title: 9-month-old APP/PS1 mice brain Replicate 3

first: Jinze

address: 2A Nanwei Road

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Biological replicate 3 of 3. APP/PS1 mouse.

hyb_protocol: Hybridization were performed based on the manufacturer’s standard protocols using the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software (version 11.0.1.1)  using default parameters (protocol GE1_1100_Jul11 and Grid: 034068_D_F_20110504) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: mouse brain, APP/PS1, replicate 3

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

tag: strain

tag: gender

value: male

value: brain


title: SCAP at c, biological rep1

status: Public on Jan 01 2021

type: RNA

city: Jinan

first: Junqing

last: Liu

address: No.44-1 Wenhua Road West

country: China

institute: Shandong University

description: Gene expression data from SCAP without differentiation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The data were analyzed with Expression Console ™ Software 1.3 using Affymetrix default analysis settings and global scaling as normalization method.The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: dental (apical papilla)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color  Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Then cells were cultured in α-minimum essential medium (HyClone, Logan, UT, United States) supplemented with 20% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA), 100 U/ml penicillin and 100 μg/ml streptomycin (HyClone) at 37°C in a 5% CO2 incubator.  The medium was changed every 3 days.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (AM1561 ) following the manufacturer's instructions.

treatment_protocol: For osteogenic differentiation, when cells reached 80% confluence, the medium was changed to osteogenic medium containing 10 mM β-glycerolphosphate (Sigma-Aldrich, St. Louis, MO, USA), 10 nM dexamethasone (Sigma-Aldrich) and 50 μg/mL L-ascorbic acid (Sigma-Aldrich). The osteogenic medium was changed every 3 days.

tag: treatment

value: control


title: WT mouse brain Replicate 2

city: Beijing

last: Li

description: Biological replicate 2 of 3. WT mouse.

organism: Mus musculus

source_name: mouse brain, WT, replicate 2

tag: age

tag: genotype/variation

value: WT

tag: tissue


title: SCAP at c, biological rep3


title: NormalDonor5_untreated_PBMC_026

type: SRA

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

source_name: Blood

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

tag: who classification

value: Normal

tag: cell type

value: Peripherial blood mononuclear cells


title: UCSF 9169_INP

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

library_source: genomic

data_processing:
FASTQ reads were trimmed to remove low quality reads and adaptors with Trim Galore.
Uniquely mapped reads were aligned to the human reference genome h19/GRCh37 with the Burrows-Wheeler Aligner to generate BAMs.
BAMs were sorted and indexed with SAMtools.
PCR duplicates were removed using PicardTools.
Peaks were called using the MACS2 callleak function on the ChIP-seq BAM file using the following parameters: BAMPE for paired-end reads, scaling to the larger dataset, the default log2 fold change enrichment of 2 vs. input and a p-value cutoff of 1e-5.
Bigwig tracks were generated using the DeepTools (v3.1.2)24 bamCoverage command with RPKM normalization
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs

molecule: genomic DNA

source_name: Meningioma tissue

growth_protocol: First-passage arachnoid granulation cells were grown in DMEM supplemented with 7% FBS and 1% penicillin/streptomycin

extract_protocol:
5–10 mg of flash-frozen primary meningioma tumors was pulverized, crosslinked using 1.5% formaldehyde and sonicated to fragment sizes of 200-800 bp. Samples were incubated overnight with 5 μg H3K27ac antibody per ChIP experiment (Active Motif; 39133).
Enriched DNA was quantified by using PicoGreen (Invitrogen) and ChIP libraries were amplified and barcoded by using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to the manufacturer’s recommendations. Following library amplification, DNA fragments were agarose gel (1.0%) size selected (<1 kb), analyzed using a Bioanalyzer (Agilent Technologies)
Samples were sequenced at Genewiz by using Illumina HiSeq 2500 150-bp paired-end reads.

tag: patient sex

value: M

tag: tumor grade

tag: tissue/sample type

value: Meningioma tissue


title: UCSF 9053_ChIP

value: F

tag: chip antibody

value: H3K27ac antibody (Active Motif; 39133)


title: WT mouse brain Replicate 1

description: Biological replicate 1 of 3. WT mouse.

source_name: mouse brain, WT, replicate 1


title: NormalDonor5_untreated_PBMC_021


title: SCAP at k, biological rep3

description: Gene expression data from SCAP after osteogenic differentiation for 7 days.

value: osteogenic differentiation for 7 days


title: WT mouse brain Replicate 3

description: Biological replicate 3 of 3. WT mouse.

source_name: mouse brain, WT, replicate 3


title: NormalDonor5_untreated_PBMC_023


title: UCSF 8867_INP


title: SCAP at c, biological rep2


title: CAM_EN_rep2

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
Illumina reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space. The minimal transcriptome was obtained as described in Gowik et al. (2011) and contains 22,079 protein coding genes.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of rpm of biological triplicate group (drought stage) were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel sheet (SupplementalData.xlsx) file including Arabidopsis Gene Identifier (AGI) and TAIR10_short_description, raw counts and rpm for each sample, mean rpm for biological triplicates.

molecule: polyA RNA

organism: Talinum fruticosum

source_name: Leaf

growth_protocol: Talinum triangulare plants were grown well-watered for 28 days and then subjected to drought treatment

extract_protocol:
Mature leaves of T. triangulare were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform.

value: leaf

tag: water-limitation

value: 12 d drought

tag: time

value: End of the night

tag: zeitgeber time

tag: photosynthetic mode

value: CAM


title: UCSF 9253_ChIP


title: NormalDonor5_untreated_PBMC_025


title: 9-month-old APP/PS1 mice brain Replicate 1

description: Biological replicate 1 of 3. APP/PS1 mouse.

source_name: mouse brain, APP/PS1, replicate 1


title: 9-month-old APP/PS1 mice brain Replicate 2

description: Biological replicate 2 of 3. APP/PS1 mouse.

source_name: mouse brain, APP/PS1, replicate 2


title: UCSF 9169_ChIP


title: reC3_EN_rep2

value: 12 d drought + 2 d re-watered


title: UCSF 8867_ChIP


title: CAM_ED_rep1

value: End of the day


title: CAM_ED_rep2


title: NormalDonor5_untreated_PBMC_018


title: CAM_EN_rep1


title: NormalDonor5_untreated_PBMC_019


title: reC3_ED_rep3


title: NormalDonor5_untreated_PBMC_022


title: UCSF 6148_ChIP


title: reC3_ED_rep2


title: UCSF 9053_INP


title: reC3_MN_rep3

value: Middle of the night


title: reC3_MN_rep1


title: reC3_ED_rep1


title: CAM_MN_rep2


title: CAM_MN_rep1


title: NormalDonor5_untreated_PBMC_015


title: CAM_EN_rep3


title: UCSF 4738_ChIP


title: NormalDonor5_untreated_PBMC_020


title: UCSF 6148_INP


title: NormalDonor5_untreated_PBMC_014


title: reC3_MN_rep2


title: CAM_ED_rep3


title: reC3_MD_rep2

value: Middle of the day


title: 17982_Flash frozen breast tumor tissue-miRNASeq

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

data_processing:
The adapter for each read was trimmed by cutadapt (version 1.12).
The trimmed reads were aligned to hg19 by Burrows−Wheeler Aligner (version 0.7.15) with no mismatches allowed.
The miRNA profiling pipeline developed by the British Columbia Genome Sciences Centre was implemented to quantify miRNA expression.
Genome_build: hg19
Supplementary_files_format_and_content: raw count data

source_name: Flash frozen breast tumor tissue

extract_protocol:
RNA extracted using RNeasy Mini Kit (Qiagen)
NEBNext Multiplex Small RNA kit for small RNA cDNA library preparation

value: breast tumor tissue

value: Female

tag: race

value: African American

tag: er

value: Negative

tag: molecule subtype

value: miRNA


title: UCSF 4738_INP

value: Meningioma tissue


title: UCSF 3806_INP

value: M


title: CAM_MN_rep3


title: Thymic γδ T lymphocytes

first: Yuan

last: Hu

state: Shandong

address: 44 Wenhuaxi Rd

data_processing:
The cell ranger1.0 software was used.
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
Single-cell trajectories were built with Monocle2 (R package) that introduced pseudotime. Genes were filtered by the following criteria: Expressed in more than 10 cells; The average expression value was greater than 0.1; Qval was less than 0.01 in different analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with filtered gene counts for every gene and every sample

source_name: γδ T lymphocytes

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V2 (10x Genomics, 120237) and Chromium Single Cell A Chip Kit (10x Genomics, 120236), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. These cells were added to each channel, and the target cell will be recovered was estimated to be about 8600 cells for sample 1 and 4500 cells for sample 2. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library Gel Bead Kit V2. The libraries were finally sequenced using an Illumina Novaseq 6000 sequencer with a sequencing depth of at least 45,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

tag: strain

value: thymus

value: primary gamma delta T lymphocytes

tag: genotype

value: wild type

value: 8 weeks old

tag: treatment

value: untreated


title: NormalDonor5_untreated_PBMC_016

value: Normal

value: Peripherial blood mononuclear cells


title: CAM_MD_rep1

tag: tissue

value: leaf

value: 12 d drought

value: CAM


title: CAM_MD_rep2

value: Middle of the day


title: NormalDonor5_untreated_PBMC_017

tag: who classification


title: reC3_MD_rep3

value: 12 d drought + 2 d re-watered


title: reC3_MD_rep1


title: CAM_MD_rep3


title: UCSF 2567_INP


title: NormalDonor5_untreated_PBMC_011

tag: cell type


title: NormalDonor5_untreated_PBMC_010


title: UCSF 3806_ChIP

tag: patient sex

value: H3K27ac antibody (Active Motif; 39133)


title: CD40LΔ5 (Mut) - rep1

city: Belle Mead

first: Bitha

last: Narayanan

state: New Jersey

address: 241 Berkley Ave

institute: Rutgers

data_processing:
The raw data were processed with CASAVA 1.8.2 (Illumina) to generate fastq files
The sequence reads were aligned to the Mus musculus reference genome (mm9) using STAR
According to the mapped data, the fragments per kilobase of exon per million reads (FPKM) was calculated with the M. musculus genome annotation NCBI build 37.2.
The differential expression analysis of two conditions/groups was performed using the DESeq2 R package.
The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Three biological replicates were used for each population.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_genename.txt, fpkm_group.txt, fpkm_sample.txt

