title: DU60-009 control

description:
Sample name:
X168

value: sperm

tag: pack years


title: GF_S_0004063

status: Public on May 23 2018

type: RNA

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

country: USA

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data

hyb_protocol: Arrays were processed using the Affymetrix GeneChip Hybridization, Washing and Staining kit, using the Affymetrix Fluidics station 450 controlled by Affymetrix GeneChip Command Console (AGCC) Software.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000, 7G controlled by AGCC Software.

data_processing: Data were analyzed and normalized by the MAS5 algorithm as implemented by the ‘affy’ package version 1.56.0 under Bioconductor version 3.6 and R version 3.4.3. Default settings were used.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary AML sample, pretreatment

label_protocol: mRNA within the total RNA (100 ng) was amplified using the 3’ IVT Express kit from Affymetrix, starting with reverse transcription to synthesize first strand cDNA. This cDNA was then converted into double stranded DNA template for transcription to generate aRNA (cRNA) and incorporate a biotin conjugated nucleotide, then fragmented for hybridization on Human Gene U133_2.0 arrays.

growth_protocol: Samples were obtained from peripheral blood, in the case of patients with a substantial proportion of circulating blast cells, or bone marrow by aspiration

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (Qiagen).

treatment_protocol: Ficoll-Hypaque density gradient separation was performed to isolate mononuclear cells

tag: disease state

value: AML

tag: tissue

value: peripheral blood

tag: cell type

value: Mononuclear cells


title: GF_S_0004062

description: Gene expression data


title: TS5.010_Inj_RNA-Seq

type: SRA

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

library_source: transcriptomic

data_processing:
RNA data was pseudoaligned to the University of California, Santa Cruz, annotated Sus scrofa (pig) genome (build 9.2)
Transcript abundances were quantified using Kallisto with default parameters
R/Bioconductor DESeq 2 was used to calculate differential expression (DE) of transcripts
R was used to analyze expression data for set analysis (GAGE), principal component analysis, and correlation of inter-treatment gene expression
Cound data was log2 transformed, after adding a pseudocount of 0.5 to all measurements
Genome_build: Rattus norvegicus (rat) genome (build 6.0)
Supplementary_files_format_and_content: Excel format worksheet for genes

organism: Rattus norvegicus

extract_protocol:
The muscles were thawed, minced and homogenized (Tissue Ruptor, Qiagen) for 30 seconds at room temperature and total RNA was isolated from the slurry using the miRNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
1 μg of isolated total RNA was used to produce cDNA libraries using the Truseq protocol (Illumina), as per the manufacturer’s instructions. Biological replicates or triplicates were produced from each condition and individual libraries were pooled and sequenced using 76 base-pair (bp) paired-end reads on a Hi-Seq. 2500 in high output mode to an average depth of 55 M reads per library.

treatment_protocol: while under isoflurane anesthesia a unilateral full-thickness VML injury was created using a 6 mm punch biopsy to the middle third of the TA muscle. On average, the tissue removed from the TA weighed 90.5 ± 3.2 mg.

tag: strain

value: Lewis rat

tag: injury

value: VML

tag: run

value: NoRun

tag: repair

value: NoRepair

tag: timepoint

value: day 3

value: tibialis anterior muscle


title: I7AZ-001 smoke

type: genomic

city: Salt Lake City

first: Kenneth

middle: Ivan

last: Aston

state: Select

address: 675 Arapeen Dr Suite 201

institute: University of Utah

description:
Sample name:
X47

hyb_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software. matrix_processed.txt contains Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: sperm

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

extract_protocol: following somatic cell lysis,  genomic DNA was extracted and purified from sperm using Qiagen DNeasy Kit according to standard instructions, with the exception of cell lysis that was performed in buffer X2 (20 mM TrisHCl [pH 8.0], 20 mM EDTA, 200 mM NaCL, 80 mM DTT, 4% SDS, 250 ug/ml proteinase K)

tag: # years smoking

tag: # cigarettes per day

tag: sperm concentration (m/ml)


title: ZQ0R-005 smoke

description:
Sample name:
X55

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


title: TS5.010_Con_RNA-Seq

value: NoVML


title: TS5.009_Inj_RNA-Seq

value: MMG


title: WV8W-017 control

description:
Sample name:
X169


title: 88NG-020 smoke

description:
Sample name:
X50


title: TS5.008_Inj_RNA-Seq

value: Run

value: day 7


title: 2YX6-015 control

description:
Sample name:
X122


title: BX6C-009 smoke

description:
Sample name:
X49


title: TS5.008_Con._RNA-Seq


title: TS5.008_Con_RNA-Seq


title: WR5B013 smoke

description:
Sample name:
X41


title: IK2D-010 smoke

description:
Sample name:
X46


title: TS5.007_Inj_2_RNA-Seq


title: TS5.007_Inj_1_RNA-Seq


title: GF_S_0004059

description: Gene expression data


title: GF_S_0004060

description: Gene expression data


title: GF_S_0004064

description: Gene expression data


title: GF_S_0004058

description: Gene expression data


title: GF_S_0004061

description: Gene expression data


title: GF_S_0004056

description: Gene expression data


title: TS5.007_Con_RNA-Seq


title: BU20-001 control

description:
Sample name:
X121


title: AB6M-008 control

description:
Sample name:
X119


title: TS5.006_Inj_2_RNA-Seq


title: GF_S_0004054

description: Gene expression data


title: GF_S_0004055

description: Gene expression data


title: GF_S_0004053

description: Gene expression data


title: GF_S_0004052

description: Gene expression data


title: TS5.006_Inj_1_RNA-Seq


title: GF_S_0004057

description: Gene expression data


title: GF_S_0004051

description: Gene expression data


title: TS5.006_Con_2_RNA-Seq


title: TD6B-016 control

description:
Sample name:
X111


title: TS5.006_Con_1_RNA-Seq


title: JF6N008 smoke

description:
Sample name:
X30


title: TS5.005_Inj_2_RNA-Seq


title: GW5W018 smoke

description:
Sample name:
X71


title: XC75015 smoke

description:
Sample name:
X21


title: CZ1S024 smoke

description:
Sample name:
X19


title: TS5.005_Con_RNA-Seq


title: GF_S_0004050

description: Gene expression data


title: TS5.005_Inj_1_RNA-Seq


title: 3YR5-015 control

description:
Sample name:
X113


title: GF_S_0004049

description: Gene expression data


title: 30PV011 smoke

description:
Sample name:
X38


title: TS5.004_Inj_2_RNA-Seq


title: GF_S_0004047

description: Gene expression data


title: GF_S_0004048

description: Gene expression data


title: IK3F016 smoke

description:
Sample name:
X34


title: GF_S_0004046

description: Gene expression data


title: TS5.004_Inj_1_RNA-Seq


title: GF_S_0004043

description: Gene expression data


title: GF_S_0004044

description: Gene expression data


title: TS5.004_Con_2_RNA-Seq


title: 5GZ4010 smoke

description:
Sample name:
X31


title: GF_S_0004042

description: Gene expression data


title: WM1S-015 control

description:
Sample name:
X133


title: TS5.004_Con_1_RNA-Seq


title: XP87-018 control

description:
Sample name:
X114


title: TS5.003_Inj_1_RNA-Seq


title: TS5.003_Inj_2_RNA-Seq


title: TS5.003_Con_RNA-Seq


title: KB90-003 control

description:
Sample name:
X108


title: TS5.002_Inj_3_RNA-Seq


title: GF_S_0004040

description: Gene expression data


title: 2BO7-014 control

description:
Sample name:
X109


title: Z8SP-010 control

description:
Sample name:
X112


title: TS5.002_Inj_2_RNA-Seq


title: 5VW6-016 control

description:
Sample name:
X105


title: WT ProB

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description:
ProB
processed data file: Raw_counts.txt

data_processing:
Fastq files were created using Cellranger 1.3.
Reads were mapped and UMIs counted using CellRanger 1.3.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_counts.txt: A raw count matrix was generated using Seurat v2.1. Genes in the rows, and cells across the columns. -1 in the cell ID denotes CLP, -2 FrA, -3 ProB.

organism: Mus musculus

source_name: Hematopoietic progenitors

growth_protocol: Bones (crista, femur, tibia) were collected from mice and bone marrow extracted by crushing bones in mortar.

extract_protocol:
After lineage depletion (DynalBeads), samples were stained with flow cytometry-antibodies, and samples were sorted on BDFacsAriaIII using 70micron nozzle and cooling. CLP=LiveLIN-FLT3+IL7R+SCA1+KIT+, FrA=LiveLIN-CD19-B220+, ProB=LiveLIN-CD19+IgM-IgD-. LIN-antibodies= Gr1, Ter119, CD3, Mac1, CD11c, NK1.1.
Libraries were constructed according to 10x genomics Chromium Single Cell 3' Reagents Kit V2 Protocol.

tag: strain/background

tag: genotype/variation

value: WT

tag: age

value: 10-11 weeks

value: Bone marrow lymphoid progenitors

tag: cell population

value: ProB


title: TS5.002_Inj_1_RNA-Seq


title: Wt Common lymphoid progenitor

description:
CLP
processed data file: Raw_counts.txt

value: Common lymphoid progenitor


title: BN2W005 smoke

description:
Sample name:
X20

value: sperm


title: 993N003 smoke

description:
Sample name:
X39


title: 09AB002 smoke

description:
Sample name:
X15


title: TS5.002_Con_RNA-Seq


title: GF_S_0004038

description: Gene expression data

value: AML

value: peripheral blood

value: Mononuclear cells


title: GF_S_0004041

description: Gene expression data


title: GF_S_0004037

description: Gene expression data


title: GF_S_0004036

description: Gene expression data


title: HFD_MeDIP

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

description: 16 weeks of 60% high fat diet

library_source: genomic

data_processing:
Libraries were sequenced with single-end reads of 75bp. Demultiplexed reads were filtered for full length reads. Filtered reads were mapped to the mouse genome build mm9 using Bowtie software allowing 2 mismatches in the read. Mapped reads were filtered to uniquely mapped reads then analyzed with MEDIPS software.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are provided as .WIG files that can be viewed in a genome browser to observe methylation signal of genomic regions.

source_name: Epididymal fat macrophages

growth_protocol: Mice were fed a 10% low fat diet (Research Diets D12450J) or 60% high fat diet (Research Diets D12492) for 16 weeks starting at 6 weeks of age.

extract_protocol:
DNA was extracted using Qiagen All Prep DNA/RNA/miRNA Universal Kit.
Purified genomic DNA was treated with dsDNA Shearase (Zymo Research, Irvine, CA). DNA fragments sized 200bp to 400 bp were isolated to construct sequencing libraries using Illumina Chip-seq Library Preparation Kit. dsDNA was then denatured and immunoprecipitated with anti 5-methylcytosine antibody using a MeDIP kit from Diagenode (Denville, NJ). Precipitated DNA was purified and sequenced.

treatment_protocol: Epididymal fat stromal vascular fractions (SVF) were isolated by collagenase digestion. F4/80+ cells (ATMs) were purified by labeling SVF cells with anti-F4/80-PE (clone: BM8) followed by immunomagnetic selection with StemCell EasySep PE Positive Selection Kit. Each biological replicate is pools of ATMs isolated from either 60 LFD-fed mice or 30 HFD-fed mice.

