title: intestinal organoids, control, biological rep-2

city: Kyoto

first: Masamichi

last: Imajo

address: Yoshidakonoe-cho, Sakyo-ku,

institute: Kyoto University

hyb_protocol: Following fragmentation, 5.5 ug of single stranded DNA was hybridized for 17 hr at 45C on the GeneChip Mouse Gene 1.0 ST arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned using an Affymetrix GeneChip Scanner.

data_processing: Images from scanned chips were processed by using the default settings of Affymetrix GeneChip Command Console (AGCC) software. The CELL files created by AGCC were imported into Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific). Expression signals of all genes (probe sets) were calculated using the RMA algorithm (default settings).

source_name: intestinal organoids cultured in the absense of CHIR99021

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Intestinal organoids were embedded in Matrigel and cultured in Advanced DMEM/F12 medium supplemented with EGF, Noggin, and R-spondin 1 (ENR medium).

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

treatment_protocol: Intestinal organoids were cultured in the ENR medium supplemented with a GSK3 inhibitor, CHIR99021, (5 microM) or vehicle (DMSO) for four days.

tag: strain

value: adult

value: intestinal epithelium

value: intestinal organoids

tag: treated with

value: vehicle (DMSO) for 4 days.


title: intestinal organoids, control, biological rep-1

status: Public on Feb 08 2018

type: RNA

country: Japan

label: biotin

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue

tag: cell type


title: Pancreatic cancer 27

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

institute: Keio University

description: Batch 2

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

scan_protocol: GeneChip Scanner 3000 7G procedure

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

organism: Homo sapiens

source_name: Patient 27

label_protocol: Standard Affymetrixt protocol

extract_protocol: QIAGEN RNeasy Plus Mini Kit procedure

value: Pancrea

tag: disease state

value: cancer


title: Pancreatic cancer 30

description: Batch 2

source_name: Patient 30


title: intestinal organoids, CHIR99021, biological rep-2

source_name: intestinal organoids cultured in the presence of CHIR99021

value: GSK3 inhibitor, CHIR99021, (5 microM) for 4 days.


title: Pancreatic cancer 31

description: Batch 2

source_name: Patient 31


title: Pancreatic cancer 32

description: Batch 2

source_name: Patient 32


title: intestinal organoids, CHIR99021, biological rep-1


title: Pancreatic cancer 24 sgRNA GATA6 long-form

description: Batch 2

source_name: Patient 24


title: CP_HuD_030

city: Providence

first: Edward

middle: G

last: Stopa

state: RI

address: 593 Eddy Street

department: Pathology & Laboratory Medicine

country: USA

institute: Brown University

hyb_protocol: Hybridization (45°C for 18 h), labeling, and scanning, using Affymetrix ovens, fluidics stations, and scanners, were conducted following the protocols recommended (NuGEN Technologies). Gene expression profiling was performed with a customized Human Affymetrix GeneChip microarray (GEO platform GPL 10379) that included 57,060 probesets (Affymetrix, Santa Clara, CA).

data_processing: Data were normalized by robust multiarray average (RMA).

source_name: choroid plexus

label_protocol: Samples were amplified and labeled using an automated version of the NuGEN Ovation WB protocol after normalizing to 50 ng total RNA input (NuGEN Technologies, San Carlos, CA).

extract_protocol:
Post-mortem tissue samples from healthy controls (Ctrl) of mean age 60 y/mean PMI 22 h; and from patients with advanced AD Braak & Braak stage III-VI (80 y/17 h), FTD (72 y/NA) and HuD (71 y/19 h), were snap frozen in liquid N2 and stored at -80°C in the Brown University Brain Tissue for Neurodegenerative Disorders Resource Center until processed.
RNA from CP was extracted using TRIzol reagent in accordance with instructions by manufacturer (Thermo-Fisher, Grand Island, NY).
Isolated RNA samples were assayed for quality via the Agilent RNA 6000 Pico Kit on Agilent Bioanalyzer (Santa Clara, CA) and RNA yield via Quanti-iT RiboGreen RNA Assay Kit (Thermo-Fisher).