source_name: splenic B cell

growth_protocol: breeding

extract_protocol:
Spleens were collected 8 days post injection. B cells were isolated using Miltenyi Pan B cell isolation kit. RNA was harvested using RNAeasy kit Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequence libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-8 week old WT and CD40LΔ5 mice were injected with SRBC

value: Spleen derived B cells

value: Day 8 after SRBC injection


title: NormalDonor5_untreated_PBMC_013


title: CD40LΔ5 (Mut) - rep3


title: NormalDonor5_untreated_PBMC_009


title: WT- rep2


title: UCSF 2366_INP

tag: tumor grade

value: Meningioma tissue


title: NormalDonor5_untreated_PBMC_008


title: Hepatic γδ T lymphocytes

value: liver

tag: age


title: WT- rep3


title: UCSF 2531_ChIP

value: M

tag: tissue/sample type

tag: chip antibody


title: WT- rep1


title: UCSF 2531_INP


title: CD40LΔ5 (Mut) - rep2


title: UCSF 2366_ChIP


title: FA_195

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR V2.6.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by HTSeq
Differeantial expression analysis with DEseq2
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

source_name: Liver

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Triple LKO

tag: Sex

value: female


title: UCSF 2567_ChIP


title: FA_141

value: male


title: NormalDonor5_untreated_PBMC_007


title: FA_180


title: UCSF 2198_ChIP

value: F


title: FA_196


title: NormalDonor5_untreated_PBMC_006

value: Normal


title: UCSF 2198_INP


title: NormalDonor5_untreated_PBMC_012

value: Peripherial blood mononuclear cells


title: FA_197

value: WT


title: FA_146


title: FA_181


title: FA_194


title: UCSF 1484_INP


title: EA149KOE

description: L1  LKO_EtOH diet

source_name: Liver RNA

value: L1  LKO_EtOH diet


title: NormalDonor5_untreated_PBMC_005


title: NormalDonor5_untreated_PBMC_003


title: EA139KOE

description: L1  LKO_EtOH diet


title: UCSF 1484_ChIP


title: EA143KOE

description: L1  LKO_EtOH diet


title: UCSF 1258_INP


title: UCSF 1258_ChIP


title: NormalDonor5_untreated_PBMC_002


title: EA142KOC

description: L1  LKO_Ctrl diet

value: L1  LKO_Ctrl diet


title: EA144KOC

description: L1  LKO_Ctrl diet


title: EA129KOC

description: L1  LKO_Ctrl diet


title: EA214WTE

description: WT_EtOH diet

value: WT_EtOH diet


title: NormalDonor5_untreated_PBMC_001


title: DI 134_INP


title: NormalDonor4_untreated_PBMC_093


title: EA150WTC

description: WT_Ctrl diet

value: WT_Ctrl diet


title: EA198KOC

description: L1  LKO_Ctrl diet


title: NormalDonor4_untreated_PBMC_092


title: EA151WTE

description: WT_EtOH diet


title: EA199KOE

description: L1  LKO_EtOH diet


title: DI 98_INP


title: EA12WTE

description: WT_EtOH diet


title: DI 134_ChIP

value: H3K27ac antibody (Active Motif; 39133)


title: EA191WTC

description: WT_Ctrl diet


title: aGVHD_V2

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited tex files include FPKM values for each samples

source_name: MSCs

growth_protocol: Cells were isolated from mice and cultured in medium containing DMEM (high-glucose), FBS and P/S.

extract_protocol:
We isolated MSCs by digesting unfractionated BM.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Cells in aGVHD_V group were treated with vehicle(DMSO) and cells in aGVHD_R group were treated with R (0.5 um).

value: MSCs

value: vehicle in vitro


title: NormalDonor4_untreated_PBMC_091


title: EA219WTC

description: WT_Ctrl diet


title: NormalDonor4_untreated_PBMC_094


title: CCF 826_INP

value: Meningioma tissue


title: NormalDonor5_untreated_PBMC_004


title: aGVHD_V1


title: NormalDonor4_untreated_PBMC_089


title: CCF 826_ChIP


title: NormalDonor4_untreated_PBMC_090


title: aGVHD_R1

value: R in vitro


title: NormalDonor4_untreated_PBMC_088


title: EA11WTC

description: WT_Ctrl diet


title: NormalDonor4_untreated_PBMC_087


title: CCF 702_ChIP

value: M


title: input for over expression of ESC

city: Shanghai

first: Yixin

last: Huang

address: Siping Road

institute: Tongji University

description: Normalized tag counts

data_processing:
ChIP-seq reads were first removed adapters and low-quality base calls by trim_galore (version 0.4.2) using the default parameters.
Chip-seq reads were aligned to the mouse genome (mm9) using Bowtie2 v.2.3.5 with the parameters  –no-mixed --no-discordant.
ChIP-seq peaks were called with MACS2 with the parameters  –nomodel --keep-dup all  --SPMR over input files
Genome_build: mm9
Supplementary_files_format_and_content: Signal track for each sample were generated using the “bamCoverage” function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM)

source_name: ESC

extract_protocol:
Lysates were clarified from sonicated nuclei and Kap1-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: ESC

value: Dcaf11 Over expression

value: none (input)


title: CCF 66_INP


title: NormalDonor4_untreated_PBMC_086


title: aGVHD_R2


title: EA192WTE

description: WT_EtOH diet


title: Kap1 for over expression of ESC, Replicate 1

description: Normalized tag counts

value: Kap1 (Abcam no. ab22553)


title: Kap1 for over expression of ESC, Replicate 2

description: Normalized tag counts


title: Kap1 for wild type of ESC, Replicate 2

description: Normalized tag counts

value: Wild type


title: Kap1 for wild type of ESC, Replicate 1

description: Normalized tag counts


title: input for wild type of ESC

description: Normalized tag counts


title: DI 98_ChIP


title: R8_4_S41_Resistant

city: La Jolla

first: Olivia

last: Osborn

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

data_processing:
Reads generated by the sequencer were first mapped to the mouse transcriptome using Bowtie2  algorithm and counted as reads per gene using RSEM  and then analyzed using the statistical algorithm limma .
Genome_build: mm9
Supplementary_files_format_and_content: Prone_Resistant_fdr.xlsx

source_name: weight gain resistant_blood

extract_protocol:
Total RNA was extracted from blood
Libraries were prepared using TruSeq Library prep kits (Illumina)

treatment_protocol: All mice were then fed a formulation of 45% HFD with olanzapine incorporated into HFD (Research Diets, Inc., D09092903).

value: female

value: 45% HFD with olanzapine

tag: mouse group

value: weight gain resistant

value: blood


title: CCF 556_INP

value: F


title: NormalDonor4_untreated_PBMC_084

value: Normal

value: Peripherial blood mononuclear cells


title: R4_4_S39_Resistant


title: CCF 702_INP


title: R2_4_S37_Resistant


title: R1_3_S36_Resistant


title: NormalDonor4_untreated_PBMC_083


title: P8_3_S33_Prone

source_name: weight gain prone_blood

value: weight gain prone


title: CCF 471_INP


title: NormalDonor4_untreated_PBMC_082


title: P7_3_S32_Prone


title: P5_4_S29_Prone


title: CCF 471_ChIP

value: H3K27ac antibody (Active Motif; 39133)


title: NormalDonor4_untreated_PBMC_081


title: CCF 66_ChIP

value: Meningioma tissue


title: CCF 3829_INP


title: 006_KO3

city: San Diego

first: Taylor

last: Doherty

address: 9500 Gilman Dr. 0678 La Jolla

department: Department of Medicine

institute: UC San Diego

description: Smart-seq2 RNA-seq

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mouse mm10 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5)  and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: Lungs

extract_protocol:
total RNA using miRNAeasy kit (Qiagen)
Smart-seq2 protocol and standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina)

value: challenged with Alternaria Alternata

value: Lin-Thy1.2+ ILC


title: NormalDonor4_untreated_PBMC_080

source_name: Blood


title: P1_4_S25_Prone


title: NormalDonor4_untreated_PBMC_085


title: 005_KO2

description: Smart-seq2 RNA-seq


title: CCF 3829_ChIP

source_name: Meningioma tissue


title: NormalDonor4_untreated_PBMC_079


title: R9_4_S43_Resistant


title: CCF 556_ChIP


title: 004_KO1

description: Smart-seq2 RNA-seq


title: CCF 3706_INP


title: 002_WT2

description: Smart-seq2 RNA-seq

value: WT


title: NormalDonor4_untreated_PBMC_078


title: NormalDonor4_untreated_PBMC_077


title: 001_WT1

description: Smart-seq2 RNA-seq


title: CCF 3706_ChIP


title: CCF 3622_INP


title: Lung BSYQF treatment rep3

first: Jie

last: Cui

address: 12 Middle Urumqi Road, Shanghai

institute: HuaShan Hospital, Fudan University

description:
BH66
treatmentVScontrol.log2FC1.Pvalue0.05
treatmentVSmodel.log2FC1.Pvalue0.05

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT.
Quality filtered reads were then mapped to mm10 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Lung

extract_protocol:
RNA was isolated using Trizol reagent.  3 ug  total RNA was used to prepare  sequencing libraries by NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: From day 14, mice in control and asthma groups were oral adminstrated with saline, and mice in BSYQF group were oral adminstrated 20g raw herbs/kg body weight. Mice were housed in a pathogen free rodent facility with food and water free available. At the end of experimental period mice were euthanized.

