSeq® sequencer with a NextSeq® 500/550 High Output v2 kit (75-cycles) (Illumina, FC-404- 2001)
Quality control of the data was verified using fastqc v0.11.2
Pair-end sequenced reads were trimmed for low-quality sequence or length using Skewer v0.1.120 with parameters -m pe -l 50 -q 15 -Q 15
Single-end sequenced reads were trimmed for low-quality sequence or length using Skewer v0.1.120 with parameters -m any -l 35 -q 15 -Q 15
Trimmed sequenced reads were mapped to the Candida parapsilosis CDC317 genome using Tophat v2.0.12 with parameters -g 1 --b2-very-sensitive --library-type fr-firststrand
Mapped reads were indexed and sorted for counting using Samtools v0.1.19
Raw number or mapped reads per gene was obtained using htseq-count from HTSeq (v0.6.1) with parameters -m union -s reverse -t exon -i Name
Differentially expressed genes from read count data were identified using the Bioconductor package DESeq2
Genome_build: Candida parapsilosis CDC 317
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads per gene for each SAMPLE

organism: Candida parapsilosis

source_name: delta-CPAR2_800890 YPD

growth_protocol: Strains were grown overnight in YPD media at 30C, diluted to an OD600 of 0.2, grown to an OD600 of 1 in YPD media at 30C

extract_protocol:
Cells filtered through a membrane and RNA was isolated using a Bioline ISOLATE II RNA Mini Kit
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq

tag: growth phase

value: log phase

tag: genotype


title: 1h_T_60_7558

tag: strain


title: ΔDAL81-YPD-1

description: delta-CPAR2_800890 YPD sample 1


title: 24h_C_10_8197


title: ΔDAL81-YPD-2

description: delta-CPAR2_800890 YPD sample 2


title: WT_CLIB214-YPD-3

description: Wild type YPD sample 3

source_name: Wild type YPD

value: wild type


title: ΔDAL81-GABA-3

description: delta-CPAR2_800890 GABA sample 3

source_name: delta-CPAR2_800890 GABA

growth_protocol: Strains were grown overnight in YPD media at 30C, diluted to an OD600 of 0.2, grown to an OD600 of 1 to 1.5  in YNB with 2% glucose and 10 mM GABA  media at 30C

extract_protocol:
Cells filtered through a membrane and RNA was isolated using a RiboPure RNA Purification Kit (Ambion)
Library preparation was performed using the Illumina NeoPrep system and the TruSeq Stranded mRNA NeoPrep kit (Illumina NP-202-1001).
Strand-specific 75bp single-end RNA-Seq


title: 1h_T_60_7423


title: WT_CLIB214-YPD-2

description: Wild type YPD sample 2


title: 1h_T_10_7592

description:
Gene expression data from normal weight trauma mouse 1h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 1h; trauma; 10% kcal fat diet; ID


title: ΔDAL81-GABA-2

description: delta-CPAR2_800890 GABA sample 2


title: MSCs, AIS group A03

tag: age


title: ΔDAL81-GABA-1

description: delta-CPAR2_800890 GABA sample 1


title: WT_CPRI-GABA-3

description: Wild type GABA sample 3

source_name: Wild type GABA

value: CPRI


title: 1h_T_10_7419


title: 1h_T_10_7415


title: WT_CPRI-GABA-2

description: Wild type GABA sample 2


title: 1h_C_60_7561

description:
Gene expression data from obese control mouse 1h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12492; started 1 week prior to breeding for prenatal influence

source_name: 1h; control; 60% kcal fat diet; ID


title: WT_CLIB214-ILE-2

description: Wild type isoleucine sample 2

source_name: Wild type isoleucine

growth_protocol: Strains were grown overnight in YPD media at 30C, diluted to an OD600 of 0.2, grown to an OD600 of 1 in YNB with 2% glucose and 10 mM Isoleucine media at 30C


title: 1h_C_10_8427

description:
Gene expression data from normal weight control mouse 1h post-injury
extensor iliotibialis anticus from female 16+-1 week old C57BL/6J mouse; fed 10% kcal diet D12450J; started 1 week prior to breeding for prenatal influence

source_name: 1h; control; 10% kcal fat diet; ID


title: 1h_C_60_8421


title: WT_CLIB214-ILE-1

description: Wild type isoleucine sample 1


title: 1h_C_10_7416


title: WT_CLIB214-YPD-1

description: Wild type YPD sample 1


title: ΔDAL81-NH4-3

description: delta-CPAR2_800890 NH4 sample 3

source_name: delta-CPAR2_800890 NH4

growth_protocol: Strains were grown overnight in YPD media at 30C, diluted to an OD600 of 0.2, grown to an OD600 of 1 to 1.5  in YNB with 2% glucose and 0.5% ammonium sulfate media at 30C


title: WT_CLIB214-NH4-3

description: Wild type NH4 sample 3

source_name: Wild type NH4

growth_protocol: Strains were grown overnight in YPD media at 30C, diluted to an OD600 of 0.2, grown to an OD600 of 1 in YNB media with 2% glucose and 0.5% ammonium sulfate at 30C


