title: nmad1 rep2 25°C

description: 1112vs910_GeneMat.results.normalized_data_matrix

data_processing:
Real-Time Analysis (RTA) software
sequencing reads were aligned to the C.elegans genome (WS220) by Bowtie2(2.2.9)
transcripts were quantified by EBSeq in RSEM (1.3.0) pipeline
Genome_build: ce10
Supplementary_files_format_and_content: Data matrix was generated by EBSeq and the reads represented normalized counts

source_name: Germline

extract_protocol:
mRNA was extracted from the germlines of 100 worms in each group using Dynabeads mRNA direct micro purification kit (Invitrogen)
8 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)


title: n2 L4 input

status: Public on Jun 21 2019

type: SRA

city: Boston

first: Eric

last: Greer

state: MA

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

country: USA

institute: Boston Children's Hospital/Harvard Medical School

library_source: genomic

data_processing:
Real-Time Analysis (RTA) software
The raw fastq files were quality checked through Fastqc(0.11.5) and the adaptors were trimmed through Trimmomatic(0.36).
The trimmed reads were mapped to Bowtie2(2.2.9) with ce10 build indexes. The sorted bam files were deduplicated and peaks were called with Picard (2.8.0) and Macs2(2.7.12) respectively.
Genome_build: ce10
Supplementary_files_format_and_content: Bigwig files are indexed binary format were generated from bam files

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
L4 stage worms were collected at 20°C. The worms were crosslinked with 1x linking buffer (11 mM HEPES-NaOH, 110 mM NaCl, 1.1 mM EDTA and 1.1 mM EGTA) with 1% formaldehyde for 10 minutes at RT. The reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at RT. Samples were washed with cold PBS twice. The samples were next dissociated with lysis buffer and sonicated by biorupter for 25 cycles in the cold room with 30 seconds on and 30 seconds off per cycle. Protein G beads were coupled to the flag antibody (F3165 Sigma) for 2 hours. Uncoupled Protein G beads were incubated with the sonicated samples to pull down non-specific binding chromatin. The precleared chromatin samples were incubated with antibody-coupled bead slurries and rotated at 4°C overnight. The bound DNA was eluted from the beads by 200  µl TE with 1% SDS after washing with low salt (0.2% SDS, 2% Triton X-100, 4 mM EDTA, 40 mM Tris-HCl), high salt (0.2% SDS, 2% Triton X-100, 4 mM EDTA, 40 mM Tris-HCl, and 1 M NaCl) and LiCl buffers (0.5 M LiCl, 2% NP-40, 1% Na deoxycholate, 2 mM EDTA, and 20 mM and Tris-HCl). The eluted DNA was next purified by phenol-chloroform.
NEBNext DNA library prep master mix set for Illumina (E6040L) was used follow the companies instructions.

tag: developmental stage

tag: genotype

value: Wild type


title: nmad1 rep1 25°C

library_source: transcriptomic

molecule: total RNA


title: 24 h C6_3

city: Oxford

first: Maricris

last: Zaidem

state: Oxfordshire

address: South Parks Rd

department: Department of Biology

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-seq reads were aligned to the CD-HIT optimized TAIR10 Col-0 reference transcripts using Bowtie 2.
Uniquely mapped reads were quantified per representative gene model using eXpress.
Supplementary_files_format_and_content: uniq_counts

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on half-strength MS medium under short-day conditions (8 h light/16 h darkness, 150 μmol/cm2s white fluorescent light, 40-60 % humidity, 22 °C).

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN), and DNA contamination was removed with the RNase-Free DNase Set (QIAGEN). RNA quantity and quality were checked with an ABI 3730xl DNA Analyzer (Applied Biosystems) and a Qubit® 2.0 Fluorometer (Invitrogen). Standard protocols provided by the kits were used for extraction.
The cDNA library was prepared from 2 μg RNA using Illumina® TruSeq® RNA Sample Preparation Kits (Illumina).  Standard protocol provided by the kits is used. For library construction.

treatment_protocol: Seedlings were moved from MS medium plate to water and soak in water overnight. Water was replace with water with/without elicitor (flg22, nlp20 or C6). Samples were harvested after 1, 6, and 24 hours.

tag: ecotype

value: wild-type

tag: time point

tag: agent


title: 6 h nlp20_3

value: 6 h


title: n2 rep1 25°C


title: 24 h flg22_2


title: n2 rep2 25°C


title: nmad1 rep2 20°C

description: 78vs56_GeneMat.results.normalized_data_matrix


title: TRIM28-1 shRNA replicate 1

type: RNA

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

country: Sweden

institute: Karolinska Institutet

description:
shT28-1_1
Gene expression data from A375 cells transduced with a TRIM28-specific shRNA.

hyb_protocol: Hybridization was performed using the Affymetrix hybridization kit. Heat cocktails at 99° for 5 minutes, followed by 42° for 5 minutes. Centrifuge at max speed for 1 minute. Transfer 200μl of hybridization solution to each array. Hybridize 16 hours at 45° at 60rpm. The fluidics protocol was FS450_0001.

scan_protocol: HTA 2.0 chips were scanned using a GeneChip Scanner 3000 7G.

data_processing: CEL files were pre-processed using the R package oligo using the robust multichip average (RMA) preprocessing methodology.

label: Biotin

organism: Homo sapiens

source_name: A375 melanoma cells transduced with shRNA targeting TRIM28

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: A375 cells were routinely tested for mycoplasma contamination. A375 cells were cultured in high-glucose DMEM (Sigma Aldrich) supplemented with fetal calf serum (10%), streptomycin (0.1 mg/ml), penicillin (100 U/ml), Sodium pyruvate (1 mM) (Sigma Aldrich), HEPES (10 mM) (Sigma Aldrich) and L-glutamine (2 mM) (Sigma Aldrich).

extract_protocol: Total RNA was isolated using RNeasy Mini Kit according to the recommended protocol (Qiagen).

treatment_protocol: For shRNA mediated knockdown, A375 cells were transduced with lentiviruses (LKO.1) that expressed non-targeting control (shSCR or shLuc) or shRNAs specific for TRIM28 (shT28-1 or shT28-2). After selection in puromycin (1 mg/ml), knockdown efficiency was validated by quantitative RT-PCR and immunoblotting.

tag: cell line

tag: cell type

value: melanoma cells

tag: shRNA


title: n2 rep1 20°C


title: 6 h flg22_2


title: n2 rep2 20°C


title: Liver, FTd3

city: Tianjing

first: Chen

last: Sheng

address: Wuqing

country: China

institute: Novogene

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for containing N or low-quality sequence, then mapped to the reference genome(ftp://ftp.ensembl.org/pub/release-88/fasta/danio_rerio/dna/) using HISAT with default parameters.
Relative expression of genes was calculated by using FPKM (expected numbers of fragments per kilobase of transcript sequence per millions base pairs sequenced) from Trapnell, Cole, et al., 2010.
Genome_build: ftp://ftp.ensembl.org/pub/release-88/fasta/danio_rerio/dna/
Supplementary_files_format_and_content: tab-delimited text file includes FPKM, readcount for each Sample

organism: Danio rerio

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: TDCIPP with DOX

tag: tissue

value: liver

tag: age

value: 3 months old


title: Scrambled shRNA replicate 1

description:
shSCR_1
Gene expression data from A375 cells transduced with a non-targeting shRNA.

source_name: A375 melanoma cells transduced with non-targeting shRNA

value: Non-targeting (shSCR)


title: Non-targeting shRNA replicate 2

description:
shLUC_2
Gene expression data from A375 cells transduced with a non-targeting shRNA.

value: Non-targeting (shLUC)


title: 1 h C6_3

value: 1 h


title: Non-targeting shRNA replicate 1

description:
shLUC_1
Gene expression data from A375 cells transduced with a non-targeting shRNA.


title: Liver, FTd2


title: 1 h C6_2


title: Liver, FTd1


title: Scrambled shRNA replicate 2

description:
shSCR_2
Gene expression data from A375 cells transduced with a non-targeting shRNA.


title: HAECs siTERF2IP+DF rep2

city: Houston

first: Jun-ichi

last: Abe

state: Texas

address: 2121 W Holcombe Blvd. IBT8 803e

institute: University of Texas MD Anderson Cacer Center

hyb_protocol: Following fragmentation and labeling, 5.2 ug of labeled ss-cDNA were hybridized for 16 hrs at 45 degree on GeneChip Mouse Transcriptome arrays. Arrays were washed and stained in Affymetrix Fluidics station 450.

scan_protocol: Arrays were scanned using Affymetrix GCS3000 scanner

data_processing: The array data were incorporated into the Transcriptome Analysis Console 3.0 software program (Affymetrix), and GeneChip data were normalized using Tukey’s biweight average algorithm and represented as a biweight average on a log2 scale. A principal component analysis and differential profile (heatmap) of the d-flow responses in TERF2IP-depleted cells were analyzed using Qlucore Omics Explorer version 3.2. The principal component analysis was performed at a stringent p = 3.3e-5 using ANOVA on the basis of TERF2IP siRNA and d-flow treatment.