value: BALB/c

value: lung

value: BSYQF for 6 weeks

tag: group

value: asthmatic mice with BSYQF treatment


title: CCF 3622_ChIP


title: NormalDonor4_untreated_PBMC_076


title: Lung BSYQF treatment rep1

description:
BH57
treatmentVScontrol.log2FC1.Pvalue0.05
treatmentVSmodel.log2FC1.Pvalue0.05


title: Lung BSYQF treatment rep2

description:
BH64
treatmentVScontrol.log2FC1.Pvalue0.05
treatmentVSmodel.log2FC1.Pvalue0.05


title: P3_4_S26_Prone

value: female


title: Lung asrhma rep3

description:
A9
modelVScontrol.log2FC1.Pvalue0.05
treatmentVSmodel.log2FC1.Pvalue0.05

value: untreated

value: asthmatic mice


title: NormalDonor4_untreated_PBMC_075


title: Lung asrhma rep2

description:
A4
modelVScontrol.log2FC1.Pvalue0.05
treatmentVSmodel.log2FC1.Pvalue0.05


title: CCF 3590_INP


title: Lung asrhma rep1

description:
A3
modelVScontrol.log2FC1.Pvalue0.05
treatmentVSmodel.log2FC1.Pvalue0.05


title: 003_WT3

description: Smart-seq2 RNA-seq


title: Lung control rep2

description:
N105
modelVScontrol.log2FC1.Pvalue0.05
treatmentVScontrol.log2FC1.Pvalue0.05

value: normal mice


title: Lung control rep3

description:
N152
modelVScontrol.log2FC1.Pvalue0.05
treatmentVScontrol.log2FC1.Pvalue0.05


title: NormalDonor4_untreated_PBMC_073


title: NormalDonor4_untreated_PBMC_074


title: CCF 3590_ChIP

value: F


title: CCF 3255_INP


title: Lung control rep1

description:
N102
modelVScontrol.log2FC1.Pvalue0.05
treatmentVScontrol.log2FC1.Pvalue0.05


title: Cers6_KO_old_8mnths

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
Raw data from Illumina was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
Raw data was filtered by Novogene Corporation Inc. according to the following steps: 1) reads containing adaptors were removed, and 2) reads containing bases that could not be determined were also removed.
STAR software was used to align reads to reference genome.
FPKM was used to estimate gene expression levels. This method considers both sequencing depth and gene length on counting of fragments. (Mortazavi et al. 2008, https://doi.org/10.1038/nmeth.1226).
The readcount from Gene Expression Analysis was used to determine the differential expression analysis.
Genome_build: Mus musculus GRCm38/mm10
Supplementary_files_format_and_content: AJ_processed_data_GEO_updated.xlsx: Excel file that includes FPKM values, gene names, length, read counts, and fold change for each Sample.

source_name: T- cells

extract_protocol:
Total RNA was extracted from mice T-cells using QIAzol Lysis Reagent (Qiagen, Cat No./ID: 79306) and processed as per manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols from Novogene Corporation Inc. (Sacramento, CA 95826).

treatment_protocol: Mice Splenic T cells were activated with anti-CD3, anti-CD28 and IL-2 for three days.

tag: background strain

value: Cers6 knockout

value: 8 months

value: Splenic T cells


title: WT_old_8mnths

value: Wild-type


title: Cers6_KO_young_2mnths

value: 2 months


title: NormalDonor4_untreated_PBMC_072

value: Normal

value: Peripherial blood mononuclear cells


title: KOEmbryo.3

data_processing:
RNA-seq raw reads were processed by BBDuk(version 38.34) to removed adapters and trim low-quality reads.  Reads( >35bp) were aligned to the mouse genome (mm9)  using STAR(version 0.6.0).
Refseq genes were quantified to FPKM using Stringtie.
Deseq2 was used to perform differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Embryos

extract_protocol:
RNAs in embryos lysis with a polyadenylated tail were captured, reverse transcripted and preamplified following the protocol for Smart-seq2 sequence library generation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dcaf11 knock out

value: Embryo


title: CCF 3255_ChIP

value: Meningioma tissue

value: H3K27ac antibody (Active Motif; 39133)


title: CCF 2847_INP


title: NormalDonor4_untreated_PBMC_071


title: WT_young_2mnths


title: NormalDonor4_untreated_PBMC_070


title: KOEmbryo.1


title: KOEmbryo.2


title: CCF 268_INP

value: M


title: CCF 268_ChIP


title: NormalDonor4_untreated_PBMC_067


title: KDES.1

source_name: Embryonic stem cells

value: Dcaf11 knock down

value: ESC


title: NormalDonor4_untreated_PBMC_066


title: NormalDonor4_untreated_PBMC_069


title: CCF 2847_ChIP


title: KOArrest.2


title: NormalDonor4_untreated_PBMC_068


title: KOArrest.1


title: CCF 2440_ChIP


title: KOArrest.3


title: CCF 2440_INP


title: controlEmbryo.2

value: Wild type


title: KDES.2


title: controlES.1


title: controlES.2


title: controlEmbryo.1


title: CCF 1724_INP


title: CCF 1935_INP


title: NormalDonor4_untreated_PBMC_064


title: NormalDonor4_untreated_PBMC_061


title: F22B6_Liver_RNA-Seq

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

data_processing:
Reads were filtered based on their length, pairing, and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the Xenopus genome (10.0 assembly) using HISAT2.
The Cufflinks (v0.0.7) tool was applied to HISAT2 alignments to enumerate the number of short reads overlapping the Ensembl annotated genes, for each library
The Cuffmerge (v0.0.6) toll was used to merge transcriptome
Cuffdiff (v0.0.7) toll was used for differential  gene expression  analysis

organism: Xenopus tropicalis

extract_protocol:
For each biological replicate, the RNAqueous®-4PCR Kit (Ambion, Austin USA) was used to extract the total RNA from 15 mg of liver according to manufacturer instructions
RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample Prep kit (Illumina, San Diego, USA) and sequenced on an Illumina GAIIx sequencer as 75 bp reads

treatment_protocol: F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1). F Females from F1 and F2 generation were not exposed.

tag: common name

value: tropical clawed frog

tag: generation and f0-treatment

value: F2generation BaP

value: female

value: Liver


title: F22B1_Liver_RNA-Seq


title: F22B3_Liver_RNA-Seq


title: F22B4_Liver_RNA-Seq


title: NormalDonor4_untreated_PBMC_063


title: NormalDonor4_untreated_PBMC_065


title: F22B2_Liver_RNA-Seq


title: CCF 1724_ChIP


title: NormalDonor4_untreated_PBMC_062


title: F12B6_Liver_RNA-Seq

value: F1 generation BaP


title: F12B4_Liver_RNA-Seq


title: AG 03_INP

source_name: Arachnoid granulation cell model

value: Arachnoid granulation cell model


title: F12B3_Liver_RNA-Seq


title: NormalDonor4_untreated_PBMC_060


title: AG 03_ChIP


title: F12B5_Liver_RNA-Seq


title: AG 02_ChIP


title: CCF 1935_ChIP

value: F


title: AG 02_INP


title: NormalDonor4_untreated_PBMC_056

value: Normal


title: F12B15_Liver_RNA-Seq


title: AG 01_ChIP


title: AG 01_INP


title: YAP-NT.30

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
Reads were aligned to the human genome (hg19) using TopHat2
Number of reads mapping to each gene was counted using HTseq and normalzed to RPKM and then further normalized using quantile normalization. Last, floor level of 1.0 was set.
Supplementary_files_format_and_content: normalized FPKM

source_name: MCF10A-YAP_control non targeting sgRNA

growth_protocol: MCF10A-YAP5SA cells were cultured in DMEM/F12 medium (Gibco), supplemented with 1% penicillin/streptomycin (Gibco), 5% horse serum, EGF 10 ng/ml(Sigma), insulin 10μg/ml (Sigma), hydrocortisone 0.5μg /ml (Sigma).

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen), following the  manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen)
Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the  manufacturer's instructions.

treatment_protocol: MCF10A-YAP5SA cells were transduced with the indicated sgRNAs. After the antibiotic selection was completed, cells were kept in cell culture until they reach 70-80% confluency. Total RNA was extracted using Trizol Reagent (Invitrogen) and following the manufacturers protocol.

tag: cell line background

tag: condition

value: MCF10A-YAP cells transduced with a control non targeting sgRNA


title: NormalDonor4_untreated_PBMC_054

value: Peripherial blood mononuclear cells


title: NormalDonor4_untreated_PBMC_053


title: NormalDonor4_untreated_PBMC_059


title: NormalDonor4_untreated_PBMC_058


title: YAP-NT.27.rep2


title: NormalDonor4_untreated_PBMC_052


title: YAP-NT.27.rep1


title: F12B2_Liver_RNA-Seq

tag: tissue


title: NormalDonor4_untreated_PBMC_057

tag: who classification


title: NormalDonor4_untreated_PBMC_051

tag: cell type


title: NormalDonor4_untreated_PBMC_050


title: YAP.sgRNA1.e24

source_name: MCF10A-YAP_sgRNA targeting Enh.G

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.G


title: YAP.sgRNA2.e25


title: NormalDonor4_untreated_PBMC_049


title: YAP-NT.28


title: NormalDonor4_untreated_PBMC_055


title: Human chondrocytes from donor 2 treated with KN92+Wnt3a, tech repl 1

city: Guildford

first: Giovanna

last: Nalesso

address: Daphne Jackson Road

country: United Kingdom

institute: University of Surrey

hyb_protocol: Hybridization cocktails were prepared according to Nugen's recommendations for Human Gene 2.0 ST arrays and hybridization took place at 45°C for 16-20 hours in an Affymetrix Genechip Hybridization oven 645

scan_protocol: The arrays were scanned using the Affymetrix on the GeneChip Fluidics station 450. The arrays were scanned using the Affymetrix GeneChip Scanner

data_processing: CEL files were QC checked using the Expression Console software package (Affymetrix, Thermo Fisher) by using standard metrics and guidelines for the Affymetrix microarray system. Data were normalised together using the Robust Multi-array Average (RMA) algorithm, incolving a background correction, quantile normalisation, and log (base 2) transformation in R using oligo::rma with target = 'core'.

label: Biotin

source_name: Human chondrocytes passage 0 stimulated with KN92+Wnt3a

label_protocol: Biotin-labelled using the NuGen Encore Biotin Module according to the manufacturer's instructions

growth_protocol: Cells grown to 90% confluency passage 0 in DMEM+Glutamax, 10% FBS and 1% antibiotics and antimicotics

extract_protocol: Trizol plus isopropanol/ethanol precipitation

treatment_protocol: Cells stimulated with Kn92, KN92+Wnt3a or KN93+Wnt3a for 24h

tag: individual

value: Human chondrocytes passage 0

tag: treatment


title: NormalDonor4_untreated_PBMC_048

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.