title: 1h_C_60_7427


title: ΔDAL81-NH4-2

description: delta-CPAR2_800890 NH4 sample 2


title: WT_CLIB214-NH4-2

description: Wild type NH4 sample 2


title: ΔDAL81-NH4-1

description: delta-CPAR2_800890 NH4 sample 1


title: WT_CLIB214-ILE-3

description: Wild type isoleucine sample 3


title: 1h_C_10_7593


title: WT_CPRI-NH4-2

description: Wild type NH4 sample 2


title: WT_CPRI-NH4-3

description: Wild type NH4 sample 3


title: WT_CPRI-GABA-1

description: Wild type GABA sample 1


title: WT_CPRI-NH4-1

description: Wild type NH4 sample 1


title: CyCam_R_Cellotriose_8h

city: Jena

first: Doreen

last: Meichsner

address: Dornburger Strasse 159

department: General Botany and Plant Physiology

institute: FSU Jena

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEX Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to a custom Gene Expression Agilent Microarray  (G4102A; DesignID 65426) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for AgilentG3_GX for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%, Tiff 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CyCam Root, Cellotriose treated, 8h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: 12 day-old Arabidopsis seedlings were transferred from MS plates to plates with solid Plant Nutritient Medium (PNM) and a nylon membrane (mesh size 70 µm) as described previously (Camehl et al., 2011). Seedlings were then grown for additional 24 h under long day conditions and light from the top (60-70 µM m-2 sec-1, 16 h light/8 h dark) at 22°C. These seedlings were then used for the incubation  with MAMPs.

extract_protocol: The PureLink® RNA Mini Kit (ThermoFisher Scientific) was used for the total RNA isolation according to the manufacturer's protocol. Total RNA from roots of transgenic A. thaliana (Col-0) expressing cytosolic apoaequorin (pMAQ2, Knight et al., 1991) and the cycam mutant (in the pMAQ2 background) from 3 independent biological experiments were exposed to CT or chitin (10µM) or mock-treated with water and harvested at 4 and 8 h after MAMP application. For each treatment, identical amounts of RNA from the three independent biological replicates were mixed and labeled and hybridized according to ArrayXS Arabidopsis Microarray-Based Gene Expression Analysis (OAK Lab GmbH, Germany). The quality of the RNA samples were checked by photometrical measurements with the Nanodrop 2000 spectrophotometer (ThermoFisher Scientific) and then analyzed on agarose gels (2%) as well as by using the 2100 Bioanalyser (Agilent Technologies, CA) for determining the RNA integrity.

treatment_protocol: For MAMP application, the roots of 13-day old seedlings were soaked in a solution containing either Cellotriose  (Sigma-Aldrich) or chitin (Hexaacetyl-chitohexaose;Megazyme), autoclaved H2O was used as control. The plates with the seedlings were then transferred back to long day conditions, before the roots and leaves were harvested at 0 h, 4 h and 8 h after the treatments. The roots were then frozen in liquid nitrogen.

value: Root


title: KO E2 rep2 (17-week-old)

status: Public on Feb 08 2018

city: New York

first: Sunil

last: Wadhwa

address: 630 West 168th Street

institute: Columbia University

data_processing:
Basecalls performed using RTA (Illumina)
Bcl2fastq2 (version 2.17) for coverting BCL to fastq format coupled with adaptor trimming
We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports raw counts and normalized counts.
.csv files including basemean, log2foldchange, IfcSE, stat, pvalue, padj values for each Sample

source_name: Mandibular condylar fibrocartilage

growth_protocol: Mice were bred and genotyped in the Columbia University vivarium. At 16-weeks of age, female mice were ovariectomized and given either placebo or estradiol (0.01 mg, 60-day release, Innovative Research) for 1 week. After 1 week, the mandibular condylar fibrocartilage was directly harvested from mice and stored in RNA later until collection of all samples was completed (≤ 1 month).

extract_protocol:
Samples were removed from RNA later solution and RNA was isolated and purified using the PureLink kit.
RNA samples (purity confirmed by Bioanalyzer with RIN values ≥ 9) were sent to the Columbia Genome Center and libraries were generated for sequencing using an Illumina TruSeq RNA prep kit and sequenced utilizing Illumina HiSeq2500/HiSeq4000. Specifically, a poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

treatment_protocol: Female mice were ovariectomized and given either placebo or estradiol (0.01 mg, 60-day release, Innovative Research) for 1 week

value: All cells in mandibular condylar fibrocartilage

value: 17-week old

value: ERalphaKO

tag: agent


title: KO E2 rep3 (17-week-old)


title: KO Plb rep4 (17-week-old)

value: Plb


title: KO E2 rep1 (17-week-old)


title: Col-0_R_Cellotriose_4h

source_name: Col-0 Root, Cellotriose treated, 4h

tag: tissue


title: CyCam_R_Cellotriose_4h

source_name: CyCam Root, Cellotriose treated, 4h


title: KO Plb rep2 (17-week-old)


title: WT E2 rep3 (17-week-old)

value: WT


title: WT Plb rep1 (17-week-old)


title: WT E2 rep2 (17-week-old)


title: WT E2 rep1 (17-week-old)


title: KO Plb rep1 (17-week-old)


title: Col-0_R_Chitin_4h

source_name: Col-0 Root, Chitin treated, 4h


title: CyCam_R_Chitin_8h

source_name: CyCam Root, Chitin treated, 8h


title: KO E2 rep2 (7-week old)

data_processing:
Basecalls performed using RTA (Illumina)
Bcl2fastq2 (version 2.17) for coverting BCL to fastq format coupled with adaptor trimming
We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports raw counts.
.csv files including basemean, log2foldchange, IfcSE, stat, pvalue, padj values for each Sample

growth_protocol: Mice were bred and genotyped in the Columbia University vivarium. At 6-weeks of age, female mice were ovariectomized and given either placebo or estradiol (0.01 mg, 60-day release, Innovative Research) for 1 week. After 1 week, the mandibular condylar fibrocartilage was directly harvested from mice and stored in RNA later until collection of all samples was completed (≤ 1 month).