label: biotin

source_name: HAECs siMAGI1 disturbed flow (DF)  24 hrs

label_protocol: Fragmented and biotinylated labeled ss-cDNA were prepared according to standard Affymetrix WT Plus protocol (P/N 703174) from 100 ng total RNA

growth_protocol: HAECs were cultured in Petri dishes or flasks coated with 0.2% gelatin type A (#901771; MP Biomedicals, Santa Ana, CA, USA), in Endothelial Cell Medium (ECM, #1001, ScienCell, Carlsbard, CA. USA) containing 465 mL of basal medium, 25 mL of fetal bovine serum (FBS, #0025, ScienCell, Carlsbard, CA, USA), 5 mL of Endothelial Cell Growth Supplement (ECGS, #1052, ScienCell, Carlsbard, CA, USA) and 5 mL of penicillin/streptomycin solution (P/S, #0503, ScienCell, Carlsbard, CA, USA).

extract_protocol: Total RNA was extracted by using an RNeasy Plus Mini Kit (catalog #74134; QIAGEN)  according to the manufacturer's instructions.

treatment_protocol: HAECs were transfected by control siRNA or TERF2IP siRNA, and after 48 hrs of transfection HAECs were exposed to disturbed flow (d-flow). After 24 hrs of disturbed flow RNA was extracted for futher microarray processing.

value: HAECs

tag: sirna

value: TERF2IP siRNA

tag: flow

value: disturbed flow (d-flow)


title: 0 h H2O_2

value: 0 h


title: Liver, FD3

value: DOX


title: nmad1 rep1 20°C


title: HAECs siTERF2IP+DF rep3


title: Liver, FD2


title: Liver, FD1


title: 24 h nlp20_2


title: Liver, FT1

value: TDCIPP


title: Liver, FT2


title: Liver, FC3

value: DMSO


title: HAECs siTERF2IP+DF rep1


title: 24 h H2O_2


title: HAECs siTERF2IP rep3

source_name: HAECs siMAGI1 static 24 hrs

value: static


title: 1 h flg22_2

value: wild-type


title: Liver, FT3


title: 1 h nlp20_2


title: AZ-LR

type: genomic

city: New York

first: Kathleen

last: Burke

state: NY

address: 475 Main St., Apt 12H

department: Pathology

institute: Memorial Sloan Kettering Cancer Center

description: SNP arrays of BT474 cell derivative genomic DNA was performed using HumanOmni2.5-8 BeadChip Kit.

hyb_protocol: Genomic DNA was analyzed with the HumanOmni2.5-8 BeadChip Kit (Illumina) per the manufacturer’s instructions.

scan_protocol: Standard protocol

data_processing: Log ratio and B-allele frequencies were exported from GenomeStudio. Allele-specific copy number alterations were estimated using ASCAT

label: Cy3, Cy5

source_name: Breast Cancer Cell Line

label_protocol: Standard protocol

growth_protocol: Source, culture media and conditions of the BT474/AZ parental (P) line were described previously (Wang et al., Breast Cancer Research 2011).

extract_protocol: Cell line genomic DNA (gDNA) was isolated using the Wizard Genomic DNA Kit (Promega).

treatment_protocol: Resistant derivatives of both BT474 P lines to HER-targeted therapies were derived independently: cells were treated with gradually increasing doses until cells resume growth in the presence of 1 μM L, 50 μg/ml T, or the combination.

tag: strain

tag: phenotype

value: resistant to Lapatinib treatment


title: Liver, FC1


title: 6 h H2O_2

value: 6 h


title: AZ-P

value: parental line


title: HAECs siTERF2IP rep2


title: HAECs siTERF2IP rep1


title: ATCC-LTR

value: resistant to the combination of Lapatinib and Trastuzumab treatment


title: ATCC-P


title: HAECs siCont+DF  rep3

source_name: HAECs siCont disturbed flow (DF)  24 hrs

value: Control siRNA


title: 6 h C6_2


title: HAECs siCont+DF  rep2


title: Liver, FC2

value: liver

value: 3 months old


title: 24 h C6_2


title: 1 h H2O_2

value: 1 h


title: HAECs siCont rep3

source_name: HAECs siCont static 24 hrs

value: HAECs


title: 6 h nlp20_2


title: CD14+CD11b+ cells from Patient 3

city: MILAN

first: BIANCA

last: CIONI

state: MI

address: Via Amadeo 41

department: Molecular Oncology

country: Italy

institute: Istituto Nazionale Tumori

data_processing:
After Illumina sequencing, Read 1 was assigned 26 base pairs and was used for identification of illumina library barcode, cell barcode
UMI tags were added to each read in order to detect and quantitfy unique mRNA transcripts
R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19
Single-cell transcriptomics analysis was done using the RaceID3 algorithm, following an adapted version of the RaceID manual (https://cran.r-project.org/web/packages/RaceID/vignettes/RaceID.html)
After removing cells with less than 2000 UMIs and only keeping genes that were detected with at least 4 UMIs in at least 3 cells, 866 cells and 7323 genes were left for further analysis
Genome_build: Hg19
Supplementary_files_format_and_content: Transcript and reads counts in .tsv

source_name: PCa-associated CD14+CD11b+ macrophages

extract_protocol:
For amplification cells were heat-lysed at 65° C followed by cDNA synthesis using the CEL-Seq2 protocol using robotic liquid handling platforms Nanodrop II (GC Biotech) and Mosquito (TTP Labtech). After second strand cDNA synthesis, the barcoded material was pooled into libraries of 384 cells and amplified using IVT.
Following amplification, the rest of the CEL-seq2 protocol was followed for preparation of the amplified cDNA library, using TruSeq small RNA primers (Illumina).
The DNA library was paired-end sequenced on an Illumina Nextseq™500, high output, with a 1x75 bp Illumina kit

tag: subject status

value: untreated prostate cancer (PCa) patient

tag: gleason score

value: Prostate cancer

value: CD14+CD11b+ macrophages


title: CD14+CD11b+ cells from Patient 2


title: HAECs siCont+DF  rep1

value: disturbed flow (d-flow)


title: HAECs siCont rep2


title: CD14+CD11b+ cells from Patient 1


title: 1 h C6_1


title: 6 h flg22_1


title: 24 h nlp20_1


title: 24 h H2O_1


title: C3-small

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: miRNA.fa.gz

data_processing:
For mRNA and lncRNA analyses, the expression levels were calculated using TopHat2 and Cufflinks followed by the annotation references of Refseq and Ensemble transcript databases with the genome release Homo sapiens, hg19. The differentially expressed mRNA and lncRNA were determined by DEseq2 with the corresponding cutoff (P value <0.001, RPKM ≥10, |log2(fold change)| ≥1 for mRNA and P value <0.05, RPKM ≥1, |log2(fold change)| ≥1 for lncRNA).
For circular RNA (circRNA) prediction, we identified the candidates with find_circ (Memczak et al., 2013) and the junction reads were calculated as Transcripts Per Kilobase Million (TPM). A criterion of P value ≤0.05, TPM ≥0.1 and |log2(fold change)| ≥1 among four pairs of samples was used to identify differentially expressed circRNAs.
After filtering out the reads shorter than 15 nt, the remaining reads were mapped to the human genome (hg19) and the miRNA database in miRBase with bowtie (-v 1). The differentially expressed miRNAs were determined by DEseq2 with the cutoff of P value <0.05, TPM ≥1, |log2(fold change)| ≥1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HCC

extract_protocol:
The clinical samples were cut into small pieces and homogenized in TRizol reagent (Life Technologies) by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor


title: C5-small

description: miRNA.fa.gz


title: P5-small

description: miRNA.fa.gz

value: paratumor


title: P3-small

description: miRNA.fa.gz


title: 1 h nlp20_1


title: C2-small

description: miRNA.fa.gz


title: 1 h flg22_1


title: 24 h flg22_1


title: HAECs siCont rep1

value: static


title: 6 h H2O_1

value: wild-type


title: P2-small

description: miRNA.fa.gz


title: C1-small

description: miRNA.fa.gz


title: ATAC-Seq_mbd9-3_R2

city: Los Angeles

first: magdalena

middle: ewelina

last: potok

state: CA

address: 4045 Terasaki Life Sciences Building

department: MCDB

institute: UCLA

data_processing:
ATAC seq read adaptors were been removed with trim_galore
Reads were mapped using Bowtie2 (-X 2000 -m 1).
Chloroplast and mitochondrial DNA aligned reads were filtered out and duplicate reads were removed using Samtools
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig, narrowPeak

source_name: flowers

growth_protocol: Plants were grown in soil in a greenhouse under long day conditions for 4 weeks. Flowers were collected for nuclei extraction. Two replicates for each genotype were collected.

extract_protocol:
Nuclei were isolated as described in Liu, W et al, 2018. ATAC-seq was performed as described in Buenrostro, J.D., et al, 2013.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

tag: developmental stage

value: 4 weeks

tag: genotype/variation

tag: background ecotype


title: P1-small

description: miRNA.fa.gz


title: ATAC-Seq_mbd9-3_R1


title: ATAC-Seq_WT_R2

value: WT


title: NeuN-sorted neurons_control (PDC026.A3A1.oxBS)

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

hyb_protocol: Genomic DNA was subjected to conventional BS-treatment as well as oxidative BS (oxBS)-conversion in parallel using TrueMethylTM 96 kit of CEGXTM (Cambridge Epigenetix Limited) at GenomeScan (GenomeScan B.V., Leiden, The Netherlands) and hybridized to the Illumina Infinium Human Methylation 450K Beadchip array according to manufacturer’s instructions

scan_protocol: BeadChip images were scanned on the iScan system using standard recommended Illumina scanner settings

data_processing: ChAMP version 1.8.0 was used for probe filter (Probes located on X and Y chromosomes, detection P value<0.01, bead count<3 in at least 5% of the samples, SNPs (Minor alelle frequency > 1% in European Population) and cross-reactivity as identified by Chen et al) and minfi version 1.16.0 was used for for subset within array normalization (SWAN) probe normalization.