title: YAP.sgRNA1.e18

source_name: MCF10A-YAP_sgRNA targeting Enh.E

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.E


title: Human chondrocytes from donor 2 treated with KN92, tech repl 1

source_name: Human chondrocytes passage 0 stimulated with KN92


title: NormalDonor4_untreated_PBMC_047


title: YAP.sgRNA2.e13

source_name: MCF10A-YAP_sgRNA targeting Enh.F

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.F


title: NormalDonor4_untreated_PBMC_046


title: Human chondrocytes from donor 1 treated with KN92+Wnt3a, tech repl 2


title: Human chondrocytes from donor 2 treated with KN92, tech repl 2


title: Human chondrocytes from donor 4 treated with KN93+Wnt3a, tech repl 2

source_name: Human chondrocytes passage 0 stimulated with KN93+Wnt3a


title: Human chondrocytes from donor 4 treated with KN92+Wnt3a


title: Human chondrocytes from donor 4 treated with KN92, tech repl 1


title: Human chondrocytes from donor 1 treated with KN93+Wnt3a, tech repl 1


title: YAP.sgRNA2.e9

source_name: MCF10A-YAP_sgRNA targeting Enh.D

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.D


title: NormalDonor4_untreated_PBMC_045


title: Human chondrocytes from donor 1 treated with KN92+Wnt3a, tech repl 1


title: Human chondrocytes from donor 4 treated with KN93+Wnt3a, tech repl 1


title: YAP.sgRNA2.e19


title: YAP.sgRNA1.e12


title: Human chondrocytes from donor 4 treated with KN92, tech repl 2


title: Human chondrocytes from donor 1 treated with KN93+Wnt3a, tech repl 2


title: NormalDonor4_untreated_PBMC_044


title: Human chondrocytes from donor 3 treated with KN92+Wnt3a


title: Human chondrocytes from donor 1 treated with KN92, tech repl 2


title: YAP.sgRNA1.e8


title: Human chondrocytes from donor 2 treated with KN93+Wnt3a, tech repl 2


title: Human chondrocytes from donor 3 treated with KN93+Wnt3a


title: Human chondrocytes from donor 2 treated with KN93+Wnt3a, tech repl 1


title: YAP.sgRNA2.e6

source_name: MCF10A-YAP_sgRNA targeting Enh.C

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.C


title: NormalDonor4_untreated_PBMC_042


title: Human chondrocytes from donor 1 treated with KN92, tech repl 1


title: Human chondrocytes from donor 2 treated with KN92+Wnt3a, tech repl 2


title: Human chondrocytes from donor 3 treated with KN92


title: YAP.sgRNA1.e5


title: NormalDonor4_untreated_PBMC_041


title: NormalDonor4_untreated_PBMC_040


title: NormalDonor4_untreated_PBMC_039


title: YAP.sgRNA1.e3

source_name: MCF10A-YAP_sgRNA targeting Enh.B

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.B


title: YAP.sgRNA2.e2

source_name: MCF10A-YAP_sgRNA targeting Enh.A

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.A


title: cGAS-WT-BIX

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

data_processing:
RNASeq raw data quality control by FastQC.
RNASeq raw data clean performed by cutadapt.
RNASeq data mapping to hg19/mm10 reference genomes by tophat2 with at most 2 mismatch for each reads. Cufflinks was used for differential expression gene analysis. Gene expression value with more than 2 fold change was defined differential expression genes.
Genome_build: Human hg19 (GRCh37); Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text format file for RNASeq gene expression level in each sample.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% penicillin and streptomycin. All the other cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin and streptomycin.

extract_protocol:
For RNASeq 10ug total RNA was used, and mRNA purification was performed using oligo-dT magnetic beads (NEBNext PolyA mRNA magnetic isolation module). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction.
RNA-seq library was performed by using Illumina TruSeq library construction kit. Using 5 μg total RNA as initiation, and then prepared according to the manufacturer's instruction. mRNA-seq libraries were sequenced using Illumina HiSeq X Ten for 100 bp paired-end sequencing.

treatment_protocol: All the cells were treated with 10 μM BIX-01294 for 12 hr.

tag: cell line

value: cGAS WT

value: 10 uM BIX-01294 for 12 hr


title: cGAS-KO-MOCK

value: cGAS KO

value: MOCK


title: NormalDonor4_untreated_PBMC_043

first: Birgit

last: Knoechel

address: 450 Brookline Ave

source_name: Blood


title: NormalDonor4_untreated_PBMC_038


title: YAP.sgRNA1.e1


title: NormalDonor4_untreated_PBMC_037


title: BM+COVID19 vs. BM_rep1

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description:
biological replicate:
1
polarity(-)

hyb_protocol: Custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3 μm resolution and 20-bit image depth using a G2565CA high-resolution laser microarray scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.12.1.1.1, Agilent)  and the  GE2_1200_Dec17  extraction protocol using standard settings with the normalization correction method Linear and Lowess.

label_protocol: RNA labeling was performed with the low Input Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: Primary human colon organoid culture were cultured in basic medium composed of Advanced Dulbecco’s Modified Eagle’s Medium/F12 (#12634,Gibco) containing 10 mM HEPES (#15630056, Gibco), 2 mM GlutaMAX (#35050061, Gibco), 1.25 mM N-acetylcysteine (#A9165, Sigma), 25% R-spondin1 conditioned medium, 1x B-27 (#17504044, Gibco), 1x N2 (#17502048, Gibco), 500 nM A83-01 (#616454, Merck), 100 µg/ml primocin (#ant-pm, Invivogen) and 10% penicillin/streptomycin (#15140122, Gibco), which was supplemented with 1 mM nicotinamide (N0636, Sigma), 10 µM SB202190 (#S7067, Sigma), 3 µM CHIR-99021 (#S1263, Selleckchem), 0.328 nM sWnt (#N001, U-Protein Express), 50 ng/ml hEGF (#PHG0311, Invitrogen), 100 ng/ml hNoggin (#120-10C, Peprotech) for maintenance in complete medium conditions. 10 µM Y-27632 (#M1817, Hölzel) was added after passaging and after the initial seeding.

extract_protocol: Organoid medium was removed and RNA was isolated using the Macherey & Nagel RNA isolation kit (#740955) according to the manufacturer’s instruction

treatment_protocol: After 4 days of culture in complete medium, differentiation was induced by further culturing in basic medium. Human organoids were passaged as organoid-crypt-fragments generated by passing 10x times through a 26G needle. IFN-γ treatment was carried out with 0-40 ng/ml human IFN-γ (#285-IF-100, R&D) for the indicated times.

value: human colon organoids

tag: medium

value: basic medium (BM)

tag: ifngamma

value: untreated

tag: covid-19 infection

value: COVID-19 infected

source_name: BM

value: non-infected


title: BM vs. BM+COVID19_rep1 dye swap

description:
biological replicate:
1
polarity(+)


title: BM+COVID19 vs. BM_rep2

description:
biological replicate:
2
polarity(-)


title: FM vs. FM+IFNg_rep2

description:
biological replicate:
2
polarity(+)

source_name: FM

value: full medium (FM)

source_name: FM+IFNg

value: treated


title: FM+IFNg vs. FM_rep2 dye swap

description:
biological replicate:
2
polarity(-)


title: cGAS-KO-BIX

tag: genotype/variation


title: FM+IFNg vs. FM_rep1 dye swap

description:
biological replicate:
1
polarity(-)


title: NormalDonor4_untreated_PBMC_036

institute: Dana Farber Cancer Institute

value: Normal

value: Peripherial blood mononuclear cells


title: X058_X_X1OD_RNASeq, biological rep3

city: Gothenborg

first: Xiaowei

last: Li

address: Kemivägen 10

department: Biology and Biological

country: Sweden

institute: Chalmers University of Technology

data_processing:
The raw reads from each sample were mapped to the CEN.PK 113-7D reference genome (http://cenpk.tudelft.nl) using TopHat (v 2.0.12), with 82.8—86.5% of the reads successfully mapped.
Cufflinks version 2.2.166 was used to calculate FPKM values, and the feature Counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: CEN.PK 113-7D

organism: Saccharomyces cerevisiae

source_name: Yeast strain X058 precultures on xylose media till OD600 equales 2.0 then transfers into fresh xylose media, cells are collected at OD600 1.0

growth_protocol: Shake flask 30 ˚C, 200rpm

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 4.8–10.6 million.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.

tag: strain

tag: genotype

value: PsXK, PsTAL1, TKL1, RPE1, RKI1,{delta}GRE3, PiXI


title: BM vs. BM+COVID19_rep2 dye swap

description:
biological replicate:
2
polarity(+)


title: X058_X_X1OD_RNASeq, biological rep2


title: X029_1OD_RNASeq, biological rep3

source_name: Yeast strain X029 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 1.0

value: PsXK, PsTAL1, TKL1, RPE1, RKI1, PiXI


title: X029_1OD_RNASeq, biological rep2


title: T47D_D538G_E2

city: Boston

first: Zheqi

state: Massachusetts

address: 450 Brookline Avenue, Smith Building SM1006

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq reads were aligned to either hg38 genome assembly using Bowtie 2.0
Peaks were called using MACS 1.4 with p value below 10E-5
DiffBind R package was used to perfrom prinicple component analysis, peak intersections and identify binding sites with differential binding intensities
Genomic feature distribution were called using ChIPseeker R package, taking the promoter region as +/- 3000 bp of the transcriptional start site (TSS).
Genome_build: Hg38
Supplementary_files_format_and_content: peaks

source_name: T47D cell line

growth_protocol: Individual clones were maintained in RPMI 1640 (T47D) and DMEM (MCF7) respectively, supplemented with 10 % FBS, 100 μg/mL penicillin and 100 mg/mL streptomycin, at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and ER-bound DNA complexes were isolated with antibody (Santa Cruz, sc-543).
ChIP was performed according to our in-house protocols. A minimum of 10ng DNA was sent to McGill University sequencing core. The library was prepared using TruSeq ChIP Library Preperation kit (Illumina) and was sequenced on Hiseq 2500 (Illumina). Over 16M single end 50bp reads were allocated for each sample.

treatment_protocol: Cells were washed with pheno-red-free CSS with 5% (MCF7) or 10% (T47D) CSS for 3 days, then treated with 1 nM E2 or 1% Ethanol for 45 minutes.