extract_protocol:
Samples were removed from RNA later solution and RNA was isolated and purified using the PureLink kit.
RNA samples (purity confirmed by Bioanalyzer with RIN values ≥ 9) were sent to the Columbia Genome Center and libraries were generated for sequencing using an Illumina TruSeq RNA prep kit and sequenced utilizing Illumina HiSeq2500/HiSeq4000. Specifically, a poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

value: 7-week old


title: KO E2 rep3 (7-week old)


title: KO Plb rep3 (7-week old)


title: Col-0_R_Cellotriose_8h

source_name: Col-0 Root, Cellotriose treated, 8h


title: CyCam_R_Chitin_4h

source_name: CyCam Root, Chitin treated, 4h


title: CyCam_R_H2O_4h

source_name: CyCam Root, H2O treated, 4h


title: KO Plb rep2 (7-week old)


title: Col-0_R_H2O_4h

source_name: Col-0 Root, H2O treated, 4h


title: KO E2 rep1 (7-week old)


title: WT E2 rep2 (7-week old)


title: KO Plb rep1 (7-week old)


title: WT E2 rep3 (7-week old)


title: Col-0_R_Chitin_8h

source_name: Col-0 Root, Chitin treated, 8h


title: WT E2 rep1 (7-week old)


title: KO Plb rep3 (17-week-old)


title: WT Plb rep2 (17-week-old)


title: RN-Leaf-T2

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

description: mRNA

data_processing:
analyses was performed on CyVerse.org
The pre-filtered reads were quality-filtered using FASTQC tools.
The RNA-seq reads that passed the quality filters were mapped to the potato reference genome (PGSC_DM_v3.4 gene models ensemblv19-preinstalled in iplantcollaborative.org) using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010).
The Tuxedo pipeline comprised TopHat2 (mapping), Cufflinks2 (transcript assembly), and Cuffmerge2 (transcript merging).
Identification of differential gene expression was conducted using Cuffdiff2, following the defaults parameters in CyVerse.
Genome_build: PGSC_DM_v3.4
Supplementary_files_format_and_content: .gtf file

organism: Solanum tuberosum

source_name: Russet Norkotah

growth_protocol: Tubers were planted in Springlake, TX and plant were grown on commercial field

extract_protocol:
Plant Sample were collected in the field place in RNA-later, kept on ice till brought back in the lab and Frozen.   and removed, flash frozen on dry ice, and RNA was harvested using Qiagen Plant RNeasy. TruSeq RNA Library Preparation Kit v2 was used on poly(A) RNA enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

value: 84 day old

tag: selection

value: Russet Norkotah


title: WT Plb rep2 (7-week old)


title: WT Plb rep1 (7-week old)


title: HCT116_VP1_mut_rep3

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using bowtie with options –k 1 –m 1 against the hg19 genome assembly.  All mapped reads were assigned to their corresponding restriction fragment and non-blind were used for quantile normalization in each sample together. After normalization profiles were smoothened using a 10kb running mean at 50bp steps.
hg19
Supplementary_files_format_and_content: WIG files contain normalized profiles smoothened using a 10kb running mean at 50bp steps.

source_name: Colorectal cancer

growth_protocol: Cells were cultured in 10% FCS RPMI with P/S

extract_protocol:
Cells were lysed, digested, religated, digested for a second time, and religated again. This template was purified and amplified with specific viewpoint primers to generate the libraries.
Cell lysis and sequential NlaIII, CviQI or sequential NlaIII, BfaI restriction followed by ethanol precipitation
4C-seq

treatment_protocol: no treatment

tag: restriction enzyme 1

value: NlaIII

tag: restriction enzyme 2

value: CviQI

tag: viewpoint primer fwd

value: AAATTTACAGATCAGGCATG

tag: viewpoint primer rev

value: ACCTGCGTAAAACACAGATT


title: HCT116_VP1_mut_rep1

tag: cell line


title: K562_VP2_mut_rep3

source_name: Leukemia

value: AAGCCCAGGTCTAGTCCATG

value: CCTAAGCTGAAAGAGGCTAA


title: HCT116_VP1_mut_rep2


title: HCT116_VP1_rep2


title: HCT116_VP1_rep3


title: K562_VP2_rep3


title: K562_VP2_mut_rep2


title: K562_VP2_mut_rep1


title: HCT116_VP1_rep1


title: K562_VP2_rep2


title: K562_VP2_rep1


title: K562_VP1_mut_rep1

growth_protocol: Cells were maintained in 10% FCS RPMI with P/S

value: BfaI

value: GCGCGCGTAGTTAATTCATG

value: AAAGAAGGGTATTAATGGGC


title: K562_VP1_mut_rep3


title: K562_VP1_rep3


title: K562_VP1_rep1


title: K562_VP1_mut_rep2

growth_protocol: Cells were maintained in 10% FCS DMEM with P/S


title: Huh7-MAVSR cells infected for 72 h

city: Shanghai

first: Yanan

address: Yueyang Road 320

institute: Institut Pasteur of Shanghai  Chinese Academy of Science

description: human hepatocytes Huh7-MAVSRcells  infected with HCVcc (JFH1 strain) for 72hs