label: Cy5 and Cy3

source_name: NeuN-sorted, White matter

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from neuronal nuclei was isolated using QIAmp DNA micro kit (QIAGEN) according to standard instructions.

tag: gender

value: F

tag: disease state

value: Non-neurological control

value: NeuN-sorted, White matter

tag: treatment of genomic dna

value: oxBS


title: NeuN-sorted neurons_MS patient (MS063.P2B4.oxBS)

source_name: NeuN-sorted, Normal-appearing white matter

value: MS


title: C5

description:
linear transcript.fa.gz
circRNA.fa.gz


title: P5

description:
linear transcript.fa.gz
circRNA.fa.gz


title: NeuN-sorted neurons_control  (C036.A4C5.oxBS)

value: M


title: NeuN-sorted neurons_control (C37.A2C1.oxBS)


title: NeuN-sorted neurons_MS patient  (MS062.P3C4.oxBS)

value: NeuN-sorted, Normal-appearing white matter


title: NeuN-sorted neurons_MS patient (MS230.A2D2.oxBS)

source_name: NeuN-sorted, Chronic lesion

value: NeuN-sorted, Chronic lesion


title: NeuN-sorted neurons_MS patient (MS060.P2E5.oxBS)


title: NeuN-sorted neurons_control (PDC029.P3D3.BS)

value: BS


title: NeuN-sorted neurons_control (C22.A1A2.oxBS)


title: NeuN-sorted neurons_control (C19.P1C3.oxBS)


title: NeuN-sorted neurons_control (C045.P4C4.oxBS)


title: NeuN-sorted neurons_control (PDC029.P3D3.oxBS)


title: ATAC-Seq_WT_R1


title: NeuN-sorted neurons_control (C37.A2C1.BS)


title: NeuN-sorted neurons_control (C19.P1C3.BS)


title: NeuN-sorted neurons_MS patient (MS071.P3D4.oxBS)


title: Obese_6

city: Linköping

first: Peter

last: Str lfors

address: Lasarettsgatan

department: Department of Biomedical and Clinical Sciences (BKV)

institute: Linköping University

data_processing:
Quality check performed with FastQC software
Sequenced reads were trimmed for adaptor sequence remnants using Trimmomatic
Sequenced reads were aligned to reference genome hg38 using STAR, and mapped reads were counted by FeatureCounts.
Differential gene expression was conducted with the R package DESeq2 (Wald test, Benjamini-Hochberg correction).
Genome_build: hg38
Supplementary_files_format_and_content: tab files with counted reads to genomic features, for each sample and summarized in the file “count_matrix.tab”, and csv files with differential expression results

source_name: Adipocytes, abdominal subcutaneous

growth_protocol: Primary abdominal subcutaneous adipocytes isolated from biopsies obtained during elective surgery.

extract_protocol:
RNA was prepared from isolated adipocytes by Trizol extraction and solid phase extraction using RNeasy MinElute Cleanup columns (Qiagen, Hilden, Germany).
Libraries were prepared, each from 1 μg of RNA, using the TruSeq stranded total RNA library preparation kit with RiboZero Gold treatment (Illumina, San Diego, CA, USA). All libraries were sequenced on Illumina HiSeq2500 generating 125bp paired-end reads.

tag: diagnosis

value: Lean woman

tag: cell type

value: Adipocytes

tag: Sex

value: female


title: NeuN-sorted neurons_MS patient (MS053.A2B5.oxBS)

tag: tissue


title: NeuN-sorted neurons_control  (C036.A4C5.BS)

tag: age


title: P3

description:
linear transcript.fa.gz
circRNA.fa.gz

value: paratumor


title: C3

description:
linear transcript.fa.gz
circRNA.fa.gz

value: tumor


title: Obese_4


title: NeuN-sorted neurons_control (C045.P4C4.BS)


title: NeuN-sorted neurons_MS patient (MS229.P5E7.oxBS)


title: NeuN-sorted neurons_control (C22.A1A2.BS)


title: Obese_5


title: NeuN-sorted neurons_MS patient  (MS051.A1C2.oxBS)


title: P2

description:
linear transcript.fa.gz
circRNA.fa.gz


title: NeuN-sorted neurons_MS patient (MS230.A2D2.BS)


title: NeuN-sorted neurons_MS patient (MS229.P5E7.BS)


title: Obese_3


title: WCt5, XCFY

city: Tokyo

first: Ryodai

last: Shindo

state: Ota-ku

address: 5-21-16 Omori-Nishi

country: Japan

institute: Toho univercity

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45℃ on Affymetrix GeneChip Whole Transcript (WT) Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using  a G2565BA Microarray Scanner System (Affymetrix).

data_processing: Data were analyzed using GeneSpring GX software (Agilent).

organism: Mus musculus

source_name: small intestine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2011, Affymetrix).

extract_protocol: Total RNAs were extracted from the small intestine of mice of the indicated genotype using Trizol according to the manufacturer’s instructions

value: small intestine

tag: genotype

value: CFLARs Tg


title: NeuN-sorted neurons_MS patient (MS050.A5D3.oxBS)


title: WCt3, XCFX


title: NeuN-sorted neurons_control (PDC026.A3A1.BS)


title: C1

description:
linear transcript.fa.gz
circRNA.fa.gz


title: NeuN-sorted neurons_MS patient (MS071.P3D4.BS)


title: S100_ancient_osteosarcoma

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

data_processing:
original fastq files were converted to fasta format and reads without Ns were kept for further analysis
3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps
reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
abundances of the reads were normalised
differential expression was called
Genome_build: GRCh38

source_name: bone cancer tissue

extract_protocol:
RNA extracted from bone tumour
Illumina compatible method using HD adapters

value: bone cells


title: NeuN-sorted neurons_MS patient (MS076.A1D4.BS)

value: F


title: Obese_2


title: WCt2, XY

value: wild-type


title: OX_NS_BAL_1259

first: Mikael

last: Ringh

state: Choose state (US & Canada)

address: Medical Epigenetics, CMM L8:00, Karolinska University Hospital Solna

hyb_protocol: Conventional bisulfite conversion as well as oxidative bisulfite conversion using TrueMethyl conversion kit from Cambridge Epigenetix (CEGX). 250 ng of DNA per reaction followed by llumina MethylationEPIC BeadChip hybridization via Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina HiScan

data_processing: SQN normalisation

source_name: Bronchoalveolar lavage cells from healthy individual

extract_protocol: DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol

value: Nonsmoker

value: NA NA

tag: fvc


title: OX_NS_BAL_1238


title: Obese_1


title: OX_S_BAL_1229

value: Smoker


title: NeuN-sorted neurons_MS patient (MS076.A1D4.oxBS)

value: MS

value: oxBS


title: OX_NS_BAL_1234

value: M


title: Lean_6

value: Obese woman


title: SC154IPFUP

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
10X Genomics' Cell Ranger 2.0 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 2.0 software's cellranger count function
Cell Ranger output of raw_gene_bc_matrices were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis.  Further filtration removed cells expressing greater than 50,000 UMI or 35% mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

molecule: polyA RNA

source_name: upper lobe lung_IPF

extract_protocol:
10X Genomics 3 Prime V2 chemistry
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide

value: idiopathic pulmonary fibrosis (IPF)

value: lung

tag: lung section/portion

value: upper lobe lung


title: OX_NS_BAL_1005


title: NeuN-sorted neurons_MS patient  (MS062.P3C4.BS)

value: NeuN-sorted, Normal-appearing white matter

value: BS


title: SC153IPFLOW

source_name: lower lobe lung_IPF

value: lower lobe lung


title: P1

description:
linear transcript.fa.gz
circRNA.fa.gz

value: paratumor


title: OX_NS_BAL_980


title: Lean_5

value: Adipocytes

value: female


title: OX_NS_BAL_972

value: F


title: SC95IPFLOW


title: OX_S_BAL_944


title: WCt1, XX

tag: strain

value: small intestine

value: wild-type


title: Lean_4


title: OX_S_BAL_943

value: Smoker


title: SC94IPFUP

tag: subject status


title: OX_NS_BAL_926

value: Nonsmoker

value: NA NA


title: NeuN-sorted neurons_MS patient  (MS051.A1C2.BS)

value: MS


title: OX_S_BAL_921


title: Lean_2

value: Obese woman


title: OX_S_BAL_920


title: SC93IPFLOW

value: idiopathic pulmonary fibrosis (IPF)


title: SC89IPFLOW

value: lung


title: OX_S_BAL_916


title: OX_S_BAL_910


title: OX_S_BAL_913


title: OX_NS_BAL_903


title: SC88IPFUP

value: upper lobe lung


title: Lean_1


title: OX_NS_BAL_879

value: M


title: Lean_3


title: OX_S_BAL_828


title: OX_S_BAL_818


title: Diabetes_5

value: Obese woman with type 2 diabetes


title: OX_S_BAL_813


title: Diabetes_4


title: NeuN-sorted neurons_MS patient (MS063.P2B4.BS)

value: NeuN-sorted, Normal-appearing white matter

value: BS


title: C2

description:
linear transcript.fa.gz
circRNA.fa.gz

value: tumor


title: SC249NORbal_fresh

source_name: fresh Brochoalvelolar lavage (BAL) + brush cells from healthy donor

value: normal/healthy donor


title: OX_NS_BAL_790


title: Diabetes_3

value: Adipocytes

value: female


title: NeuN-sorted neurons_MS patient (MS053.A2B5.BS)


title: OX_NS_BAL_785


title: Diabetes_6


title: Diabetes_1


title: Diabetes_2


title: SC87IPFLOW

value: lower lobe lung


title: OX_NS_BAL_726


title: OX_NS_BAL_708


title: OX_NS_BAL_719

value: F


title: OX_S_BAL_809

value: Smoker


title: OX_NS_BAL_722

value: Nonsmoker

value: NA NA


title: CS_seedlings_lncRNA_seq_rep1

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq and DNaseI-seq  data,  HISAT2 2.1.020 for RNA-seq data ,  Bismark_v0.19.0 for bisulfite-seq data , all with default settings.
For ChIP-seq  and DNaseI-seq data, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–50 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In RNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided;In DNaseI-seq , peak files were provided ; In Bisulfite-seq ,BigWig files with position and  methylation ratio were provided.

