title: 254706910094_b2 - 4_Col0-DEX_1 vs 1_Col0-EtOH_1

description: Discover TT1 donwstream targets

hyb_protocol: 1_Col0-EtOH_1 Cy5 / 4_Col0-DEX_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: H2009 RUVBL2 PCRmutant -dox

status: Public on Dec 18 2019

type: SRA

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Reads were mapped to amplicon sequence using bwa (v.0.7.15)
Extracted mismatched reads and pielup was generated using samtools
Computed the perbase composition from pileup using pileup2base
Calculated per base error rate
Supplementary_files_format_and_content: tab-separated file & perbase composition from mismatched reads

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: H2009 cells lentivirally transduced with doxycycline-inducible PCR mutated RUVBL1 or RUVBL2 cDNAs were grown to confluency

extract_protocol:
Cells harvested via trypsinization and then genomic DNA was isolated using Qiagen Blood & Cell Culture DNA Mini Kit
RUVBL1 or RUVBL2 cDNAs were amplified via nested-PCR with primers containing a unique barcode for each sample. Adapators and sequencing barcodes were added using the KAPA Hyper Prep Kit
DNAsequencing using MiSeq

treatment_protocol: For + dox samples: Cells were treated with doxycycline to induce PCR-mutated RUVBL1 or RUVBL2 alleles, and then a toxic dose (500 nM) of the RUVBL1/RUVBL2 inhibitor Compound B was added. Cells were kept in Compound B + doxycycline for ~1 month until resistant cells emerged. For - dox samples: these are the parental, untreated cells used in the +dox experiments.

tag: cell type

value: non-small cell lung cancer cell line

tag: cell line

tag: genotype

value: RUVBL2 PCRmutant

tag: treatment

value: no dox


title: NCD_wt_1

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: SupplementaryData1_RNA-Seq[HFD--CD].xlsx

library_source: transcriptomic

data_processing:
barcode and adapter removal using flexbar 3.4.0
computational rRNA depletion by filtering reads that map to known rRNAs in mice using Bowtie2 2.2.9
alignment of non-rRNA reads to the mm10 reference genome using STAR 2.6.0c
transcript assembly using cufflinks followed by cuffmerge
differential expression analysis using cuffdiff (Cufflinks suite 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx spreadsheet containing results of the transcript-level differential expression testing comparing two levels. Includes locus, FPKM values, log2FC as well as test statistics. For a complete description see https://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
Following initial quality checks, 1ug of total RNA of each sample was depleted for cytoplasmic and mitochondrial rRNA with Ribo-Zero and strand-specific library preparation was performed using TruSeq RNA Gold Kit from Illumina. All libraries were sequenced in parallel on a HiSeq 2000 for 2 x 100 PE sequencing.

treatment_protocol: Diet-induced obesity (DIO) was achieved by feeding a high-fat diet (HFD, D12492 (I) mod; Sniff) containing 22 kJ% carbohydrates, 24 kJ% protein and 54 kJ% fat from starting at 6-7-weeks-of-age. NCD (D12450B* mod LS; Sniff): containing 62 kJ% carbohydrates, 27 kJ% protein and 11 kJ% fat.

tag: strain

tag: tissue

value: liver

value: wt

tag: diet

value: NCD


title: ChIP_E55Epi_H3K4me3_rep2

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

description: processed data file: E55Epi_H3K4me3.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
STEM-seq datasets were trimmed adaptors by Trim galore and then aligned to the mm9 reference genome though BSSeeker2 with the parameters: --bt2-p 8 --XS 0.2,3 --a CCCCCC --m 4. Multiple mapped and duplicated reads were also removed.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bed files contains reads count for each CpG site. The txt file of RNA-seq contains quantile normalized FPKM for each sample.

source_name: embryo

growth_protocol: Tissues of post-implantation embryos were collected as described previously (Zhang, et al., 2018).

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol.
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

value: epiblast

value: WT

tag: chip antibody

value: H3K4me3(home made)


title: H2009 RUVBL1 PCRmutant +dox rep3

value: RUVBL1 PCRmutant

value: dox


title: CCl4 rep-1

city: Columbus

first: David

last: Brigstock

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description:
CCl4_1
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx

data_processing:
Quality of libraries was determined via Agilent 4200 Tapestation using a High Sensitivity D1000 ScreenTape Assay kit, and quantified by KAPA qPCR (KAPA BioSystems).
Approximately 60-80 million paired-end 150 bp sequence reads were generated for each library on the Illumina HiSeq 4000 platform.
Each sample was aligned to the GRCm38.p3 assembly of the Mus musculus reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.23/) using version 2.6.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635).
Features were identified from the GFF file that came with the assembly from Gencode (Release M19).
Feature coverage counts were calculated using featureCounts (http://bioinf.wehi.edu.au/featureCounts/).
Differentially expressed features were calculated using DESeq2 (http://genomebiology.com/2014/15/12/550).
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: CCl4_vs_Oil_3511_DEGs.xlsx: Excel spreadsheet containing normalized read counts and differential expression data for each comparison.

source_name: liver tissue

extract_protocol:
Tissues were lysed in Trizol and a miRNeasy mini kit was used for RNA extraction with on-column DNase I treatment.
RNA-seq libraries (n = 3 per group) were prepared using the TruSeq Stranded protocol (Illumina, San Diego CA).

treatment_protocol: Cut the liver tissue, save at -80C before RNA extraction.

value: Swiss Webster

tag: Sex

value: Male

value: Liver


title: ChIP_E55Epi_H3K4me3_rep1


title: NCD_db_3

description: SupplementaryData4_RNA-Seq[Dock7M—DBDB].xlsx

value: Leprdb


title: H2009 RUVBL1 PCRmutant +dox rep2


title: ATAC_End_rep2

description: processed data file: End_ATAC.bed.gz

extract_protocol:
The DNA extraction follows miniATAC-seq protocol.
The miniATAC-seq libraries were generated following the protocol as described previously(Wu et al., 2018).

value: endoderm


title: Oil+EV rep-2

description:
Oil_E_2
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx

value: Oil+EV


title: H2009 RUVBL1 PCRmutant +dox rep1

value: non-small cell lung cancer cell line


title: NCD_db_1


title: ATAC_End_rep1

description: processed data file: End_ATAC.bed.gz


title: ATAC_Mes_rep2

description: processed data file: Mes_ATAC.bed.gz

value: mesoderm


title: Oil+EV rep-1

description:
Oil_E_1
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: H2009 RUVBL1 PCRmutant -dox

value: no dox


title: Oil rep-3

description:
Oil_3
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx

value: Oil


title: NCD_misty_3

value: liver

value: Dock7m +/+ Leprdb


title: NCD_misty_2

value: NCD


title: ATAC_PS_rep2

description: processed data file: PS_ATAC.bed.gz

value: primitive streak

value: WT


title: Oil rep-2

description:
Oil_2
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: Oil rep-1

description:
Oil_1
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: ATAC_Mes_rep1

description: processed data file: Mes_ATAC.bed.gz


title: ATAC_PS_rep1

description: processed data file: PS_ATAC.bed.gz


title: Non-treated rep-3

description:
NA_3
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: ATAC_Ect_rep2

description: processed data file: Ect_ATAC.bed.gz

value: ectoderm


title: Non-treated rep-2

description:
NA_2
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: NCD_db_2


title: ATAC_Ect_rep1

description: processed data file: Ect_ATAC.bed.gz


title: Oil+EV rep-3

description:
Oil_E_3
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: Non-treated rep-1

description:
NA_1
processed data file: CCl4_vs_Oil_3511_DEGs.xlsx


title: NCD_misty_1


title: PZH_6

city: Shanghai

first: Jinhang

last: Zhu

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

data_processing:
Trim low quality reads and adapters using Trimmomatic software
Mapping trimmed reads to mouse reference genome using Hisat2 software
Transcript assembly and quantification using Stringtie software
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Table-delimited text files include FPKM value of 29883 protein coding transcripts across 12 samples
Supplementary_files_format_and_content: Table-delimited text files include FPKM value of 1432 lncRNA transcripts across 12 samples

source_name: Tissue

growth_protocol: The mice of control group received intraperitoneal injection of CCl4 solvent twice a week and the double distilled by intragastric administration water once a day, while the mice of PZH group underwent intraperitoneal injection of CCl4 solvent twice a week and the PZH prepared reagent by intragastric administration once a day

extract_protocol:
RNA from each hepatic fibrosis tissue sample was extracted using Trizol reagent (Invitrogen, CA, USA)
The RNA library was constructed into strand-specific sequencing technologies by manufacturer’s recommended protocol of TruseqTM RNA sample prep Kit
RNA-seq based on ribosome RNA minus

treatment_protocol: We construct two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group didn’t treatment.

tag: agent

value: PZH


title: ATAC_E65VE_rep1

description: processed data file: E65VE_ATAC.bed.gz

value: visceral endoderm


title: PZH_5


title: PZH_4


title: ATAC_E65Epi_rep2

description: processed data file: E65Epi_ATAC.bed.gz

value: epiblast


title: Sample 13 BM from patient with  100% spleen size reduction

type: RNA

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

label: biotin

source_name: BM

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: Bone marrow cells were extracted from patients under sterile conditions. Cells were flash frozen.