tag: esr1 genotype

tag: treatments

value: 1 nM E2

tag: chip antibody

value: ERα (Santa Cruz Biotechnologies, sc543)


title: FM vs. FM+IFNg_rep1

description:
biological replicate:
1
polarity(+)


title: T47D_D538G_Vehicle

value: Vehicle


title: cGAS-WT-MOCK

value: cGAS WT


title: YAP.sgRNA2.e4

tag: cell line background

value: MCF10A-YAP cells transduced with a sgRNA targeting Enh.B


title: X058_X_X1OD_RNASeq, biological rep1


title: NormalDonor4_untreated_PBMC_035


title: T47D_D538G_Input


title: X058_4OD_RNASeq, biological rep3

source_name: Yeast strain X058 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 4.0


title: T47D_Y537S_E2


title: NormalDonor4_untreated_PBMC_034


title: X029_1OD_RNASeq, biological rep1


title: X058_0.5OD_RNASeq, biological rep3

source_name: Yeast strain X058 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 0.5


title: X058_4OD_RNASeq, biological rep2


title: X058_4OD_RNASeq, biological rep1


title: NormalDonor4_untreated_PBMC_033


title: X058_0.5OD_RNASeq, biological rep2


title: X058_0.5OD_RNASeq, biological rep1


title: T47D_Y537S_Vehicle


title: NormalDonor4_untreated_PBMC_032


title: X058_E_X1OD_RNASeq, biological rep3

source_name: Yeast strain X058 precultures on ethanol media till OD600 equales 2.0 then transfers into xylose media, cells are collected at OD600 1.0


title: X058_E_X1OD_RNASeq, biological rep2


title: T47D_Y537S_Input


title: NormalDonor4_untreated_PBMC_030


title: X058_E_X1OD_RNASeq, biological rep1


title: X058_G_X1OD_RNASeq, biological rep3

source_name: Yeast strain X058 precultures on glucose media till OD600 equales 2.0 then transfers into xylose media, cells are collected at OD600 1.0


title: T47D_WT_E2

value: Wild-type


title: X058_G_X1OD_RNASeq, biological rep2


title: X058_E_RNASeq, biological rep3

source_name: Yeast strain X058 cultures on ethanol media, cells are collected at OD600 2.0


title: T47D_WT_Vehicle


title: NormalDonor4_untreated_PBMC_031


title: T47D_WT_Input


title: NormalDonor4_untreated_PBMC_029


title: X058_E_RNASeq, biological rep2


title: NormalDonor4_untreated_PBMC_028


title: MCF7_D538G_E2

source_name: MCF7 cell line


title: X058_E_RNASeq, biological rep1


title: X058_1OD_RNASeq, biological rep3

source_name: Yeast strain X058 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 1.0


title: NormalDonor4_untreated_PBMC_027


title: X058_1OD_RNASeq, biological rep2


title: X058_1OD_RNASeq, biological rep1


title: MCF7_D538G_Vehicle


title: NormalDonor4_untreated_PBMC_026


title: X158_4OD_RNASeq, biological rep3

source_name: Yeast strain X158 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 4.0

value: PsXK, PsTAL1, TKL1, RPE1, RKI1,{delta}GRE3,{delta}ASK10,{delta}YPR1, PiXI


title: X158_4OD_RNASeq, biological rep2


title: MCF7_D538G_Input


title: NormalDonor4_untreated_PBMC_025


title: X158_4OD_RNASeq, biological rep1


title: MCF7_Y537S_E2


title: X058_G_X1OD_RNASeq, biological rep1


title: X109_1OD_RNASeq, biological rep3

source_name: Yeast strain X109 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 1.0

value: PsXK, PsTAL1, TKL1, RPE1, RKI1,{delta}GRE3,{delta}ASK10, PiXI


title: X058_G_RNASeq, biological rep1

source_name: Yeast strain X058 cultures on glucose media, cells are collected at OD600 2.0


title: X058_G_RNASeq, biological rep3


title: X109_1OD_RNASeq, biological rep2


title: MCF7_Y537S_Vehicle


title: X109_1OD_RNASeq, biological rep1


title: NormalDonor4_untreated_PBMC_024

source_name: Blood


title: MCF7_Y537S_Input


title: NormalDonor4_untreated_PBMC_022


title: MCF7_WT_E2


title: X058_G_RNASeq, biological rep2


title: X158_1OD_RNASeq, biological rep1

source_name: Yeast strain X158 precultures on glucose media for 12 to 15 h then transfers into xylose media, cells are collected at OD600 1.0


title: MCF7_WT_Vehicle


title: NormalDonor4_untreated_PBMC_023


title: X158_1OD_RNASeq, biological rep2


title: NormalDonor4_untreated_PBMC_019


title: NormalDonor4_untreated_PBMC_021


title: NormalDonor4_untreated_PBMC_018


title: MCF7_WT_Input


title: Cells at timepoint Day 7, repeat 3 (29580)

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
Cells at timepoint Day 7, repeat 3
cellular miRNA expression data

hyb_protocol: The standard Affymetrix chip hybridization protocol was followed to hybridize the labeled miRNAs onto Affymtrix miRNA array 4.0 in the hybridization oven at 48 C and 60 rpm for 18 hours.

scan_protocol: After washing and staining, the chips were scanned using the Affymetrix 7G scanner with standard settings to capture the signal intensities for the miRNAs.

data_processing: The raw signal data were loaded into Affymetrix Expression Console (v1.4) and subjected to RMA background correction, median summarization of multiple probes, and quantile normalization. This was done only within the probes for Human miRNAs on chip.

source_name: cells treated with osteogenic induction medium at day 7

label_protocol: 500 ng of total RNA from whole cell were first subjected to poly-A tailing with Poly A Polymerase and substrate ATP. Then the FlashTag Ligation Mix and ligase were added to carry out the ligation reaction so that the Biotin-labeled, dendritic structutre of 3DNAs were ligated onto miRNA molecules to archieve the miRNA labeling and the amplification of detection signals.

growth_protocol: MSCs were cultured and expanded in growth medium containing DMEM (low glucose), 10% fetal bovine serum, 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 1ng/ml basic FGF.

extract_protocol: Total RNA was isolated from whole cell extracts using the Norgen Total RNA purification kit following the manufacturer's protocol.

treatment_protocol: MSCs were cultured in MSC growth medium (described above) and used as controls. The treatment (differentiation) protocol involved culturing MSCs in the presence of osteogenic induction (differentiation) medium containing aMEM base medium, 10% fetal bovine serum, 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin, 10mM β-glycerol phosphate, 50µM ascorbic acid and 10µM dexamethasone.

tag: repeat id

tag: timepoint


title: NormalDonor4_untreated_PBMC_017

tag: who classification


title: Cells at timepoint Day 0, repeat 3 (29578)

description:
Cells at timepoint Day 0, repeat 3
cellular miRNA expression data

source_name: cells treated with growth medium at day 0


title: Cells at timepoint Day 3, repeat 3 (29579)

description:
Cells at timepoint Day 3, repeat 3
cellular miRNA expression data

source_name: cells treated with osteogenic induction medium at day 3


title: Cells at timepoint Day 14, repeat 2 (29577)

description:
Cells at timepoint Day 14, repeat 2
cellular miRNA expression data

source_name: cells treated with osteogenic induction medium at day 14


title: NormalDonor4_untreated_PBMC_016

tag: cell type


title: NormalDonor4_untreated_PBMC_015


title: NormalDonor4_untreated_PBMC_020


title: synpo2 -/- - rep3

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

country: Canada

institute: Sunnybrook Research Institute

data_processing:
adapter trimming using Trimmomatic (v0.36),
Read mapped to danio rerio GRCz10.89 using STAR aligner (v2.5.2b)
Genome_build: danio rerio GRCz10
Supplementary_files_format_and_content: raw counts

organism: Danio rerio

source_name: whole embryo

extract_protocol: Whole embryo directly immersed in Trizol after ethunasia with Tricaine

tag: Stage

value: 22 hours post fertilization

value: synpo2 -/-

tag: tissue

value: whole embryo


title: NormalDonor4_untreated_PBMC_014


title: Cells at timepoint Day 7, repeat 2 (29576)

description:
Cells at timepoint Day 7, repeat 2
cellular miRNA expression data


title: synpo2 -/- - rep1


title: NormalDonor4_untreated_PBMC_013


title: X158_1OD_RNASeq, biological rep3


title: synpo2 wt/wt - rep3

value: synpo2 wt/wt


title: Cells at timepoint Day 0, repeat 2 (29574)

description:
Cells at timepoint Day 0, repeat 2
cellular miRNA expression data


title: Cells at timepoint Day 14, repeat 1 (29573)

description:
Cells at timepoint Day 14, repeat 1
cellular miRNA expression data


title: synpo2 wt/wt - rep2


title: NormalDonor4_untreated_PBMC_012


title: synpo2 wt/wt - rep1


title: Cells at timepoint Day 7, repeat 1 (29572)

description:
Cells at timepoint Day 7, repeat 1
cellular miRNA expression data


title: NormalDonor4_untreated_PBMC_011


title: Cells at timepoint Day 3, repeat 2 (29575)

description:
Cells at timepoint Day 3, repeat 2
cellular miRNA expression data


title: synpo2 -/- - rep2


title: NormalDonor4_untreated_PBMC_010


title: NormalDonor4_untreated_PBMC_009


title: Cells at timepoint Day 3, repeat 1 (29571)

description:
Cells at timepoint Day 3, repeat 1
cellular miRNA expression data


title: Cells at timepoint Day 0, repeat 1 (29570)

description:
Cells at timepoint Day 0, repeat 1
cellular miRNA expression data


title: NormalDonor4_untreated_PBMC_008


title: Baso IL-3 rep 3

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

hyb_protocol: 500 ng of Cy3-labelled cRNA  from each sample was hybridized to Agilent SurePrint G3 Human Gene Expression 8×60K V2 microarray  according to the manufacturer's instructions

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

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were Quantile normalized using R.

source_name: Baso IL-3 rep 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 55ng total RNA using using the Agilent One-Color Microarray-Based Exon Analysis (Low Input Quick Amp Labeling) kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Purified basophils were cultured in RPMI 1640 medium supplemented with 2 mM L-glutamine, 10% heat-inactivated FCS, and 50 ug/mL gentamicin.  For gene expression microarray analysis, purified basophils at a density of 2×105 cells/well in a 96-well plate were cultured either with or without human IL-3 (50 ng/mL) (n = 3) for 24 hours.