organism: Triticum aestivum

source_name: Triticum aestivum 12-days-old seedlings

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Chromatin or RNA was extracted from 12-days-old seedlingss, using standard protocols. 2 microgram mRNA ,2 microgram total RNA (rRNA depleted) were used to prepare mRNA-seq and lncRNA-seq. 2.2 microgram DNA extracted from the harvested seedlings were used to prepare ChIP-seq, DnaseI-seq and Bisulfite-seq
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions  (Illumina) to produce 150bp paired-end reads.

treatment_protocol: No treatment applied.

tag: cultivar

value: Chinese Spring

value: 12-days-old seedlings


title: CS_seedlings_lncRNA_seq_rep2


title: CS_seedlings_DNaseI_seq_rep2

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq and DNaseI-seq  data,  HISAT2 2.1.020 for RNA-seq data ,  Bismark_v0.19.0 for bisulfite-seq data , all with default settings.
For ChIP-seq  and DNaseI-seq data, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–50 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In RNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided;In DNaseI-seq, peak files were provided; In Bisulfite-seq, BigWig files with position and  methylation ratio were provided.

extract_protocol:
Chromatin or RNA was extracted from 12-days-old seedlingss, using standard protocols. 2 microgram mRNA, 2 microgram total RNA (rRNA depleted) were used to prepare mRNA-seq and lncRNA-seq. 2.2 microgram DNA extracted from the harvested seedlings were used to prepare ChIP-seq DnaseI-seq and Bisulfite-seq   .
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions  (Illumina) to produce 150bp paired-end reads.


title: SC228NORbal_frozen

source_name: frozen Brochoalvelolar lavage (BAL) cells from healthy donor

value: lung


title: OX_NS_BAL_703


title: OX_NS_BAL_724


title: CS_seedlings_DNaseI_seq_rep1


title: NeuN-sorted neurons_MS patient (MS060.P2E5.BS)

value: MS


title: OX_NS_BAL_707


title: CS_seedlings_ Bisulfite_seq

description: CS_seedlings_ Bisulfite_seq


title: OX_S_BAL_696

value: M


title: OX_S_BAL_698


title: CS_seedlings_H3K36me3_ChIP_seq_rep2

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: CS_seedlings_H3K36me3_ChIP_seq_rep1


title: OX_NS_BAL_682


title: OX_NS_BAL_641


title: BS_NS_BAL_1259


title: CS_seedlings_mRNA_seq


title: NeuN-sorted neurons_MS patient (MS050.A5D3.BS)

tag: gender

value: NeuN-sorted, Normal-appearing white matter


title: CS_seedlings_H3K9ac_ChIP_seq_rep2

value: Upstate


title: CS_seedlings_H3K9ac_ChIP_seq_rep1


title: BS_NS_BAL_1238


title: CS_seedlings_H3K9me2_ChIP_seq_rep1


title: OX_NS_BAL_694


title: BS_NS_BAL_1234


title: CS_seedlings_H3K27ac_ChIP_seq_rep2


title: CS_seedlings_H3K27ac_ChIP_seq_rep1


title: CS_seedlings_H3K4me1_ChIP_seq_rep1


title: BS_NS_BAL_1005


title: BS_S_BAL_1229


title: BS_NS_BAL_972


title: BS_NS_BAL_980


title: BS_S_BAL_944


title: CS_seedlings_H3K4me3_ChIP_seq


title: ChIPSeq_H3Ac_WT

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie57 using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized read coverage tracks were generated using the USeq package Sam2Useq application
ChIP-Seq peaks were called using callpeak function in MACS2 (v2.1.1.)
ChIP-seq data metaplots and k-means clustering were generated by  NGSPLOT (v4.02.48)59
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using bioloobox bam2wig.pl application

source_name: seedlings

growth_protocol: 13 DAG seedlings grown on plantes containing 1%MS  under long day conditions were collected and flash frozen.   About 0.5 g of seedlings was used for the H3Ac ChIP.

extract_protocol:
Following in-vivo fixation, isolated nuclei were sonicate, cell lysates were cleared and  histone-DNA complexes were isolated with  antibody.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

tag: developmental stage

value: 13 DAG shoots

value: H3Ac (Active Motif:39140)

tag: ecotype

tag: genotype/variation

value: wildtype


title: control5_Cy5

type: protein

city: Borstel

first: Xinhua

last: Yu

address: Parkallee 22

institute: Research Center Borstel

description:
raw data file:
20171020-9002559-control5.gpr
non-COPD smoker 5

hyb_protocol: Microarrays were then washed with 1 x TBS-T and probed with Cy3-labeled anti-human IgG and Cy5-labeled anti-human IgM at room temperature for 1 h.

scan_protocol: Microarrays were scanned in a GenePix 4200A (Molecular Devices, Sunnyvale, CA).

data_processing:
Signal intensities were measured by using GenePix Pro 6.0 Software (Molecular Devices, Sunnyvale, CA).
The median foreground and background intensities for each spot on the protein microarrays were obtained, and the raw intensity for each spot was defined as the difference between foreground and background median intensity. Then the quantile normalization algorithms were used to adjust the values of the background-subtracted mean pixel intensities of microarray by using LIMMA (Linear Models for Microarray Data) package.

molecule: protein

source_name: serum from non-COPD smoker

label_protocol: Microrrays were blocked with 1% BSA at 4 oC for 3 h, and probed with a total of 5 mL of diluted serum sample (1:200 diluted in Tris-buffered saline containing 0.1% Tween 20 detergent (TBS-T)) at room temperature for 1 h.

extract_protocol: Serum samples were prepared from patients or control subjects.

tag: diagnosis

value: non-COPD smoker

value: sera

tag: autoantibody

value: IgM


title: Human_CELSS180_Post30_04_BloodCell

city: Shenzhen

first: Yuan

last: Quan

state: Guangdong

address: Space Institute of Southern China, Shenzhen, Guangdong

department: Lab of Epigenetics and Advanced Health Technology

institute: Space Institute of Southern China

hyb_protocol: Bisulfite modification of DNA (≥500ng for each sample) was conducted using an EZ DNA Methylation Kit (Zymo Research) according to the manufacturer’s procedure.

scan_protocol: The Infinium Methylation 450K assay was performed according to Illumina’s standard protocol.

data_processing: minfi package (version: 1.30.0) in R Language (version: 3.6)

source_name: Blood Cell

extract_protocol: DNA was extracted from frozen blood samples by standard proteinase K/RNase treatment and phenol/chloroform extraction.

treatment_protocol: Peripheral whole blood cells were extracted from all crew members before breakfast. After extraction, whole blood cells were immediately treated with EDTA anticoagulation, transferred outside of the module and centrifuged stored at -70℃ untill the DNA extraction performed.

tag: tissue

value: whole blood


title: Human_CELSS180_R175_04_BloodCell


title: BS_S_BAL_943

tag: Sex

value: F

tag: age

value: Smoker


title: Human_CELSS180_R60_04_BloodCell


title: control4_Cy5

description:
raw data file:
20171020-9002558-control4.gpr
non-COPD smoker 4


title: Human_CELSS180_R2_04_BloodCell


title: ChIPSeq_H2AZ_arp6-1,mbd9-3_R2

growth_protocol: 13 DAG shoots grown on plantes containing 1%MS supplemented with 1% sucrose under long day conditions were collected and flash frozen. Two replicates grown on separate plates were collected for each genotype.  About 0.5 g of seedlings were used for each replicate. Each replicate was split into H2AZ and H3 ChIP.

value: H2AZ (Polyclonal antibodies specific to Arabidopsis H2A.Zs HTA11 and HTA9 were produced in rabbits  and further purified using the peptides described in Deal, R.B et al, 2007.