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: human hepatocytes Huh7-MAVSR cells infected for 72 h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Huh7-MAVSRcells were grown in complete Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 10 mM HEPES, 2 mM L-glutamine, 100 U of penicillin/ml, and 100 mg of streptomycin/ml. Cells were incubated at 37°C in a CO2 incubator.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The cells were seeded 1 day prior to viral infection, and infected with HCVcc (JFH1 strains) at an MOI of 5. The cells were lysed  by TRIZOL Reagent at 12, 24, 48, 72 hours post-infection.

value: HCVcc infection 72 hours


title: Huh7-MAVSR cells that are mock infected for 72 h

description: human hepatocytes Huh7-MAVSRcells  72hs mock cells

source_name: human hepatocytes Huh7-MAVSR cells mock infected for 72 h

value: Mock infection for 72 hours


title: Huh7-MAVSR cells infected for 48 h

description: human hepatocytes Huh7-MAVSRcells  infected with HCVcc (JFH1 strain) for 48hs

source_name: human hepatocytes Huh7-MAVSR cells infected for 48 h

value: HCVcc infection 48 hours


title: nonSmoker1

city: Borstel

first: Lena

last: Heinbockel

address: Parkallee 3

department: Pathology

institute: Research Center Borstel

description: Gene expression

hyb_protocol: The labeled cRNA was hybridized on Agilent Human Gene Expression 4 × 44k V2 arrays.

scan_protocol: The arrays were scanned with the Agilent SureScan microarray scanner.

data_processing: Data were analysed with the Agilent GeneSpring GX software version 12.6

source_name: tumor-free tissue of non-smoker

label_protocol: The One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol was performed.

extract_protocol: Sections of paraffin blocks were deparaffinized and the RNA was isolated by using the Rneasy Mini Kit (Qiagen).

treatment_protocol: After pneumonectomy tumor-free lung tissue was fixed in HOPE and embedded in paraffin.

value: female

value: lung


title: Huh7-MAVSR cells infected for 12 h

description: human hepatocytes Huh7-MAVSRcells  infected with HCVcc (JFH1 strain) for 12hs

source_name: human hepatocytes Huh7-MAVSR cells infected for 12 h

value: HCVcc infection 12 hours


title: nonSmoker5

description: Gene expression


title: nonSmoker4

description: Gene expression


title: K562_VP1_rep2


title: nonSmoker3

description: Gene expression


title: siRELA 10Gy4h rep2

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description:
siRELA-transfected-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_2_si_RelA_lib80471_4027_4_1

data_processing:
alignment to hg19, hisat 2.0.5
feature counting, featureCounts
normalization, DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: txt file, normalized expression values

growth_protocol: The wild-type U2-OS cells were purchased from ATCC (HTB-96) and used as a primary model. Cells were grown in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (HyClone) and gentamicin (40 mg/mL; Krka) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from 1x10^6 cells using RNeasy Mini Kit (Qiagen) and treated on-column with DNase using the RNase-Free DNase Set (Qiagen).
RNA libraries were prepared for sequencing using 1ug RNA according to the standard Illumina protocols

treatment_protocol: Any treatment started 48 h after inoculation of cells; all steps, with the exception of irradiation, were carried out at 37 °C and 5% CO2. For gene expression analysis cells were incubated with TNFα cytokine and harvested after 0.5 or 4 hours of stimulation. Alternatively, cells were irradiated with 4 or 10 Gy IR dose at a 1Gy/min dose, the medium was replaced with a fresh one, and cells were analyzed 4 hours after irradiation

tag: tumor

value: osteosarcoma

tag: Sex

value: 15 years

tag: tissue/cells

value: bone


title: Huh7-MAVSR cells infected for 24 h

description: human hepatocytes Huh7-MAVSRcells  infected with HCVcc (JFH1 strain) for 24hs

source_name: human hepatocytes Huh7-MAVSR cells infected for 24 h

tag: treatment

value: HCVcc infection 24 hours


title: COPD9

description: Gene expression

source_name: tumor-free tissue of smoker with COPD

tag: gender

value: male


title: COPD11

description: Gene expression

source_name: tumor-free tissue of ex-smoker with COPD


title: COPD10

description: Gene expression


title: COPD12

description: Gene expression


title: COPD7

description: Gene expression


title: COPD8

description: Gene expression


title: COPD14

description: Gene expression


title: COPD4

description: Gene expression


title: siRELA 4Gy4h rep3

description:
siRELA-transfected-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_3_si_RelA_lib80486_4027_7_1


title: siRELA 10Gy4h rep3

description:
siRELA-transfected-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_3_si_RelA_lib80490_4027_7_1


title: siRELA 10Gy4h rep1

description:
siRELA-transfected-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_1_si_RelA_lib80452_3949_1_1


title: COPD13

description: Gene expression


title: COPD3

description: Gene expression


title: siRELA TNF4h rep1

description:
siRELA-transfected-transfected cells treated with TNFalpha for 4h
NG.7926_tnf_4_1_si_RelA_lib80445_3949_1_1


title: siRELA 4Gy4h rep2

description:
siRELA-transfected-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_2_si_RelA_lib80467_4027_4_1


title: COPD5

description: Gene expression


title: siRELA 4Gy4h rep1

description:
siRELA-transfected-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_1_si_RelA_lib80448_3900_3949_1_1


title: siRELA TNF4h rep2

description:
siRELA-transfected-transfected cells treated with TNFalpha for 4h
NG.7926_tnf_4_2_si_RelA_lib80464_3949_7_1