value: Epididymal fat macrophages

tag: gender

value: Male

value: 22 weeks

tag: weeks of diet

value: 16 weeks


title: TS5.001_Inj_RNA-Seq

value: Lewis rat

value: VML

value: NoRepair

value: day 3

value: tibialis anterior muscle


title: GF_S_0004034

description: Gene expression data

tag: disease state


title: HV22-021 control

description:
Sample name:
X110

tag: tissue

tag: pack years


title: GF_S_0004035

description: Gene expression data

tag: cell type


title: GF_S_0004039

description: Gene expression data


title: GF_S_0004032

description: Gene expression data


title: GF_S_0004031

description: Gene expression data


title: TS5.001_Con_RNA-Seq

tag: strain

tag: injury

value: NoVML

value: Run


title: 9YV6012 smoke

description:
Sample name:
X25


title: LFD_MeDIP

description: 16 weeks of 10% low fat diet


title: 7XL6-018 control

description:
Sample name:
X117


title: E11 wIAHCs

city: Utrecht

first: Chloé

last: Baron

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: .csv file containing transcript count

source_name: whole intra-aortic hematopoietic cluster cells

extract_protocol:
YS were carefully collected and vitelline vessels were cut off. After removal of the head and tail, the blood was flushed away by injecting PBS/FCS/PS or antibodies with a glass capillary directly inside the aorta of the embryo trunk.  Aorta-Gonad-Mesonephros (AGM) regions were dissected, pooled and dissociated by collagenase treatment (0.125% collagenase type I in PBS/FCS/PS) for 1 hour at 37°C. After dissociation, cells were washed, stained with various antibodies. Cells were sorted with a FACS Aria III flow cytometer. Single whole (w)IAHCs were mechanically picked-up from live thick embryo slices by using a CellCelector mechanical cell-picker. Location (dorsal or ventral) of the picked wIAHC was recorded.
Single cells were sorted in the wells of 96-well PCR plates, each well containing 100ml of TRIzol reagent and 0.2ul of a 1:250,000 dilution of ERCC spike ins (Thermo Fisher). wIAHCs were collected after pick-up in tubes containing the above solution. Total RNA was extracted from single cells, according to TRIzol manufacturer’s instructions (Thermo Fisher) with few alterations. GlycoBlue reagent (0.2μl) was added to each sample to facilitate RNA precipitation. After overnight isopropanol precipitation, RNA pellets were air dried for up to 15 minutes, and suspended in CEL-Seq first-strand primer solution
Single cells (or wIAHCs) RNA obtained after TRIzol extraction was suspended in primer solution, denatured at 70˚C for 2 minutes and quickly chilled. First strand synthesis was carried out at 42˚C for 1 hour followed by a second strand synthesis step at 16˚C for 1 hour. cDNA was cleaned-up and in vitro transcription was set-up overnight at 37˚C. Amplified RNA was fragmented and cleaned-up for 3’ adapter ligation, reverse transcription reaction and PCR amplification. Libraries were sequenced with an Illumina NextSeq 2500 by using 75 bp paired end sequencing.

tag: genotype

value: WT

tag: developmental stage

value: Aorta-Gonad-Mesonephros

tag: phenotype

value: c-kit+


title: WT Fraction A

description:
FrA
processed data file: Raw_counts.txt

value: 10-11 weeks

value: Bone marrow lymphoid progenitors

value: Fraction A


title: TS4.038_Right_RNA-Seq

value: Sham

tag: run

value: NoRun

tag: repair

tag: timepoint

value: day 0


title: LZ6K030 control

description:
Sample name:
X103

value: sperm

tag: # years smoking

tag: # cigarettes per day

tag: sperm concentration (m/ml)


title: TS4.038_Left_RNA-Seq

value: Lewis rat


title: TS4.037_Right_RNA-Seq


title: 7O69004 smoke

description:
Sample name:
X17


title: E11 pre-HSCs

source_name: Single pre-HSCs

value: c-kit+ Cdh5+ CD45 index


title: GF_S_0004029

description: Gene expression data

value: AML

value: peripheral blood

value: Mononuclear cells


title: GF_S_0004028

description: Gene expression data


title: aorta of LysM-Cre/Dicerflox/flox/Apoe–/– mouse fed a HFD for 12 weeks, Replicate 2

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

description:
Biological replicate 2 of 3. aortas from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Aorta-KO2

data_processing:
The Applied Biosystems TaqMan Rodent miRNA A+B Cards Set v2.0  (catalog number 4400239) was used for this study. Taqman low density arrays were run on the 7900HT Fast Real-Time PCR System. The ABI TaqMan SDS v2.4 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software. Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRNAs from card A and B was used for analysis. Data were calculated using qBase software. Input data for analysis consisted of all samples. CT values were normalized to multiple endogenous controls (snoRNA202, snoRNA135 and MammU6 for Card A, snoRNA202, snoRNA135, MammU6 and snoRNA429 for Card B).
Normalization: qBase-software computed signal (target gene signal normalized to endogenous controls and then scaled to WT group); Fold_Change:  KO/WT

label: FAM

source_name: aorta, macrophage Dicer knockout

label_protocol: cDNA was obtained by TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems) and amplified by TaqMan PreAmp Master Mix (Applied Biosystems)

extract_protocol: mirVana miRNA Isolation Kit, see manufacturer's web site

treatment_protocol: high-fat diet feeding

value: aorta

value: macrophage

value: LysM-Cre/Dicerflox/flox/Apoe–/–

tag: age

value: 6-8 weeks

tag: Sex

value: Male

tag: diet

value: high fat diet (HFD)


title: M8YN016 smoke

description:
Sample name:
X18

tag: tissue


title: GF_S_0004033

description: Gene expression data

tag: disease state


title: aorta of LysM-Cre/Dicerflox/flox/Apoe–/– mouse fed a HFD for 12 weeks, Replicate 3

description:
Biological replicate 3 of 3. aortas from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Aorta-KO3

tag: cell type


title: TS4.037_Left_RNA-Seq

tag: strain

value: NoRepair

value: tibialis anterior muscle


title: E11 IAHC cells_2

source_name: Single Intra-aortic hematopoietic cluster cells

value: WT

value: Aorta-Gonad-Mesonephros

value: c-kit+


title: F9WY-015 control

description:
Sample name:
X118

value: sperm

tag: pack years


title: H89S-009 control

description:
Sample name:
X93


title: E11 IAHC cells

tag: genotype

value: c-kit+ CD31+


title: aorta of LysM-Cre/Dicerflox/flox/Apoe–/– mouse fed a HFD for 12 weeks, Replicate 1

description:
Biological replicate 1 of 3. aortas from LysM-Cre/Dicerflox/flox/Apoe–/– mice
Sample name: Aorta-KO1


title: E11 EHT cells

source_name: Single EHT cells

value: ICR

value: Gfi+/tomato/ Gfi1b+/GFP

tag: developmental stage

value: Cdh5+ Gfi1+ Gfi1b- c-kit+


title: ZU52010 smoke

description:
Sample name:
X5


title: QD2Z012 smoke

description:
Sample name:
X1


title: aorta of LysM-Cre/Dicerwt/wt/Apoe–/– mouse fed a HFD for 12 weeks, Replicate 2

description:
Biological replicate 2 of 3. aortas from LysM-Cre/Dicerwt/wt/Apoe–/– mice
Sample name: Aorta-WT2

source_name: aorta, macrophage Dicer wild type

value: LysM-Cre/Dicerwt/wt/Apoe–/–


title: 9W1S009 smoke

description:
Sample name:
X3


title: E10 YS cells

source_name: Single yolk sac cells

value: Yolk-Sac

tag: phenotype


title: E11 non-HE cells

source_name: Single non-hemogenic endothelial cells

value: Cdh5+ Gfi1- Gfi1b- c-kit-


title: aorta of LysM-Cre/Dicerwt/wt/Apoe–/– mouse fed a HFD for 12 weeks, Replicate 1

description:
Biological replicate 1 of 3. aortas from LysM-Cre/Dicerwt/wt/Apoe–/– mice
Sample name: Aorta-WT1

value: aorta

value: macrophage


title: HL1C-005 control

description:
Sample name:
X97


title: E11 YS cells


title: E10 IAHC cells


title: D1GG-012 control

description:
Sample name:
X95


title: AD2U-020 control

description:
Sample name:
X116


title: E10 HE cells

source_name: Single hemogenic endothelial cells

value: Cdh5+ Gfi1+ Gfi1b- c-kit-


title: aorta of LysM-Cre/Dicerwt/wt/Apoe–/– mouse fed a HFD for 12 weeks, Replicate 3

description:
Biological replicate 3 of 3. aortas from LysM-Cre/Dicerwt/wt/Apoe–/– mice
Sample name: Aorta-WT3

value: 6-8 weeks

value: Male

value: high fat diet (HFD)


title: 5UO9-002 control

description:
Sample name:
X100


title: E10 non-HE cells


title: E11 HE cells


title: ATACseq in AdnpKO mES cells.  Clone2, replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on two independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
RNAseq: Sequenced reads were aligned using Bowtie 1.0.0 ( -m1 --best –strata) or STAR 2.5.0a (--outFilterMultimapNmax 20 --outMultimapperOrder Random --outSAMmultNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000)
ChIPseq: Sequenced reads were aligned using Bowtie 1.0.0 (-m 1 —best –strata) or STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within )
For RNAseq and ChIPseq, QuasR was used to count aligned reads (qCount) and to generate depth normalized bigWig files (qExportWig). Differential expression analysis was perfored using EdgeR on the raw gene count tables generated by QuasR.
ATACseq data was mapped using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType Local --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix  --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using QuasR. Read counts were binned in 50bp intervals and normalized to average sequencing depth. For ATACseq, data was not binned and the bigwig files display the full sequencing reads normalized to 1 mio genome mapping reads. Bed files containing peak positions were generated from the .narrowPeak output file from MACS2.

source_name: ATACseq in AdnpKO mES cells.  Clone2

growth_protocol: Mouse ES cells were grown under standard conditions in 2i medium containing LIF.

extract_protocol:
50000 ES cells of the respective genotype were used to perform ATAC seq according to a previously published protocol ( Buentrostro et al, Curr Protoc Mol Biol, 2015). ATACseq was performed in two biological replicates for each of the two independent wild type and Adnp KO clones.
Libraries were prepared according to Buentrostro et al, Curr Protoc Mol Biol, 2015.

tag: strain background

value: hybrid 129-C57BL/6

tag: genotype/variation

value: Adnp KO

value: embryonic stem (ES) cells

tag: treatment

value: no


title: JE82-011 control

description:
Sample name:
X98

value: sperm

tag: # years smoking


title: ATACseq in AdnpKO mES cells.  Clone2 replicate 1


title: VJ30011 smoke

description:
Sample name:
X14

tag: # cigarettes per day


title: ATACseq in AdnpKO mES cells.  Clone1, replicate 2

source_name: ATACseq in AdnpKO mES cells.  Clone1


title: 0XG3009 smoke

description:
Sample name:
X10

tag: sperm concentration (m/ml)


title: ATACseq in AdnpKO mES cells.  Clone1, replicate 1


title: ATACseq in wt mES cells.  Clone2, replicate 1

source_name: ATACseq in wt mES cells.  Clone2

value: wt


title: ATACseq in wt mES cells.  Clone2, replicate 2


title: E10 EHT cells

value: ICR

value: Gfi+/tomato/ Gfi1b+/GFP

value: Aorta-Gonad-Mesonephros


title: ZA5H007 smoke

description:
Sample name:
X11


title: vein graft_7 day_rep6

city: Nanchang

first: Qun

state: Jiangxi Province

address: No.461, Bayi Road,

country: China

institute: First Affiliated Hospital of Nanchang University

description:
Gene expression 7 day after surgery in vein graft
vein graft, 7 day after surgery, replicate6
C6

hyb_protocol: 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. 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 at 60 °C for 30 min, and 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.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryctolagus cuniculus

source_name: vein graft, 7 day after surgery

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: RNA was prepared using, TRIzol® Reagent (Invitrogen life technologies),Biopulverizer(biospec),Mini-Bead-Beater-16(biospec), following the manufacture's recommendations.