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

value: Bone Marrow

value: myelofibrosis

tag: overall survival months from rx

tag: vital status

value: ALIVE

tag: race

value: White

value: F

tag: age at rx

tag: overall response

value: Clinical Improvement

tag: wbc

tag: hgb

tag: plt

tag: pb bl

tag: alb

tag: cyto


title: Sample 11 BM from patient with  100% spleen size reduction

tag: genotype

value: M


title: Sample 14 BM from patient with  100% spleen size reduction

tag: tissue

value: DEAD


title: Sample 12 BM from patient with  100% spleen size reduction


title: NRK-52E cells(TGF-β1-treated+ shCtrl),biological rep3

city: Shenyang

first: Xiaoming

last: Yin

state: Liaoning

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description: Gene expression data from NRK-52E cells treated with TGF-β1 and transfected with control lentivirus

hyb_protocol: Following fragmentation, 130 ul of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with R programming language software package.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the protocol of Affymetrix One-Cycle Target Labeling kit and Control Reagents kit(Affymetrix, Santa Clara, CA) from 10 ug total RNA.

growth_protocol: The NRK-52E cells (Baihaobio, Liaoning, China) were cultured in Dulbecco's Modified Eagle's Medium (DMEM/high glucose; ca. no.SH30022.01; Hyclone, UT, USA) supplemented with 10% fetal bovine serum (FBS) (ca. no.SH30071.03; Hyclone, UT, USA) and 3% penicillin-streptomycin solution (ca. no.SV30010; Hyclone, UT, USA). Cell culture was maintained at 37°C in a humidified atmosphere at 5% CO2. Cell medium was changed every 2 days.

treatment_protocol: The NRK-52E cells were transfected with AMPKα2 short hairpin RNA (shRNA) lentivirus (LV) or control LV according to the manufacturer’s protocol (GeneChem, Shanghai, China). For the TGF-β1 treatment, all cells were stimulated with 10 ng/mL recombinant TGF-β1 (Proteintech Group, IL,USA) for 24 h.

tag: cell line

value: normal rat renal tubular epithelial (NRK-52E) cells

value: control


title: PZH_2

tag: strain

value: Liver


title: NRK-52E cells(TGF-β1-treated+shAMPKα2 Knockdown),biological rep3

description: Gene expression data from NRK-52E cells treated with TGF-β1 and transfected with AMPKα2 short hairpin RNA lentivirus

value: AMPKalpha2 knockdown


title: ATAC_E65VE_rep2

description: processed data file: E65VE_ATAC.bed.gz

value: WT


title: NRK-52E cells(TGF-β1-treated+shAMPKα2 Knockdown),biological rep1

source_name: NRK-52E cells treated with TGF-β1 and transfected with AMPKα2 short hairpin RNA lentivirus


title: Sample 10 BM from patient with  100% spleen size reduction

tag: Sex


title: Gastric cancer biopsy. Biological replicate 3

city: Ciudad de Mexico

first: Gonzalo

last: Castillo

state: Ciudad de Mexico

address: Av. Universidad 3000, Circuito Escolar s/n, Col. Universidad Nacional Autónoma de México-Copilco, Del. Coyoacán

department: Microbiologia y Parasitologia

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

hyb_protocol: Fragmented and labeled cDNA was hybridized onto Affymetrix Human Gene 1.0 ST by means of GeneChip Hybridization, Wash and Stain Kit (Affymetrix, USA).

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

data_processing:
Raw data were background-corrected using Robust Multiarray Average (RMA) and normalized using Quantile Normalization.
Differential expression was determined using statistical linear models with arbitrary coefficients, contrasts of interest were analyzed using the bioconductor library limma. Correction for multiple hypotheses was applied using false discovery rate (FDR). Genes were selected based on a Fold-change in base 2 log scale within -0.85 ≥ logFCh ≥ 0.85 and statistical significance according to a B-statistic ≥ 1 (which corresponds to an adjusted p-value ≤ 0.01).

label: Biotin

source_name: Gastric tissue with gastric cancer

label_protocol: Target cDNA was prepared according to the WT Expression Sense Target Kit (Ambion, USA). Purified sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, USA).

growth_protocol: Patients undergoing routine endoscopic evaluation for chronic abdominal complaints were recruited and biopsy samples were taken for histological and molecular analysis. An expert pathologist performed histological examination, according to Sydney classification. After histological examination, samples classified as gastritis and intestinal metaplasia were selected. Within samples corresponding to gastritis, chronic and follicular gastritis were distinguished.

extract_protocol: Total RNA was extracted using RNAqueous Kit (Ambion, USA) according to the manufacturer’s instructions

value: gastric tissue

tag: patient diagnosis

value: gastric cancer

tag: gender

value: female

tag: age


title: NRK-52E cells(TGF-β1-treated+ shCtrl),biological rep1

source_name: NRK-52E cells treated with TGF-β1 and transfected with control lentivirus


title: NRK-52E cells(TGF-β1-treated+ shCtrl),biological rep2


title: NRK-52E cells(TGF-β1-treated+shAMPKα2 Knockdown),biological rep2


title: RNA_E65Epi_Kmt2b_WT_rep3

description: processed data file: RNA.FPKM.txt.gz

extract_protocol:
The RNA extraction follows smart-seq2 protocol.
The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).

value: epiblast


title: PZH_1

tag: agent

value: PZH


title: Gastric cancer biopsy. Biological replicate 2


title: Sample 8 BM from patient with  100% spleen size reduction

value: Bone Marrow

value: myelofibrosis

tag: overall survival months from rx

tag: vital status

tag: race

tag: age at rx


title: ATAC_E65Epi_rep1

description: processed data file: E65Epi_ATAC.bed.gz


title: ATAC_E65Epi_rep3

description: processed data file: E65Epi_ATAC.bed.gz


title: Sample 9 BM from patient with  100% spleen size reduction

value: White

tag: overall response

tag: wbc

tag: hgb

tag: plt


title: PZH_3


title: Gastric cancer biopsy. Biological replicate 1


title: Chronic atrophic gastritis biopsy. Biological replicate 3

source_name: Gastric tissue with chronic atrophic gastritis

value: chronic atrophic gastritis


title: Sample 7 BM from patient with  less than 25% spleen size reduction

tag: genotype

value: Clinical Improvement

tag: pb bl

tag: alb

tag: cyto


title: Sample 6 BM from patient with  less than 25% spleen size reduction

tag: tissue

value: ALIVE

tag: Sex

value: M

value: No Response


title: Control_6

tag: strain


title: Sample 5 BM from patient with  less than 25% spleen size reduction

value: DEAD


title: RNA_E65Epi_Kmt2b_WT_rep1

description: processed data file: RNA.FPKM.txt.gz


title: RNA_E85_Head_Kmt2b_WT_rep1

description: processed data file: RNA.FPKM.txt.gz

growth_protocol: To obtain E8.5 brain tissue, embryos were firstly collected and removed amniotic membrane in PBS buffer, and then directly made a cut near their neck region. The head part was collected as brain tissues.

value: head


title: Control_4

value: Liver


title: Control_3


title: RNA_E85_Head_Kmt2b_KO_rep2

description: processed data file: RNA.FPKM.txt.gz


title: Chronic atrophic gastritis biopsy. Biological replicate 1

tag: patient diagnosis

tag: gender

tag: age


title: RNA_E85_Head_Kmt2b_KO_rep1

description: processed data file: RNA.FPKM.txt.gz


title: RNA_E65Epi_Kmt2b_KO_rep3

description: processed data file: RNA.FPKM.txt.gz


title: Control_1

tag: agent


title: RNA_E65Epi_Kmt2b_WT_rep2

description: processed data file: RNA.FPKM.txt.gz

value: WT


title: Follicular gastritis biopsy. Biological replicate 7

source_name: Gastric tissue with follicular gastritis

value: gastric tissue

value: follicular gastritis


title: RNA_E65Epi_Kmt2b_KO_rep2

description: processed data file: RNA.FPKM.txt.gz


title: lncIRS2_HFD_4

data_processing:
barcode and adapter removal using flexbar 3.4.0
computational rRNA depletion by filtering reads that map to known rRNAs in mice using Bowtie2 2.2.9
alignment of non-rRNA reads to the mm10 reference genome using STAR 2.6.0c
transcript assembly using cufflinks followed by cuffmerge
differential expression analysis using cuffdiff (Cufflinks suite 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx spreadsheet containing containing results of the transcript-level differential expression testing comparing two levels. Includes locus, FPKM values, log2FC as well as test statistics. For a complete description see https://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
Following initial quality checks, 1ug of total RNA of each sample was depleted for cytoplasmic and mitochondrial rRNA with Ribo-Zero Gold and strand-specific library preparation was performed using TruSeq RNA Gold Kit from Illumina. All libraries were sequenced in parallel on a HiSeq 4000 for 2 x 76 PE sequencing.

treatment_protocol: Diet-induced obesity (DIO) was achieved by feeding a high-fat diet (HFD, D12492 (I) mod; Sniff) containing 22 kJ% carbohydrates, 24 kJ% protein and 54 kJ% fat from starting at 6-7-weeks-of-age. NCD (D12450B* mod LS; Sniff): containing 62 kJ% carbohydrates, 27 kJ% protein and 11 kJ% fat. Mice were injected for 12 weeks with control (Scr), Mafg or LncIRS2 LNA.