tag: Sex

value: female

tag: post mortem interval (hr)

tag: apoe genotype

value: HD (grade IV)


title: CP_FTD_027

scan_protocol: Hybridization (45°C for 18 h), labeling, and scanning, using Affymetrix ovens, fluidics stations, and scanners, were conducted following the protocols recommended (NuGEN Technologies). Gene expression profiling was performed with a customized Human Affymetrix GeneChip microarray (GEO platform GPL 10379) that included 57,060 probesets (Affymetrix, Santa Clara, CA).

value: FTD


title: Pancreatic cancer 26

description: Batch 2

source_name: Patient 26


title: CP_FTD_026

value: male

value: FTD Pick's disease


title: CP_FTD_025

value: FTD & motor neuron disease


title: Pancreatic cancer 29

description: Batch 2

source_name: Patient 29


title: Pancreatic cancer 28

description: Batch 2

source_name: Patient 28


title: Pancreatic cancer 34

description: Batch 2

source_name: Patient 34


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

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit.

scan_protocol: Affymetrix GeneChip Scanner.

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

label: Biotin

source_name: Muscle

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: TriZol

tag: genetic background

tag: genotype/variation

value: 8 Weeks

value: Male

tag: injury

value: Cardiotoxin

tag: time point (days after injury)

value: muscle macrophages

tag: phenotype markers

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

tag: separation method

value: Dissection / Trimming


title: Pancreatic cancer 41

description: Batch 2

source_name: Patient 41


title: CP_HuD_031


title: Pancreatic cancer 25 normal like

description: Batch 2

source_name: Patient 25


title: CP_HuD_029


title: CP_CTR_012

value: normal control


title: Pancreatic cancer 24 shRNA GATA6

description: Batch 2


title: scBS-hSP3

type: SRA

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

description: Raw data not provided due to patient privacy concerns

library_source: genomic

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

molecule: genomic DNA

source_name: Sperm

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

value: Sperm

tag: gender

tag: bulk or single cell

value: single cell


title: Pancreatic cancer 23 normal like

description: Batch 2

source_name: Patient 23

value: Pancrea

value: cancer


title: CP_FTD_024


title: Pancreatic cancer 22 normal like

description: Batch 2

source_name: Patient 22


title: CP_CTR_009


title: Pancreatic cancer 24

description: Batch 2


title: CP_ALZ_023

value: AD (severe Braak V-VI)


title: CP_CTR_008

value: female


title: Pancreatic cancer 24 shRNA control

description: Batch 2


title: Pancreatic cancer 18 normal like

description: Batch 1

source_name: Patient 18


title: CP_CTR_010


title: e14.5 Lgr5+ interzone cells from developing forelimb digits

city: Hong Kong S.A.R.

first: Kathryn

last: Cheah

state: Hong Kong

address: 3/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

department: School of Biomedical Sciences

institute: University of Hong Kong

description: e14.5, forelimb digit, Lgr5+, Lgr5-GFP-CreERT mouse

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with default parameter setting.
Fragment Per Kilobase of exon per Megabase of library size value for each gene was calculated by using the Gencode mouse annotation file version 16. Cufflink program was used to normalize the gene expression levels with default parameter setting.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: All mice were kept in the Minimal Disease Area in the Laboratory Animal Unit, the University of Hong Kong, a member of the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC).

extract_protocol:
Digested in a mixture of TrypLE Express (Gibco) and 0.1% (w/v) DNase I for 20 min. The isolated cells were filtered through 40μm cell strainer.
cDNA libraries were constructed with 10ng of total RNA using SMARTer Ultra Low Input RNA Kit for Sequencing (v3, Illumina).

tag: strain/background

tag: developmental stage

value: forelimb digits, interzone


title: Pancreatic cancer 21 normal like

description: Batch 2

source_name: Patient 21


title: CP_ALZ_022

tag: age

value: male


title: Pancreatic cancer 19

description: Batch 1

source_name: Patient 19

tag: tissue


title: CP_CTR_007


title: CP_ALZ_018


title: Pancreatic cancer 13

description: Batch 2

source_name: Patient 13


title: CP_ALZ_019

value: AD (severe + Lewy body disease)


title: e14.5 Lgr5- non-interzone cells from developing forelimb digits

description: e14.5, forelimb digit, Lgr5-, Lgr5-GFP-CreERT mouse

value: forelimb digits, non-interzone


title: Pancreatic cancer 17

description: Batch 2

source_name: Patient 17


title: Pancreatic cancer 16

description: Batch 1

source_name: Patient 16


title: CP_CTR_011

source_name: choroid plexus


title: CP_ALZ_015

value: AD (Braak III-IV)