treatment_protocol: vein graft were removed 1 day, 7 day after surgery, and sham surgery were conducted in control group

tag: protocol

value: vein graft, 7 day after surgery

value: vein tissue

tag: gender

value: male


title: ATACseq in wt mES cells. Clone1, replicate 2

source_name: ATACseq in wt mES cells. Clone1


title: vein graft_7 day_rep4

description:
Gene expression 7 day after surgery in vein graft
vein graft, 7 day after surgery, replicate4
C4


title: vein graft_sham surgey_rep2

description:
Gene expression  in sham surgery vein graft
vein graft, sham surgery, replicate2
O2

source_name: vein graft, sham surgery

value: vein graft, sham surgery


title: vein graft_sham surgey_rep1

description:
Gene expression  in sham surgery vein graft
vein graft, sham surgery, replicate1
O1


title: vein graft_sham surgey_rep3

description:
Gene expression  in sham surgery vein graft
vein graft, sham surgery, replicate3
O3


title: vein graft_7 day_rep1

description:
Gene expression 7 day after surgery in vein graft
vein graft, 7 day after surgery, replicate1
C1


title: vein graft_7 day_rep3

description:
Gene expression 7 day after surgery in vein graft
vein graft, 7 day after surgery, replicate3
C3


title: vein graft_7 day_rep5

description:
Gene expression 7 day after surgery in vein graft
vein graft, 7 day after surgery, replicate5
C5


title: vein graft_1 day_rep5

description:
Gene expression 1 day after surgery in vein graft
vein graft, 1 day after surgery, replicate5
A5

source_name: vein graft, 1 day after surgery

value: vein graft, 1 day after surgery


title: ATACseq in wt mES cells. Clone1, replicate 1


title: vein graft_sham surgey_rep4

description:
Gene expression  in sham surgery vein graft
vein graft, sham surgery, replicate4
O4


title: vein graft_7 day_rep2

description:
Gene expression 7 day after surgery in vein graft
vein graft, 7 day after surgery, replicate2
C2


title: vein graft_1 day_rep4

description:
Gene expression 1 day after surgery in vein graft
vein graft, 1 day after surgery, replicate4
A4


title: Organoid 4

city: Parkville

first: Luke

last: Zappia

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

description:
org4_barcodes.tsv
org4_counts.csv
org4_genes.tsv
org4_matrix.mtx

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Count matrics from the kidney samples were combined using cellranger aggr with no normalisation, as were those from the organoid samples. The resulting datasets consist of matrix files (kid_matrix.mtx, org_matrix.mtx) containing the UMI count values, barcode files (kid_barcodes.tsv, org_matrix.tsv) containing the detected cell barcodes and genes files (kid_genes.tsv, org_genes.tsv) containing the ENSEMBL ids of the detected genes. These have been converted to dense matrices in CSV format (kidney_counts.csv, org_counts.csv).
Genome_build: mm10 / hg38
Supplementary_files_format_and_content: CSV files containing raw count matrices.

source_name: C32 human embryonic stem cell

growth_protocol: Kidney organoids were made according to a published protocol (Takasata et al., Generation of kidney organoids from human pluripotent stem cells, Nature protocols 2016, PMID:27560173.

extract_protocol:
Mouse kidneys were dissected into ice cold PBS then digested over 15 minutes at 37C in Accutase, with manual dissociation via pippetting through a P1000 tip every 5 minutes. Following dissociation, cells were passed through a 30 micron filter and stored on ice in 50% PBS, 50% DMEM with 10% FCS. Human kidney organoids were dissociated via a similar protocol using Trypsin instead of Accutase and stored on ice in APEL media.
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: ES-derived kidney organoid

tag: day of differentiation


title: vein graft_1 day_rep1

description:
Gene expression 1 day after surgery in vein graft
vein graft, 1 day after surgery, replicate1
A1

tag: tissue


title: pTSPO-PDC1-5 drought_rep3

city: Yokohama-Shi, Tsurumi Ku

first: Khurram

last: Bashir

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: Gene expression drought stressed

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: Quantile normalization was performed with Gene Spring (Agilent Technology v14.9) with median transformation. One way ANOVA was performed and Tuckey's HSD was performed as posthoc test.

organism: Arabidopsis thaliana

source_name: pTSPO-PDC1-5  shoot from drought stressed

label_protocol: Total RNA (400 ng) was labeled with fluorescently-labeled Cy3, using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: WT and pTSPO-PDC1-5 seeds were sown in trays containing Dio propagation mix no. 2 professional soil (Dio Chemicals, Japan) and germinated and grown at 22°C under a 16 h light/8 h dark cycle, and a 60 µmol m−2 s−1 photon flux density.

extract_protocol: RNA was extracted from PureLink™ Plant RNA Reagent (Thermo Fisher)

treatment_protocol: Two weeks after germination, plants were subjected to drought treatment by removing excess water from the trays and ceasing any subsequent watering. Shoot samples were collected 11 days after drought stress treatment. Plants not subjected to drought stress treatment were used as control. Samples were immediately frozen in liquid nitrogen and stored at -80 degrees until RNA extraction.

tag: condition

value: Drought stressed

value: Shoot


title: YL4

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

description: YL.peaks.txt

data_processing:
Raw reads of MeDIP-seq were preprocessed using fastx (version: 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/index.html) by removing reads containing adapters, low-quality reads, less than 20 bp reads. Subsequently, the remaining reads (clean reads) were mapped to the pig reference genome Sus scrofa 10.2.69.
Methylated enrichment peaks were counted (diffScore >= 50) using MACS1.4. The MEDIPS package was used to calculate DMRs by window size = 500 bp, fold-change (FC) ≥ 1.33 or ≤ 0.75), and P-value ≤ 0.001
We annotated DMGs from the DMRs in combination with the UCSC database. According positions of the DMRs, we annotated related genes and genome elements ("promoter","5’-UTR","CDS","3’-UTR", "exon", "intron" and "TTR", where promoter is 5000 bp upstream of the transcription initiation site, TTR is 5000 bp downstream of the transcription termination site) and CpG island ("shore" is CpG island 2000bp upstream, "shelf" is CpG island 2000bp downstream and "open sea" is not located in the CpG island region)
The DMGs were classified for functional categories using the annotation of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway with the DAVID online software.
Genome_build: Sscrofa10.2.69
Supplementary_files_format_and_content: tab-delimited text files include distribution of peaks varies with peak length in four groups

organism: Sus scrofa

source_name: Yorkshire raised at lowland

extract_protocol:
DNA of heart tissue samples was isolated using TuSeq DNA Sample Preparation Kit, Box A (Illumina)
DNA (1μg) was sonicated to obtain about 250bp fragments using a Covarias sonication system (Covarias, USA) according to the parameters. DNA fragments were end repaired, added “A” to the 3’ end, ligated with the Agencourt® AMPure XP Beads (Beckman), and MeDIP was performed using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode). The enriched DNA in MeDIP was PCR with TruSeq DNA Sample Preparation Kit and PCR Prep Box (Illumina). Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a cBot User Guide (Illumina).

value: heart

tag: breed

value: Yorkshire

tag: location

value: lowland

tag: age

value: 6 months

tag: Sex


title: YL3

description: YL.peaks.txt


title: WT Drought_rep3

description: Gene expression control conditions

source_name: WT shoot from drought stressed plants

tag: genotype

value: WT

value: Control


title: Mammary gland PRA transgenic Replicate 3

city: New York

first: Maria

middle: Jose

last: Carlini

state: NY

department: Neurology

institute: Columbia University

hyb_protocol: 300ng of Cy5/Cy3-labeled cRNA was fragmented and prepared for hybridization using the Gene Expression Hybridization Kit (Agilent Technologies Inc.) following manufacturer's instructions and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K (Agilent Technologies Inc.) for 17 h at 65 °C in a rotating hybridization oven. After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent Technologies Inc.) and 1 min with 37 °C GE Wash buffer 2 (Agilent Technologies Inc.) containing 0.005% Triton X-100.

scan_protocol: Slides were scanned immediately after washing using the G4900DA SureScan microarray scanner system, features were extracted with Agilent Feature Extraction Software (Agilent Technologies Inc.)

data_processing: Data was processed with Agilent Feature Extraction 12.0 using GE2_1200_Jun14 protocol. Data analysis were conducted with GeneSpring GX software (Agilent Technologies Inc.). Input data was pre-processed by baseline transformation to the median of all samples.

source_name: Preneoplastic mammary gland from nulliparous adult PRA transgenic FVB mouse (20-25 weeks)

label_protocol: RNA integrity was assessed using the RNA 6000 Nano Assay and Agilent 2100 Bioanalyzer (Agilent Technologies Inc.). Labeled cRNA was prepared from 50 ng RNA using the Low Input QuickAmp Labeling Kit Two-Color and RNA Spike-In Kit for Two colors v4.0 (Agilent Technologies Inc.) according to manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen Inc.) purification.

growth_protocol: Nulliparous adult FVB mice (20-25 weeks) were used in this study. PRA transgenic mice have been described previously (G. Shyamala et al, Proc. Natl. Acad. Sci. U. S. A., vol. 95, 1998) . Mice were housed and treated in accordance with the NIH Guide for Humane Use of Animals in Research. Mice were euthanized, and mammary glands were harvested from all mice at diestrus, given that serum progesterone levels and the morphological grade, epithelial proliferation, and apoptosis in the mammary gland all peak at this stage (J. E. Fata, V. Chaudhary, and R. Khokha, Biol. Reprod., 2001). A total of seven animals were used (3 wild-type, 4 PRA transgenic).

extract_protocol: Tissue was pulverized in a Thermo-vac tissue pulverizer (Thermovac Industries Corp.) at liquid nitrogen temperature. The resulting powder was transferred into tubes containing 1.5ml of Trizol reagent (Thermo Fisher Scientific Inc.) and homogenized by passing the lysate through sterile, disposable 21G needle 5 times twice. Following homogenization, samples were centrifuged at 12,000 × g for 10 minutes at 4°C. The fatty layer above the supernatant was removed and discarded, and the cleared supernatant was transferred to a new tube. Total RNA was extracted according to manufacturer's instructions, followed by additional column purification (RNeasy Mini Kit, Qiagen Inc.)

treatment_protocol: In each case, a single abdominal gland was removed following excision of lymph nodes, immediately frozen in liquid nitrogen and stored at -80C until used.