value: liver

value: wt

tag: lna

value: lncIRS2 LNA

tag: diet

value: HFD


title: RNA_E65Epi_Kmt2b_KO_rep1

description: processed data file: RNA.FPKM.txt.gz

value: epiblast


title: Control_5


title: Chronic atrophic gastritis biopsy. Biological replicate 2

value: female


title: Sample 4 BM from patient with  less than 25% spleen size reduction

value: Bone Marrow

value: myelofibrosis

tag: overall survival months from rx

tag: vital status

tag: race

value: White

value: F

tag: age at rx

tag: overall response


title: DNp73_FLAG

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street Hansen Life Sciences Bldg, HANS, 225

department: Biochemistry and Computer Science

institute: Purdue University

data_processing:
The expression values obtained by RSEM v1.2.21 using the following parameters (rsem-calculate-expression --forward-prob 0 --no-bam-output --bowtie-n 1 --bowtie-m 100 --seed-length 28). Rsem index was created based on mm10.
Differentially expressed genes between any two conditions were obtained using edgeR. The raw read counts were obtained from the "expected counts" column in rsem results. The criteria for selecting differentially expressed genes are Fold Change >2, FDR<0.05, and RPKM>2 in at least one of the two compared conditions.
Peak calling for ChIP-seq data was done using macs14 using the default parameters
The TDF files for IGV browser are created using “igvtools count -z 5 -w 5 -e 100 --minMapQuality 30”
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements(text file)
Supplementary_files_format_and_content: MACS peaks peak-calling(text file)
Supplementary_files_format_and_content: tile data file format for IGV browser

source_name: Spleen

growth_protocol: Naïve CD4+ T cells were purified from spleens of 7-8 week old mice using a CD4+CD62L+ T cell Isolation Kit II (Miltenyi).  Mouse naïve CD4+ T cells were cultured at 106/ml in RPMI 1640 medium containing 10 mM Hepes, 10% fetal bovine serum, 2 mM L-glutamine, and antibiotics, including 50 µM 2-ME, and polarized under Th1 conditions with plate-bound anti-CD3 (2 µg/ml), soluble anti-CD28 (1 µg/ml, PharMingen), 10 ng/ml mouse IL-12 (PeproTech), and 10 µg/ml of anti-mIL-4 antibody

extract_protocol:
Total RNA was extracted from cells by trizol. ChIP-Seq from 10million Th1 cells overexpressing Trp73 or vector control cells were performed using anti-FLAG (M2) antibody (Sigma) as previously described.
RNA-Seq libraries from 2 μg total of mRNA and ChIP-seq library were prepared using the KAPA kit per the manufacturer’s protocol.
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: Trp73 overexpressed Th1 cells were isolated by FACS sorting as GFP+ cells three days after retroviral transduction.

tag: genotype/variation

tag: cell type

value: In vitro culture Th1

tag: antibody

value: anti-FLAG (M2) antibody (Sigma)


title: lncIRS2_HFD_2

tag: tissue

tag: genotype


title: Follicular gastritis biopsy. Biological replicate 6


title: lncIRS2_HFD_1

tag: strain


title: TAp73 Over-expression

value: TAp73 Over-expression


title: DNp73 Over-expression

value: DNp73 Over-expression


title: MafG_HFD_4

description: SupplementaryData7_RNA-Seq[MAFG_LNA_HFD--SCR_LNA_HFD].xlsx

value: MafG LNA


title: Follicular gastritis biopsy. Biological replicate 3

value: gastric tissue

tag: patient diagnosis

value: male


title: Follicular gastritis biopsy. Biological replicate 1

value: follicular gastritis

tag: gender


title: Vector

value: Vector


title: MafG_HFD_3

value: liver

value: wt


title: Sample 1 BM from patient with  less than 25% spleen size reduction

value: DEAD

tag: Sex

value: M

value: No Response

tag: wbc

tag: hgb

tag: plt

tag: pb bl

tag: alb

tag: cyto


title: lncIRS2_HFD_3

tag: lna

value: lncIRS2 LNA

tag: diet

value: HFD


title: Follicular gastritis biopsy. Biological replicate 2

value: female

tag: age


title: Sample 2 BM from patient with  less than 25% spleen size reduction

value: Bone Marrow

value: myelofibrosis

tag: overall survival months from rx

tag: vital status

tag: race

value: White

tag: age at rx

tag: overall response

value: Clinical Improvement


title: wt_dss_lif_LPLs

city: Suzhou

first: Yanan

middle: S

last: Zhang

state: Jiangsu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lamina propria lymphocytes, day 10

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug 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.

extract_protocol: RNA were prepared with TRIzol reagent. Breifly, add 1ml of TRIzol per 1*10^6 cells, which were solubilized for 5 min at room temperature (RT). Then, add 0.2ml of coloroform per ml of TRIzol, mix vigorously for 15 sec, and stand the mixture for 2-3 min at RT, following by a centrifuge at 13,000rpm for 15 min at 4℃. Transfer the upper clear phase to a panel of fresh tubes. Add 0.5ml of isopropanol per each milliliter of the clear phase, mix vigorously, and stand the mixture for 10 min, following by a centrifuge at 13,000rpm for 10 min at 4℃. Decant the supernatant. Resuspend the pellet immediately with 1ml of 75% ethanol, following by a centrifuge at 13,000rpm for 5 min at 4℃. Decant the supernatant, and remove any remaining liquid. Resolve the RNA with RNase-free water, and store it at -80℃.

treatment_protocol: Freshly isolated LPLs from mice on day 10 after exposure to mock water, dextran sulfate sodium (DSS) solution, or DSS solution and LIF-treatment were were collected and stored in TRIzol reagent at -80℃ fridge.

tag: cell type

value: lamina propria lymphocytes (LPLs)

tag: strain

tag: genotype

value: wild type

tag: treatment

value: DSS and LIF


title: Vector_FLAG

tag: genotype/variation

value: In vitro culture Th1

tag: antibody

value: anti-FLAG (M2) antibody (Sigma)


title: Follicular gastritis biopsy. Biological replicate 4

tag: tissue

value: gastric tissue

tag: patient diagnosis

value: follicular gastritis

tag: gender

value: male


title: Sample 3 BM from patient with  less than 25% spleen size reduction

value: DEAD

value: Black

tag: Sex

value: M

tag: wbc

tag: hgb

tag: plt

tag: pb bl

tag: alb

tag: cyto


title: Control_2

value: Liver

tag: agent


title: MafG_HFD_2

value: liver

value: wt

tag: lna

value: MafG LNA

tag: diet

value: HFD


title: Follicular gastritis biopsy. Biological replicate 5

value: female

tag: age


title: CIC KD_RNASeq (T47D)

city: Pohang

first: Jeehyun

last: Yoe

state: Gyungbuk

address: 77 Cheongam-Ro. Nam-Gu

department: Life Science

country: South Korea

institute: POSTECH

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
Artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed to reduce biases.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads, to provide information of known transcripts, novel transcripts, and alternative splicing transcripts.
Expression profiles are represented as read count and normalization value, based on the transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
In case of known gene annotation, functional annotation and gene-set enrichment analysis are performed using GO and KEGG database on differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: The total number of bases, reads, GC (%), Q20 (%), Q30 (%) are calculated for control and test samples and presented in throughput.stats file.
Supplementary_files_format_and_content: Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data and presented in throughput.stats file.
Supplementary_files_format_and_content: Known transcript expression level per sample in expression value assembled with StringTie based on reference genome model, UCSC hg38, and presented in GRCh38.transcript.txt file
Supplementary_files_format_and_content: Known gene expression level per sample in expression value assembled with StringTie based on reference genome model, UCSC hg38, and presented in GRCh38.gene.txt file
Supplementary_files_format_and_content: Expression level for each sample for each known transcript, novel transcript and novel alternative splicing transcript, and presented in Novel.GRch38.transcript.txt file.
Supplementary_files_format_and_content: Expression level for each sample for gene containing known transcripts and novel alternative splicing transcript or novel gene, and presented in Novel.GRCh38.gene.txt file.
Supplementary_files_format_and_content: List of novel transcripts filtered by transcripts with class code ‘u’ from the results of known and novel transcripts, and presented in Novel_transcript_list.txt file.
Supplementary_files_format_and_content: List of novel alternative splicing transcripts filtered by class code ('j', 'c', 'k', 'e', 'i', 'o', 'p', 's', 'x') from the results of known and novel transcripts, and presented in Novel_splicing_variant_list.txt file.
Supplementary_files_format_and_content: For 4 samples, if more than one FPKM value was 0, it was not included in the analysis. Therefore, from total of 46,732 genes, 26,268 were excluded and only 20,464 genes were used for statistical analysis. This is shown in box plots diagram.
Supplementary_files_format_and_content: Sample's expression distribution based on percentile (median, 50 percentile, 75 percentile, maximum and minimum) based on raw signal (FPKM), Log2 transformation of FPKM+1 and Quantile Normalization shown in boxplots diagram.
Supplementary_files_format_and_content: Sample's expression distribution before and after of raw signal (FPKM), Log2 transformation of FPKM+1 and Quantile Normalization shown as density plots diagram.
Supplementary_files_format_and_content: The similarity between samples are obtained through Pearson’s coefficient of the normalized value. For range: -1≤ r ≤ 1,the closer the value is to 1, the more similar the samples are. This is presented in diagram showing correlation matrix of all samples.
Supplementary_files_format_and_content: List of differentially expressed genes (DEGs) between control and CIC knockdown secondary mammospheres, after filtering, log2 transformation of FPKM+1, and quantile normalization. This is presented in data2.xlsx file.

source_name: CIC knockdown secondary mammospheres derived from T47D breast cancer cells

growth_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence. Secondary mammospheres were generated using control and CIC knockdown T47D breast cancer cells, seeded at a density of 1.0 × 10^4 per well in a 24-well ultralow attachment plate (Corning Inc., Corning, NY, USA) with MammoCult Basal Medium (STEMCELL Technologies, Vancouver, BC, Canada) containing 10% MammoCult Proliferation Supplements (STEMCELL Technologies, Durham, NC, USA) and grown for 7 days as primary mammospheres, and then subsequently passaged and grown for additional 7 days as secondary mammospheres.

extract_protocol:
Secondary mammospheres were collected and total RNA was extracted using TRIzol Reagent (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
DNA library for mRNA sequencing was prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) according to the manufacturer’s protocols. Libraries were sequenced on the NovaSeq sequencer accompanying the NovaSeq 6000 S4 Reagent Kit following the manufacturer’s protocols.