title: Human_CELSS180_R150_04_BloodCell


title: BS_NS_BAL_926

value: Nonsmoker

value: NA NA

tag: fvc


title: CS_seedlings_H3K4me1_ChIP_seq_rep2

value: Chinese Spring

value: 12-days-old seedlings


title: ChIPSeq_H2AZ_arp6-1_R2


title: control3_Cy5

description:
raw data file:
20171020-9002557-control3.gpr
non-COPD smoker 3


title: Human_CELSS180_R105_04_BloodCell


title: Human_CELSS180_R120_04_BloodCell


title: BS_S_BAL_921


title: Human_CELSS180_R75_04_BloodCell


title: Human_CELSS180_R90_04_BloodCell


title: Human_CELSS180_R175_03_BloodCell


title: ChIPSeq_H2AZ_mbd9-3_R2


title: control1_Cy5

description:
raw data file:
20171020-9002555-control1.gpr
non-COPD smoker 1


title: control2_Cy5

description:
raw data file:
20171020-9002556-control2.gpr
non-COPD smoker 2


title: COPD5_Cy5

description:
raw data file:
20171020-9002539-COPD5.gpr
COPD patient 5

source_name: serum from COPD patient

value: COPD


title: BS_S_BAL_920


title: Human_CELSS180_Pre15_04_BloodCell


title: ChIPSeq_H2AZ_WT_R2


title: BS_S_BAL_916


title: Human_CELSS180_R30_04_BloodCell


title: Human_CELSS180_Post30_03_BloodCell


title: ChIPSeq_H2AZ_arp6-1_R1


title: Human_CELSS180_Pre45_04_BloodCell


title: Human_CELSS180_R120_03_BloodCell


title: BS_S_BAL_910


title: ChIPSeq_H2AZ_mbd9-3_R1


title: Human_CELSS180_R150_03_BloodCell


title: COPD2_Cy5

description:
raw data file:
20171020-9002536-COPD2.gpr
COPD patient 2


title: COPD4_Cy5

description:
raw data file:
20171020-9002538-COPD4.gpr
COPD patient 4


title: Human_CELSS180_R90_03_BloodCell


title: COPD1_Cy5

description:
raw data file:
20171020-9002535-COPD1.gpr
COPD patient 1


title: COPD3_Cy5

description:
raw data file:
20171020-9002537-COPD3.gpr
COPD patient 3


title: ChIPSeq_H2AZ_WT_R1


title: control5_Cy3

value: IgG


title: BS_NS_BAL_879

value: M


title: BS_S_BAL_828


title: Human_CELSS180_R60_03_BloodCell


title: BS_NS_BAL_903


title: Human_CELSS180_R2_03_BloodCell


title: ChIPSeq_H3_arp6-1,mbd9-3_R2

value: 13 DAG shoots

value: H3 (Abcam:ab1791)


title: ChIPSeq_H3_arp6-1_R2


title: BS_S_BAL_818


title: BS_S_BAL_813


title: ChIPSeq_H2AZ_arp6-1,mbd9-3_R1


title: Human_CELSS180_Pre15_03_BloodCell


title: Human_CELSS180_R30_03_BloodCell


title: ChIPSeq_H3_mbd9-3_R2


title: ChIPSeq_H3_WT_R2

value: wildtype


title: control4_Cy3

value: non-COPD smoker


title: Human_CELSS180_R75_03_BloodCell


title: control3_Cy3

value: sera


title: Human_CELSS180_Pre45_03_BloodCell


title: control2_Cy3


title: BS_NS_BAL_790


title: ChIPSeq_H3_arp6-1_R1


title: ChIPSeq_H3_arp6-1,mbd9-3_R1


title: BS_NS_BAL_785


title: Human_CELSS180_R105_03_BloodCell


title: Human_CELSS180_R175_02_BloodCell


title: BS_NS_BAL_726


title: control1_Cy3


title: ChIPSeq_H3_mbd9-3_R1


title: COPD3_Cy3


title: Human_CELSS180_Post30_02_BloodCell


title: ChIPSeq_H3_WT_R1


title: BS_S_BAL_913


title: BS_NS_BAL_724


title: COPD2_Cy3


title: Human_CELSS180_R120_02_BloodCell


title: SFS

city: Habin

first: Ai min

last: Zhou

address: 59 wood street, xiangfang district

institute: Northeast Agricultural University

data_processing:
After obtaining clean reads, the clean reads need to be spliced to obtain a reference sequence for subsequent analysis
We use Trinity to assemble clean reads,then use Tgicl to cluster the transcripts to obtain Unigene
After the assembly, we will perform seven major functional database annotations on the assembled Unigene.(NR 、NT 、GO 、KOG 、  KEGG,SwissPprot and InterPro)
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample

organism: Adonis amurensis

source_name: senescing flower stage

growth_protocol: Adonis amurensis plants were grown in an open field at Northeast Agricultural University

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The floral organs of A. amurensis were sampled simultaneously at different developmental stages

value: flower


title: Human_CELSS180_R105_02_BloodCell

value: whole blood


title: BS_NS_BAL_722

value: F


title: COPD1_Cy3


title: arp6-1,mbd9-3_R3

data_processing:
Reads were aligned using Tophat by allowing up to two mismatches and mapping only to one location.
FRPKM values were analyzed using Cufflinks
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each genes generated by Cufflinks

extract_protocol:
Total RNA was extracted from 13dag shoots grown on 1%MS supplemented with 1% sucrose under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of three seedlings. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina).


title: BS_NS_BAL_719


title: Human_CELSS180_R150_02_BloodCell


title: FBS

source_name: full bloom stage


title: EFS

source_name: early flowering stage


title: Human_CELSS180_R75_02_BloodCell


title: Human_CELSS180_R90_02_BloodCell


title: BS_NS_BAL_708


title: arp6-1,mbd9-3_R1


title: BS_NS_BAL_707


title: arp6-1_R4


title: YA

source_name: young alabastrum

value: flower bud


title: BS_NS_BAL_703


title: arp6-1_R3


title: Human_CELSS180_R2_02_BloodCell


title: COPD5_Cy3


title: FBD

source_name: flower bud differentiation


title: Human_CELSS180_R30_02_BloodCell


title: BS_S_BAL_698

value: Smoker


title: Human_CELSS180_R60_02_BloodCell


title: arp6-1_R2


title: arp6-1_R1


title: Human_CELSS180_Pre15_02_BloodCell


title: BS_S_BAL_696


title: arp6-1,mbd9-3_R2


title: BS_NS_BAL_694

value: Nonsmoker


title: Human_CELSS180_Pre45_02_BloodCell


title: mbd9-3_R4


title: arp6-1,mbd9-3_R4


title: VCA

source_name: visible color alabastrum


title: Human_CELSS180_Post30_01_BloodCell


title: BS_NS_BAL_641

value: NA NA


title: BS_NS_BAL_682


title: BS_S_BAL_809


title: mbd9-3_R3


title: PLv NonIR 3

city: SEVILLA

first: Vivian

last: Capilla-Gonzalez

state: Sevilla

address: Avda. Americo Vespucio 24

country: Spain

institute: CABIMER

description: Gene expression data from the PLv isolated from untreated mice

hyb_protocol: Following fragmentation, 2.3 µg of single-stranded cDNA were hybridized for 16 hr at 45ºC on  Clariom™ S Assay Mouse Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

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

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

source_name: PLv from mouse 3 that was not irradiated

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2ng total RNA Labeling Protocol (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression ArraysWT Pico Reagent Kit, ©2015 Affymetrix Inc.)

growth_protocol: Hipp and PLv from mouse brains were isolated and immediately frozen in liquid nitrogen and stored at -80 degrees C.

extract_protocol: Total RNA was extracted using the RNAeasy Mini kit (Qiagen) following the instructions of the manufacturer.

treatment_protocol: Frozen tissues were used for RNA isolation

value: brain lateral ventricles

tag: treatment


title: COPD4_Cy3


title: PLv NonIR 2

source_name: PLv from mouse 2 that was not irradiated


title: Human_CELSS180_R150_01_BloodCell


title: PLv NonIR 1

source_name: PLv from mouse 1 that was not irradiated


title: mbd9-3_R1


title: ZEN [Z2 ]

city: Guangzhou

first: Yu

last: Sun

address: Tianhe Qu, Wushan

institute: South China Agricultural University

data_processing:
The index of the reference genome was built using Bowtie v2.2.3
Paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
The read numbers mapping to each gene were calculated by HTSeq v0.6.1
FPKM of each gene was calculated based on the length of the gene and the reads count mapped to that gene
Differential expression analysis was performed using the DESeq R package
Genome_build: GenBank Assembly ID GCA_000002315.3
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample

organism: Gallus gallus

source_name: primary hepatocytes

growth_protocol: Eighteen-day embryonated specific-pathogen-free (SPF) chicken eggs were purchased from the Institute of Animal Science, Guangdong Academy of Agricultural Sciences (Guangzhou, China).

extract_protocol:
Chicken embryo primary hepatocytes were re-suspended in Williams E medium
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hepatocytes were prepared using a collagenase digestion method

value: primary hepatocytes

tag: agent

value: ZEN treated


title: mbd9-3_R2


title: PLv IR 3

description: Gene expression data from the PLv isolated from mice receiving radiation

source_name: PLv from mouse 3 receiving cranial radiation

value: radiation


title: PLv IR 2

source_name: PLv from mouse 2 receiving cranial radiation


title: ZEN [Z3 ]


title: Human_CELSS180_R175_01_BloodCell


title: Columbia-0_R4


title: A549_ 12 h_ R6-NLS-p53(380–386-3Ac)_25µM_Rep 3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array (AMADID: 039494). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

source_name: non-small cell lungs carcinoma

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: A549 were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: RNA extraction was performed by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: A549 cells were treated with 25 µM R6-NLS-p53(380–386-3Ac) peptide and incubated for two different time points (12 h and 24 h) in 5% CO2 at 37°C. Trypsinized cells were collected and mixed with RNA-later.