tag: strain

value: FVB

tag: estrous cycle stage

value: Diestrus

value: PRA transgenic

source_name: Universal Mouse Reference RNA (UMRR) composed of total RNA from 11 mouse cell lines

tag: cell line derivations

value: Embryo; T-lymphocyte (thymus); embryo, fibroblast; mammary gland; kidney; muscle myoblast; liver, hepatocyte; skin; lung, alveolar macrophage; testis; B-lymphocyte


title: vein graft_1 day_rep2

description:
Gene expression 1 day after surgery in vein graft
vein graft, 1 day after surgery, replicate2
A2

value: vein tissue


title: pTSPO-PDC1-5 control_rep3

description: Gene expression drought stressed

source_name: pTSPO-PDC1-5  shoot from control


title: pTSPO-PDC1-5 drought_rep1

description: Gene expression drought stressed


title: pTSPO-PDC1-5 drought_rep2

description: Gene expression drought stressed


title: WT Drought_rep1

description: Gene expression control conditions


title: Control_2_miRNA

city: Whitechapel

first: John

last: Bladen

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

description:
CTRL.2
Control sample

hyb_protocol: Nanostring experiment carried out at UCL Genomics Core Facility.

data_processing: R/BioConductor to quantile normalise data

source_name: Control

extract_protocol: Qiagen FFPE kit used for microRNA and messengerRNA

treatment_protocol: FFPE

value: non-cancerous eyelid/tarsal plate


title: vein graft_1 day_rep3

description:
Gene expression 1 day after surgery in vein graft
vein graft, 1 day after surgery, replicate3
A3

value: male


title: WT Drought_rep2

description: Gene expression control conditions


title: vein graft_1 day_rep6

description:
Gene expression 1 day after surgery in vein graft
vein graft, 1 day after surgery, replicate6
A6

value: vein graft, 1 day after surgery


title: Control_3_miRNA

description:
CTRL.5
Control sample

scan_protocol: Nanostring experiment carried out at UCL Genomics Core Facility.


title: Mammary gland PRA transgenic Replicate 1

tag: genotype/variation


title: YL2

description: YL.peaks.txt


title: Mammary gland PRA transgenic Replicate 2


title: Mammary gland PRA transgenic Replicate 4


title: Mammary gland wild-type Replicate 3

source_name: Normal mammary gland from nulliparous adult wild-type FVB mouse (20-25 weeks)

value: wild type


title: Mammary gland wild-type Replicate 2


title: RECTUM_BIOPSY_P0311 [Agilent]

city: Goettingen

first: Alexander

last: Wolff

state: Lower Saxony

address: Humboldtallee 32

department: Medical Statistics

institute: UMG

hyb_protocol: 1.5 mg of Cy3-labeled cRNA was hybridized to an oligonucleotide-based Whole Human Genome Microarray (4x44K, Agilent Technologies) and incubated at 65˚C for 17 hours.

scan_protocol: Slides were washed and scanned using an Agilent G2565BA scanner.

data_processing: Raw data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies). Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

source_name: Pretherapeutic rectal cancer patient biopsy

label_protocol: 1 µg of total RNA was labeled with Cy3 using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent Technologies, Santa Clara, CA). Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Biospies from patients not cell lines were used for analyses

extract_protocol: Biopsies were immediately stored in RNAlater (Qiagen, Hilden, Germany). Subsequently, RNA and DNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer´s instructions.  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: No treatment prior to expression profiling analysis was performed.

tag: development of distant metastasis


title: pTSPO-PDC1-5 control_rep1

description: Gene expression drought stressed

value: Drought stressed


title: WT control_rep1

description: Gene expression control conditions

source_name: WT shoot from control

value: Shoot


title: WT control_rep3

description: Gene expression control conditions


title: pTSPO-PDC1-5 control_rep2

description: Gene expression drought stressed


title: Mammary gland wild-type Replicate 1


title: E10 wIAHCs

source_name: whole intra-aortic hematopoietic cluster cells

tag: developmental stage

value: Aorta-Gonad-Mesonephros

tag: phenotype

value: c-kit+


title: WT control_rep2

description: Gene expression control conditions


title: YH4

description: YH.peaks.txt

source_name: Yorkshire pigs raised at highland

value: heart

value: Yorkshire

value: highland


title: YL1

description: YL.peaks.txt

value: lowland

value: 6 months


title: YH1

description: YH.peaks.txt


title: YH3

description: YH.peaks.txt


title: Control_1_miRNA

description:
CTRL.1
Control sample

label_protocol: Nanostring experiment carried out at UCL Genomics Core Facility.


title: SGC_pagetoid_3_miRNA

description:
SCC.11
Sebaceous gland carcinoma pagetoid  sample

value: Sebaceous gland carcinoma pagetoid


title: SGC_pagetoid_2_miRNA

description:
SCC.9
Sebaceous gland carcinoma pagetoid sample


title: SGC_pagetoid_1_miRNA

description:
SCC.7
Sebaceous gland carcinoma pagetoid sample


title: TL4

description: TL.peaks.txt

source_name: Tibetan pigs raised at lowland

value: Tibetan


title: TL3

description: TL.peaks.txt


title: TL2

description: TL.peaks.txt


title: SGC_nodular_1_miRNA

description:
SCC.1
Sebaceous gland carcinoma nodular  sample

value: Sebaceous gland carcinoma nodular


title: PV.026_L_PT7 RNA-Seq

data_processing:
RNA data was pseudoaligned to the University of California, Santa Cruz, annotated Sus scrofa (pig) genome (build 9.2)
Transcript abundances were quantified using Kallisto with default parameters
R/Bioconductor DESeq 2 was used to calculate differential expression (DE) of transcripts
R was used to analyze expression data for set analysis (GAGE), principal component analysis, and correlation of inter-treatment gene expression
Cound data was log2 transformed, after adding a pseudocount of 0.5 to all measurements
Genome_build: University of California, Santa Cruz, annotated Sus scrofa (pig) genome (build 9.2)
Supplementary_files_format_and_content: Excel format worksheet for genes

organism: Sus scrofa domesticus

source_name: Sham_PT muscle

extract_protocol:
During the harvest for histologic samples, samples from the PT muscle were collected for whole tissue RNA isolation. The muscles were thawed, minced and homogenized (Tissue Ruptor, Qiagen) for 30 seconds at room temperature and total RNA was isolated from the slurry using the miRNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
1 μg of isolated total RNA was used to produce cDNA libraries using the Truseq protocol (Illumina), as per the manufacturer’s instructions. Biological replicates or triplicates were produced from each condition and individual libraries were pooled and sequenced using 76 base-pair (bp) paired-end reads on a Hi-Seq. 2500 in high output mode to an average depth of 55 M reads per library.

treatment_protocol: While under isoflurane anesthesia and appropriate aseptic conditions, a ~3 × 3 × 1 cm area of muscle (5.10 ± 0.03 g) was surgically removed using sharp dissection from the middle third of the PT muscle. The fascia and skin were closed in layers with absorbable suture and compressive bandages were wrapped around each limb.

value: Yorkshire Cross pig

tag: timepoint

value: Sham

value: peroneous tertius (PT) muscle


title: PV.025_L_PT9 RNA-Seq


title: RECTUM_BIOPSY_P0300 [Agilent]


title: TL1

description: TL.peaks.txt

value: male


title: PV.024_R_PT8 RNA-Seq

source_name: ECM-SIS_PT muscle

value: ECM-SIS


title: TH4

description: TH.peaks.txt

source_name: Tibetan pigs raised at highland


title: RECTUM_BIOPSY_P0112 [Agilent]


title: YH2

description: YH.peaks.txt


title: RECTUM_BIOPSY_P0294 [Agilent]


title: RECTUM_BIOPSY_P0291 [Agilent]


title: RECTUM_BIOPSY_P0048 [Agilent]


title: SGC_nodular_3_miRNA

description:
SCC.5
Sebaceous gland carcinoma nodular  sample


title: TH3

description: TH.peaks.txt


title: PV.023_R_PT4 RNA-Seq

source_name: No repair_PT muscle

value: No repair


title: RECTUM_BIOPSY_P0123 [Agilent]


title: TH1

description: TH.peaks.txt


title: PV.022_L_PT3 RNA-Seq


title: TH2

description: TH.peaks.txt


title: PV.021_R_PT7 RNA-Seq


title: PV.018_L_PT2 RNA-Seq


title: RECTUM_BIOPSY_P0160 [Agilent]


title: PV.017_R_PT3 RNA-Seq

source_name: HA_PT muscle

value: HA


title: RECTUM_BIOPSY_P0022 [Agilent]


title: Fo 37°C Replicate 2

city: Amherst

first: Gregory

middle: Alan

last: DeIulio

address: 240 Thatcher Road

department: Biochemistry and Molecular Biology

institute: Umass Amherst

description: F_oxysporum_temp_rpkm.txt (col 5)

data_processing:
Fastq files were mapped using Rsubread to the Fo4287 genome and a GTF file containing gene annotations
Replicate information was tracked
Genome_build: The reference genome used was fusarium_oxysporum_f._sp._lycopersici_4287_2_supercontigs.fasta.gz (available from the broad institue)
Supplementary_files_format_and_content: Processed data included the Gene ID for each gene and the predicted FPKM value as given by R for each sample and replicate

organism: Fusarium oxysporum f. sp. lycopersici 4287

source_name: Hyphae

growth_protocol: 14 hours at 28°C (in the case of 28° growth experiment) or for 10 hours at 28°C and switched to 37°C for 4 hours (in the case of 37° growth experiment) in 200 ml of Minimal Medium supplemented with GluNa 25 mM and buffered with HEPES (20 mM final concentration) to pH 7.4 at 170 rpm

extract_protocol:
Fungal tissue was collected with filter paper and RNA was extracted using a standard TRIzol RNA Isolation Reagent extraction
RNA Library was constructed using Illumina TruSeq Stranded mRNA Library Prep Kit

value: Hyphae

tag: temperature


title: Fo 37°C Replicate 3

description: F_oxysporum_temp_rpkm.txt (col 6)


title: PV.017_L_PT8 RNA-Seq


title: RECTUM_BIOPSY_P0028 [Agilent]


title: Fo 28°C Replicate 3

description: F_oxysporum_temp_rpkm.txt (col 3)


title: PV.014_R_PT1 RNA-Seq


title: Fo 28°C Replicate 2

description: F_oxysporum_temp_rpkm.txt (col 2)


title: Fo 28°C Replicate 1

description:
This dataset was excluded from the final data analysis due to high variability with the other 2 replicates
Excluded


title: PV.013_L_PT4 RNA-Seq


title: CD4 T cells sorted from PBMC at baseline from patient 4

status: Public on May 22 2018

city: Nanjing

first: Shiping

last: JIAO

state: Jiangsu

address: Zhongshan Road #321

department: Department of Hepatobiliary Surgery

institute: Nanjing Drum Tower Hospital

data_processing:
Raw reads were filtered by standard Illumina chastity filtering (removing “non pass-filter” reads).
Filtered reads were aligned to reference genome by TopHat v2.1.0 with the following settings: tophat-2.1.0.Linux_x86_64/tophat -p 32 -r 50 --no-coverage-search --library-type fr-firststrand -g 1 -G genes_hg19.gtf hg19 [FASTQ 1] [FASTQ 2] (genes_hg19.gtf file was obtained from the Illumina iGenomes server).
Raw counts were calculated by htseq-count with the following settings: -a 10 -s no -m union.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts from htseq-count

source_name: Human peripheral blood

extract_protocol:
RNAeasy plus mini kit (Qiagen) as per manufacturers recommended protocol with DNase digestion.
Directional PolyA RNA-seq library (NEBNext kit, New England Biolabs)

treatment_protocol: Patients with metastatic melanoma who received Ipilimumab as a standard of care. Perpheral T cells were sorted at baseline and after 3 doses of therapy with ipilimumab

tag: cell type

value: PBMC


title: CD4 T cells sortted from PBMC after 3 doses of Ipi from patient 1


title: CD4 T cells sortted from PBMC after 3 doses of Ipi from patient 4


title: CD4 T cells sortted from PBMC after 3 doses of Ipi from patient 2


title: CD4 T cells sortted from PBMC after 3 doses of Ipi from patient 3


title: CD4 T cells sorted from PBMC at baseline from patient 3


title: 07_R106_SC

city: Glostrup

first: Lisette

last: Kogelman

address: Nordre Ringvej 67

department: Danish Headache Centre

country: Denmark

institute: Rigshospital Glostrup

data_processing:
Filtering using NGSQC toolkit, default settings
Alignment using STAR
Quantification of reads using HTSeq.
Genome_build: Rattus Norvegicus 6.0.83
Supplementary_files_format_and_content: txt files, resulting from HTSeq

molecule: polyA RNA

source_name: spinal cord dorsal horn

growth_protocol: reversed night/day conditions, food and water ad lib.