title: WT_CLIB214-NH4-1

description: Wild type NH4 sample 1

source_name: Wild type NH4

tag: growth phase

value: log phase

value: wild type


title: siRELA ctr rep3

description:
untreated control siRELA-transfected-transfected cells
NG.7926_ctr_3_si_RelA_lib80475_4027_5_1


title: siRELA ctr rep2

description:
untreated control siRELA-transfected-transfected cells
NG.7926_ctr_2_si_RelA_lib80456_3949_6_1


title: siRELA TNF30min rep3

description:
siRELA-transfected-transfected cells treated with TNFalpha for 30min
NG.7926_tnf_05_3_si_RelA_lib80479_4027_4045_1_1


title: siRELA TNF4h rep3

description:
siRELA-transfected-transfected cells treated with TNFalpha for 4h
NG.7926_tnf_4_3_si_RelA_lib80483_4027_1_1


title: COPD2

description: Gene expression


title: nonSmoker2

description: Gene expression


title: siRELA TNF30min rep2

description:
siRELA-transfected-transfected cells treated with TNFalpha for 30min
NG.7926_tnf_05_2_si_RelA_lib80460_3949_6_1


title: siCTR 4Gy4h rep3

description:
siCTR-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_3_si_ctr_lib80485_4027_6_1


title: siCTR 10Gy4h rep2

description:
siCTR-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_2_si_ctr_lib80470_4027_4_1


title: siCTR 10Gy4h rep3

description:
siCTR-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_3_si_ctr_lib80489_4027_7_1


title: siCTR TNF4h rep3

description:
siCTR-transfected cells treated with TNFalpha for 4h
NG.7926_tnf_4_3_si_ctr_lib80482_4027_6_1


title: siCTR 4Gy4h rep2

description:
siCTR-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_2_si_ctr_lib80466_4027_4_1


title: siRELA TNF30min rep1

description:
siRELA-transfected-transfected cells treated with TNFalpha for 30min
NG.7926_tnf_05_1_si_RelA_lib80441_3899_1_1


title: COPD1

description: Gene expression


title: siCTR TNF4h rep1

description:
siCTR-transfected cells treated with TNFalpha for 4h
NG.7926_tnf_4_1_si_ctr_lib80444_3949_4027_1_1


title: siCTR TNF4h rep2

description:
siCTR-transfected cells treated with TNFalpha for 4h
NG.7926_tnf_4_2_si_ctr_lib80463_3949_7_1


title: siCTR TNF30min rep3

description:
siCTR-transfected cells treated with TNFalpha for 30min
NG.7926_tnf_05_3_si_ctr_lib80478_4027_6_1


title: siCTR TNF30min rep2

description:
siCTR-transfected cells treated with TNFalpha for 30min
NG.7926_tnf_05_2_si_ctr_lib80459_3949_6_1


title: siCTR ctr rep3

description:
untreated control siCTR-transfected cells
NG.7926_ctr_3_si_ctr_lib80474_4027_5_1


title: siRELA ctr rep1

description:
untreated control siRELA-transfected-transfected cells
NG.7926_ctr_1_si_RelA_lib80437_3900_3949_1_1


title: siCTR ctr rep2

description:
untreated control siCTR-transfected cells
NG.7926_ctr_2_si_ctr_lib80455_3949_6_1


title: siCTR TNF30min rep1

description:
siCTR-transfected cells treated with TNFalpha for 30min
NG.7926_tnf_05_1_si_ctr_lib80440_3900_5_1


title: siCTR ctr rep1

description:
untreated control siCTR-transfected cells
NG.7926_ctr_1_si_ctr_lib80436_3900_1_1


title: siCTR 10Gy4h rep1

description:
siCTR-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_1_si_ctr_lib80451_3949_4013_1_1


title: COPD6

description: Gene expression


title: siCTR 4Gy4h rep1

description:
siCTR-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_1_si_ctr_lib80447_3900_1_1


title: WT 4Gy4h rep1

description:
wild type cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_1_wt_lib80446_3949_4013_1_1


title: WT 4Gy4h rep2

description:
wild type cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_2_wt_lib80465_3949_7_1


title: WT TNF30min rep3

description:
wild type cells treated with TNFalpha for 30min
NG.7926_tnf_05_3_wt_lib80477_4027_5_1


title: WT ctr rep2

description:
untreated control wild type cells
NG.7926_ctr_2_wt_lib80454_3949_4_1

source_name: untreated control wild type cells


title: WT TNF4h rep1

description:
wild type cells treated with TNFalpha for 4h
NG.7926_tnf_4_1_wt_lib80443_3899_1_1


title: WT ctr rep3

description:
untreated control wild type cells
NG.7926_ctr_3_wt_lib80473_4027_5_1


title: WT ctr rep1

description:
untreated control wild type cells
NG.7926_ctr_1_wt_lib80435_3949_1_1


title: WT TNF30min rep2

description:
wild type cells treated with TNFalpha for 30min
NG.7926_tnf_05_2_wt_lib80458_3949_6_1


title: WT TNF4h rep2

description:
wild type cells treated with TNFalpha for 4h
NG.7926_tnf_4_2_wt_lib80462_3949_7_1


title: WT TNF4h rep3

description:
wild type cells treated with TNFalpha for 4h
NG.7926_tnf_4_3_wt_lib80481_4027_6_1


title: WT 10Gy4h rep2

description:
wild type cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_2_wt_lib80469_4027_4_1


title: WT 4Gy4h rep3

description:
wild type cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG.7926_4Gy_3_wt_lib80484_4027_1_1


title: WT TNF30min rep1

description:
wild type cells treated with TNFalpha for 30min
NG.7926_tnf_05_1_wt_lib80439_3899_1_1


title: WT 10Gy4h rep3

description:
wild type cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_3_wt_lib80488_4027_7_1


title: WT 10Gy4h rep1

description:
wild type cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG.7926_10Gy_1_wt_lib80450_3949_1_1


title: A11-1 Breast T

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
A11 Tumor
H1AUNC-1565-C-A11-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken.