extract_protocol: Total RNA was extracted using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA).

value: whole blood

tag: gender

value: male


title: Baso IL-3 rep 2

source_name: Baso IL-3 rep 2


title: Baso IL-3 rep 1

source_name: Baso IL-3 rep 1


title: NormalDonor4_untreated_PBMC_006

value: Normal

value: Peripherial blood mononuclear cells


title: Cells at timepoint Day 14, repeat 3 (29581)

description:
Cells at timepoint Day 14, repeat 3
cellular miRNA expression data


title: Baso Control (IL-3  control) rep 2

source_name: Baso Control rep 2


title: Baso Control (IL-3  control) rep 3

source_name: Baso Control rep 3


title: Baso Control (IL-3  control) rep 1

source_name: Baso Control rep 1


title: hDF_F64Br_TGFb1_24h_rep3

city: London

first: Oliver

middle: J

last: Culley

address: Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond

department: Centre for Stem Cells and Regenerative Medicine

institute: King’s College London

hyb_protocol: Sample preparations were mixed, collected and incubated at 60°C for 30 min to fragment the cRNA using the gene expression hybridisation kit (Agilent): Cy3-labelled cRNA (600 ng) with nuclease-free water, 2X blocking agent, 1X fragmentation buffer. The fragmentation reaction was stopped by adding 1X hybridisation buffer Hi-RPM. Each SurePrint microarray (Agilent) was incubated in a rotisserie oven at 65°C for 17h to allow hybridisation. Following hybridisation, microarrays were added to gene expression wash buffer 1 (Agilent), incubated at room temperature for 1 min. Microarrays were washed in wash buffer 2 (Agilent) at 37°C for 1 min. Arrays were incubated in acetonitrile (Sigma-Aldrich) at room temperature for 10 sec, dried and covered with ozone protection covers (Agilent).

scan_protocol: Arrays were imaged using the Agilent G2565BA microarray scanner system. All three experiments were run using the SurePrint G3 Human GE 8x60K V2 kit (Agilent).

data_processing: Scanned images were analysed with G2567AA feature extraction software (v.9.5.1; Agilent) using default parameters (protocols GE1-v5_91_0806; grid 039494_D_F_20150612). Gene expression values were normalised using Agilent GeneSpring GX software (v.14.8).

label_protocol: One colour Quick-Amp labelling kit (Agilent) was used to derive cyanine 3 (Cy3)-labelled cRNA from the extracted RNA. A one colour RNA spike-in kit (Agilent) was used to monitor sample amplification and labelling efficiency. For each sample, 300 ng total RNA was used; universal human reference RNA (Agilent) was used as a reference. The concentration of labelled cRNA was measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific).

growth_protocol: Human dermal fibroblasts (hDF) were cultured in phenol red-free, low glucose DMEM (Sigma-Aldrich) supplemented with 10% foetal bovine serum; 450 µg/ml L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich). Referred to as complete DMEM.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was measured using the Bioanalyser 2100 (Agilent) and RNA 6000 Nano kit (Agilent) according to the manufacturer’s instructions.

treatment_protocol: hDF were seeded into 6-well microplates and cultured in complete DMEM for four days at 37°C in 5% CO2. hDF were equilibrated in low (1%) serum DMEM for 24h and treated with or without TGF-β1 (10 ng/ml; R&D) in low (1%) serum DMEM for a further 12h or 24h.

tag: donor id

tag: Sex

value: Female

tag: age

value: Breast

value: enzyme-derived, human dermal fibroblasts (hDF)

tag: treatment

tag: treatment time


title: NormalDonor4_untreated_PBMC_005


title: omentum (stomach); tissue; M73

city: Stanford

first: Heather

last: Clemons

address: Beckman Center

department: Dept of Biochemistry

institute: Stanford School of Medicine

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79475.gif

hyb_protocol: not provided

scan_protocol: Model: GenePix 4200A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Human Universal Reference

source_name: omentum (stomach); tissue; M73, 10 ug labeled aRNA

extract_protocol:
Adipose Tissue Samples; Specimen Collection Adipose tissue specimens were collected either from the Stanford Tissue Bank, Stanford Dermatology Clinic, Stanford Surgical Pathology or directly from the surgeon at the time of surgery. All surgeries were performed at Stanford Hospital and Clinics. When necessary a trained pathologist dissected the desired adipose specimen from the organ/limb/skin to which it was attached. Samples acquired by Stanford Tissue Bank or Surgical Pathology may have been stored at 4C for up to several hours but were always processed on the same day as the surgery was performed. All samples are considered normal human tissues and were originally collected under the IRB Study of Messenger RNA Expression in Normal Human Tissues ID: 76363, which did not require patient consent as very little patient information (age, gender, procedure) was provided. Subsequently it was determined that our sample collection does not meet the definitions of human subject research under Stanfords Human Research Protection Program and therefore an IRB protocol was no longer required.
Tissue Fractionation - Clemons; Tissue Fractionation Adipose tissue samples were thoroughly rinsed with 70% ethanol to minimize risk of microbial contamination of cell cultures. Tissues were then rinsed with Hanks Balanced Salt Solution (HBSS) and transferred to a clean dish. At this time 1-4 g of tissue were removed and stored at -80C. Additionally a thin slice of each tissue was placed in 10% formalin for paraffin embedding. The remainder of each tissue sample was minced using surgical scissors. Tissue pieces were transferred to 50 ml conical tubes (up to 25 ml tissue per tube), and an equivalent volume of collagenase solution* was added to the tube. Tissue was again minced with scissors until no large pieces remained. Tubes were shaken to mix and incubated at 37C for 30 min to 4 hours, until pieces of tissue were no longer visible. Shin/calf adipose tissue in general took the longest and abdominal and thigh lipoaspirate the shortest time to digest. Digested tissues were then passed through a 180-micron nylon net filter and centrifuged at 100g for 5 minutes to pellet stromal-vascular cells. A 16-gauge needle attached to a 20 ml syringe was passed through the top visible lipid/adipocyte layer and the entire bottom layer containing buffer, cell pellet and blood cells was aspirated from the bottom and transferred to a new conical, tube. This cell suspension (stromal-vascular fraction) was thoroughly mixed by pipetting and divided equally into 2 conical tubes. One of these was set aside for cell culture (see Cell Culture) and the other was centrifuged at 400g for 7 minutes. Buffer was carefully aspirated with a pipette to avoid losing pelleted cells and 15 ml Trizol was added. The remaining lipid/adipocyte layer was washed 1-2 times depending on the amount of visible blood cells: 25 ml HBSS was added to the adipocytes, and gently inverted to mix. Adipocytes were centrifuged at 100g and excess buffer along with contaminating cells was aspirated from the bottom using a needle and syringe as described above. An equal volume of Trizol was added to the washed adipocytes. The stromal-vascular pellet sample and the adipocyte sample were stored in Trizol at -80C.  Collagenase Solution: For stock solution 1000 U/ml Sigma Type II Collagenase (Cat# C6885) was dissolved in HBSS and centrifuged at 1000g for 20 minutes. Resulting liquid fraction was filtered (.22 micron) and stored at -20C and pelleted crystals were discarded. For working solution 1000 U/ml collagenase stock solution was diluted 3x in HBSS containing 5mM CaCl2
Amplification 1 ug of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to manufacturers protocol

value: 73 years

tag: organism part

value: omentum (stomach)

tag: sample fraction

value: tissue

value: Male


title: hDF_F22Br_TGFb1_24h_rep3


title: NormalDonor4_untreated_PBMC_007


title: hDF_F60Br_Control_24h_rep3

value: Control


title: omentum (colon); tissue; M60a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79477.gif

source_name: omentum (colon); tissue; M60a, 10 ug labeled aRNA

value: 60 years

value: omentum (colon)


title: hDF_M50F_Control_24h_rep3

value: Face


title: NormalDonor4_untreated_PBMC_004


title: shin; tissue; M77

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79490.gif

scan_protocol: Model: GenePix 4000A

source_name: shin; tissue; M77, 10 ug labeled aRNA

value: 77 years

value: shin


title: hDF_M50F_TGFb1_24h_rep3


title: abdominal; tissue; F42

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79486.gif

source_name: abdominal; tissue; F42, 10 ug labeled aRNA

value: 42 years

value: abdominal

value: female


title: NormalDonor4_untreated_PBMC_003

source_name: Blood

value: Normal

value: Peripherial blood mononuclear cells


title: shin/calf; stromal pellet; F71

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79500.gif

source_name: shin/calf; stromal pellet; F71, 10 ug labeled aRNA

value: 71 years

value: shin/calf

value: stromal pellet


title: NormalDonor4_untreated_PBMC_002


title: omentum (colon); stromal pellet; F72

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79474.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); stromal pellet; F72, 10 ug labeled aRNA

value: 72 years


title: shin/calf; adipocyte; F71

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79501.gif

source_name: shin/calf; adipocyte; F71, 10 ug labeled aRNA

value: adipocyte


title: hDF_F22Br_Control_24h_rep3

value: Female

value: Breast

value: enzyme-derived, human dermal fibroblasts (hDF)

value: Control


title: hDF_F64Br_TGFb1_12h_rep3


title: hDF_F22Br_TGFb1_12h_rep3


title: abdominal; tissue; F52c

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79489.gif

source_name: abdominal; tissue; F52c, 10 ug labeled aRNA

value: 52 years

value: tissue


title: hDF_M50F_Control_12h_rep3

value: Male

value: Face


title: NormalDonor4_untreated_PBMC_001


title: hDF_F60Br_Control_12h_rep3


title: hDF_F60Br_TGFb1_12h_rep3


title: omentum (colon); adipocyte; F75

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79492.gif

source_name: omentum (colon); adipocyte; F75, 10 ug labeled aRNA

value: 75 years

value: omentum (colon)

value: female


title: abdominal lipo; tissue; M58a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79484.gif

source_name: abdominal lipo; tissue; M58a, 10 ug labeled aRNA

value: 58 years

value: abdominal lipo


title: NormalDonor3_untreated_PBMC_094

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor3_untreated_PBMC_092


title: hDF_F60Br_TGFb1_24h_rep3


title: hDF_F60Br_Control_24h_rep2


title: hDF_F60Br_TGFb1_24h_rep2


title: NormalDonor3_untreated_PBMC_090


title: abdominal; tissue; UUg

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79479.gif

value: Stratagene Human Universal Reference

source_name: abdominal; tissue; UUg, 10 ug labeled aRNA

value: unknown

value: abdominal


title: hDF_F64Br_Control_24h_rep3

value: Female

value: Breast


title: hDF_F64Br_TGFb1_24h_rep2

value: enzyme-derived, human dermal fibroblasts (hDF)