extract_protocol:
tissues embedded in tissue-tek O.C.T. compound, but in 14 um slices, mounted on glass slides. Slides fixed and stained. Laser capture microdissection performed using arcturusXT LCM system.
RNA extracted using NucleoSpin RNA kit in combination with QIAzol
sequencing on Illumina HiSeq 2500 platform; mRNA isolated using poly(A) selection.

treatment_protocol: anaesthetized wit intraperitoneal injection of pentobarbital with lidocaine, perfused with cold saline to remove blood from tissue

value: Wistar Han

value: 10 weeks

tag: tissue

value: spinal cord dorsal horn


title: 07_R106_TNC

source_name: Trigeminal nucleus caudalis

value: Trigeminal nucleus caudalis


title: CD4 T cells sorted from PBMC at baseline patient 1


title: 07_R104_SC


title: 07_R104_TNC


title: 07_R105_TNC


title: 07_R103_SC


title: Fo 37°C Replicate 1

description: F_oxysporum_temp_rpkm.txt (col 4)


title: PV.016_L_PT5 RNA-Seq

city: Lexington

first: Darrell

institute: MIT Lincoln Laboratory


title: 07_R102_SC


title: 07_R102_TNC


title: 07_R101_TNC


title: CD4 T cells sorted from PBMC at baseline from patient 2


title: BE2C Input combined

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: This sample includes combined data from GSM2311765 and a new BE2C_Input sample. Raw data are available for both samples from the SRX below.

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
Aligned reads from two samples (GSM2311765,this sample) were combined
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Neuroblastoma

growth_protocol: Cells were cultured according to the suggested guidelines in RPMI media containing 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

tag: chip antibody


title: BE2C H3K27ac combined

description: This sample includes combined data from GSM1680107 and GSM2037779. Raw data are available for both samples from the SRX below.

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
Aligned reads from two samples (GSM1680107,GSM2037779) were combined and used for peak calling.  The output of two MACS runs was collapsed.  MACS run 1 used -p 1e-9  --keep-dup=all and corresponding input control.  MACS run 2 used -p 1e-9  --keep-dup=auto and corresponding input control.
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

tag: antibody manu.

value: Abcam

tag: antibody catalog


title: 07_R105_SC

tag: age


title: 07_R103_TNC

tag: Sex


title: RACHX_2h-B

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
CASAVA 1.8.2 software was used for demultiplexing
Quality check was performed using Babraham Bioinformatics FastQC v.0.10.1
Sequenced reads were mapped to Xenopus laevis 9.1 whole genome using bowtie v 2.1.0
Read Counting and detection of differentially regulated genes was performed using edgeR
Candidate genes with log2Foldchange of 2 and p-value 0.05 were filtered
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: Tab-delimited text file containing normalized values, candidate genes

organism: Xenopus laevis

source_name: animal cap explants

growth_protocol: Ectodermal explants were dissected from the blastocoel roof of stage 8/9 embryos and cultured in salt solution (88 mM NaCl, 1 mM KCl, 0.82 mM MgSO4, 2.4 mM NaHCO3, 0.41 mM CaCl2, 0.33 mM Ca(NO3)2, 10 mM HEPES, pH 7.8 ) with antibiotics (Ampicillin (100 µg/ml), Kanamycin (10µg/ml) and Gentamycin (10 µg/ml)) on 0.7% agarose at 14°C until control embryos had reached the desired stage.

extract_protocol:
Total RNA was isolated using peqGOLD Trifast reagent (peQlab)
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit removing both cytoplasmic and mitochondrial rRNA (Illumina, Cat. No. RS-122-2201, San Diego, CA, USA). About 200 ng of total RNA was used as start material. Accurate quantitation of cDNA libraries was performed  by using the QuantiFluorTM dsDNA System (Promega,Madison, WI, USA). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina with 50bp Single-end chemistry.

treatment_protocol: Treatments with 5 µM RA (all-trans RA, SIGMA) were done in the corresponding buffer at stage 11 for one hour at 12 °C under light protection.  Treatments with 10 µg/ml Cyclohexamide (SIGMA) started 30 min prior to additional treatments.

tag: injected rna

tag: treatment

value: RA and Cyclohexamide

tag: time


title: CYP_2h-B

value: untreated


title: RACHX_2h-A


title: CYP_2h-A


title: CYPCHX_2h-B

value: Cyclohexamide


title: RA_2h-A

value: RA


title: CYPCHX_2h-A


title: RA_2h-B


title: 07_R101_SC

tag: strain


title: wt_TetR-EGFP_Rep1

city: Urbana

first: Ipek

last: Tasan

state: IL

address: 600 S. Mathews Avenue

institute: University of Illinois at Urbana-Champaign

description: CUT and RUN analysis. biological replicate 1

data_processing:
Raw reads were first trimmed for adapters with Trimmomatic, version 0.36 and then aligned to the human reference genome hg19 using bowtie2, version 2.3.2
Deduplication was performed with MarkDuplicates, part of picard tools (http://broadinstitute.github.io/picard) version 2.1.0
Further filtering was performed with samtools, version 1.4.1, in order to keep only properly paired non-duplicate reads
Normalization was performed using bamCoverage using the following command:
bamCoverage –b ${filterBam} –o ${filterBam}.bw   --binSize 1000 –normalizeTo1x ${params.genomeEfSize} –ignoreForNormalization chrX
Genome_build: UCSC hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were washed twice in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, a tablet of Roche complete protease inhibitor EDTA-free in 50 ml final volume) at room temperature. Cells were resuspended in 1 ml wash buffer, mixed with BioMag Plus Concanavalin A-coated magnetic beads, rotated 10 minutes. Samples were placed on a magnet stand and the supernatant was removed. Beads were resuspended in antibody buffer (2 mM EDTA and antibody at 1:100 dilution in dig-wash buffer (Wash buffer with 0.05% digitonin)). Samples were rotated overnight at 4°C. Beads were captured on a magnet stand and washed once in dig-wash buffer. Afterwards, beads were resuspended in Protein A-MNase diluted to ~700 ng/ml in 50 µl dig-wash buffer and rotated for 1 hour at 4°C. Beads were washed twice in dig-wash buffer, followed by resuspending in 100 µl dig-wash buffer. After the samples were placed at 0°C, 2 µl 100 mM CaCl2 was added. Samples were incubated at 0°C for 45 min, followed by addition of 100 µl 2XSTOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.1% digitonin, 50 µg/ml RNAse A, 50 µg/ml glycogen, and 10 pg mono-nucleosomal S. cerevisiae (spike-in) DNA). Samples were incubated 10 min at 37°C and centrifuged 5 min 16,000×g at 4°C. DNA in the supernatant was isolated by spin column.
Libraries for next generation sequencing were prepared by using KAPA Hyper Prep Kit, following manufacturer’s instructions. IDT for Illumina-TruSeq DNA UD Indexes (Illumina, San Diego, CA) were used as adapters. To minimize representation of large DNA fragments in the libraries, 14 cycles and a combined annealing/extension step at 60°C, 10 seconds were used for library amplification.

tag: genotype

value: wildtype

tag: cell line

tag: antibody

value: Anti-H3K9me3 Abcam (ab8898)

tag: viral transduction

value: Cells were transduced with TetR-EGFP. 2 days after transduction, selected with 0.5 ug/ml puromycin for 3 days. Afterwards, cells were grown without puromycin for 2 days before collection.


title: wt_Rep2

description: CUT and RUN analysis. biological replicate 2

value: no transduction


title: 48-15_TetR-EGFP_Rep1

value: 48-mer TetO repeat knock-in. CRISPR target site chr6:31,813,898-31,813,920 (hg19)


title: HT29_Ctrl

city: Tokyo

first: Masaru

last: Koido

address: 4-6-1, Shirokanedai, Minato-ku

institute: Institute of Medical Science, The University of Tokyo

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression measurement was carried out using Affymetrix Microarray Suite version 5.0 from R package affy v1.40.0. Expression values were normalized to a mean target level of 100

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were cultured in PRMI-1640 (WAKO, Osaka, Japan), supplemented with 10% heat-inactivated FBS and 100 ug/ml of kanamycin.

extract_protocol: Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: ON-TARGETplus SMART pool siRNA (GE Healthcare, Little Chalfont, UK) was used for knockdown of MYC expression. ON-TARGETplus Non-targeting Pool (GE Healthcare) was used as the control. HT-29 cells were seeded at a density of 8×104 cells/well on a 6-well plate, and were transfected for 24 hours with each 20 nM siRNA in Opti-MEM (Thermo Fisher Scientific) with lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s reverse transfection protocol. After for 48 hours, the cells were used for further experiments.


title: A1A3_Brg1KD_Dex3_RNAseq

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
Brg1KD_Dex_3

data_processing:
Adapter sequences were trimmed from ChIP-seq reads using Cutadapt
low quality reads were removed from analysis using Sickle
For ChIP-seq, alignment was performed with Bowtie2, aligned reads were sorted and processed with Samtools, and de-duplicated using Picard Tools
Peaks were called using MACS2 and Homer using a false discovery rate cutoff and 0.001, and regions of high depth or with high signal in untreated or input samples were used to filter out false positive peak calls
For RNA-seq, alignment was performed using STAR to generate coverage tracks and using Salmon and to obtain gene counts for differential expression analysis using limma-voom with cutoffs of Fold Change > 1.5, p-Value < 0.01, and False Discovery Rate < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Coverage files and heatmaps were generated using Deeptools

growth_protocol: Cells were cultured in Dulbecco's modified Eagle medium (DMEM) containing 10% fetal bovine serum containing 250 μg/ml G418. Media for A1A3 cells also contatined 1 μg/ml Puromycin