value: lungs epithelial cells

tag: cell line

value: 12 h treatment with 25µM R6-NLS-p53(380–386-3Ac)


title: PLv IR+MSC 2

description: Gene expression data from the PLv isolated from mice receiving radiation and MSCs

source_name: PLv from mouse 2 receiving cranial radiation and MSC

value: radiation and MSCs


title: A549_ 24 h_ R6-NLS-p53(380–386-3Ac)_25µM_Rep 1

value: 24 h treatment with 25µM R6-NLS-p53(380–386-3Ac)


title: A549_ 24 h_ R6-NLS-p53(380–386-3Ac)_25µM_Rep 2


title: Columbia-0_R2

source_name: seedlings

value: 13 DAG shoots

value: wildtype


title: Human_CELSS180_R75_01_BloodCell

source_name: Blood Cell


title: ZEN [Z1 ]


title: Columbia-0_R3


title: Human_CELSS180_R120_01_BloodCell


title: PLv IR+MSC 3

source_name: PLv from mouse 3 receiving cranial radiation and MSC


title: PLv IR 1

source_name: PLv from mouse 1 receiving cranial radiation


title: OTA [O3 ]

value: OTA treated


title: A549_ 12 h_ R6-NLS-p53(380–386-3Ac)_25µM_Rep 2


title: Human_CELSS180_R60_01_BloodCell

value: whole blood


title: Human_CELSS180_R105_01_BloodCell


title: OTA [O1 ]


title: AFB1 [A3 ]

value: AFB1 treated


title: OTA [O2 ]


title: siSGK_4

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

data_processing:
Illumina bcl2fastq version 2.19 were used to the basecalling.
Clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Hisat2 v2.0.5 and  paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of  splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample

source_name: ME180 cell lines

extract_protocol:
RNAs were isolated from ME180 cells using the TRIzol (Invitrogen) reagent by following the company manual. RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0  Flurometer (Life Technologies, CA, USA).  RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: ME180 cells were transfected with siControl or siSGK1 for 48 hours.

tag: origin

value: Cervical cancer

tag: morphology

value: Epithelial

value: siSGK1 transfected


title: Human_CELSS180_R90_01_BloodCell


title: Hipp NonIR 2

description: Gene expression data from the Hipp isolated from untreated mice

source_name: Hipp from mouse 2 that was not irradiated

value: hippocampus


title: Human_CELSS180_Pre15_01_BloodCell


title: A549_ 12 h_ R6-NLS-p53(380–386-3Ac)_25µM_Rep 1


title: Human_CELSS180_R30_01_BloodCell


title: siSGK_3


title: A549 _ Untreated_Rep 2

value: untreated


title: Hipp NonIR 1

source_name: Hipp from mouse 1 that was not irradiated


title: KI_Homo_0_day_2

first: Jun

last: Tanihata

address: 3-25-8 Nishishinbashi, Minato-ku

institute: The Jikei Univ Sch of Med

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally, 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: Hybridization signals were immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc, CA, USA).

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.

label_protocol: Total RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA was labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen).

extract_protocol: Total RNAs were extracted from ventricular tissue in wild-type and TNNT2ΔK210/ΔK210 mice at 0-day old and 1-week old, using TRIZOL reagent (Thermo Fisher Scientific, MA). Three ventricular samples from each group were combined for comparison. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: Ventricle

value: immediately at birth

tag: genotype


title: PLv IR+MSC 1

source_name: PLv from mouse 1 receiving cranial radiation and MSC

value: brain lateral ventricles


title: WT_0_day_2

value: wild-type


title: Hipp NonIR 3

source_name: Hipp from mouse 3 that was not irradiated


title: siSGK_2


title: A549 _ Untreated_Rep 1

value: lungs epithelial cells


title: AFB1 [A2 ]

value: primary hepatocytes


title: Human_CELSS180_Pre45_01_BloodCell


title: NC_4

value: siControl transfected


title: AFB1 [A1 ]


title: WT_0_day_1


title: Human_CELSS180_R2_01_BloodCell


title: KI_Homo_0_day_1


title: NC_3


title: control [C3 ]

value: no toxin treatment


title: NC_2


title: Hipp IR 1

description: Gene expression data from the Hipp isolated from mice receiving radiation

source_name: Hipp from mouse 1 receiving cranial radiation

value: radiation


title: KI_Homo_1w_2

value: 1 week old


title: Hipp IR 3

source_name: Hipp from mouse 3 receiving cranial radiation


title: Hipp IR 2

source_name: Hipp from mouse 2 receiving cranial radiation


title: control [C2 ]

source_name: primary hepatocytes


title: KI_Homo_1w_1


title: Hipp IR+MSC 2

description: Gene expression data from the Hipp isolated from mice receiving radiation and MSCs

source_name: Hipp from mouse 2 receiving cranial radiation and MSC

value: radiation and MSCs


title: Hipp IR+MSC 1

source_name: Hipp from mouse 1 receiving cranial radiation and MSC


title: Hipp IR+MSC 3

source_name: Hipp from mouse 3 receiving cranial radiation and MSC


title: control [C1 ]


title: panicle  of heat tolerant line 252 under optimal temperature, biological rep3

status: Public on Jun 20 2019

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road Furong district

institute: Hunan Agricultural University

description: Gene expression data from panicle under optimal temperature treatment

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

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0,The gene classification based on gene ontology was conducted as previously described(Hobo et al. 2008). The pathway analysis was performed with MapMan

organism: Oryza sativa

source_name: Rice panicle under optimal temperature treatment

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

growth_protocol: panicles were collected,frozen in liquid nitrogen immediately,and stored at -80 ℃.

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

treatment_protocol: High temperature treatment( 37 ℃ day/30 ℃ night cycle for 5 d),optimal temperature treatment(30 ℃day/ 25 ℃ night cycle) .

value: Panicle


title: panicle  of heat sensitive line 082 under optomal temperature, biological rep1


title: WT_1W_2

source_name: WT_Ventricle _1W_2


title: panicle  of heat sensitive line 082 under optimal temperature, biological rep3


title: NPC_INI1-/-_TP53-/-

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data analyses were processed using Genespring software (version13.0). For the analysis of hiPSC_INI1-/-_TP53-/- and NPC_INI1-/-_TP53-/-,201B7_TP53_INI1_loss.CEL and NE_TP53_INI1_loss.CEL were loaded using Genespring. For the analysis of hiPSC_INI1-/-_TP53-/--derived_tumor and NPC_INI1-/-_TP53-/--derived_tumor, hiPSC_INI1-/-_TP53-/--derived_tumor.CEL and NPC_INI1-/-_TP53-/--derived_tumor.CEL were loaded using Genespring.

source_name: NPCs

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: hiPSC were cultured in AK03N on cell culture plates coated with laminin-511. NPCs were cultured in neural expansion medium containing 50% Neurobasal medium, 50% Advanced DMEM/F12 and neural induction supplement on cell culture plates coated with laminin-511.

extract_protocol: RNeasy Plus Mini kit

tag: cell type

value: 201B7-derived cells


title: CHLA_04_AT/RT

source_name: AT/RT cell line

value: AT/RT cell line


title: WT_1W_1

source_name: WT_Ventricle _1W_1


title: panicle of heat tolerant line 252 under high temperature, biological rep3

description: Gene expression data from panicle under high temperature treatment

source_name: Rice panicle under high temperature treatment


title: panicle of heat sensitive line 082 under high temperature, biological rep1


title: hiPSC_INI1-/-_TP53-/-

source_name: hiPSCs


title: panicle  of heat sensitive line 082 under optimal temperature, biological rep2


title: panicle  of heat sensitive line 082 under high temperature, biological rep3


title: panicle of heat tolerant line 252 under high temperature, biological rep2


title: panicle  of heat sensitive line 082 under high temperature, biological rep2


title: hiPSC_INI1-/-_TP53-/--derived_tumor

source_name: hiPSC-derived tumor


title: panicle  of heat tolerant line 252 under optomal temperature, biological rep1


title: NPC_INI1-/-_TP53-/--derived_tumor

source_name: NPC-derived tumor


title: panicle  of heat tolerant line 252 under optimal temperature, biological rep2


title: GBM822

city: Beijing

first: tao

middle: bo

address: No. 17 South Panjiayuan, Chaoyang District

institute: Cancer Hospital

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 p/n 5188-5325) and 1 minute with 37°C GE Wash buffer 2 (Agilent p/n 5188-5326).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with the Agilent's Feature Extraction Software (v10.5)  using default parameters (protocol GE1_105_Dec08 and Grid 014850_D_20070207) to obtain background subtracted and spatially detrended processed signal intensities. The raw data was normalized by the GenespringGX Software (Agilent, version 11.5).

source_name: brain tissue

label_protocol: 500ng purified total RNA was reverse transcribed into cDNA, transcribed into cRNA and labeled with Cyanine-3 (Cy3) using the Agilent’s Quick Amp Labeling Kit (Agilent p/n 5190-0442) 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: Total RNA was extracted from frozen tissue using the mirVana miRNA Isolation kit (Ambion 1561) according to the manufacturer’s specifications, and purified by the RNeasy mini Kit (Cat No.74106, Qiagen, Germany). RNA integrity was detected using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: The brain tissue samples were rinsed with normal saline after surgical resection and divided into two parts, one of which was placed in liquid nitrogen immediately and then stored at -80°C until use, and the other was placed in formaldehyde solution and for hematoxylin-eosin stained to assess the percentage of tumor cells.