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

growth_protocol: samples were taken from patients at autopsy

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: Reference

source_name: A11-1 Breast T

extract_protocol: Qiagen Rneasy Kit

value: breast tumor

value: flash frozen tissue


title: 11W-PBAT-villus-2

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (RefXXX) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads passed quality control were mapped to human or mouse reference genome (version: hg19 or mm9) using bismark (version: 0.7.6) for bisulfite sequencing reads with paired-end alignment mode (parameters: --non-directional --fastq) and tophat for RNA-seq reads. To rescue more bisulfite sequencing reads, unmapped reads were realigned to the same reference genome in single-end alignment mode.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: For bisulfite sequencing samples, the processed files include the DNA methylation levels of cytosines in CpG, CHH and CHG context, in bed format. Processed data of RNA-seq samples were gene expression tables obtained from cufflinks.

source_name: Villus

extract_protocol:
single cell or small amounts of cells were seeded into the lysis buffer using the mouth pipette, and DNAs were released after proteinase treatment at 50C and then bisulfite converted.
After purification, DNAs were complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer. For RNA-Seq, transcriptome of single cells or low amount of cells were amplified using a modified Smart-seq2. We reversely transcribed RNA molecules using a oligo (dT) primer anchored with 8bp unique molecular identifiers (UMI). Amplified cDNAs were fragmented into around 300 bp using a Covaris S2 and the sequencing libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems).