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde at 37C for 10 minutes for all targets except BRG1, for which cells were fixed for 20 minutes. After quenching with glycine, cell pellets were washed Hypotonic buffer (10mM HEPES-NaOH pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 340 mM sucrose, 10% glycerol, 0.1% Triton X-100, and HALT protease inhibitors (ThermoFisher)) and resuspended in Shearing buffer (10 mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, 0.5mM PMSF, 5mM Sodium Butyrate, 0.1% SDS, and HALT protease inhibitors (ThermoFisher) and chromatin was fragmented by sonication with the Covaris S220. Chromatin was diluted two-fold in 2xIP buffer (20 mM Tris-HCl pH 8.0, 300mM NaCl, 2mM EDTA, 20% Glycerol, 1% Triton X-100, 0.5mM PMSF, 5mM Sodium Butyrate, and HALT protease inhibitors (ThermoFisher)) and immunoprecipitation was performed with 1ug antibody per 100ug chromatin. Immune complexes were captured using protein A and G dynabeads, washed once each with low salt (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.1 % SDS), high salt (same as low salt buffer, except 500 mM NaCl), and LiCl buffer (Tris-HCl pH 8.0, 250 mM LiCl, 2 mM EDTA, 1 % NP-40, 1 % (wt/vol) sodium deoxycholate), and twice with TE. Eluted DNA was RNaseA and Proteinase K  treated and purified using Qiagen PCR purification columns. For RNA-seq, RNA was isolated from treated A1-2 and A1A3 cells using Qiagen RNeasy kits with on-column DNase treatment.
ChIP-seq libraries were generated using the Illumina Nextara-XT library generation kit, RNA-seq libraries were generated at the National Intramural Sequencing Center using Ribo-Zero Gold

treatment_protocol: Dexamethasone treatments were performed using 100 nM Dexamethasone or ethanol vehicle for 1 hour or 8 hours for ChIP-seq and RNA-seq experiments, respectively. To knockdown BRG1 expression in A1-A3 cells, cells were treated for 72 hours with Doxycycline.

tag: cell line/type

value: A1A3 breast cancer cells

value: 8hr Dex

value: 72hrs Doxycycline


title: wt_Rep1


title: 96-8_TetR-EGFP_Rep1

value: 96-mer TetO repeat knock-in. CRISPR target site chr6:31,813,898-31,813,920 (hg19)


title: 48-15_TetR-EGFP_Rep2


title: wt_TetR-EGFP_Rep2


title: A1A3_Brg1KD_Dex1_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
Brg1KD_Dex_1


title: A1A3_Brg1KD_Dex2_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
Brg1KD_Dex_2


title: HT29_siMYC

value: MYC siRNA


title: 96-8_TetR-EGFP_Rep2


title: A1A3_Brg1KD_EtOH3_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
Brg1KD_EtOH_3

value: 8hr EtOH


title: A1A3_Brg1KD_EtOH2_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
Brg1KD_EtOH_2


title: A1A3_control_Dex3_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
WT_Dex_3

value: 72hrs PBS


title: A1A3_Brg1KD_EtOH1_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
Brg1KD_EtOH_1


title: A1A3_control_Dex2_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
WT_Dex_2


title: A1A3_control_Dex1_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
WT_Dex_1


title: A1A3_control_EtOH3_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
WT_EtOH_3


title: A1A3_control_EtOH1_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
WT_EtOH_1


title: A1A3_control_EtOH2_RNAseq

description:
processed data file: A1A3_RNAseq_log2normalized_geneCounts.xlsx
WT_EtOH_2


title: smallRNA Medicago HM106

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
RNA-seq: RNA-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
small RNAseq was performed using Illumina small RNA TruSeq library prep kit,and using bowtie for sequence mapping
Genome_build: Mtruncatula_285_Mt4.0
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "smallRNA.processedfile_description.txt" and "RNA_column_header_descriptions.txt" for column headers

organism: Medicago truncatula

source_name: plant

extract_protocol: MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.

treatment_protocol: the plant was grown in the greenhouse under long day conditions during the winter

tag: ecotype

value: mature leaves

value: 45 days


title: smallRNA Medicago HM105


title: smallRNA Medicago HM109


title: smallRNA Medicago HM099


title: smallRNA Medicago HM091


title: smallRNA Medicago HM095


title: smallRNA Medicago HM089


title: smallRNA Medicago HM085


title: smallRNA Medicago HM092


title: smallRNA Medicago HM088


title: smallRNA Medicago HM101


title: smallRNA Medicago HM079


title: smallRNA Medicago HM086


title: smallRNA Medicago HM093


title: smallRNA Medicago HM098


title: smallRNA Medicago HM112


title: smallRNA Medicago HM107


title: smallRNA Medicago HM080


title: smallRNA Medicago HM108


title: smallRNA Medicago HM111


title: smallRNA Medicago HM082


title: smallRNA Medicago HM087


title: smallRNA Medicago HM096


title: smallRNA Medicago HM083


title: smallRNA Medicago HM084


title: smallRNA Medicago HM078


title: smallRNA Medicago HM097


title: smallRNA Medicago HM077


title: smallRNA Medicago HM076


title: smallRNA Medicago HM074


title: smallRNA Medicago HM062


title: smallRNA Medicago HM061


title: smallRNA Medicago HM065


title: smallRNA Medicago HM064


title: smallRNA Medicago HM060


title: smallRNA Medicago HM068


title: smallRNA Medicago HM075


title: smallRNA Medicago HM057


title: smallRNA Medicago HM048


title: smallRNA Medicago HM073


title: smallRNA Medicago HM070


title: smallRNA Medicago HM071


title: smallRNA Medicago HM063


title: smallRNA Medicago HM046


title: smallRNA Medicago HM050


title: smallRNA Medicago HM058


title: smallRNA Medicago HM056


title: smallRNA Medicago HM053


title: smallRNA Medicago HM054


title: smallRNA Medicago HM055


title: smallRNA Medicago HM049


title: smallRNA Medicago HM069


title: smallRNA Medicago HM044


title: smallRNA Medicago HM052


title: smallRNA Medicago HM047


title: smallRNA Medicago HM066


title: smallRNA Medicago HM059


title: SGC_nodular_2_miRNA

description:
SCC.2
Sebaceous gland carcinoma nodular sample

value: Sebaceous gland carcinoma nodular


title: smallRNA Medicago HM041


title: smallRNA Medicago HM043


title: smallRNA Medicago HM042


title: smallRNA Medicago HM035


title: smallRNA Medicago HM039


title: smallRNA Medicago HM040


title: smallRNA Medicago HM036


title: smallRNA Medicago HM038


title: smallRNA Medicago HM031


title: smallRNA Medicago HM027


title: smallRNA Medicago HM045


title: smallRNA Medicago HM026


title: smallRNA Medicago HM015


title: smallRNA Medicago HM012


title: smallRNA Medicago HM010


title: smallRNA Medicago HM028


title: smallRNA Medicago HM034


title: smallRNA Medicago HM011


title: smallRNA Medicago HM032


title: smallRNA Medicago HM033


title: smallRNA Medicago HM007


title: smallRNA Medicago HM014


title: smallRNA Medicago HM006


title: smallRNA Medicago HM013


title: smallRNA Medicago HM009


title: smallRNA Medicago HM005


title: smallRNA Medicago HM004


title: smallRNA Medicago HM037


title: smallRNA Medicago HM003


title: mRNA Medicago HM112


title: smallRNA Medicago HM002


title: mRNA Medicago HM108


title: mRNA Medicago HM111


title: mRNA Medicago HM104


title: mRNA Medicago HM110


title: smallRNA Medicago HM001


title: mRNA Medicago HM105


title: mRNA Medicago HM097


title: mRNA Medicago HM101


title: mRNA Medicago HM103


title: smallRNA Medicago HM008


title: mRNA Medicago HM095


title: mRNA Medicago HM093


title: mRNA Medicago HM091


title: mRNA Medicago HM099


title: mRNA Medicago HM092


title: mRNA Medicago HM098


title: mRNA Medicago HM090


title: mRNA Medicago HM096


title: mRNA Medicago HM089


title: mRNA Medicago HM088


title: mRNA Medicago HM087


title: mRNA Medicago HM086


title: mRNA Medicago HM084


title: mRNA Medicago HM083


title: mRNA Medicago HM081


title: mRNA Medicago HM109


title: mRNA Medicago HM080


title: mRNA Medicago HM077


title: mRNA Medicago HM078


title: mRNA Medicago HM079


title: mRNA Medicago HM074


title: mRNA Medicago HM068


title: mRNA Medicago HM072


title: mRNA Medicago HM070


title: mRNA Medicago HM071


title: mRNA Medicago HM067


title: mRNA Medicago HM075


title: mRNA Medicago HM066


title: mRNA Medicago HM065


title: mRNA Medicago HM059


title: mRNA Medicago HM063


title: mRNA Medicago HM062


title: mRNA Medicago HM056


title: mRNA Medicago HM085


title: mRNA Medicago HM057


title: inducible regulatory T cells+CPI-1205 2D_iTreg-CPI

data_processing:
Raw reads were filtered by standard Illumina chastity filtering (removing “non pass-filter” reads).
Filtered reads were aligned to reference genome by TopHat v2.1.0 with the following settings: tophat-2.1.0.Linux_x86_64/tophat -p 32 -r 50 --no-coverage-search --library-type fr-firststrand -g 1 -G genes_mm10.gtf mm10 [FASTQ 1] [FASTQ 2] (genes_mm10.gtf file was obtained from the Illumina iGenomes server)
Raw counts were calculated by htseq-count with the following settings: -a 10 -s no -m union.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts from htseq-count

source_name: Mouse spleen and lymph node

treatment_protocol: Naïve CD4 T cells were sorted from FoxP3-eGFP mice. Naïve T cellswere activated with plate bound anti-CD3 and soluble CD28  and differentiated into inducible regulatory T cells with and without EZH2 inhibitor (CPI-1205). Following differentiation, indicuble T-regs were sorted based on GFP expression and subjected to RNA-seq.

tag: cell type

value: inducible regulatory T cells+CPI-1205


title: mRNA Medicago HM058

tag: tissue


title: mRNA Medicago HM061


title: inducible regulatory T cells+CPI-1205 2C_iTreg-CPI


title: inducible regulatory T cells+CPI-1205 2B_iTreg-CPI


title: mRNA Medicago HM053


title: mRNA Medicago HM052


title: mRNA Medicago HM051


title: inducible regulatory T cells+CPI-1205 2A_iTreg-CPI


title: mRNA Medicago HM076


title: mRNA Medicago HM049


title: mRNA Medicago HM064


title: mRNA Medicago HM050


title: mRNA Medicago HM048


title: inducible regulatory T cells 1C_iTreg

value: inducible regulatory T cells


title: inducible regulatory T cells 1B_iTreg


title: mRNA Medicago HM046


title: inducible regulatory T cells 1D_iTreg


title: mRNA Medicago HM047


title: mRNA Medicago HM060


title: mRNA Medicago HM041


title: mRNA Medicago HM045


title: mRNA Medicago HM044


title: mRNA Medicago HM042


title: WT-40min pair #2

city: Stony Brook

first: Nurit

last: Ballas

address: 100 Nicolls Road

department: Department of Biochemistry and Cell Biology

institute: Stony Brook University

description: processed data file: GeneCountTable_invivo.txt

data_processing:
The raw reads were done by STAR.
Normalization and differential gene analysis were done using DESeq2 and DESeq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GeneCountTable_invitro.txt
Supplementary_files_format_and_content: GeneCountTable_invivo.txt

source_name: Hippocampus, WT, kainic acid, T40

growth_protocol: Cortical cells were isolated from P0-P1 wild-type and MeCP2-null male littermate mice, and cultured on poly-L-lysine-coated dishes. To enrich for neurons, the cells were cultured for 10 days with neuronal medium, and Arabinoside C (AraC) was added between day 2 and 4 in a final concentration of 1 uM.