tag: cell type

value: breast cancer secondary mammospheres

tag: cell line

value: CIC knockdown


title: ko_dss_lif_LPLs

value: lamina propria lymphocytes (LPLs)

tag: strain

tag: genotype

tag: treatment

value: DSS and LIF


title: ko_dss_LPLs

value: DSS


title: wt_dss_LPLs

value: wild type


title: MafG_HFD_1

tag: tissue


title: Control_RNASeq (T47D)

source_name: Control secondary mammospheres derived from T47D breast cancer cells

tag: genotype/variation

value: control


title: CTRL_HFD_2

description:
SupplementaryData7_RNA-Seq[MAFG_LNA_HFD--SCR_LNA_HFD].xlsx
SupplementaryData8_RNA-Seq[SCR_LNA_CD--SCR_LNA_HFD].xlsx

value: CTRL NEG A


title: lncIRS2_NCD_4

description: SupplementaryData9_RNA-Seq[SCR_LNA_CD--LNCIRS2_LNA_CD].xlsx

value: lncIRS2 LNA

value: NCD


title: CTRL_HFD_1


title: lncIRS2_NCD_2


title: CTRL_HFD_4


title: lncIRS2_NCD_3


title: H2009_siNT_rep2

description: H2009 transfected with siNTC siRNA for 2.5 days

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
Reads were aligned to hg19 geneome assembly and transcript assembly was performed using tophat (v.2.0.12)
FPKM calculation and differential expression analysis was performed using cufflinks (v.2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample … Genes that have FPKM of >=1 in any sample in a given treatment were listed.

growth_protocol: For siRNA experiments, 100,000 cells were reverse transfected with indicated siRNA in 3 wells of a 6-well plate, and after 2.5 or 3 days (noted in description) RNA was harvested by direct lysis on plate using buffer RLT plus. For Compound B, Compound C and untreated samples, 1 million cells were plated in a 10cm dish then treated for 24 hours with indicated treatment, or left untreated. RNA was harvested directly from the plate using buffer RLT plus

extract_protocol:
Total RNA was extracted and genomic DNA discarded using Qiagen RNAeasy plus kit
4ug of RNA, using Illumina's TruSeq Stranded mRNA library prep kit and following manufacterers protocol
Illumina's TruSeq Stranded mRNA library prep kit

treatment_protocol: 2.5 or 3 days of siRNA treatment, or 24 hours of 100 nM Compound B or Compound C

value: non-small cell lung cancer

tag: histology

value: Adenocarcinoma

tag: passage

value: unknown - Immortal

value: WT


title: lncIRS2_NCD_1

value: liver

value: wt


title: CTRL_HFD_3

value: HFD


title: Caco2brafv600e_3

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina HumanMethylation450 BeadChip using standard Illumina protocol.

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

data_processing: Data was normalized using the DASEN method in R.

label: Cy5 and Cy3

source_name: Colorectal adenocarcinoma cell line Caco2, BRAFV600E

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.

treatment_protocol: Caco2 cells stably expressing oncogenic BRAF (BRAFV600E) or GFP. Genomic DNA was extracted after 14 days of virus infection.

value: colorectal adenocarcinoma cell line

tag: transduction

tag: replicate


title: H2009_siNT_rep1

source_name: H2009 transfected with siNTC siRNA for 2.5 days


title: MafG_NCD_4

value: MafG LNA


title: H2009_siBL1_rep2

description: H2009 transfected with siRUVBL1 siRNA for 2.5 days


title: MafG_NCD_3


title: Caco2gfp_1

source_name: Colorectal adenocarcinoma cell line Caco2, GFP

value: GFP


title: Caco2gfp_3


title: Caco2brafv600e_1


title: RT2.Cdkn2a-/--in vivo #2

city: Tübingen

first: Ellen

last: Brenner

state: Baden-Württemberg

address: Liebermeisterstraße 25

department: Dermatology

country: Germany

institute: Eberhard Karls University Tuebingen

description:
Replicate of in vivo Cdkn2a loss cell line 1
ICB resistant cell line developed from precursor #1

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: female beta-cancer cells

label_protocol: 1 µg of total DNA were denaturated at 98°C  for 3 min, then labelled with 19 µl of the Labeling Master Mix  according to Agilents CGH_Enzymatic_Protocol_7.2

growth_protocol: beta cancer cells were cultivated ) in DMEM supplemented with 10% foetal calf serum (FCS), nonessential amino acids, sodium pyruvate, antibiotics, and 50 µM 2-mercaptoethanol at 37°C and 7.5% CO2

extract_protocol: Total DNA extracted using Qiagen AllPrep DNA/RNA Mini Kit following manufacturer's instructions

value: beta cancer cell

value: Cdkn2a deficient

value: 12 weeks

value: RIP-Tag2 (RT2)

source_name: male spleen cells (reference)

value: > 12 week < 20 week

value: spleen


title: MafG_NCD_2

source_name: liver

value: NCD


title: H-Z-24-R2

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 24 hours, replicate 2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to turbot custom Oligo Microarrays (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extended dynamic range implemented in the Agilent software was applied to avoid saturation in the highest intensity range. The Agilent feature extraction was used as raw data for further preprocessing. The processed signal (gProcessed-Signal) value was chosen for the statistical analysis.

organism: Ruditapes philippinarum

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 24 hours, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA  of each strain and time using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, 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: Clams were collected from a P. olseni infection-free natural bed in Camariñas (Galicia, NW Spain) as confirmed by PCR (Casas et al., 2002a) and incubation of gill pieces in Ray’s fluid thioglycollate medium. These clams were kept at 14-17 oC in filtered (1 µm) seawater (35 ‰) with aeration for 1 week to adapt to indoor conditions. The details for collection of hemocytes have been described in Hasanuzzaman et al. (2017).

extract_protocol: Hemocyte samples for RNA extraction were collected at 1, 8 and 24 h after the start of the challenge. Total RNA was extracted using the Qiagen RNeasy mini kit with DNase following manufacturer’s instructions.

treatment_protocol: R. philippinarum hemocytes (5x106) were challenged in vitro with P. olseni trophozoites (5x106), zoospores (5x106) and extracellular products (2.5 mL of culture media enriched with extracellular products) separately in IWAKI 6-well plates. For the challenges, trophozoites and zoospores, obtained just before the challenge, were separately suspended in 2.5 mL filtered seawater (FSW) and added into a permeable insert (0.2 μm Anopore® membrane NUNC 25 mm) in each well. For hemocyte-extracellular products challenge, 2.5 mL of culture media enriched with hemocyte extracellular products were added into the inserts of the respective wells. The inserts allowed the flow of media but not the cells; hence, hemocytes and parasite cells were never in contact.

value: haemocyte cells


title: RT2-precursor #2

description:
Precursor 2
Primary RT2-cancer cell line precursor #2

value: control


title: RT2.Cdkn2a-/--in vivo #3


title: H2009_siBL1_rep1

source_name: H2009 transfected with siRUVBL1 siRNA for 2.5 days

value: non-small cell lung cancer

value: Adenocarcinoma

value: unknown - Immortal


title: RT2.Cdkn2a-/--in vitro #2

description:
Replicate of in vitro Cdkn2a loss cell line 1
CIS resistant cell line developed from precursor #1


title: RT2.Cdkn2a-/--in vitro #1

description:
in vitro Cdkn2a loss cell line 1
CIS resistant cell line developed from precursor #1


title: RT2.CRISPR-Cdkn2a

description:
CRISPR-Cas9 Cdkn2a transfected cell line from precursor #2
CRISPR-Cas9 Cdkn2a transfected cell line from precursor #2


title: RT2.Cdkn2a-/--in vivo #1

description:
in vivo Cdkn2a loss cell line 1
ICB resistant cell line developed from precursor #1


title: MafG_NCD_1

value: liver

value: wt


title: Caco2

source_name: Colorectal adenocarcinoma cell line Caco2

value: colorectal adenocarcinoma cell line

tag: braf mutation status

value: BRAF wild type


title: RT2.CRISPR-Ctr

description:
CRISPR-Cas9 contol transfected cell line from precursor #2
CRISPR-Cas9 contol transfected cell line from precursor #2


title: RT2.Cdkn2a-/--in vivo #4


title: H-Z-8-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 8 hours, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 8 hours, replicate 2


title: PP rep3

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

data_processing:
The clean data were obtained by removing reads containing adapters, reads containing over 10 % of poly(N), and low-quality reads (>50 % of the bases had Phred quality scores ≤ 10) from the raw data.
All the downstream analyses were based on the high quality clean data. Pig reference genome and gene annotation files were downloaded from NCBI database (Sscrofa11.1, NCBI). Paired-end clean reads were aligned to the reference genome using Tophat package, the parameters were set as default.
Next, we filtered the assembled novel transcripts from the different libraries to obtain putative lncRNAs following the steps in the pipeline as follows. First, we excluded transcripts that shorter than 200 nt in length, containing less than 2 exons, and containing less than three reads. Next, the coding potential of the remaining transcripts was calculated using the Coding Potential Calculator (CPC) and Coding-Non-Coding Index (CNCI). A transcript with a CPC value lower than -1 and a CNCI value lower than 0 was taken to be an lncRNA.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: identified lncRNAs and reads count  for each Sample. The file lncRNA.fa includes the transcript sequences for all lncRNA MSTRG* IDs.