title: CP_ALZ_017


title: Pancreatic cancer 15

description: Batch 2

source_name: Patient 15


title: Pancreatic cancer 8

description: Batch 2

source_name: Patient 8


title: Pancreatic cancer 20

description: Batch 2

source_name: Patient 20


title: Pancreatic cancer 11

description: Batch 2

source_name: Patient 11


title: Pancreatic cancer 14

description: Batch 2

source_name: Patient 14


title: Pancreatic cancer 5

description: Batch 2

source_name: Patient 5


title: Pancreatic cancer 12

description: Batch 2

source_name: Patient 12


title: XFG10

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cell Biology and Anatomy

institute: Medical College of Georgia

hyb_protocol: Purified and labeled target/probe complexes were hybridized to the manufacturer supplied cartridge, according to the manufacturer's instructions.

scan_protocol: The cartridges were digitally imaged and analyzed using the nCounter Digital Analyzer.

data_processing: The raw miRNA counts were normalized based on RNA content using the trimmed geometric mean, using the miRNAs with the median 40% of the counts, and the geometric mean of the positive control probes POS_C, POS_D, and POS_E using the nSolver 3.0 software. After normalization, data was imported into R, and batch effects were adjusted for using the limma package.

label: not provided

source_name: Aqueous humor, XFG

label_protocol: RNA were hybridized to color codes and washed using a two step-magnetic bead method, according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from the AH samples using the miRCURY RNA Isolation Kit for Cell and Plant (Exiqon, Woburn, MA), according to the manufacturer’s instructions.

tag: disease status

value: Exfoliation glaucoma (XFG)

value: Aqueous humor

tag: age (years)

tag: race

value: Female


title: XFG12

tag: Sex


title: XFG9


title: XFG8

value: Male


title: XFG7


title: XFG11


title: XFG6


title: Pancreatic cancer 7

description: Batch 2

source_name: Patient 7

tag: disease state


title: Pancreatic cancer 4 normal like engineered KCTS Wnt adapted

description: Batch 2

source_name: Patient 4


title: Pancreatic cancer 4 normal like engineered KCTS Wnt control

description: Batch 2


title: Pancreatic cancer 4 normal like engineered KCTS

description: Batch 2


title: Pancreatic cancer 4 normal like engineered KCT

description: Batch 2


title: Pancreatic cancer 4 normal like engineered KTS

description: Batch 2


title: T12_0x_48

city: Wyndmoor

first: Gaylen

middle: C

last: Ulrich

state: PA

address: 600 East Mermaid Lane

institute: USDA/ARS/Eastern Regional Research Center

data_processing:
RNA-seq data were mapped to the E. coli O157:H7 Sakai genome using the Subjunc aligner program from the Subread package (v1.4.6)   (http://bioinf.wehi.edu.au/subread/).
The alignment Bam files were compared against the gene annotation general feature format (GFF) file, and raw counts for each gene were  generated using the featureCounts tool from Subread. The raw counts data of the expressed genes was normalized for RNA composition using the trimmed mean of M values (TMM) method (http://www.ncbi.nlm.nih.gov/pubmed/20196867) from the Empirical analysis of Digital Gene Expression Data in R (EdgeR) package   (https://bioconductor.org/packages/release/bioc/html/edgeR.html), then transformed to log2CPM (counts per million) values using the voom method   (http://www.ncbi.nlm.nih.gov/pubmed/24485249) from the R LIMMA package  (https://bioconductor.org/packages/release/bioc/html/limma.html).
Next, a linear model was built for each comparison using the R LIMMA package and statistics for differential expression analysis were computed. To filter for differential expression, two fold or three-fold change with a FDR ≤0.05 were used as the threshold.
Functional annotation was done using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources 6.7, NIAID, NIH (http://david.abcc.ncifcrf.gov).
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample

organism: Escherichia coli

source_name: PA20 cultures

growth_protocol: PA20 cultures for RNA-seq were grown on T-agar with and without added Sulfamethoxazole-  Trimethoprim at designated levels for the indicated times and temperatures. Working stocks were tested and maintained using LB (Miller formulation) or LB agar. Plasmid pSE380 derivatives were induced by IPTG.