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen).
RNA sequencing (RNA-Seq) libraries were prepared using the KAPA Stranded RNASeq Kit with RiboErase (Kapabiosystems) in accordance with the manufacturer's instructions. Briefly, 500ng of total RNA were used for ribosomal depletion and fragmentation. Depleted RNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 9 cycles). Final libraries were evaluated using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (Invitrogen) and Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent2100).

treatment_protocol: For membrane depolarization of neurons, 10 DIV (days in vitro) WT and MT cultures were treated with 35 mM KCl for 3 hours. For the kainic acid (KA) treatment, 7-week-old WT and MT littermates were treated with KA by intra-peritoneal injection at a dosage of 23mg/kg body weight. Hippocampi were dissected after 40 min or 68 min of injection.

tag: strain/background

tag: genotype/variation

value: WT

value: Hippocampus

value: Kainic acid

value: 40 min

tag: experiment type

value: in vivo


title: MT-40min pair #2

source_name: Hippocampus, MT, kainic acid, T40


title: WT-68min pair #1

source_name: Hippocampus, WT, kainic acid, T68

value: 68 min


title: mRNA Medicago HM039

tag: age


title: WT-40min pair #1


title: mRNA Medicago HM037


title: MT-N pair #2

source_name: Hippocampus, MT, untreated


title: WT-68min pair #2


title: MT-40min pair #1


title: mRNA Medicago HM036


title: mRNA Medicago HM043


title: WT-N pair #2

source_name: Hippocampus, WT, untreated


title: mRNA Medicago HM034


title: MT-N pair #1


title: mRNA Medicago HM033


title: inducible regulatory T cells 1A_iTreg


title: MT-68min pair #2

source_name: Hippocampus, MT, kainic acid, T68


title: mRNA Medicago HM032


title: MT-68min pair #1


title: Exp #3-WT-3hr KCl

description: processed data file: GeneCountTable_invitro.txt

source_name: Cortical neurons, WT, KCl

value: Cortical culture

value: KCl

value: in vitro


title: WT-N pair #1


title: mRNA Medicago HM031


title: Exp #2-WT-3hr KCl


title: mRNA Medicago HM040


title: mRNA Medicago HM030


title: mRNA Medicago HM029


title: Exp #1-WT-3hr KCl


title: Exp #2-WT-N

source_name: Cortical neurons, WT, untreated


title: mRNA Medicago HM026


title: Exp #2-MT-N

source_name: Cortical neurons, MT, untreated


title: mRNA Medicago HM015


title: mRNA Medicago HM018


title: Exp #3-MT-3hr KCl

source_name: Cortical neurons, MT, KCl


title: Exp #3-MT-N


title: mRNA Medicago HM013


title: mRNA Medicago HM028


title: mRNA Medicago HM014


title: Exp #1-WT-N


title: mRNA Medicago HM012


title: Exp #1-MT-3hr KCl


title: mRNA Medicago HM010


title: Exp #1-MT-N


title: mRNA Medicago HM011


title: mRNA Medicago HM009


title: Exp #3-WT-N


title: P8 DTA/DTA_T28 RNAseq

city: Montreal

first: Michel

last: Cayouette

state: Québec

address: 110 Ave des Pins O

department: Cellulary Neurobiology

country: Canada

institute: Institut de Recherches Cliniques de Montreal

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC.
Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.
The cleaned reads were aligned to the Mus musculus genome (mm10) using STAR
Read counts for each gene were calculated using htseq-count, in conjunction with a gene annotation file for mm10 obtained from UCSC
Differential expression was determined using DESeq2
The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05
Genome_build: mm10

source_name: P8 retinal extracts_Opn4DTA/DTA

extract_protocol:
RNA from retinas was extracted in using the Qiagen RNAeasy kit (Qiagen, cat no. 74104)
To generate RNA sequencing libraries, RNA quality and quantity were determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of > 7 and quantities of 100 nanograms or more per sample. Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per manufacturer’s instructions. Polyadenylated mRNAs were captured from total RNA using oligo-dT selection. Samples were converted to cDNA by reverse transcription. Each sample was ligated to Illumina sequencing adapters containing unique barcode sequences. Barcoded samples were PCR amplified, resulting cDNA libraries were quantified using qPCR. Equimolar concentrations of each cDNA library were pooled and sequenced on the Illumina HiSeq2500.

value: dissociated mouse retinal cells

tag: strain background

value: Postnatal day 8


title: mRNA Medicago HM008


title: P8 DTA/DTA_T27 RNAseq


title: mRNA Medicago HM006


title: P8 WT_T25 RNAseq

source_name: P8 retinal extracts_wild-type

value: Wild-type


title: P8 WT_T26 RNAseq


title: mRNA Medicago HM003

value: mature leaves


title: Spermatogonia PolyA-Seq 2

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

data_processing:
Reads consisting of two or more consecutive N’s or all poly(A) were filtered out, then remaining reads were processed to remove adapter and poly(A) sequences. Remaining reads were mapped to mouse genome mm9 with GSNAP allowing 2 mismatches. Reads with identical genomic footprint and 4N’s were then collapsed into single reads as likely PCR duplicates. Mapped reads that were likely internal priming events rather than true poly(A) tails were discarded if they had 6 or more consecutive A’s or 7 or more A’s in the 10 nt window downstream of the read 3’ end (cleavage and polyadenylation site). We accepted only 3’ ends with 1 of 14 hexamers within 50 nt upstream of the 3’ end (as described in (Martin et al., 2012))
Genome_build: mm9
Supplementary_files_format_and_content: Excel sheet containing the genomic coordinates of 16502 3'UTRs

source_name: Testes

extract_protocol: PolyA+ RNA was selected by oligodT-hybridization (Dynal) and fragmented by alkaline hydrolysis.  RNA fragments 50-100 nt long were gel purified from 10% PAGE/Urea gels, and used as template for reverse transcriptions with SuperScript III (Invitrogen).  First strand cDNA was gel purified, then circularized with CircLigase (EpiCentre).  Circularized DNA was used as the template for PCR.  After cycle number optimization to obtain the minimal amount of PCR product detectable by Sybr Gold (Invitrogen), the PCR product was gel purified and used as template for a second PCR with primers containing Illumina adaptor sequences.

treatment_protocol: Spermatogonia PolyA-Seq libraries were generated from 400ng of RNA from spermatogonia isolated by FACS from 8 week old Stra8-iCre+; IRG+ males as previously described (Zagore et al., 2015).

tag: Sex

value: Male

value: spermatogonia


title: mRNA Medicago HM005

value: 45 days


title: Exp #2-MT-3hr KCl

tag: treatment


title: mRNA Medicago HM001


title: Dazl KO GFP+ RNA-seq S5

description:
FACS sorted GFP+ germ cells
RPKM KO2

data_processing:
Read mapping and gene expression quantification was performed using Olego and Quantas
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

extract_protocol: Illumina TruSeq/Clontech ultra low input library preparation with Nextera XT indexing was used to generate RNA-Seq libraries

treatment_protocol: Isolations of GFP+ cells was performed using dual fluorescence labeling as previously described (Zagore et al., 2015), except P6 cells were not stained with Hoechst and were collected using either BD Biosciences Aria or iCtye Reflection cytometry instrumentation.

value: Stra8-iCre+; IRG+; DAZLTm1hgu/Tm1hgu (DAZL KO)


title: Methylome Medicago HM112


title: Dazl KO GFP+ RNA-seq S6

description:
FACS sorted GFP+ germ cells
RPKM KO3


title: Methylome Medicago HM111


title: Methylome Medicago HM110


title: Dazl WT GFP+ RNA-seq S2

description:
FACS sorted GFP+ germ cells
RPKM WT2

value: Stra8-iCre+; IRG+; DAZL++ (DAZL WT)


title: Dazl WT GFP+ RNA-seq S1

description:
FACS sorted GFP+ germ cells
RPKM WT1


title: Methylome Medicago HM108


title: Spermatogonia PolyA-Seq 1


title: Dazl p6 iCLIP 2

data_processing:
Reads were filtered by quality, collapsed and adapters removed using Galaxy
Reads mapped using Olego (Wu et al., 2013).
Genome_build: mm9
Supplementary_files_format_and_content: BED file contains processed reads from individual samples (color coded:)

extract_protocol:
Testes were detunicated in cold HBSS and seminiferous tubules UV-irradiated on ice.
Libraries were processed similarly to HITS-CLIP libraries (Hannigan et al., 2017) with the following changes -  No 5’linker ligation step was performed.  The 3’linker contained a iSp18 spacers and phosphorylated 5’ end permitting circularization of first strand cDNA (after gel purification) to generate a PCR template without linearization (as described by (Ingolia, 2010))


title: Methylome Medicago HM105


title: Methylome Medicago HM109


title: Dazl p6 iCLIP 1


title: Methylome Medicago HM106


title: Methylome Medicago HM101


title: Methylome Medicago HM104


title: Methylome Medicago HM107


title: Methylome Medicago HM099


title: Methylome Medicago HM103


title: Methylome Medicago HM098


title: Methylome Medicago HM097


title: Dazl KO GFP+ RNA-seq S4

description:
FACS sorted GFP+ germ cells
RPKM KO1


title: Diabetic benzo-lipoxin replicate 1

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

data_processing:
Used HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data
Reads were trimmed for quality using a minimum phred value of 20 and minimum length of 18 using Skewer (Jiang et al, 2014).
Reads were mapped with STAR (Dobin et al, 2013) to the mouse genome downloaded from Ensembl (GRCm38).
FeatureCounts (Liao et al, 2014) was used to count reads mapped to gene bodies on the correct strand with a minimum mapping quality of 20 using Ensembl genome annotation (Mus musculus.GRCm38.86.gtf).
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression count matrix

source_name: kidney cortex

extract_protocol:
Kidney cortex was harvested and homogenised in Trizol. RNA was isolated from Trizol homogenates using the Direct-zol™ RNA MiniPrep Kit by Zymo Research. RNA quality was assessed by MultiNA bioanalyzer.
200 ng of total RNA was subject to ricosomal RNA depletion using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) followed by  library preparation with the Ultra Directional RNA-seq library prep kit. Both kits were urchased from New England Biolabs.

treatment_protocol: Six-week-old ApoE−/− male mice (C57BL/6 background) were rendered diabetic by 5 daily intraperitoneal (I.P.) injections of streptozotocin (Sigma-Aldrich, St Louis, MO) at a dose of 55 mg/kg. ApoE−/− mice were administered either ethanol (0.1%), LXA4 (5 ug/kg; Merck, Calbiochem) or Benzo-LXA4 (1.7 ug/kg; synthesized at University College Dublin, Ireland_Fieldmark__989_1362782350__Fieldmark__990_1362782350__Fieldmark__990_136278235038__Fieldmark__989_1362782350) twice weekly by I.P injection. For the Interis ntion study design, mice  ere followed for 16 weeks, and were administered ethanol, LXA4, or Benzo-LXA4 between weeks 10-16. Blood glucose levels were monitored weekly after STZ injections for the duration of the studies to confirm the diabetic status of these mice. Detailed methods are available in the Online Article’s Supplement.