organism: Sus scrofa

source_name: longissimus dorsi muscle

growth_protocol: Qinyu pigs were feeded at growth curve inflection point (maximum matabolism rate) (178 days old)  and plateau phase (395 days old)

extract_protocol:
Total RNAs are extracted by Trizol (Invitrogen).Only the RNA samples that had RNA Integrity Number (RIN) scores > 8 were used for further sequencing. .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Qinyu Pig

value: muscle

value: 178 days old


title: H-Z-24-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 24 hours, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 24 hours, replicate 1


title: PP rep2


title: H2009_untreat_rep2

description: H2009 with no treatment

source_name: H2009 with no treatment

value: WT


title: H2009_untreat_rep1

description: H2009 with no treatment


title: PP rep1


title: CTRL_NCD_4

description:
SupplementaryData8_RNA-Seq[SCR_LNA_CD--SCR_LNA_HFD].xlsx
SupplementaryData9_RNA-Seq[SCR_LNA_CD--LNCIRS2_LNA_CD].xlsx

value: CTRL NEG A


title: RT2-precursor #1

description:
Precursor 1
Primary RT2-cancer cell line precursor #1

value: beta cancer cell

value: 12 weeks

value: RIP-Tag2 (RT2)

value: > 12 week < 20 week


title: Co115

source_name: Colorectal adenocarcinoma cell line Co115


title: CTRL_NCD_3

value: NCD


title: H-Z-8-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 8 hours, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 8 hours, replicate 1

value: haemocyte cells


title: Sw620

source_name: Colorectal adenocarcinoma cell line Sw620


title: H-Z-1-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 1 hour, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 1 hour, replicate 3


title: CTRL_NCD_2


title: CTRL_NCD_1


title: H2009_compC_rep1

description: H2009 treated with 100 nM Compound C for 1 day

value: non-small cell lung cancer

value: Adenocarcinoma


title: IP rep2


title: IP rep3


title: H-Z-1-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 1 hour, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 1 hour, replicate 2


title: H2009_compB_rep2

description: H2009 treated with 100 nM Compound B for 1 day

value: unknown - Immortal


title: MafG20

description: SupplementaryData6_RNA-Seq[Ad-MAFG--Ad-CMV].xlsx

value: liver

value: wt

tag: virus

value: Ad-MAFG


title: H2009_compC_rep2

source_name: H2009 treated with 100 nM Compound C for 1 day


title: IP rep1

value: Qinyu Pig


title: H2009_compB_rep1

source_name: H2009 treated with 100 nM Compound B for 1 day


title: H596_untreat_rep2

description: H596 with no treatment

source_name: H596 with no treatment


title: H-Z-1-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 1 hour, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, 1 hour, replicate 1


title: Mi-II

city: Santiago

first: macarena

middle: del pilar

last: Barra Jimenez

address: 1600 Tobalaba

country: Chile

institute: AAFC

data_processing:
The libraries were sequenced on a HiSeq 2500 instrument (Illumina, USA, San Diego, California) in Paired-end mode (2x125bp). Software : Illumina package bcl2fastq v1.8.4
Sequencing data was aligned to the reference genome of S. tuberosum v3_2.1.10 using the TopHat v. 2.0.9 with the "fr-unstranded" library mode.
The quality of the alignments was verified using the 'flagstat' tool of the SAMtools v software. 0.1.19.
Transcripts were then assembled with CuffLinks v. 2.1.1 [33], using the ITAG1.0 annotation system of S. tuberosum from Sol Genomics Network [34,35]. The assembly of the transcriptome was performed with the "multi read correct" and "bias correct" modes activated.
The assembled transcripts of different replicates and treatments were combined into a single reference transcriptome for each variety using the CuffMerge tool included in CuffLinks. Raw and processed transcriptome sequence data was deposited at the National Centre for Biotechnology Information Gene Expression Omnibus (NCBI GEO). Differentially expressed genes between control and water stressed were identified for each cultivar using CuffDiff and fragment per kilobase per million mapped reads (FPKM) was calculated
Genome_build: S. tuberosum v3_2.1.10
Supplementary_files_format_and_content: differential expression

organism: Solanum tuberosum

source_name: MIJE  LEAF DROUGHT 2-1

extract_protocol:
The libraries were prepared with the TruSeq RNA kit (Illumina, USA, San Diego, California.). The mRNA was purified from 1 μg of total RNA using oligo-dT beads, and then fragmented using divalent cations and at 95 °C. Reverse transcription was performed to obtain cDNA fragments of approximately 200 bp. After repair, adenylation and ligation of indexed adapters, the libraries were completed and amplified by PCR. The libraries were sequenced on a HiSeq 2500 instrument (Illumina, USA, San Diego, California) in Paired-end mode (2x125bp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf cell

tag: cultivar

value: MIJE

value: DROUGHT

tag: leaf type

value: third leaf unfolded


title: Mi-III

source_name: MIJE  LEAF DROUGHT 3-1


title: H-Z-POOL-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with zoospores from P. olseni, 1 hour, control

source_name: Ruditapes philippinarum hemocytes cells-zoospores in vitro challenge, control pool


title: MafG12

source_name: liver

tag: diet


title: H-T-24-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 24 hours, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 24 hours, replicate 3


title: H596_untreat_rep1

description: H596 with no treatment

value: WT


title: Mi-I

source_name: MIJE  LEAF DROUGHT 1-1


title: CMV19

value: Ad-CMV


title: CL-III

source_name: CLON 37FB  LEAF DROUGHT 3-1

value: CLON


title: H-T-24-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 24 hours, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 24 hours, replicate 2


title: H-T-24-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 24 hours, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 24 hours, replicate 1


title: H596_compC_rep1

description: H596 treated with 100 nM Compound C for 1 day


title: MafG4


title: H-T-24-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 24 hours, control

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 24 hours, control


title: CL-II

source_name: CLON 37FB  LEAF DROUGHT 2-1


title: H596_compB_rep2

description: H596 treated with 100 nM Compound B for 1 day


title: CL-I

source_name: CLON 37FB  LEAF DROUGHT 1-1


title: CMV3


title: RF_4

treatment_protocol: Animals were allowed Ad libitum access to control diet (CD, D12450B* mod LS; Sniff) containing 62 kJ% carbohydrates, 27 kJ% protein and 11 kJ% fat and drinking water. Fasting group was deprived of food for 16 h. Refeeding group was subsequently allowed Ad libitum food access for 6 h.

tag: feeding regime

value: 6 hours refeeding


title: DE-III

source_name: DESIEE  LEAF DROUGHT 3-1

value: DESIEE


title: H596_compB_rep1

source_name: H596 treated with 100 nM Compound B for 1 day


title: H-T-8-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 8 hours, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 8 hours, replicate 3

tag: cell type

value: haemocyte cells


title: H596_compC_rep2

source_name: H596 treated with 100 nM Compound C for 1 day

tag: cell line

value: non-small cell lung cancer


title: RF_3

tag: strain

value: NCD


title: H596_siNT_rep2

description: H596 transfected with siNTC siRNA for 3 days

value: Adenocarcinoma

value: unknown - Immortal

tag: genotype


title: DE-II

source_name: DESIEE  LEAF DROUGHT 2-1

tag: treatment


title: RF_2

tag: tissue

value: liver

value: wt


title: Colo320brafv600e_2

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina HumanMethylation850 BeadChip using standard Illumina protocol.

data_processing: Data was normalized using preprocessQuantile method using Bioconductor package minfi.

source_name: Colorectal adenocarcinoma cell line Colo320, BRAFV600E

treatment_protocol: Colo320 cells stably expressing oncogenic BRAF (BRAFV600E) or GFP. Genomic DNA was extracted after 14 days of virus infection.

value: colorectal adenocarcinoma cell line

tag: gender

value: female


title: RF_1


title: H596_siNT_rep1

source_name: H596 transfected with siNTC siRNA for 3 days

tag: histology


title: DE-I

source_name: DESIEE  LEAF DROUGHT 1-1

value: leaf cell


title: CA-III

source_name: CARDINAL LEAF DROUGHT 3-1

value: CARDINAL

value: DROUGHT


title: FA_4

description:
SupplementaryData2_RNA-Seq[AL--FA].xlsx
SupplementaryData3_RNA-Seq[FA--RF].xlsx

source_name: liver

value: 16 hours fasted


title: H-T-8-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 8 hours, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 8 hours, replicate 1


title: H-T-8-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 8 hours, control

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 8 hours, control


title: H596_siBL1_rep2

description: H596 transfected with siRUVBL1 siRNA for 3 days

tag: passage

value: WT


title: Colo320brafv600e_1

tag: transduction


title: FA_3


title: H596_siBL1_rep1

source_name: H596 transfected with siRUVBL1 siRNA for 3 days


title: CA-II

source_name: CARDINAL LEAF DROUGHT 2-1

value: third leaf unfolded


title: H-T-1-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 1 hour, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 1 hour, replicate 3


title: H-T-8-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 8 hours, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 8 hours, replicate 2


title: H-T-1-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 1 hour, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 1 hour, replicate 2


title: Colo320gfp_2

source_name: Colorectal adenocarcinoma cell line Colo320, GFP

value: GFP

tag: replicate


title: HCASMC TCF21 ChIPseq_reanalyzed

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description:
IP DNA
TCF21_peaks.bed
TCF21_pooled.bw
GSM1503214

data_processing:
ChIP was performed with approximately 4e6 HCAMSC cells using SRF antibody (sc-335). Two biological replicates GAII for 36bp paired-end sequencing. Quality control of ChIPseq data was performed using Fastqc, and then low-quality bases and adaptor contamination were trimmed by cutadapt. Filtered reads were mapped to hg19 using BWA mem algorithm. Duplicate reads were marked by Picard Markduplicate module and removed with unmapped reads by samtools view -f 2 -F 1804. macs2 callpeak was used for peaks calling with --broad parameters and input as control. The fastq files of TCF21 (SRR1573744&SRR1573745), H3K27ac ChIPseq (GSE72696) and ATACseq (GSE72696) were extracted from GEO database by fastq-dump. These samples have been included here so that the entire study can be downloaded from a single SRP.
Genome_build: hg19
Supplementary_files_format_and_content: bed with called peaks and bw

source_name: Cultured coronary artery smooth muscle cells

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from Lonza (Lonza 0000317155) at passage 2 and were cultured in smooth muscle cell basal media along with hEGF, insulin, hFGF-B and fetal bovine serum (FBS) (Lonza # CC-3182) according to the manufacturer’s instructions. HCASMCs between passages 5-8 were used for all the experiments.