tag: gender

value: M

tag: history

value: GBM

tag: grade

tag: idh1 mutation


title: panicle of heat tolerant line 252 under high temperature, biological rep1


title: GBM775


title: GBM798

value: F


title: GBM778


title: GBM764


title: GBM741


title: GBM709


title: GBM729


title: GBM683


title: GBM714


title: GBM700


title: GBM684


title: GBM734


title: GBM699


title: GBM646


title: GBM693


title: GBM664


title: GBM719


title: GBM654


title: GBM606


title: GBM680


title: GBM713


title: GBM628


title: GBM604


title: GBM612


title: GBM609


title: GBM640


title: GBM594


title: GBM593


title: GBM597


title: Columbia-0_R1

first: magdalena

last: potok

address: 4045 Terasaki Life Sciences Building

institute: UCLA

source_name: seedlings

tag: developmental stage

value: 13 DAG shoots

tag: ecotype

tag: genotype/variation

value: wildtype


title: GBM588


title: GBM649


title: GBM549


title: GBM570


title: GBM464


title: GBM527


title: GBM573


title: GBM575


title: GBM547


title: GBM557


title: GBM462


title: GBM530


title: GBM518


title: GBM454


title: GBM404


title: GBM512


title: GBM437


title: GBM401


title: GBM444


title: GBM451


title: GBM371


title: GBM375


title: GBM442


title: GBM366


title: GBM504


title: GBM373


title: GBM380


title: GBM439


title: GBM419


title: GBM436


title: GBM377


title: GBM342


title: GBM370


title: GBM346


title: GBM311


title: GBM335


title: GBM292


title: GBM308


title: GBM345


title: GBM221


title: GBM324


title: GBM287


title: GBM156


title: GBM240


title: GBM011


title: GBM210


title: GBM104


title: GBM195


title: GBM255


title: GBM203


title: GBM178


title: GBM225


title: GBM168


title: GBM205


title: GBM126


title: GBM124


title: GBM218


title: GBM172


title: GBM264


title: MSC3 GRN treated

city: Heidelberg

first: Lena

last: Schulze-Edinghausen

address: Im Neuenheimer Feld 580

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center (DKFZ) Heidelberg

hyb_protocol: Standard Illumina Hybridisation Protocol  Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355 (Whole-Genome Gene Expression  Direct Hybridization Assay Guide).

data_processing: Analysis of gene expression data was performed based on unique Illumina probes (instead of transcripts or genes). First, samples were processed by background correction and detection filtering to exclude non-expressed probes (results provided as normalized matrix). Pairwise comparison of untreated (MSCs cultured alone) versus treated samples (MSCs in CLL co-culture or GRN treated MSCs) was then performed using the empirical Bayes approach by Smyth (analyzed data table for deregulated genes by MSCs in CLL co-culture is provided). For each probe a linear model was fitted with factors characterizing treatment and donor. Significant transcripts were selected based on the moderated t statistic. The Benjamini-Hochberg correction was applied in order to control the false discovery rate.

source_name: MSC

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) was used to generate single-stranded cRNA from input amounts of 200ng total RNA. Label: Biotin, Cy3-Streptavidin.

growth_protocol: 5x 10^5 MSCs were cultured in 2 ml MSC-growth medium (MSCGM Bulletkit, Lonza, Walkersville, MD, USA) in 6 cm dishes for 5 days.

extract_protocol: RNA was isolated using TRIzol reagent (Invitrogen/Thermo Fisher Scientific, Waltham, MA, USA) and the Qiagen 74004 RNeasy Micro Kit (Quiagen, Hilden, Germany) according to manufacturers´ instructions.

treatment_protocol: MSCs were either left untreated, treated with 3 µg/ml GRN (R&D Systems, Minneapolis, MN, USA) daily or co-cultured with 5x 10^6 CD19-purified CLL cells (purities >99% CD5+ CD20+ cells).

tag: msc donor

value: treated with 3 microg/ml GRN daily


title: MSC1 CLL15 co-culture

value: co-cultured with 5x 10^6 CD19-purified CLL cells


title: MSC4 GRN treated


title: MSC2 CLL15 co-culture


title: MSC4 untreated

value: untreated


title: MSC2 GRN treated


title: MSC3 untreated


title: MSC1 CLL16 co-culture


title: MSC2 CLL16 co-culture


title: MSC1 GRN treated


title: Kidney_M1IKO_Input

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
ChIP-seq runs were all 50-100bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Genome_build: mm9
Supplementary_files_format_and_content: *.bedGraph files are for display in the UCSC genome browser

source_name: kidney

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB, Mol Endo. 2012). Briefly, samples were subjected to immuno-precipitation using either a control IgG antibody or the indicated experimental antibody.  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50-100mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The ChIP samples were repeated in biological triplicate in the same manner. Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Mice were injected with indicated hormone and concentration. pBMC samples were treated ex vivo in a cell culture dish.

value: vehicle (ethanol and PBS)