extract_protocol:
Total RNA samples were isolated using RNAzol RT (Molecular Research Center) by following manufature's instructions. Contaminating DNA was   removed from RNA samples by DNase I digestion using the TURBO DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols; rRNAs were removed by Ribozero (gram negative), libraries were prepared using TruSeq protocol.

tag: incubation time

value: 12 hr

tag: ug/ml smx / ug/ml tm


title: POAG10

source_name: Aqueous humor, POAG

value: Primary open angle glaucoma (POAG)

value: Caucasian


title: POAG8


title: POAG9


title: POAG12


title: XFG4


title: POAG11


title: XFG5


title: XFG3


title: XFG1


title: XFG2


title: POAG7


title: POAG4


title: POAG5

value: African-American


title: POAG3


title: T12_0x_40


title: T12_27x_41


title: T12_1x_44


title: POAG6


title: T12_1x_36


title: CP_ALZ_020

tag: post mortem interval (hr)

tag: apoe genotype


title: T12_27x_33


title: T12_27x_25


title: T5_0x_24

value: 5 hr


title: T12_0x_32


title: Pancreatic cancer 4 normal like engineered KT

description: Batch 2

value: Pancrea

value: cancer


title: Pancreatic cancer 4 normal like engineered KC

description: Batch 2


title: Pancreatic cancer 1

description: Batch 2

source_name: Patient 1


title: Pancreatic cancer 3

description: Batch 2

source_name: Patient 3


title: Pancreatic cancer 4 normal like

description: Batch 2


title: T12_1x_28


title: Pancreatic cancer 2

description: Batch 2

source_name: Patient 2


title: T5_1x_20


title: T5_27x_17


title: POAG2


title: T5_1x_12


title: T5_27x_9


title: Control10

source_name: Aqueous humor, control

value: Non-glaucoma control


title: POAG1


title: T5_1x_4


title: T5_27x_1


title: T5_0x_8


title: Control6


title: Control3


title: T5_0x_16


title: H1299 KRAS G12D 3

city: Manchester

first: Michela

last: Garofalo

address: Wilmslow Road

country: United Kingdom

institute: University of Manchester

description:
microRNA expression profile after transfection of H1299 cells with KRAS mutant (G12D)
D3

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Hybridization reactions were performed with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies) following the manufacturer’s instructions

scan_protocol: For each assay, a high density scan (600 fields of view) was performed.

data_processing: Raw data was normalized by calculating the geometric mean of the top 100 miRNAs in all samples, as recommended by NanoString, followed by quantile normalization.

source_name: H1299 cells transfected with KRAS G12D

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies). Preparation of small RNA samples involves the ligation of a specific DNA tag onto the 3’ end of each mature miRNA. These tags are designed to normalize the Tm’s of the miRNAs as well as to provide a unique identification for each miRNA species in the sample. Following the ligation reaction, excess tags and bridges were removed,

growth_protocol: cells were grown in RPMI media, transfected for 48h with an empty vector, KRAS wild type or KRAS G12D

extract_protocol: Trizol extraction was performed following the manufacturer's instructionsm. RNA was purified and concentrated by Norgen RNA clean up and concentration kit

tag: cell line

tag: transfection

value: KRAS G12D plasmid


title: Control4


title: Control8


title: H1299 KRAS G12D 2

description:
microRNA expression profile after transfection of H1299 cells with KRAS mutant (G12D)
D2


title: H1299 KRAS G12D 1

description:
microRNA expression profile after transfection of H1299 cells with KRAS mutant (G12D)
D1


title: Control9


title: H1299 KRAS WT 1

description:
microRNA expression profile after transfection of H1299 cells with KRAS wild type
WT1

source_name: H1299 cells transfected with KRAS WT

value: KRAS WT plasmid


title: H1299 KRAS WT 2

description:
microRNA expression profile after transfection of H1299 cells with KRAS wild type
WT2


title: Control7


title: Control2


title: SV40 BSC40 PA-m6A-seq early mutant Tm2 validation

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Aligned to the SV40 genome (RefSeq NC_001669.1)