extract_protocol:
Briefly, approximately 4e6 HCASMC cells were fixed with 1 % formaldehyde and quenched by glycine. The cells were washed three times with PBS and then harvested in ChIP lysis buffer (50 mM Tris-HCl, pH 8, 5 mM EDTA, 0.5 % SDS). Crosslinked chromatin was sheared for 3x1 min by sonication (Branson SFX250 Sonifier) before extensive centrifugation. Four volumes of ChIP dilution buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100) was added to the supernatant. The resulting lysate was then incubated with Dynabeads™ Protein G (Thermo Scientific, 10009D) and antibodies at 4°C overnight. Beads were washed once with buffer 1 (20 mM Tris pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton X100, 0.1% SDS), once with buffer 2 (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 1% Triton X100, 0.1% SDS), once with buffer 3 (10 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate monohydrate) and twice with TE buffer. DNA was eluted by ChIP elution buffer (0.1 M NaHCO3, 1 % SDS, 20 μg/ml proteinase K). The elution was incubated at 65 °C over-night and DNA was extracted with DNA purification kit (Zymo D4013). The purified DNA was assayed by quantitative PCR with ABI ViiA 7 and Power SYBR Green Master Mix (ABI 4368706).
Two biological replicates DNA was combined for library preparation. Libraries were prepared with KAPA Hyper Prep kit (KK8502).

value: Cultured HCASMC

tag: growth medium

value: Grown in serum

tag: chip antibody

value: TCF21 (Sigma HPA013189)


title: CA-I

source_name: CARDINAL LEAF DROUGHT 1-1

tag: cultivar


title: H-T-1-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 1 hour, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 1 hour, replicate 1

value: haemocyte cells


title: FA_2

value: NCD


title: Mi-3

source_name: MIJE  LEAF IRRIGATION 3-1

value: MIJE

value: IRRIGATION

tag: leaf type


title: FA_1

value: liver

value: wt

tag: diet


title: HCASMC SRF ChIPseq [TQ40]

description:
IP DNA
SRF_137_peaks.bed
SRF.bw

value: anti-SRF (Santa Cruz sc-335)


title: HCASMC SRF ChIPseq [TQ37]

description:
IP DNA
SRF_137_peaks.bed
SRF.bw


title: AL_4

tag: feeding regime

value: ad libitum


title: Mi-2

source_name: MIJE  LEAF IRRIGATION 2-1

value: leaf cell


title: Mi-1

source_name: MIJE  LEAF IRRIGATION 1-1


title: HCASMC INPUT DNA

description: Input DNA

value: none (input)


title: AL_3


title: H-T-1-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with trophozoites from P. olseni, 1 hour, control

source_name: Ruditapes philippinarum hemocytes cells-trophozoites in vitro challenge, 1 hour, control

tag: cell type


title: H-ECP-24-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 24 hours, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 24 hours, replicate 3


title: CL-3

source_name: CLON 37FB  LEAF IRRIGATION 3-1

value: CLON


title: H-ECP-24-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 24 hours, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 24 hours, replicate 2


title: AL_2

source_name: liver


title: H-ECP-24-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 24 hours, control

source_name: Ruditapes philippinarum hemocytes cells-extracellular products  in vitro challenge, 24 hours, control


title: CL-2

source_name: CLON 37FB  LEAF IRRIGATION 2-1


title: CL-1

source_name: CLON 37FB  LEAF IRRIGATION 1-1


title: H-ECP-8-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 8 hours, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 8 hours, replicate 3


title: H-ECP-8-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 8 hours, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 8 hours, replicate 2


title: DE-3

source_name: DESIEE  LEAF IRRIGATION 3-1

value: DESIEE


title: DE-2

source_name: DESIEE  LEAF IRRIGATION 2-1

value: third leaf unfolded


title: DE-1

source_name: DESIEE  LEAF IRRIGATION 1-1


title: CA-3

source_name: CARDINAL LEAF IRRIGATION 3-1

value: CARDINAL


title: H-ECP-24-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 24 hours, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 24 hours, replicate 1


title: AL_1


title: H-ECP-8-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 8 hours, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 8 hours, replicate 1


title: H-ECP-8-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 8 hours, control

source_name: Ruditapes philippinarum hemocytes cells-extracellular products  in vitro challenge, 8 hours, control


title: H-ECP-1-R3

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 1 hour, replicate 3

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 1 hour, replicate 3


title: H-ECP-1-R2

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 1 hour, replicate 2

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 1 hour, replicate 2


title: Trp1 CD4+ TILs, Th-ctx condition sample 3

city: London

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

hyb_protocol: Following fragmentation,  cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array as per the standard affymetrix protocol. GeneChips were washed and stained as per the standard affymetrix protocol.

scan_protocol: GeneChips were scanned following standard Affymetric protocol

data_processing: Raw expression values were normalized using the robust multi-array average (RMA) procedure

source_name: CD4+ Trp1 from Th-ctx treated B16 tumour

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

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

treatment_protocol: B16-bearing mice were treated with 0.6 × 10^5 naïve CD4+ Foxp3GFP Trp1 cells, GVAX and aCTLA-4 (Th condition) or  0.6 × 10^5 naïve Foxp3GFP Trp1 cells, irradiation (5Gy) and aCTLA-4 (Th-ctx condition). Control mice received naïve Trp1 cells only (control). 8 days after transfer, Trp1 GFP- cells were FACS purified from tumours and draining lymph nodes.

tag: tumour type

value: B16 melanoma

value: tumour

value: Foxp3GFP- CD4+ Trp-1 cells


title: CMV1

city: Odense

first: Jan

last: Kornfeld

address: Campusbej 50

institute: University of Southern Denmark

description: SupplementaryData6_RNA-Seq[Ad-MAFG--Ad-CMV].xlsx

tag: strain

tag: virus

value: Ad-CMV


title: K562 Cells with miR-543 vector replicate 2

source_name: K562 Cell line

growth_protocol: K562  cells were cultured  under sterile conditions..

tag: genotype/variation

value: miR-543 overexpressed

value: Bone Marrow

tag: genotype

value: erythroleukemia


title: H-ECP-1-R1

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 1 hour, replicate 1

source_name: Ruditapes philippinarum hemocytes cells-extracellular products in vitro challenge, 1 hour, replicate 1

value: haemocyte cells

tag: treatment


title: Trp1 CD4+ TILs, Th-ctx condition sample 2

tag: tissue


title: CA-2

source_name: CARDINAL LEAF IRRIGATION 2-1

value: IRRIGATION


title: Trp1 CD4+ TILs, Th-ctx condition sample 1


title: K562 Cells with miR-543 vector replicate 3


title: Trp1 CD4+ LN , ctrl condition sample 1

source_name: CD4+ Trp1 from ctrl treated LN

value: draining Lymph nodes


title: Trp1 CD4+ LN , ctrl condition sample 2


title: K562 Cells with miR-543 vector replicate 1


title: CA-1

source_name: CARDINAL LEAF IRRIGATION 1-1


title: K562 Cells with control vector replicate 3

value: control


title: Trp1 CD4+ LN , ctrl condition sample 3


title: Trp1 CD4+ TILs, Th condition sample 2

source_name: CD4+ Trp1 from Th treated B16 tumour


title: K562 Cells with control vector replicate 2


title: Trp1 CD4+ TILs, Th condition sample 3


title: Trp1 CD4+ TILs, Th condition sample 1


title: H-ECP-1-C

description: Gene expression of Ruditapes philippinarum hemocytes in vitro challenged with extracellular products from P. olseni, 1 hour, control

source_name: Ruditapes philippinarum hemocytes cells-extracellular products  in vitro challenge, 1 hour, control


title: Rice seedling degradome

status: Public on Dec 17 2019

city: Xinxiang

first: Miao

last: Zhao

state: Henan

address: Jianshe east road

department: Life sciences college

institute: Henan Normal University

data_processing:
Getting rid of low quality reads
Getting rid of reads which proportion of N
Getting rid of reads with 5' primer contaminants and reads without the insert fragments
Getting rid of reads without 3' primer
Getting rid of reads with poly A and reads shorter than 25 nt
Getting unique reads and frequency
Supplementary_files_format_and_content: txt file with unique reads sequence and frequency

organism: Oryza sativa

source_name: seedlings

growth_protocol: Rice seedlings were grown in hydropic media at 22°C with 16h/8h light/dark cycle for three week-old,media was changed every two days.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacture's protocol,poly(A) RNA was purified.
RNA possessing 5’monophosphate was ligated to an RNA adapter consisting Ecop15I recognition site at 3’end. After ligation and RT-PCR, the PCR product was digested with Ecop15I and then ligated to a double-stranded DNA oligo. The final degradome library is enriched by primer pairs used for small RNA library preparation. Therefore, the generated degradome library can be sequenced as easily as small RNA library using Illumina sequencing platform.

treatment_protocol: three week old seedlings were collected.