tag: diabetic status

value: diabetic

tag: treatment group

value: benzo-lipoxin


title: Diabetic benzo-lipoxin replicate 6

tag: strain


title: Diabetic benzo-lipoxin replicate 3


title: Diabetic benzo-lipoxin replicate 5


title: Diabetic benzo-lipoxin replicate 4


title: Dazl p6 iCLIP 3


title: Methylome Medicago HM096


title: Methylome Medicago HM095


title: Diabetic lipoxin replicate 4

value: lipoxin


title: Diabetic lipoxin replicate 6


title: Diabetic lipoxin replicate 3


title: Diabetic lipoxin replicate 2


title: Methylome Medicago HM091


title: Diabetic lipoxin replicate 5


title: Methylome Medicago HM093


title: Diabetic lipoxin replicate 1


title: Diabetic vehicle replicate 6

value: vehicle


title: Diabetic vehicle replicate 5


title: Diabetic benzo-lipoxin replicate 2


title: Methylome Medicago HM089


title: Diabetic vehicle replicate 4


title: Methylome Medicago HM088


title: Methylome Medicago HM087


title: Diabetic vehicle replicate 3


title: Diabetic vehicle replicate 2


title: Methylome Medicago HM085


title: Diabetic vehicle replicate 1


title: Methylome Medicago HM084


title: Methylome Medicago HM083


title: Methylome Medicago HM092


title: Methylome Medicago HM086


title: Nondiabetic benzo-lipoxin replicate 6

value: nondiabetic


title: Nondiabetic benzo-lipoxin replicate 5


title: Methylome Medicago HM081


title: Nondiabetic benzo-lipoxin replicate 3


title: Methylome Medicago HM090


title: Methylome Medicago HM079


title: Nondiabetic benzo-lipoxin replicate 2


title: Nondiabetic benzo-lipoxin replicate 1


title: Nondiabetic benzo-lipoxin replicate 4


title: Methylome Medicago HM077


title: Nondiabetic lipoxin replicate 5


title: Methylome Medicago HM076


title: Methylome Medicago HM075


title: Nondiabetic lipoxin replicate 3


title: Methylome Medicago HM074


title: Nondiabetic lipoxin replicate 2


title: Methylome Medicago HM082


title: Nondiabetic vehicle replicate 6


title: Methylome Medicago HM080


title: Methylome Medicago HM072


title: Methylome Medicago HM070


title: Methylome Medicago HM071


title: Nondiabetic vehicle replicate 5


title: Nondiabetic lipoxin replicate 6


title: Nondiabetic vehicle replicate 3


title: Methylome Medicago HM069


title: Nondiabetic vehicle replicate 4


title: Nondiabetic vehicle replicate 1


title: Methylome Medicago HM068


title: Methylome Medicago HM065


title: Methylome Medicago HM078


title: Methylome Medicago HM067


title: Nondiabetic lipoxin replicate 4


title: A1A3_Brg1KD_Dex_Input_ChIPseq

value: A1A3 breast cancer cells

value: 1hr Dex

value: 72hrs Doxycycline


title: Methylome Medicago HM066


title: Methylome Medicago HM064


title: Methylome Medicago HM073


title: A1A3_Brg1KD_Dex_FoxA1_ChIPseq

tag: chip antibody

value: Abcam ab23738


title: Methylome Medicago HM063


title: Nondiabetic lipoxin replicate 1


title: Methylome Medicago HM062


title: A1A3_Brg1KD_Dex_Gata3_ChIPseq

value: Cell Signaling D13C9


title: A1A3_Brg1KD_EtOH_Input_ChIPseq

value: 1hr EtOH


title: Methylome Medicago HM061

value: mature leaves


title: A1A3_Brg1KD_EtOH_FoxA1_ChIPseq


title: A1A3_Brg1KD_EtOH_Gata3_ChIPseq


title: Methylome Medicago HM060


title: Nondiabetic vehicle replicate 2


title: A1A3_control_Dex_Input_ChIPseq

value: 72hrs PBS


title: Methylome Medicago HM059


title: A1A3_control_EtOH_Input_ChIPseq


title: A1A3_control_Dex_FoxA1_ChIPseq


title: Methylome Medicago HM058


title: Methylome Medicago HM057


title: Methylome Medicago HM056


title: A1A3_control_EtOH_Gata3_ChIPseq


title: Methylome Medicago HM055


title: Methylome Medicago HM054


title: Methylome Medicago HM053


title: A1A3_control_EtOH_FoxA1_ChIPseq


title: EtOH_ATACseq

value: A1-2 breast cancer cells

value: 15min EtOH


title: Input_Dex_ChIPseq


title: Methylome Medicago HM050

value: 45 days


title: Methylome Medicago HM052


title: Dex_ATACseq

value: 15min Dex


title: Methylome Medicago HM048


title: Gata3_Dex_ChIPseq


title: Input_EtOH_ChIPseq


title: FoxA1_Dex_ChIPsep


title: Methylome Medicago HM047


title: Methylome Medicago HM049


title: Methylome Medicago HM046


title: Gata3_EtOH_ChIPseq


title: Methylome Medicago HM045


title: A1A3_control_Dex_Gata3_ChIPseq


title: FoxA1_EtOH_ChIPsep


title: Methylome Medicago HM044


title: K4me1_Dex_ChIPseq

value: Abcam ab8895


title: Methylome Medicago HM043


title: K4me1_EtOH_ChIPseq


title: Methylome Medicago HM042


title: K27me3_Dex_ChIPseq

value: Active Motif 39155


title: K27ac_Dex_ChIPseq

value: Abcam ab4729


title: K27me3_EtOH_ChIPseq


title: K27ac_EtOH_ChIPseq


title: Methylome Medicago HM041


title: Methylome Medicago HM039


title: Methylome Medicago HM040


title: Input_EtOH


title: Input_Dex


title: Methylome Medicago HM038


title: Brg1_EtOH_ChIPseq

value: lab-made rabbit anti-Brg1


title: Methylome Medicago HM036


title: GR_Dex_ChIPseq

value: Santa Cruz M-20


title: Methylome Medicago HM035


title: Brg1_Dex_ChIPseq


title: Methylome Medicago HM034


title: Methylome Medicago HM033


title: Methylome Medicago HM031


title: Methylome Medicago HM030


title: Methylome Medicago HM029


title: Methylome Medicago HM028


title: Methylome Medicago HM027


title: Kelly_MYCN (NBoncoSE batch 2)

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
Peaks were called using MACS 1.4 with parameters -p 1e-9 --keep-dup=auto and corresponding input control.
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Neuroblastoma

value: Kelly

value: n-Myc

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: antibody lot


title: Methylome Medicago HM026

source_name: plant

tag: ecotype


title: Kelly_TBX2 (NBoncoSE batch 2)

tag: cell type


title: Kelly_PHOX2B_B11X (NBoncoSE batch 2)

value: Santa Cruz


title: Methylome Medicago HM014

tag: tissue


title: Methylome Medicago HM015


title: Methylome Medicago HM037


title: Methylome Medicago HM012


title: Methylome Medicago HM018


title: Methylome Medicago HM013


title: Methylome Medicago HM007


title: Methylome Medicago HM011


title: Methylome Medicago HM008


title: GR_EtOH_ChIPseq

tag: cell line/type


title: Methylome Medicago HM010


title: Methylome Medicago HM032


title: Methylome Medicago HM003


title: Methylome Medicago HM009


title: Methylome Medicago HM002


title: Methylome Medicago HM001


title: Methylome Medicago HM006


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl31: BIOMARKERS)

city: La Laguna

first: Emma

last: Carmelo

state: SANTA CRUZ DE TENERIFE

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

department: University Institute of Tropical Diseases and Public Health

country: Spain

institute: University of La Laguna

description:
Ba-rl31
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION

data_processing: Cq values from the 61 samples analyzed were exported for normalization using geNorm (qBasePLUS software (Biogazelle, Gent, Belgium)). Two genes showed the most stable expression (Stat6 and Itgb2)  and were used for normalization.

source_name: SPLEEN

label_protocol:
The reverse transcription was performed with 2 ug of RNA with random hexamers using the High Capacity cDNA Reverse Transcription Kit (Life Technologies, Carlsbad, CA) according to manufacturer’s instructions.
Real-time PCR and fluorescence detection were performed using QuantStudio 12K Flex Real-Time PCR System (Life  Technologies, Carlsbad, CA) following manufacturer’s instructions, using Custom TaqMan OpenArray Real-Time PCR Plates

growth_protocol: 61 BALB/c (purchased to Charles River Laboratories, France) mice (14-15 weeks old) were used  in this study. Mice were randomly separated in two groups: (i) 30 control mice and (ii) 31 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70ºC (Sigma-Aldrich, St. Louis, USA). F

extract_protocol: Total RNA isolation from spleens (9-11 mg) was performed by cell disruption using FastPrep®  System (ProScientific, Cedex, France) and Lysing Matrix D (MP Biomedicals, Solon, USA) in TRI-Reagent (Sigma-Aldrich, St. Louis, USA). RNeasy Mini Kit (Qiagen) was subsequently used for mRNA enrichment following manufacturer’s instructions

treatment_protocol: 31 out of the 61 mice were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein.

value: Balb/c


title: Spleen of non-infected Balb/c mice (Ba-nr30: BIOMARKERS)

description:
Ba-nr30
LOGISTIC MODEL EVALUATION


title: Spleen of non-infected Balb/c mice (Ba-nr29: BIOMARKERS)

description:
Ba-nr29
LOGISTIC MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl29: BIOMARKERS)

description:
Ba-rl29
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of non-infected Balb/c mice (Ba-nr28: BIOMARKERS)

description:
Ba-nr28
LOGISTIC MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl28: BIOMARKERS)

description:
Ba-rl28
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl26: BIOMARKERS)

description:
Ba-rl26
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of non-infected Balb/c mice (Ba-nr24: BIOMARKERS)

description:
Ba-nr24
LOGISTIC MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl27: BIOMARKERS)

description:
Ba-rl27
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of non-infected Balb/c mice (Ba-nr26: BIOMARKERS)

description:
Ba-nr26
LOGISTIC MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl25: BIOMARKERS)

description:
Ba-rl25
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of non-infected Balb/c mice (Ba-nr25: BIOMARKERS)

description:
Ba-nr25
LOGISTIC MODEL EVALUATION


title: Spleen of non-infected Balb/c mice (Ba-nr27: BIOMARKERS)

description:
Ba-nr27
LOGISTIC MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL24: BIOMARKERS)

description:
Ba-rL24
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rl30: BIOMARKERS)

description:
Ba-rl30
LOGISTIC MODEL EVALUATION
LINEAR REGRESSION MODEL EVALUATION


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL23: BIOMARKERS)

description:
Ba-rL23
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL22: BIOMARKERS)

description:
Ba-rL22
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL20: BIOMARKERS)

description:
Ba-rL20
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL21: BIOMARKERS)

description:
Ba-rL21
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT


title: Spleen of Leishmania-infected Balb/c mice (Ba-rL19: BIOMARKERS)

description:
Ba-rL19
LOGISTIC MODEL DEVELOPMENT
LINEAR REGRESSION MODEL DEVELOPMENT