data_processing:
Library strategy: PA-m6A-seq
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the SV40 genome using Bowtie 0.12.7: bowtie -m 9 -v 1 -a --best --strata --chunkmbs 2048
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand": BEGIN{FS=OFS="\t"} { chromosome=$3; startC=$4+1; endC=(length($5) + $4); strand=$2; split($1,sc,"-"); name=sc[1]; score= (sc[2] / [Total 15nt+ read count of each run]); if($2!="") print(chromosome"\t"startC"\t"endC"\t"score"\t"strand); }
Genome_build: RefSeq NC_001669.1
Supplementary_files_format_and_content: bed files, aligned to SV40 NC_001669.1

molecule: polyA RNA

organism: Chlorocebus aethiops

source_name: BSC40 infected with SV40 776 mutant "Tm2"

extract_protocol:
PAR-CLIP
All samples were processed with the Illumina Tru-seq small RNA-seq kit

tag: virus strain

value: SV40 776 mutant "Tm2"

tag: virus genotype

value: mutant "Tm2"

tag: host cell line

value: Cercopithecus aethiops cell line BSC40

tag: technique

tag: antibody

value: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4


title: SV40 BSC40 PA-m6A-seq early mutant Tm1 validation

source_name: BSC40 infected with SV40 776 mutant "Tm1"

value: SV40 776 mutant "Tm1"

value: mutant "Tm1"


title: Control5

tag: tissue

value: Aqueous humor

value: Female


title: SV40 BSC40 PA-m6A-seq early mutant Tm12 validation

source_name: BSC40 infected with SV40 776 mutant "Tm12"

value: SV40 776 mutant "Tm12"

value: mutant "Tm12"


title: H1299 CTL 2

description:
N/A
C2

source_name: H1299 cells transfected with an empty vector

value: empty vector


title: H1299 CTL 1

description:
N/A
C1


title: Control1

tag: disease status

value: Caucasian

value: Male


title: H1299 KRAS WT 3

description:
microRNA expression profile after transfection of H1299 cells with KRAS wild type
WT3


title: H1299 CTL 3

description:
microRNA expression profile after transfection of H1299 cells with an empty vecto
C3


title: EpiSC_day9_rep1 (mRNA)

status: Public on Feb 07 2018

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

description:
Primary cells
EpiSC at day9 replicate 1
US11263921_252800520995_S01_GE2_1105_Oct12_2_1.txt

hyb_protocol: Hybridization was performed following manufacturer’s instructions

scan_protocol: Scanning was performed accordingly with the Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with an agilent SureScan Microarray scanner

data_processing: The raw data was processed in statistical language R, using a limma package (limma_3.20.9). Samples were background corrected with Normexp (offset = 50) and normalized with cyclic loess. Only probes that were deemed expressed (10 % greater signal than the negative controls) in at least 5 samples were maintained for differential expression analysis. Array weights were applied to data to down-weight lesser-quality arrays, improving the precision and power of the overall differential expression analysis. Probes were summarised at the miRNA level. Data was adjusted for multiple testing using Benjamini and Hochberg method to control for false discovery rate.

source_name: EpiSC at day9

label_protocol: gene expression profiling was performed using SurePrint mouse mRNA microarray technology, (G4852A, Agilent Technologies). Briefly, 200 ng of total RNA was retrotranscribed and labelled using the Two-Color

extract_protocol: RNA was extracted using TRI-Reagent (Sigma) and treated with DNAase I (Ambion)

tag: cell type

value: EpiSC

tag: treatment

value: control cells

tag: time (day of isolation)

value: day 9


title: DA_day14_rep3 (mRNA)

description:
Primary cells
DA cells at day14 replicate 3
US11263921_252800520995_S01_GE2_1105_Oct12_1_2.txt

source_name: DA cells at day14

value: DA cells

value: DA induction

value: day 14


title: EpiSC_day5_rep3 (mRNA)

description:
Primary cells
EpiSC at day5 (before DA induction) replicate 3
US11263921_252800520995_S01_GE2_1105_Oct12_1_3.txt

source_name: EpiSC at day5 (before DA induction)

value: before DA induction

value: day 5


title: EpiSC_day9_rep2 (mRNA)

description:
Primary cells
EpiSC at day9 replicate 2
US11263921_252800520995_S01_GE2_1105_Oct12_1_4.txt


title: EpiSC_day9_rep3 (mRNA)

description:
Primary cells
EpiSC at day9 replicate 3
US11263921_252800520994_S01_GE2_1105_Oct12_2_2.txt


title: DA_day14_rep1 (mRNA)

description:
Primary cells
DA cells at day14 replicate 1
US11263921_252800520995_S01_GE2_1105_Oct12_1_4.txt


title: KO2, biological rep2

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. Then, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix Expression Console Software (version 1.2.1) was used for microarray analysis. Raw data (CEL files) were normalized at transcript level using robust multiaverage method (RMA workflow). Median summarization of transcript expressions was calculated. Gene-level data was then filtered to include only those probe sets that are in the ‘core’ metaprobe list, which represent RefSeq genes.