tag: cell type

value: Villus

tag: bulk or single cell

value: bulk cells


title: 9W_husband_blood

source_name: Peripheral Blood

value: Peripheral Blood


title: 7W-PBAT-heart-2

source_name: Heart

value: Heart


title: 9W_wife_blood


title: 7W-PBAT-heart-1


title: Sperm-WGS

source_name: Sperm

value: Sperm


title: 11W-PBAT-villus-1


title: 11W-PBAT-heart-1


title: 11W-PBAT-heart-2


title: scBS-Q-s8

source_name: Blastocyst

value: Blastocyst

value: single cell


title: scBS-Q-s7


title: scBS-Q-s6


title: scBS-Q-s4


title: scBS-O-bst-4


title: scBS-Q-s3


title: scBS-Q-s1


title: scBS-N-TE-2b

source_name: TE

value: TE


title: scBS-L-TE-2b


title: scBS-L-TE2-s4


title: scBS-L-TE2-s3


title: scBS-L-TE2-s5


title: scBS-N-ICM-2b

value: ICM


title: scBS-L-TE2-s2


title: scBS-L-ICM2-s5

source_name: ICM


title: scBS-L-TE2-s1


title: scBS-Q-s5


title: scBS-L-ICM2-s1


title: scBS-L-ICM-2b


title: scBS-X-M-4b

source_name: Morula embryo#X

value: Morula


title: scBS-L-ICM2-s4


title: scBS-8C-8-5

source_name: 8-cell embryo#8


title: scBS-8C-8-4


title: scBS-L-ICM2-s2


title: scBS-L-ICM2-s3


title: Mor08-W-s168

source_name: Morula embryo#W


title: scBS-8C-8-7


title: scBS-Y-M-1b

source_name: Morula embryo#Y


title: scBS-Q-s2


title: Mor08-W-s167


title: scBS-8C-8-1


title: scBS-8C-8-2


title: scBS-8C-2-6

source_name: 8-cell embryo#2


title: scBS-8C-2-8


title: scBS-8C-2-3


title: scBS-Q-8C-8

source_name: 8-cell embryo#Q1


title: scBS-8C-8-8


title: scBS-Q-8C-5


title: scBS-W-M-13b


title: scBS-8C-8-6


title: scBS-8C-2-7


title: scBS-8C-2-5


title: scBS-Q-8C-4


title: scBS-Q-8C-1


title: scBS-E-4C-4

description: Raw data not provided due to patient privacy concerns

source_name: 4-cell embryo#E1


title: scBS-8C-2-4


title: scBS-E-4C-3


title: scBS-E-4C-1


title: scBS-4C-1-3

source_name: 4-cell embryo#1


title: scBS-8C-8-3


title: scBS-4C-1-2


title: scBS-E-4C-2


title: scBS-Q-8C-3


title: scBS-4C-1-4


title: scBS-Q-8C-7


title: scBS-4C-1-1


title: scBS-2C-9-1

source_name: 2-cell embryo#9


title: scBS-2C-4-2

source_name: 2-cell embryo#4


title: scBS-2C-3-1

source_name: 2-cell embryo#3


title: scBS-2C-9-2


title: scBS-2C-11-1

source_name: 2-cell embryo#11


title: scBS-Q-8C-6


title: scBS-2C-7-2

source_name: 2-cell embryo#7


title: scBS-2C-10-1

source_name: 2-cell embryo#10


title: scBS-2C-7-1


title: scBS-2C-5-2

source_name: 2-cell embryo#5


title: scBS-Q-8C-2


title: scBS-MPN3-2


title: scBS-2C-4-1


title: scBS-2C-5-1


title: scBS-2C-3-2


title: scBS-MPN3-1


title: scBS-D-PN2-2


title: scBS-2C-2-2

source_name: 2-cell embryo#2


title: scBS-2C-2-1


title: scBS-2C-1-2

source_name: 2-cell embryo#1


title: scBS-2C-1-1


title: scBS-C-PN5-2


title: scBS-MPN4-2


title: scBS-MPN4-1


title: scBS-2C-10-2


title: scBS-C-PN1-2


title: scBS-D-PN2-1


title: scBS-C-PN5-1


title: scBS-B-PN13-1


title: scBS-C-PN1-1


title: scBS-MPN7-1


title: scBS-L-MII-2

source_name: metaphase II oocyte

value: metaphase II oocyte

value: female


title: scBS-B-PN13-2


title: scBS-B-PN2-1


title: scBS-L-MII-4


title: scBS-MPN7-2


title: scBS-B-PN2-2


title: scBS-L-MII-3


title: scBS-G-MII-11


title: scBS-E-MII-3


title: scBS-L-MII-1


title: scBS-D-MII-9


title: scBS-E-MII-10


title: scBS-G-MII-10


title: scBS-E-MII-21


title: scBS-D-MII-8


title: scBS-D-MII-7


title: scBS-D-MII-6


title: scBS-D-MII-5


title: scBS-D-MII-4


title: scBS-G-MII-12


title: scBS-D-MII-1


title: scBS-D-MII-3


title: scBS-D-MII-2


title: scBS-C-MII-9


title: scBS-B-GV1

source_name: GV oocyte

value: GV oocyte


title: scBS-hSP-10ng

source_name: Sperm


title: Day7.DTR+.F4-80+.MHCII+#2

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit.

scan_protocol: Affymetrix GeneChip Scanner.

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Muscle

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: TriZol

tag: genetic background

tag: genotype/variation

tag: age

value: 10 Weeks

value: Male

tag: injury

value: Cardiotoxin

tag: time point (days after injury)

value: muscle macrophages

tag: phenotype markers

value: Ly6g- CD11b+ F4-80+ MHCII-

tag: separation method

value: Dissection / Trimming


title: Day7.DTR-.F4-80+.MHCII+#2


title: Day7.DTR+.F4-80+.MHCII+#1


title: Day7.DTR-.F4-80+.MHCII+#1


title: Day1.24hrDT.DTR-.F4-80+.MHCII+#2

value: 8 Weeks

value: CD45+ DAPI- CD11b+ Ly6g- SiglecF- F4-80+ MHCII-


title: scBS-hSP5

value: Sperm


title: Day4.DTR-.F4-80+.MHCII-#2


title: scBS-hSP-1ng

value: bulk cells


title: Day4.DTR-.F4-80+.MHCII+#3


title: Day1.24hrDT.DTR-.F4-80+.MHCII-#1


title: Day1.24hrDT.DTR-.F4-80+.MHCII-#2


title: Day1.24hrDT.DTR+.F4-80+.MHCII-#2


title: Day1.24hrDT.DTR+.F4-80+.MHCII-#1


title: Day1.24hrDT.DTR+.F4-80+.MHCII+#1


title: Day4.DTR-.F4-80+.MHCII-#1


title: Day1.24hrDT.DTR-.F4-80+.MHCII+#1


title: Day4.DTR-.F4-80+.MHCII+#2


title: Day1.24hrDT.DTR+.F4-80+.MHCII+#2


title: Day0.DTR-.F4-80+.MHCII-#1


title: Day0.DTR-.F4-80+.MHCII-#2


title: Day0.DTR-.F4-80+.MHCII+#1

value: Ly6g- CD11b+ F4-80+ MHCII+


title: Day0.DTR-.F4-80+.MHCII+#2


title: 8hrDT.D7.DTR-.F4-80+.MHCII-#5

value: 12 Weeks

value: Ly6g- SiglecF- CD11b+ F4-80+ MHCII-


title: scBS-Sp12

value: single cell


title: 8hrDT.D7.DTR-.F4-80+.MHCII-#2


title: 8hrDT.D7.DTR-.F4-80+.MHCII-#3


title: 8hrDT.D7.DTR-.F4-80+.MHCII-#1


title: 8hrDT.D7.DTR-.F4-80+.MHCII+#1


title: 8hrDT.D7.DTR-.F4-80+.MHCII+#2


title: PAR-CLIP AEG1

city: Durham

first: David

last: Reid

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

description:
AEG-1–14 is a HepG3-based cell line with stable expression of C-terminal HA-tagged AEG1.
PAR-CLIP AEG1

data_processing:
Map to Refseq transcriptome using Bowtie, allowing one mismatch
Define clusters as overlapping regions of reads with at least one mutation (only T→ C mutations for PAR-CLIP)
A cluster score was score was defined as log 2 (1000 * (1-D) * M / R), where M is the number of mutations in the cluster and R is the abundance of the RNA from RNA-seq. D represents the breadth of read distribution, defined as (1/N)^N, where N is the number of unique read starts or stops in the cluster. Clusters with scores of less than 0 were discarded.
Genome_build: Refseq Release 73
Supplementary_files_format_and_content: Cluster information: gene, cluster boundaries, and score