title: hDF_M50F_Control_24h_rep2

value: Control


title: hDF_M50F_TGFb1_12h_rep3


title: NormalDonor3_untreated_PBMC_091


title: hDF_F22Br_Control_12h_rep3


title: hDF_F64Br_Control_12h_rep3


title: abdominal; adipocyte; F52c

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79488.gif

source_name: abdominal; adipocyte; F52c, 10 ug labeled aRNA

value: 52 years

value: adipocyte


title: NormalDonor3_untreated_PBMC_093


title: hDF_M50F_TGFb1_24h_rep2

value: Male

value: Face


title: hDF_F22Br_TGFb1_24h_rep2


title: NormalDonor3_untreated_PBMC_089


title: NormalDonor3_untreated_PBMC_088


title: shin/calf; adipocyte; M23

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79499.gif

source_name: shin/calf; adipocyte; M23, 10 ug labeled aRNA

value: 23 years

value: shin/calf


title: NormalDonor3_untreated_PBMC_087


title: abdominal; tissue; M59a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79480.gif

source_name: abdominal; tissue; M59a, 10 ug labeled aRNA

value: 59 years

value: tissue


title: NormalDonor3_untreated_PBMC_086

value: Normal


title: hDF_F64Br_TGFb1_12h_rep2


title: hDF_F64Br_Control_24h_rep2


title: A10-CTR-ChIP

city: Chongqing

first: Junyi

address: 10th Changjiangzhilu Road, Yuzhong District

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University, Chongqing, P.R. China.

data_processing:
Fastqs were qualified by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and they were mapped to UCSC reference genome Rnor.6.0 using Bowtie2
SAMtools was used to manipulate SAM files into sorted BAM files
To capture ChIP signals, MACS2 was applied with the option qvalue cutoff = 0.05
Peaks were annotated by annotatePeaks.pl in Homer using Rat gtf files from ENSEMBL.
Genome_build: Rnor6

organism: Rattus norvegicus

source_name: A10 cell (ATCC CRL-1476)

growth_protocol: Rat thoracic aortic vascular smooth muscle A10 cells was purchased from ATCC (CRL-1476), and cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% FBS, 100U/mL penicillin and 100g/mL streptomycin at 37 °C in a 95% air-5% CO2 atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext ChIP-seq library prep master mix set for Illumina was used to prepare the sequencing library with custom-synthesized primers (Wang et al., 2019). 50 nt single end reads (Arteridin ChIP-Seq) were generated on Illumina Hiseq 2500 platform and 150bp pair end reads (YBX1 ChIP-Seq) were generated on Illumina HiSeq X Ten.

treatment_protocol: Lipofactamine 3000 was used for plasmid transfection.

value: aorta, thoracic/medial layer

tag: passages

tag: chip antibody

value: rabbit multiconal customized antibody targerting full-length Arteridin


title: hDF_F22Br_Control_24h_rep2


title: NormalDonor3_untreated_PBMC_085

value: Peripherial blood mononuclear cells


title: omentum (colon); stromal pellet; F85

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79497.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: omentum (colon); stromal pellet; F85, 10 ug labeled aRNA

value: 85 years

value: omentum (colon)

value: stromal pellet

value: female


title: abdominal; stromal pellet; F52c

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79487.gif

source_name: abdominal; stromal pellet; F52c, 10 ug labeled aRNA

value: 52 years

value: abdominal


title: A10-input


title: hDF_F60Br_Control_12h_rep2

value: Female

value: Breast

value: enzyme-derived, human dermal fibroblasts (hDF)

value: Control


title: omentum (colon); tissue; M82

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79476.gif

source_name: omentum (colon); tissue; M82, 10 ug labeled aRNA

value: 82 years

value: Male


title: hDF_M50F_Control_12h_rep2

value: Face


title: hDF_F64Br_Control_12h_rep2


title: omentum (stomach); tissue; F73

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79496.gif

source_name: omentum (stomach); tissue; F73, 10 ug labeled aRNA

value: 73 years

value: omentum (stomach)

value: tissue


title: hDF_M50F_TGFb1_12h_rep2


title: hDF_F22Br_TGFb1_12h_rep2


title: hDF_F22Br_Control_12h_rep2


title: NormalDonor3_untreated_PBMC_084

source_name: Blood

value: Normal

value: Peripherial blood mononuclear cells


title: A10-ORF-ChIP

value: aorta, thoracic/medial layer

value: rabbit multiconal customized antibody targerting full-length Arteridin


title: NormalDonor3_untreated_PBMC_082


title: hDF_F64Br_TGFb1_24h_rep1


title: hDF_M50F_Control_24h_rep1


title: abdominal lipo; stromal pellet; M58a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79483.gif

value: Stratagene Human Universal Reference

source_name: abdominal lipo; stromal pellet; M58a, 10 ug labeled aRNA

value: 58 years

value: abdominal lipo

value: stromal pellet


title: NormalDonor3_untreated_PBMC_081


title: omentum (stomach); stromal pellet; F73

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79495.gif

source_name: omentum (stomach); stromal pellet; F73, 10 ug labeled aRNA

value: female


title: hDF_F60Br_TGFb1_12h_rep2

value: Female

value: Breast

value: enzyme-derived, human dermal fibroblasts (hDF)


title: hDF_F60Br_Control_24h_rep1

value: Control


title: abdominal; tissue; F60

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79491.gif

source_name: abdominal; tissue; F60, 10 ug labeled aRNA

value: 60 years

value: abdominal


title: NormalDonor3_untreated_PBMC_080


title: hDF_M50F_TGFb1_24h_rep1

value: Male

value: Face


title: abdominal; stromal pellet; F42

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79485.gif

source_name: abdominal; stromal pellet; F42, 10 ug labeled aRNA

value: 42 years


title: omentum (colon); adipocyte; F72

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79494.gif

source_name: omentum (colon); adipocyte; F72, 10 ug labeled aRNA

value: 72 years

value: omentum (colon)

value: adipocyte


title: calf; tissue; M24a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79478.gif

value: Stratagene Human Universal Reference

source_name: calf; tissue; M24a, 10 ug labeled aRNA

value: 24 years

value: calf

value: tissue


title: hDF_M50F_Control_12h_rep1


title: hDF_F22Br_TGFb1_24h_rep1


title: Newly diagnosed elderly multiple myeloma 179

city: Rotterdam

first: P

last: Sonneveld

address: Wytemaweg 80

department: Department of Hematology

country: Netherlands

institute: ErasmusMC cancer institute

hyb_protocol: 13 ug of fragmented and biotin labeled cRNA hybridized to the microarray in an Affymetrix GeneChip® Hybridization Oven 645 and washed / stained in Affymetrix GeneChip Fluidics Station FS450DX2v2.

scan_protocol: Affymetrix GeneChip® System 3000Dx v.2

data_processing: MAS5.0 (Bioconductor affy package v1.36.2) default values with a  trimmed mean target intensity value set to 1500. Values below 30 were truncated. Log2 transformed.

source_name: CD138 purified myeloma plasma cells

label_protocol: Affymetrix GeneChip® 3' IVT PLUS Reagent Kit or Gene Profiling MDx IVD Expression Reagent Kit in accordance with Affymetrix protocols.

extract_protocol: Bone marrow aspirates were processed by CD138 based magnetic bead sorting (Stem Cell Technologies) to a purity of >80% plasma cells as verified by CD38 positivity by flowcytometry. Purified cells are prepared for RNA isolation using Qiagen Allprep.

tag: diagnosis

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

tag: sky92 status

value: Standard risk

tag: reagents

value: IVT


title: hDF_F60Br_TGFb1_24h_rep1

value: Female

value: Breast

tag: cell type

value: enzyme-derived, human dermal fibroblasts (hDF)


title: NormalDonor3_untreated_PBMC_083

tag: who classification

value: Normal

value: Peripherial blood mononuclear cells


title: hDF_F22Br_Control_24h_rep1

tag: tissue

value: Control


title: hDF_F60Br_Control_12h_rep1


title: Newly diagnosed elderly multiple myeloma 154


title: shin/calf; tissue; M55

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79498.gif

source_name: shin/calf; tissue; M55, 10 ug labeled aRNA

value: 55 years

value: shin/calf

value: Male


title: hDF_F64Br_TGFb1_12h_rep1


title: hDF_F64Br_Control_24h_rep1


title: Newly diagnosed elderly multiple myeloma 180


title: omentum (colon); stromal pellet; F75

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79481.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); stromal pellet; F75, 10 ug labeled aRNA

value: 75 years

value: omentum (colon)

value: stromal pellet

value: female


title: hDF_F64Br_Control_12h_rep1


title: NormalDonor3_untreated_PBMC_078


title: hDF_M50F_TGFb1_12h_rep1

value: Face


title: Newly diagnosed elderly multiple myeloma 145

value: multiple myeloma

value: bone marrow

value: CD138 purified myeloma plasma cells

value: Standard risk


title: NormalDonor3_untreated_PBMC_079


title: NormalDonor3_untreated_PBMC_077


title: hDF_F60Br_TGFb1_12h_rep1

value: Female

value: Breast

value: enzyme-derived, human dermal fibroblasts (hDF)


title: NormalDonor3_untreated_PBMC_076

value: Normal

value: Peripherial blood mononuclear cells


title: PD_pMFH774_slide495

type: genomic

city: New York

first: Nicholas

middle: D

last: Socci

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: array-based comparative genomic hybridization (CGH)

scan_protocol: per Agilent protocols

data_processing:
Custom GC-Normalization full methods are here: http://cbio.mskcc.org/CGCC/
Copy number segmentation using Circular Binary Segmentation CBS in (https://bioconductor.org/packages/release/bioc/html/DNAcopy.html)
genome build: HG18 (N.B. not b37)
[singerS_CAN-19-1269R_IGV.seg]  Segmentation file (.seg) primary output of CBS