value: spp japonica cv. Nipponbare


title: cM1 non-recoverd (ID in manuscript: 17)

city: Palo Alto

first: Michelle

last: Cheng

address: 1201 Welch Rd., MSLS P352

department: Neurosurgery

description:
Primary motor cortex transcriptome
SP4.1.3.cM1_no_recovery

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence using Trimmomatic 0.38,  then mapped to mm10 whole genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf provided from genecode ( vM13)
Sequences were imported into R , scaled, filter for low counts ( < 1 cpm) and  TMM normalized using the edgeR package.
cpm data adjusted with prior.count = 2 prior to log2 transform
Genome_build: mm10
Supplementary_files_format_and_content: single tab delimited file containing normalize log2 (cpm) adjusted with prior.count=2

source_name: RNA from contralesional primary motor cortex

extract_protocol:
study protocol: Mice underwent stroke and behavior recovery was evalulated using horizontal rotating beam test
RNA from the brain samples were extracted using the Trizol reagent (Invitrogen) followed by QIAGEN RNeasy Plus kit. RIN was 7-9.
A cDNA library was prepared using the TruSeq Stranded mRNA Library Prep Kit.

tag: sample name in manuscript

value: Primary motor cortex

tag: condition

value: non-recovered stroke mice


title: cM1 recoverd (ID in manuscript: 6)

description:
Primary motor cortex transcriptome
SP4.4.2.cM1_spon_recovery

value: recovered stroke mice


title: iM1 recoverd (ID in manuscript: 28)

description:
Primary motor cortex transcriptome
SP4.6.2.iM1_spon_recovery

source_name: RNA from ipsilesional primary motor cortex


title: cM1 non-recoverd (ID in manuscript: 29)

description:
Primary motor cortex transcriptome
SP4.6.3.cM1_no_recovery


title: iM1 recoverd (ID in manuscript: 6)

description:
Primary motor cortex transcriptome
SP2.7.1.iM1_spon_recovery


title: cM1 recoverd (ID in manuscript: 23)

description:
Primary motor cortex transcriptome
SP2.7.1.cM1_spon_recovery


title: cM1 non-recoverd (ID in manuscript: 20)

description:
Primary motor cortex transcriptome
SP4.3.3.cM1_no_recovery


title: cM1 non-recoverd (ID in manuscript: 19)

description:
Primary motor cortex transcriptome
SP4.3.2.cM1_no_recovery


title: iM1 non-recoverd (ID in manuscript: 20)

description:
Primary motor cortex transcriptome
SP4.3.3.iM1_no_recovery


title: iM1 non-recoverd (ID in manuscript: 21)

description:
Primary motor cortex transcriptome
SP4.3.4.iM1_no_recovery


title: iM1 non-recoverd (ID in manuscript: 19)

description:
Primary motor cortex transcriptome
SP4.3.2.iM1_no_recovery


title: cM1 non-recoverd (ID in manuscript: 21)

description:
Primary motor cortex transcriptome
SP4.3.4.cM1_no_recovery


title: cM1 recoverd (ID in manuscript: 28)

description:
Primary motor cortex transcriptome
SP4.6.2.cM1_spon_recovery


title: iM1 recoverd (ID in manuscript: 23)

description:
Primary motor cortex transcriptome
SP4.4.2.iM1_spon_recovery


title: iM1 non-recoverd (ID in manuscript: 17)

description:
Primary motor cortex transcriptome
SP4.1.3.iM1_no_recovery


title: JIM609A50_S38_L007: thymus-2

first: Patricia

last: Barral

address: Guy's Campus

department: Immunobiology

institute: King's College London

data_processing:
cutadapt  v1.7.1 with a minlength of 25 and a quality of 10
quantify reads using rsem (v1.2.31) with bowtie2 (v2.2.9)
Genome_build: GRCm38
Supplementary_files_format_and_content: fastq are gzipped, rsem are tab delimited columns of expected counts

molecule: polyA RNA

source_name: iNKT cells

extract_protocol:
RNA was isolated using RNA Mini Kit (QIAGEN). RNAseq including cDNA library preparation was processed at the Advanced sequencing facility in the Francis Crick Institute (London, UK).
NuGEN Ovation Ultralow (v2) kit was used for library preparation

treatment_protocol: NKT cells were sort-purified from lymphoid tissues from WT C57BL/6 mice (as CD1d-tetramer+TCR-b+B220-CD11b-CD11c-CD8-). Four biological replicates were performed.

value: iNKT

value: THYMUS

tag: unit

tag: batch

value: Second


title: JIM609A47_S35_L007: mLN-2

value: MLN


title: JIM609A48_S36_L007: iLN-2

value: INGLN


title: JIM609A46_S34_L007: spleen-2

value: SPLEEN


title: K562 Cells with control vector replicate 1

first: George

last: Calin

address: 1881 East Road

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

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


title: ShBCL11B H9 Replicate 2

city: Beijing

first: Wenjing

last: Fu

address: No.1 Xianmen Street, Xicheng District

department: Department of Dermatology and Venerology

institute: Peking University First Hospital

description: Biological replicate 2 of 3. ShBCL11B-treated H9 cells, RNA was extracted 96h post-transfection.

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R. The normalized data were analyzed according to Fold-Change(fold change(abs)>= 2.0 or 1.5 respectively) and Student's t-test(P-value<0.05) to select the differentially expressed genes. foldchange:the ratio ( not logarithm) of normalized intensities between two conditions ; Formula : foldchange=average(power(2,signal(CASE)))/average(power(2,signal(CONTROL))). foldchange (abs):the absolute ratio (not logarithm) of normalized intensities between two conditions ; Formula : if foldchange>1,foldchange(abs)=foldchange,foldchange<1,foldchange(abs)=1/foldchange.

source_name: H9-ShBCL11B H9 cells

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

growth_protocol: H9 cells with transfection were cultured in RPMI 1640 medium with 10% fetal bovine(Life technology)  serum

extract_protocol: Total RNA extracted using EZNA total RNA kit II(Omega)  following 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).

tag: cell line

value: cutaneous T-cell lymphoma (CTCL)


title: ShBCL11B H9 Replicate 3

description: Biological replicate 3 of 3. ShBCL11B-treated H9 cells, RNA was extracted 96h post-transfection.


title: ShBCL11B H9 Replicate 1

description: Biological replicate 1 of 3. ShBCL11B-treated H9 cells, RNA was extracted 96h post-transfection.


title: Vehicle control H9 Replicate 2

description: Biological replicate 2 of 3. Vehicle control H9 cells, transfected with empty vector, RNA was extracted 96h post-transfection.

source_name: H9-vehicle control transfected H9 cells


title: Vehicle control H9 Replicate 1

description: Biological replicate 1 of 3. Vehicle control H9 cells, transfected with empty vector, RNA was extracted 96h post-transfection.


title: Vehicle control H9 Replicate 3

description: Biological replicate 3 of 3. Vehicle control H9 cells, transfected with empty vector, RNA was extracted 96h post-transfection.


title: iM1 non-recoverd (ID in manuscript: 29)

description:
Primary motor cortex transcriptome
SP4.6.3.iM1_no_recovery


title: Colo320gfp_1

source_name: Colorectal adenocarcinoma cell line Colo320, GFP

value: colorectal adenocarcinoma cell line

tag: transduction

value: GFP

tag: gender

value: female

tag: replicate


title: JIM609A45_S33_L007: thymus-1


title: JIM609A42_S30_L007: mLN-1


title: JIM609A41_S29_L007: spleen-1


title: Subject 115, Whole Blood

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

data_processing: Quality control checks (>90% fields of view imaged to ensure complete scanning coverage & <2 binding density to avoid issues of saturation); positive control normalization; negative controls used to establish background threshold for filtering of lowly abundant transcripts; total sum scaling normalization

label: NanoString Oligonucleotide Probe

source_name: Allergic Asthmatic_whole blood

extract_protocol: Whole blood was drawn into PAXgene tubes and extracted for total RNA using PAXgene Blood miRNA kit (PreAnalytiX)

tag: subject id

value: Subject 115

tag: subject status

value: Allergic Asthmatic

tag: age

value: F

tag: sample type

value: Whole blood preserved in PAXgene


title: Subject 102, PBMC

source_name: Healthy Control_PBMC

extract_protocol: Peripheral blood mononuclear cell lysates were isolated by ficoll separation and loaded onto NanoString cartridges for RNA analysis

value: Subject 102

value: Healthy Control


title: Subject 112, Whole Blood

source_name: Healthy Control_whole blood

value: Subject 112

value: M


title: Subject 114, Whole Blood

value: Subject 114


title: Subject 105, PBMC

source_name: Allergic Asthmatic_PBMC

value: Subject 105

value: Peripheral blood mononuclear cell lysates


title: Subject 101, Whole Blood

value: Subject 101


title: Subject 109, Whole Blood

value: Subject 109


title: Subject 110, Whole Blood

value: Subject 110


title: Subject 116, PBMC

value: Subject 116


title: Subject 111, Whole Blood

value: Subject 111


title: Subject 115, PBMC


title: Subject 112, PBMC


title: Subject 114, PBMC


title: Subject 110, PBMC


title: Subject 109, PBMC


title: Subject 105, Whole Blood


title: Subject 102, Whole Blood


title: BW_fadr_1

city: San Diego

first: Anand

last: Sastry

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample

organism: Escherichia coli BW25113

source_name: E. coli BW25113 fadR KO

growth_protocol: glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2.