source_name: Hepatoblastoma cell line (HepG3)

growth_protocol: Cells were cultured at 37ºC and 5% CO2 in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were lysed, partially RNase I-digested, and immunoprecipitated with anti-HA antibody (https://www.thermofisher.com/antibody/product/HA-Tag-Antibody-clone-2-2-2-14-Monoclonal/26183). The RNA moiety was dephosphorylated and radioisotope-labeled. The complexes were subsequently eluted, resolved by SDS-PAGE, transferred to nitrocellulose membranes, and analyzed by phosphorimaging. RNA fragments were extracted by proteinase K digestion from the nitrocellulose membranes and purified by phenol/chloroform extraction. cDNA libraries were constructed by  NEBNext® Small RNA Library Prep Set for Illumina. Libraries were then sequenced on the Illumina HiSeq with 50-nucleotide single-read runs.
cDNA libraries were constructed according to the manufacturer's instructions (New England Biolabs; E7330).

treatment_protocol: Cells were UV-irradiated at 254 nm for HITS-CLIP and 365 nm for PAR-CLIP  on ice. The negative controls have no UV irradiation treatments.

tag: cell line

tag: cell line background


title: 8hrDT.D7.DTR+.F4-80+.MHCII-#3

tag: Sex


title: 8hrDT.D7.DTR-.F4-80+.MHCII+#3


title: scBS-hSp10


title: HITS-CLIP negative ctrl 2

description:
AEG-1–14 is a HepG3-based cell line with stable expression of C-terminal HA-tagged AEG1.
HITS-CLIP negative ctrl 2


title: 8hrDT.D7.DTR+.F4-80+.MHCII-#5


title: 8hrDT.D7.DTR+.F4-80+.MHCII-#6


title: 8hrDT.D7.DTR+.F4-80+.MHCII+#4


title: 8hrDT.D7.DTR+.F4-80+.MHCII+#3


title: HITS-CLIP negative ctrl 1

description:
AEG-1–14 is a HepG3-based cell line with stable expression of C-terminal HA-tagged AEG1.
HITS-CLIP negative ctrl 1


title: scBS-Sp14


title: PAR-CLIP negative ctrl

description:
AEG-1–14 is a HepG3-based cell line with stable expression of C-terminal HA-tagged AEG1.
PAR-CLIP negative ctrl


title: HITS-CLIP AEG1 1

description:
AEG-1–14 is a HepG3-based cell line with stable expression of C-terminal HA-tagged AEG1.
HITS-CLIP AEG1 1


title: HITS-CLIP AEG1 2

description:
AEG-1–14 is a HepG3-based cell line with stable expression of C-terminal HA-tagged AEG1.
HITS-CLIP AEG1 2


title: Pancreatic cancer 49

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

country: Japan

institute: Keio University

description: Batch 2

hyb_protocol: Affymetrics GeneChip® 3 ' IVT PLUS Reagent Kit or 3 ' IVT Express Reagent Kit procedure

scan_protocol: GeneChip Scanner 3000 7G procedure

data_processing: The data was normalized by RMA (R package affy). Batch effect was compensated by ComBat (R package sva). The pre-processed data was median-centered.

source_name: Patient 49

label_protocol: Standard Affymetrixt protocol

extract_protocol: QIAGEN RNeasy Plus Mini Kit procedure

tag: tissue

value: Pancrea

tag: disease state

value: cancer


title: 8hrDT.D7.DTR+.F4-80+.MHCII+#1


title: 24hrDT.D7.DTR-.F4-80+.MHCII-#1


title: Normal pancrea 1

description: Batch 2

source_name: Patient 50

value: normal


title: Pancreatic cancer 48

description: Batch 2

source_name: Patient 48


title: Pancreatic cancer 47

description: Batch 2

source_name: Patient 47


title: Normal pancrea 3

description: Batch 2

source_name: Patient 51


title: 24hrDT.D7.DTR-.F4-80+.MHCII-#3


title: 24hrDT.D7.DTR-.F4-80+.MHCII-#2


title: 24hrDT.D7.DTR-.F4-80+.MHCII+#1


title: Pancreatic cancer 45

description: Batch 2

source_name: Patient 45


title: 24hrDT.D7.DTR-.F4-80+.MHCII+#2


title: Pancreatic cancer 44

description: Batch 2

source_name: Patient 44


title: Pancreatic cancer 40

description: Batch 2

source_name: Patient 40


title: 24hrDT.D7.DTR+.F4-80+.MHCII-#3


title: Pancreatic cancer 42

description: Batch 2

source_name: Patient 42


title: Pancreatic cancer 43

description: Batch 2

source_name: Patient 43


title: 24hrDT.D7.DTR+.F4-80+.MHCII-#1


title: 24hrDT.D7.DTR-.F4-80+.MHCII+#4


title: Pancreatic cancer 35

description: Batch 2

source_name: Patient 35


title: 24hrDT.D7.DTR-.F4-80+.MHCII+#3


title: 24hrDT.D7.DTR+.F4-80+.MHCII-#2


title: Pancreatic cancer 39

description: Batch 2

source_name: Patient 39


title: Pancreatic cancer 36

description: Batch 2

source_name: Patient 36


title: 24hrDT.D7.DTR+.F4-80+.MHCII+#5


title: Pancreatic cancer 37

description: Batch 2

source_name: Patient 37


title: Pancreatic cancer 38

description: Batch 2


title: Pancreatic cancer 33

description: Batch 2

source_name: Patient 33