source_name: Tumor

label_protocol: per Agilent protocols

growth_protocol: Tumor tissue was obtained from human patients

extract_protocol:
Cryomolds were generated from human patient tumor tissue. Cryomolds containing > 75% cellularity were macrodissected to remove normal, fibrotic, inflammatory, and necrotic tissue. Genomic DNA was then prepared using a Dneasy Blood and Tissue kit (QIAGEN)
DNA libraries were prepared as per Agilent protocols

tag: histology

value: Undifferentiated pleomorphic sarcoma

tag: tumor site

value: Groin

tag: tumor length

source_name: Promega ref DNA

tag: sample type

value: Promega ref


title: NormalDonor3_untreated_PBMC_075


title: NormalDonor3_untreated_PBMC_074


title: PD_pMFH767_slide800

value: Thigh


title: NormalDonor3_untreated_PBMC_073


title: PD_pMFH765_slide802

value: Shoulder


title: PD_pMFH766_slide801


title: Newly diagnosed elderly multiple myeloma 138

value: IVT


title: PD_pMFH764_slide381

value: Chest Wall


title: PD_pMFH762_slide804

value: Calf


title: hDF_F22Br_Control_12h_rep1

tag: donor id

tag: Sex

tag: age

tag: treatment

value: Control


title: Newly diagnosed elderly multiple myeloma 111

value: multiple myeloma

value: bone marrow


title: PD_pMFH760_slide562


title: SGC-7901 cells knockdown NUAK1-2

city: Nanchang

first: Suhong

last: Di

state: China

address: Medicalcollege of Nanchang University

institute: Nanchang University

description: The microarrays from gastric cancer SGC-7901 cells transfected with NUAK1-specific siRNA

hyb_protocol: RNA were hybridized for 16 hr at 45℃ on GeneChip Hybridization Oven 645. GeneChips were washed and stained in GeneChip Fluidics Station 450.The hyb protocol was completed in Genechem company(shanghai,China) with Affymetrix microarray analysis products.

scan_protocol: GeneChips were scanned using theGeneChip Scanner 3000.The scan protocol was completed in Genechem company(shanghai,China) with Affymetrix microarray analysis products.

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Human gastric cancer cells knockdown NUAK1

label_protocol: In vitro reversal (IVT reaction) is used to GeneChip 3’IVT Express Kit for 16 hr at 40 ℃ to obtain biotinylated aRNA.The label protocol was completed in Genechem company(shanghai,China) with Affymetrix microarray analysis products.

growth_protocol: Human gastric cancer SGC-7901 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum at 37℃ with an atmosphere composed  of 5% CO2

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

treatment_protocol: The control group is gastic cancer cells transfected with control siRNA.Other group is gastric cancer cells transfected with NUAK1-specific siRNA

tag: cell line

value: gastric cancer

tag: tumor stage

value: Moderate differentiation

tag: transfected with

value: NUAK1-specific siRNA


title: SGC-7901 cells control-3

description: The microarrays from gastric cancer SGC-7901 cells transfected with control siRNA

source_name: Human gastric cancer SGC-7901 cells

value: control siRNA


title: NormalDonor3_untreated_PBMC_072

value: Normal


title: NormalDonor3_untreated_PBMC_071

value: Peripherial blood mononuclear cells


title: Newly diagnosed elderly multiple myeloma 122

tag: diagnosis

value: CD138 purified myeloma plasma cells

value: Standard risk


title: SGC-7901 cells knockdown NUAK1-1


title: Newly diagnosed elderly multiple myeloma 107

tag: sky92 status

value: High risk


title: SGC-7901 cells knockdown NUAK1-3


title: Newly diagnosed elderly multiple myeloma 54

tag: reagents


title: SGC-7901 cells control-2

tag: cell type


title: SGC-7901 cells control-1


title: Newly diagnosed elderly multiple myeloma 50


title: PD_MXF776_slide616

value: Myxofibrosarcoma

value: Thigh

value: Promega ref


title: PD_MXF772_slide776

value: Upper arm


title: PD_MXF771_slide777


title: NormalDonor3_untreated_PBMC_070

tag: who classification


title: PD_MFH9_slide376

value: Undifferentiated pleomorphic sarcoma


title: NormalDonor3_untreated_PBMC_069


title: Newly diagnosed elderly multiple myeloma 1

tag: tissue

value: IVT


title: Newly diagnosed elderly multiple myeloma 59

value: multiple myeloma


title: PD_pMFH759_slide779

tag: histology


title: PD_MFH7671_slide431

tag: tumor site


title: PD_MFH742_slide367

tag: tumor length


title: PD_MFH683_slide429

value: Buttock

tag: sample type


title: PD_MFH682_slide433

value: Abdominal Wall


title: NormalDonor3_untreated_PBMC_068


title: PD_MFH679_slide154


title: PD_MFH675_slide153

value: Chest Wall


title: NormalDonor3_untreated_PBMC_066


title: NormalDonor3_untreated_PBMC_065


title: PD_MFH666_slide152

value: Retroperitoneum


title: NCI-H292_CT45A1-negative_rep1

city: Suzhou

first: Gaochuan

last: Zhang

address: 199 Ren-Ai Road

institute: Soochow university

description: Gene expression data from CT45A1-negative  human lung cancer cell line NCI-H292

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: DMEM complete medium, 10%FBS, 37 ̊C, 5% CO2

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

treatment_protocol: NCI-H292 cells were stably transcfected with CT45A1-Venus or the vector Venus as a control

tag: genotype


title: PD_MFH658_slide151

value: Paraspinal


title: PD_MFH0224_slide386


title: PD_MFH628_slide150


title: NormalDonor3_untreated_PBMC_064

value: Normal


title: NCI-H292_CT45A1-negative_rep3


title: NormalDonor3_untreated_PBMC_067

value: Peripherial blood mononuclear cells


title: NormalDonor3_untreated_PBMC_062


title: NormalDonor3_untreated_PBMC_063


title: NCI-H292_CT45A1-negative_rep2


title: Blood QT4

city: Tianjin

first: huanxin

last: chen

address: No.61, third avenue, tianjin economic and technolo

institute: Teda International Cardiovascular Hospital

description: Hybridized to Affymetrix SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The overall hybridization quality was estimated by the call rate obtained from Genotyping Console Software 4.2 (birdseed algorithm with default parameter settings). Partek Genomics Suite (version 6.5, Partek Inc., St. Louis, MO) was used for copy number analysis. Regions of CNV were detected using a Hidden Markov Model (HMM) algorithm in the Partek workflow for unpaired samples.

source_name: TOF patient_blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood for each patient and control subject, using QIAamp® DNA blood mini kit according to the manufacturer’s instruction

tag: group

value: TOF patient

value: blood


title: Blood QT5

description: Hybridized to Affymetrix SNP 6.0


title: Blood QT3

description: Hybridized to Affymetrix SNP 6.0


title: Blood QT2

description: Hybridized to Affymetrix SNP 6.0


title: NCI-H292_CT45A1-overexpression_rep3

description: Gene expression data from CT45A1-overexpressed human lung cancer cell line NCI-H292


title: PD_MFH6221_slide430


title: NCI-H292_CT45A1-overexpression_rep1


title: Blood QT6

description: Hybridized to Affymetrix SNP 6.0


title: Blood PQC389

description: Hybridized to Affymetrix SNP 6.0


title: Blood PQC372

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_060

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.


title: Blood PQC367

description: Hybridized to Affymetrix SNP 6.0


title: Blood PQC355

description: Hybridized to Affymetrix SNP 6.0


title: Blood PQC349

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_059


title: NCI-H292_CT45A1-overexpression_rep2


title: NormalDonor3_untreated_PBMC_061


title: Newly diagnosed elderly multiple myeloma 176

value: bone marrow

value: CD138 purified myeloma plasma cells

value: Standard risk

value: GPR


title: Blood QT1

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 174


title: Newly diagnosed elderly multiple myeloma 172


title: Newly diagnosed elderly multiple myeloma 178


title: Newly diagnosed elderly multiple myeloma 177

value: High risk


title: Blood P198

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 175


title: Blood P196

description: Hybridized to Affymetrix SNP 6.0


title: hDF_F22Br_TGFb1_12h_rep1

tag: donor id

tag: Sex

value: Female

tag: age

value: Breast

value: enzyme-derived, human dermal fibroblasts (hDF)

tag: treatment time


title: NormalDonor3_untreated_PBMC_057


title: Newly diagnosed elderly multiple myeloma 173

value: multiple myeloma


title: Blood P191

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_055


title: Blood P192

description: Hybridized to Affymetrix SNP 6.0


title: Blood P190

description: Hybridized to Affymetrix SNP 6.0


title: Blood P189

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_058


title: NormalDonor3_untreated_PBMC_054


title: Blood PQC307

description: Hybridized to Affymetrix SNP 6.0


title: Blood P188

description: Hybridized to Affymetrix SNP 6.0


title: Blood PQC343

description: Hybridized to Affymetrix SNP 6.0


title: Blood P19R

description: Hybridized to Affymetrix SNP 6.0


title: Blood P186

description: Hybridized to Affymetrix SNP 6.0


title: Blood P187

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 171


title: NormalDonor3_untreated_PBMC_052


title: NormalDonor3_untreated_PBMC_053


title: shin/calf; stromal pellet; M23

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79482.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

tag: reference

value: Stratagene Human Universal Reference

source_name: shin/calf; stromal pellet; M23, 10 ug labeled aRNA

value: 23 years

tag: organism part

value: shin/calf

tag: sample fraction

value: stromal pellet

value: Male


title: Blood P185

description: Hybridized to Affymetrix SNP 6.0


title: Blood P184

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 169

tag: diagnosis

tag: sky92 status

tag: reagents


title: Newly diagnosed elderly multiple myeloma 168

tag: tissue

tag: cell type


title: Newly diagnosed elderly multiple myeloma 166


title: Blood P182

description: Hybridized to Affymetrix SNP 6.0


title: Blood P183

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor3_untreated_PBMC_050

source_name: Blood

tag: who classification

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor3_untreated_PBMC_051


title: Blood P178

description: Hybridized to Affymetrix SNP 6.0

value: TOF patient

value: blood


title: Blood P180

description: Hybridized to Affymetrix SNP 6.0


title: Newly diagnosed elderly multiple myeloma 167

value: bone marrow

value: CD138 purified myeloma plasma cells