source_name: LSKs from the bone marrow of KO mice

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: All mice were housed in specific pathogen-free conditions and fed with autoclaved food.  autoclaved food

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Darmstadt, Germany) according to the manufacturer's instructions.

treatment_protocol: Mouse bone marrow cells were flushed from the femur and tibia. Then, red blood cells were lysed using a red cell lysis buffer. After stained with LSK markers, cells were sorted by flow cytometry.

tag: genotype/variation

value: SRC-3 knockout (KO)

tag: gender

tag: age

value: Bone marrow

value: lineage- Sca1+ c-Kit+ cells (LSKs)


title: EpiSC_day14_rep3 (mRNA)

description:
Primary cells
EpiSC at day14 replicate 3
US11263921_252800520994_S01_GE2_1105_Oct12_2_2.txt

source_name: EpiSC at day14


title: DA_day9_rep1 (mRNA)

description:
Primary cells
DA cells at day9 replicate 1
US11263921_252800520995_S01_GE2_1105_Oct12_2_2.txt

source_name: DA cells at day9


title: EpiSC_day14_rep1 (mRNA)

description:
Primary cells
EpiSC at day14 replicate 1
US11263921_252800520994_S01_GE2_1105_Oct12_1_3.txt


title: EpiSC_day14_rep2 (mRNA)

description:
Primary cells
EpiSC at day14 replicate 2
US11263921_252800520995_S01_GE2_1105_Oct12_2_4.txt


title: KO1, biological rep1


title: DA_day9_rep2 (mRNA)

description:
Primary cells
DA cells at day9 replicate 2
US11263921_252800520995_S01_GE2_1105_Oct12_2_4.txt


title: DA_day9_rep3 (mRNA)

description:
Primary cells
DA cells at day9 replicate 3
US11263921_252800520995_S01_GE2_1105_Oct12_1_2.txt


title: EpiSC_day5_rep2 (mRNA)

description:
Primary cells
EpiSC at day5 (before DA induction) replicate 2
US11263921_252800520995_S01_GE2_1105_Oct12_2_2.txt


title: DA_day14_rep2 (mRNA)

description:
Primary cells
DA cells at day14 replicate 2
US11263921_252800520995_S01_GE2_1105_Oct12_1_3.txt


title: 5500254131233090312330_B02

city: Atlanta

first: Hanjoong

last: Jo

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

hyb_protocol: Biotin-labeled cRNA was generated from the cDNA and used to probe a Human Genome HT_HG-U133A plate (Affymetrix, Sunnyvale, CA, USA) Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

data_processing: CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm

source_name: Whole blood

label_protocol: Double-stranded cDNAs were synthesized from 1 μg of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and converted to double-strand using the cDNA Synthesis System (Invitrogen). Biotin-labeled cRNA was generated from the cDNA. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix.

extract_protocol: Total RNA was isolated, treated with DNase I, and cleaned up using a Qiagen RNeasy MinElute Cleanup Kit. RNA concentrations were determined using NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and RNA quality was evaluated using the Experion electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA).

treatment_protocol: PAXgene tubes were stored at -20C until processing for RNA extraction.

tag: neuta

tag: protocol

tag: group

value: control

value: peripheral blood from SLE patients and normal healthy controls were collected directly into PAXgene tubes.


title: 5500254131233090312330_E03

scan_protocol: Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.