tag: antibody


title: Kidney_M21IKO_Input


title: pBMC_WT_Input

source_name: peripheral blood monocytes


title: TPTG_C27KO_H3K9Ac_Veh_rep1

source_name: thyroparathyroid


title: Kidney_WT_Input


title: TPTG_C27KO_Input


title: TPTG_WT_H3K36me3_Veh_rep1


title: Kidney_VKO_Input

value: VDR-KO


title: TPTG_WT_H3K36me3_125_rep1


title: TPTG_WT_Input


title: Kidney_C27KO_Input


title: TPTG_M1IKO_Input


title: TPTG_WT_H3K9Ac_Veh_rep1


title: TPTG_WT_H3K4me1_Veh_rep1


title: TPTG_M1IKO_H3K9Ac_Veh_rep1


title: TPTG_WT_H3K4me1_125_rep1


title: pBMC_WT_pCREB_Fsk_rep2

value: 10 nM forskolin


title: pBMC_WT_pCREB_Fsk_rep1


title: pBMC_WT_pCREB_Veh_rep3


title: MSC2 untreated


title: pBMC_WT_pCREB_Veh_rep2


title: pBMC_WT_pCREB_Veh_rep1


title: TPTG_M1IKO_H3K4me1_Veh_rep1


title: MSC1 untreated


title: pBMC_WT_VDR_125_rep1

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: pBMC_WT_VDR_125_rep2


title: TPTG_C27KO_H3K4me1_Veh_rep1


title: pBMC_WT_VDR_Veh_rep2


title: pBMC_WT_VDR_Veh_rep3


title: pBMC_WT_VDR_Veh_rep1


title: Kidney_C27KO_H3K9Ac_Veh_rep1


title: Kidney_C27KO_H3K9Ac_Veh_rep2


title: Kidney_C27KO_H3K9Ac_Veh_rep3


title: TPTG_WT_H3K9Ac_125_rep1


title: Kidney_VKO_H3K9Ac_Veh_rep3


title: Kidney_M21IKO_pCREB_Veh_rep1


title: Kidney_M21IKO_pCREB_Veh_rep3


title: Kidney_VKO_H3K9Ac_Veh_rep1


title: Kidney_M21IKO_VDR_125_rep2


title: Kidney_M21IKO_VDR_125_rep3


title: Kidney_VKO_H3K9Ac_Veh_rep2


title: Kidney_M21IKO_pCREB_Veh_rep2


title: Kidney_M21IKO_VDR_125_rep1


title: pBMC_WT_VDR_125_rep3


title: Kidney_M21IKO_VDR_Veh_rep3


title: Kidney_M21IKO_VDR_Veh_rep2


title: Kidney_M21IKO_VDR_Veh_rep1


title: Kidney_M1IKO_H3K9Ac_125_rep3


title: Kidney_M1IKO_H3K9Ac_125_rep2


title: Kidney_M1IKO_H3K9Ac_Veh_rep1


title: Kidney_M1IKO_VDR_125_rep3


title: Kidney_M1IKO_pCREB_Veh_rep2


title: Kidney_M1IKO_H3K9Ac_Veh_rep2


title: Kidney_M1IKO_H3K9Ac_125_rep1


title: Kidney_M1IKO_pCREB_Veh_rep3


title: Kidney_M1IKO_pCREB_Veh_rep1


title: Kidney_M1IKO_VDR_Veh_rep2


title: Kidney_M1IKO_VDR_Veh_rep3


title: Kidney_M1IKO_VDR_Veh_rep1


title: Kidney_M1IKO_H3K9Ac_Veh_rep3


title: Kidney_M1IKO_VDR_125_rep2


title: Kidney_WT_H3K36me3_PTH_rep2

value: 230 ng/g bw PTH


title: Kidney_WT_H3K36me3_PTH_rep3


title: Kidney_WT_H3K36me3_FGF23_rep3

value: 50 ng/g bw FGF23


title: Kidney_WT_H3K36me3_PTH_rep1


title: Kidney_WT_H3K36me3_125_rep3


title: Kidney_WT_H3K36me3_FGF23_rep1


title: Kidney_WT_H3K36me3_FGF23_rep2


title: Kidney_M1IKO_VDR_125_rep1


title: Kidney_WT_H3K36me3_Veh_rep2


title: Kidney_WT_H3K36me3_125_rep1


title: Kidney_WT_H3K36me3_Veh_rep3


title: Kidney_WT_H3K36me3_Veh_rep1


title: Kidney_WT_H3K9Ac_FGF23_rep3


title: Kidney_WT_H3K9Ac_FGF23_rep2


title: Kidney_WT_H3K9Ac_FGF23_rep1


title: Kidney_WT_H3K9Ac_PTH_rep3


title: Kidney_WT_H3K9Ac_PTH_rep1


title: Kidney_WT_H3K9Ac_PTH_rep2


title: TPTG_WT_VDR_125_rep1


title: Kidney_WT_H3K9Ac_125_rep3


title: Kidney_WT_H3K9Ac_125_rep2


title: Kidney_WT_H3K9Ac_125_rep1


title: Kidney_WT_H3K9Ac_Veh_rep3


title: Kidney_WT_H3K9Ac_Veh_rep1


title: Kidney_WT_H3K9Ac_Veh_rep2


title: Kidney_WT_H3K36me3_125_rep2


title: Kidney_WT_H3K4me1_FGF23_rep2


title: Kidney_WT_H3K4me1_125_rep1


title: Kidney_WT_H3K4me1_FGF23_rep1


title: Kidney_WT_H3K4me1_125_rep2


title: Kidney_WT_H3K4me1_FGF23_rep3


title: Kidney_WT_H3K4me1_PTH_rep3


title: Kidney_WT_H3K4me1_125_rep3


title: Kidney_WT_H3K4me1_PTH_rep1


title: Kidney_WT_H3K4me1_PTH_rep2


title: Kidney_WT_H3K4me1_Veh_rep2


title: Kidney_WT_pCREB_PTH_rep3


title: Kidney_WT_H3K4me1_Veh_rep1


title: Kidney_WT_pCREB_PTH_rep2


title: Kidney_WT_pCREB_Veh_rep3


title: Kidney_WT_VDR_Veh_rep3


title: Kidney_WT_pCREB_Veh_rep2


title: Kidney_WT_VDR_125_rep3


title: Kidney_WT_VDR_125_rep1


title: Kidney_WT_VDR_125_rep2


title: Kidney_WT_pCREB_PTH_rep1


title: Kidney_WT_pCREB_Veh_rep1


title: Kidney_WT_VDR_Veh_rep1


title: Kidney_WT_H3K4me1_Veh_rep3


title: SS2_17_449_star_mm10_P2

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

institute: KI

description:
Lung
Day 10 Lymph node and MLN mouse 1

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file

source_name: Day 10 Lymph node and MLN mouse 1

extract_protocol:
Single memory T helper cells (CD4+CD3+CD44+) sorted directly inflammed tissues (either BAL, lung or mLN) into 2% titron.
SMART-SEQ2 (see Picelli et al 2014)
Single cell RNA-Seq

tag: tissue

value: Lymph Node

tag: model

value: HDM


title: SS2_17_449_star_mm10_P6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Kidney_WT_VDR_Veh_rep2

tag: treatment


title: SS2_17_449_star_mm10_P13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_P17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_O11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_N13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: pBMC_WT_pCREB_Fsk_rep3


title: SS2_17_449_star_mm10_L8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: TPTG_WT_VDR_Veh_rep1


title: SS2_17_449_star_mm10_L7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L20

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_M11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_L14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K3

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: NNI-11_Clone3_KD [AFG1252-8]

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

description: Gene expression data from GPCs

hyb_protocol: 100 ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create biotin-labeled aRNA (amplified RNA). The aRNA was then fragmented and hybridized to Affymetrix Human U133 Plus 2.0 Arrays for 16 hours at 45oC with rotation at 60 rpm.

scan_protocol: GeneChips were scanned using the FS450_0001 fluidics protocol on 2 fluidics station and scanned using an Affymetrix 3000 7G scanner

data_processing: The data were processed with dChip normalization strategy using R/packages

source_name: Patient-Derived Glioma-propagating cells KD for STAT3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: GPCs were cultured as per standard protocols described in PMID: 21196406

treatment_protocol: GPCs were perturbed with lentiviral-mediated knock-down (KD) for STAT3

value: GBM cells

value: KD for STAT3

tag: age


title: NNI-11_Clone1_KD [AFG1252-6]

description: Gene expression data from GPCs


title: NNI-12_Clone2_KD [AFG1252-23]

description: Gene expression data from GPCs


title: NNI-12_Clone3_KD [AFG1252-24]

description: Gene expression data from GPCs


title: NNI-12_NT_NT [AFG1252-9]

description: Gene expression data from GPCs

source_name: Patient-Derived Glioma-propagating cells non-targeting

value: non-targeting


title: NNI-11_Clone1_KD [AFG1252-18]

description: Gene expression data from GPCs


title: Beta-Like_Late

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

data_processing:
Reads were mapped on mm10 using bowtie2.
Reads were converted to reads per million.
Coverage data in 10 kb bins are calculated from mapped reads using samtools and bedtools.
Replication timing score is calculated as base 2 log of early to late coverage ratio in 10 kb windows.
Genome_build: hg38
Supplementary_files_format_and_content: The proceesed data file ("Differentiation_Repli-seq.txt") is the replication timing caluclated as the base 2 log ratio between early and late S fraction. Column 1 and 2 are CHR and POS. Remaining columns are scaled , smoothed quantile normalized replication timing score.

source_name: human ESC (H9)

growth_protocol: H9 hESCs were cultured under feeder-free conditions on Geltrex (Thermo Fisher, A14133) coated dishes, and maintained in StemPro (Thermo Fisher, A100701) culture media per manufacture’s specifications.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Marchal et al., 2018). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: Differentiation towards Definitive Endoderm for 24 h and 48 h time-points were carried out after adapting protocol from Schulz et al., 2012 to adherent culture. Briefly, hESC cultures at ~70% confluency were washed 2x with cold PBS and stimulated to differentiate by the addition of RPMI (Invitrogen), 50ng/ml Wnt (CellGS, GFM77), 100ng/ml Activin A (CellGS, GFH6). 24 hours after stimulation, media was replaced with RPMI containing 0.2% FBS, and 100 ng/ml Activin A. Definitive Endoderm, Pancreatic Progenitor, Poly-Hormonal cells and Pancreatic Beta-like cells were made from hESCs as previously described in Pagliuca et al., 2014 with modifications. H9 hESC aggregates were made by seeding cells at 1 million/ml in 5.5-6ml HAIF with 10M ROCK-inhibitor (Y27632) per well in a 6-well plate. Cells were incubated on rotator (97 rpm) at 37oC with 5% CO2 overnight.  Aggregates were washed 3x with MCDB 131 media and re-suspend in DE media with 3uM CHIR and 10M Y27632. On day 1 and 2, the media was replaced with DE media (MCB131, 1% Probumin (10% stock made in MCB131), 1x NEAA, 2mM Glutagro, 1x Trace Elements A, B, & C, 10ug/ml Human Transferrin, 50ug/ml L- Ascorbic acid, 100ng/ml Activin, 8ng/ml bFGF.). On Day 3 Definitive Endoderm cells were collected. From day 3 onwards the method in Pagliuca et al., 2014 was followed to collect Pancreatic Progenitor, Poly-Hormonal cells and Pancreatic Beta-like cells.

tag: s-phase fraction

value: Late S fraction

tag: replicate

tag: differentiation state

value: Beta-Like


title: SS2_17_449_star_mm10_K6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: NNI-11_Clone2_KD [AFG1252-19]

description: Gene expression data from GPCs

tag: genotype


title: NNI-11_Clone2_KD [AFG1252-7]

description: Gene expression data from GPCs


title: NNI-12_NT_NT [AFG1252-21]

description: Gene expression data from GPCs


title: NNI-11_NT_NT [AFG1252-17]

description: Gene expression data from GPCs


title: Beta-Like_Early

value: Early S fraction


title: NNI-12_Clone1_KD [AFG1252-10]

description: Gene expression data from GPCs


title: SS2_17_449_star_mm10_K1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: NNI-11_Clone3_KD [AFG1252-20]

description: Gene expression data from GPCs


title: NNI-11_NT_NT [AFG1252-5]

description: Gene expression data from GPCs


title: SS2_17_449_star_mm10_K21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Polyhormonal_Late

value: Polyhormonal


title: NNI-12_Clone2_KD [AFG1252-11]

description: Gene expression data from GPCs


title: NNI-12_Clone1_KD [AFG1252-22]

description: Gene expression data from GPCs


title: NNI-12_Clone3_KD [AFG1252-12]

description: Gene expression data from GPCs


title: Polyhormonal_Early


title: SS2_17_449_star_mm10_K16

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K17

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K18

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Definitve Endoderm_Early

value: Definitve Endoderm


title: Definitve Endoderm_Late


title: Pancreatic Progenitor_Early

value: Pancreatic Progenitor


title: SS2_17_449_star_mm10_K14

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K13

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K12

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 48 h_Rep1_Early

value: 48 hours


title: 48 h_Rep2_Late


title: SS2_17_449_star_mm10_K11

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 48 h_Rep1_Late


title: SS2_17_449_star_mm10_K10

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 24 h_Rep2_Late

value: 24 hours


title: SS2_17_449_star_mm10_J9

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J8

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: Pancreatic Progenitor_Late


title: 24 h_Rep1_Early


title: SS2_17_449_star_mm10_J6

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 24 h_Rep1_Late


title: 12 h_Rep2_Late

value: 12 hours


title: 12 h_Rep2_Early


title: SS2_17_449_star_mm10_J4

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_K15

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 12 h_Rep1_Late


title: 12 h_Rep1_Early


title: SS2_17_449_star_mm10_J2

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 6 h_Rep2_Early

value: 6 hours


title: 6 h_Rep2_Late


title: 48 h_Rep2_Early


title: SS2_17_449_star_mm10_J23

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 6 h_Rep1_Late


title: SS2_17_449_star_mm10_J24

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: 6 h_Rep1_Early


title: SS2_17_449_star_mm10_J22

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: H9 ESC_Rep2_Late

value: ESC


title: H9 ESC_Rep2_Early


title: 24 h_Rep2_Early


title: SS2_17_449_star_mm10_J1

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J21

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J19

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J7

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J5

description:
Lung
Day 10 Lymph node and MLN mouse 1


title: SS2_17_449_star_mm10_J17

description:
Lung
Day 10 Lymph node and MLN mouse 1