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: media

value: M9 minimal media w/ 0.2% glucose

tag: knock-out

value: FadR


title: Subject 101, PBMC

extract_protocol: Peripheral blood mononuclear cell lysates were isolated by ficoll separation, lysed with RLT buffer, and loaded onto NanoString cartridges for RNA analysis


title: Subject 116, Whole Blood

value: Allergic Asthmatic


title: BW_cbl_2

source_name: E. coli BW25113 cbl KO

value: cbl


title: BW_fabr_1

source_name: E. coli BW25113 fabR KO

value: FabR


title: BW_cbl_1


title: Subject 111, PBMC


title: BW_fadr_2


title: BW_fabr_2


title: white adipose tissue_MSx-added diet_biological rep7

city: Gunma

first: Tsudoi

last: Toyoda

address: 54 Nakaorui-machi, Takasaki-shi

country: Japan

institute: Tkasaki University of Health and Welfare

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to a Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) with the GeneChip 3' IVT PLUS Reagent kit (Thermo Fisher Scientific). The array was stained using the GeneChip Hybridization, Wash and Stain kit and on a GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: The fluorescence signals of probes were scanned with a GeneChip Scanner 3000 7G (Thermo Fisher Scientific) and converted to an intensity value with Affymetrix GeneChip Command Console software (Thermo Fisher Scientific).

data_processing: The signal intensity of probe sets was normalized by the distribution free weighted method. Data were compared between control and the MSx groups by rank products method. Probe sets with false discovery rate < 0.02 were considered as showing significant differences in expression. Probe sets sorted as both up- and downregulated were excluded, and the remaining probe sets were treated as differentially expressed genes. Normalization and between-group comparisons were performed with R v.3.2.2 (https://cran.r-project.org/) and Bioconductor v.3.1 (http://www.bioconductor.org/).

source_name: MSx-added diet

label_protocol: Biotinylated cRNA was prepared from purified total RNA with the GeneChip 3' IVT PLUS Reagent kit (Thermo Fisher Scientific).

growth_protocol: Male KK-Ay mice (4 weeks old) were purchased from CLEA Japan (Tokyo, Japan). The mice were individually housed in a room maintained at 21°C–23°C and 50%–70% relative humidity on a 12:12-h light/dark cycle. Control and MSx diets were prepared based on the AIN-93G formula by Oriental Yeast Co. (Tokyo, Japan) . After 4 days of acclimation, the mice were divided into two groups (n = 8 each) with approximately equal mean body weights. Mice were fed the control or MSx diet for 42 days and allowed free access to the diet and ultrapure water during this period.

extract_protocol: Total RNA was isolated from epididymal white adipose tissue with TRIzol reagent (Thermo Fisher Scientific) and purified with an RNeasy Mini kit and RNase-Free DNase Set (Qiagen, Venlo, the Netherlands).

treatment_protocol: Epididymal white adipose tissue was immediately frozen in liquid nitrogen and stored at −80°C until use.

value: KK-A[y]

value: male

value: 11 weeks old

value: epididymal white adipose tissue

tag: diet

value: MSx-added diet


title: white adipose tissue_MSx-added diet_biological rep6

tag: tissue


title: white adipose tissue_MSx-added diet_biological rep8


title: Detroit562 H3K27ac ChIP seq

city: La Jolla

first: Nathan

last: Jameson

state: CALIFORNIA

department: Pathology

institute: UC San Diego

data_processing:
Raw reads were aligned to hg19 with the Bowtie2 software with default parameters
Non-uniquely mapped reads were removed with “awk” command
Peaks were called by first creating TagDirectories of H3K27Ac and Input samples using the “makeTagDirectory” command in HOMER. Peaks were identified from the H3K27Ac tag directories using the input directories for normalization with the “findPeaks” command from HOMER with the following parameters: -style histone -size 250 -minDist 250.
Genome-wide read coverage was calculated by igvtools count
Genome_build: hg19
Supplementary_files_format_and_content: tiled data files (tdf) include average feature density for each sample for easy viewing in IGV; Browser Extensible Data (BED) files contain H3K27Ac peak calls with the given parameters across the whole genome

source_name: Pharynx

growth_protocol: GBM cell lines U87, T98G, LN229, LNZ308, SF767 and head and neck cell lines HN12, Cal27 and Detroit562 were maintained in DMEM (Hyclone, #SH30022.01) supplemented with 10% fetal bovine serum (Atlanta Biologicals, #S12450) and 1% penicillin-streptomycin (Gibco, #15140-122) and grown as adherent cultures. GBM neurosphere cell lines GSC23 and TS576 were maintained in DMEM/F12 (Gibco, #11320-033) supplemented with B27 supplement (Gibco, #12504-044) and 1% penicillin-streptomycin and grown in suspension.

extract_protocol:
Chromatin was sheared in diluted lysis buffer (1% SDS, 50mM Tris-HCl, 20mM EDTA, 1x protease inhibitor) to 200-500bp using a Covaris M220 Focused-Ultrasonicator with the following parameters: 10 minutes, peak incident power 75, duty factor 10%, 200 cycles/burst. 3ug antibody anti-H3K27Ac (Active Motif, #39133) was incubated with Dynabeads Protein G beads (Invitrogen, #10004D) for 4 hours. Beads were washed 3 times with 5mg/ml BSA, and incubated with 50% crosslinked chromatin (500ul) and 50% ChIP master mix (1% Triton-X, 0.1% DOC, 1X protease inhibitor, 1x TE) at 4°C overnight. 10% of the chromatin was not exposed to antibody and was used as control (input). Immunoprecipitated DNA was washed with RIPA buffer (50mM Hepes, 1% NP-40, 0.7% DOC, 0.5M LiCl, 1mM EDTA, 1x protease inhibitor) and eluted from the beads in elution buffer (10mM Tris, 1mM EDTA, 1% SDS). Along with input, immunoprecipitated DNA was reverse crosslinked at 65°C overnight, and purified via Phenol:Chloroform extraction
DNA libraries were prepared with either the TruSeq ChiP Library Prep Kit (Illumina, #IP-202-1012) or the Accel-NGS 2S Plus DNA Library kit (Swift Bioscience, #21024) and sequenced using 75 bp single-end sequencing method on an Illumina Hi-seq 4000

value: Pharynx

tag: tumor type

value: HNSCC

tag: chip antibody

value: anti-H3K27Ac (Active Motif, #39133)


title: Detroit562 Input


title: Cal27 Input

source_name: Tongue

value: Tongue


title: Alpha_WGBS_rep1

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using BSMap (Xi and Li, 2009) in bisulfite mode with default parameters. CpG methylation was called as described in (Ziller et al., 2013), excluding low-quality, duplicate, and >10%-mismatched reads.
Genome_build: hg19
Supplementary_files_format_and_content: bed. Column headers are: Chr, Start, End, methylatedCpG/TotalCpG, Score, Strand

source_name: Primary human adult islets

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
DNA was fragmented with a Covaris S2 sonicator for 6min, purified using the DNA Clean and Concentrator kit (Zymo Research), and bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research).
Sequencing libraries were generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences), pooled, and sequenced on a HiSeq 4000 instrument.

tag: cell type

value: Primary adult alpha cell


title: SCbeta_WGBS_rep1

source_name: HUES 8 hESC line

value: HUES 8 hESC line

value: hPSC-derived beta cell

tag: Stage

value: Stage 6 day 15


title: Beta_WGBS_rep1

value: Primary adult beta cell


title: DE_WGBS_rep1

tag: cell line

value: hPSC-derived definitive endoderm

value: Stage 1 day 3


title: PP1_WGBS_rep1

value: hPSC-derived pancreatic progenitor 1

value: Stage 3 day 2


title: PH_WGBS_rep1

value: hPSC-derived poly-hormonal cell


title: Cal27 H3K27ac ChIP seq


title: HN12 Input


title: white adipose tissue_normal diet_biological rep8

source_name: normal diet

value: KK-A[y]

value: male

value: 11 weeks old

value: normal diet


title: white adipose tissue_normal diet_biological rep3

value: epididymal white adipose tissue


title: white adipose tissue_normal diet_biological rep4


title: white adipose tissue_normal diet_biological rep6


title: white adipose tissue_normal diet_biological rep1


title: HN12 H3K27ac ChIP seq

value: HNSCC

value: anti-H3K27Ac (Active Motif, #39133)


title: EN_WGBS_rep1

value: hPSC-derived endocrine progenitor

value: Stage 5 day 3


title: white adipose tissue_normal diet_biological rep7


title: white adipose tissue_MSx-added diet_biological rep4

value: MSx-added diet


title: white adipose tissue_MSx-added diet_biological rep2


title: white adipose tissue_MSx-added diet_biological rep5


title: white adipose tissue_MSx-added diet_biological rep1


title: white adipose tissue_normal diet_biological rep2


title: white adipose tissue_MSx-added diet_biological rep3


title: SF767 Input

source_name: Brain

value: Brain

value: GBM


title: SF767 H3K27ac ChIP seq


title: TS576 Input


title: TS576 H3K27ac ChIP seq


title: GSC23 Input


title: GSC23 H3K27ac ChIP seq


title: LNZ308 Input


title: LN229 Input


title: liver_MSx-added diet_biological rep8

data_processing: The signal intensity of probe sets was normalized by the distribution free weighted method. Data were compared between control and the MSx groups by rank products method. Probe sets with false discovery rate < 0.001 were considered as showing significant differences in expression. Probe sets sorted as both up- and downregulated were excluded, and the remaining probe sets were treated as differentially expressed genes. Normalization and between-group comparisons were performed with R v.3.2.2 (https://cran.r-project.org/) and Bioconductor v.3.1 (http://www.bioconductor.org/).

extract_protocol: Total RNA was isolated from liver with TRIzol reagent (Thermo Fisher Scientific) and purified with an RNeasy Mini kit and RNase-Free DNase Set (Qiagen, Venlo, the Netherlands).

treatment_protocol: The liver was treated with RNAlater (Thermo Fisher Scientific, Waltham, MA, USA) at 4°C overnight and stored at −80°C until use.

value: liver


title: white adipose tissue_normal diet_biological rep5


title: T98G Input


title: T98G H3K27ac ChIP seq


title: LN229 H3K27ac ChIP seq


title: liver_MSx-added diet_biological rep5


title: liver_MSx-added diet_biological rep7


title: liver_MSx-added diet_biological rep4


title: liver_MSx-added diet_biological rep3


title: liver_MSx-added diet_biological rep6


title: liver_normal diet_biological rep7


title: liver_MSx-added diet_biological rep1


title: U87 H3K27ac ChIP seq