title: 5500254131233090312330_C03


title: WT2, biological rep2

source_name: LSKs from the bone marrow of WT mice

value: wild-type (WT)


title: 5500254131233090312330_G01


title: 5500254131233090312330_G07


title: 5500254131233090312330_G05


title: 5500254131233090312330_E02


title: 5500254131233090312334_C05


title: 5500254131233090312334_C09


title: 5500254131233090312330_A09


title: EpiSC_day5_rep1 (mRNA)

description:
Primary cells
EpiSC at day5 (before DA induction) replicate 1
US11263921_252800520994_S01_GE2_1105_Oct12_1_3.txt


title: WT1, biological rep1


title: 5500254131233090312334_B10

value: Low

value: SLE


title: 5500254131233090312334_H12


title: 5500254131233090312334_A07

value: Medium


title: 5500254131233090312334_F11


title: 5500254131233090312334_E11


title: 5500254131233090312334_D01

value: High


title: 5500254131233090312330_D06


title: 5500254131233090312334_C06


title: 5500254131233090312334_E07


title: 5500254131233090312334_D05


title: 5500254131233090312334_E06


title: 5500254131233090312334_A12


title: 5500254131233090312334_D12


title: 5500254131233090312334_E08


title: 5500254131233090312330_D05


title: 5500254131233090312334_C07


title: 5500254131233090312334_E03


title: 5500254131233090312334_B09


title: 5500254131233090312334_E01


title: 5500254131233090312334_G01


title: 5500254131233090312334_D09


title: 5500254131233090312330_D08


title: 5500254131233090312334_H05


title: 5500254131233090312334_F06


title: 5500254131233090312334_H06


title: 5500254131233090312330_H04


title: 5500254131233090312330_H08


title: 5500254131233090312334_G10


title: 5500254131233090312334_H10


title: Control11

value: Non-glaucoma control

value: Aqueous humor

tag: age (years)

tag: race

value: Caucasian

tag: Sex

value: Female


title: 5500254131233090312334_B02


title: 5500254131233090312330_D04


title: 5500254131233090312334_C11


title: 5500254131233090312334_A03


title: 5500254131233090312330_C04


title: 5500254131233090312334_A11


title: 5500254131233090312330_H01


title: 5500254131233090312330_E01


title: 5500254131233090312330_D02


title: 5500254131233090312334_C03


title: 5500254131233090312330_H05


title: 5500254131233090312330_E06


title: 5500254131233090312334_E05


title: 5500254131233090312330_C01


title: 5500254131233090312330_H07


title: 5500254131233090312334_F01


title: 5500254131233090312334_F02


title: 5500254131233090312334_A05


title: 5500254131233090312334_A08


title: 5500254131233090312330_D01


title: 5500254131233090312330_F04


title: 5500254131233090312330_E07


title: 5500254131233090312334_E02


title: 5500254131233090312334_E04


title: 5500254131233090312334_G04


title: 5500254131233090312330_C07


title: 5500254131233090312334_H03


title: 5500254131233090312334_G09


title: 5500254131233090312330_A05


title: 5500254131233090312334_G07


title: 5500254131233090312330_G02


title: 5500254131233090312330_A08


title: 5500254131233090312334_H04


title: 5500254131233090312334_D02


title: 5500254131233090312334_H11


title: 5500254131233090312334_B07


title: 5500254131233090312334_B03


title: 5500254131233090312330_A07


title: 5500254131233090312334_G11


title: 5500254131233090312334_F08


title: 5500254131233090312330_H06


title: 5500254131233090312334_H02


title: 5500254131233090312330_C08


title: 5500254131233090312330_B03


title: 5500254131233090312334_F07


title: 5500254131233090312330_C06


title: 5500254131233090312334_A02


title: 5500254131233090312334_D06


title: 5500254131233090312330_B01


title: 5500254131233090312334_B08


title: 5500254131233090312334_B01


title: 5500254131233090312330_B06


title: 5500254131233090312330_B09


title: 5500254131233090312334_A04


title: 5500254131233090312330_B07


title: 5500254131233090312330_F05


title: 5500254131233090312334_F10


title: 5500254131233090312330_C02


title: 5500254131233090312330_A01


title: 5500254131233090312334_C12


title: 5500254131233090312334_B06


title: 5500254131233090312334_G06


title: 5500254131233090312330_B04


title: 5500254131233090312334_A10


title: 5500254131233090312334_H07


title: 5500254131233090312334_C02


title: 5500254131233090312330_G03


title: 5500254131233090312334_H01


title: 5500254131233090312334_G12


title: 5500254131233090312330_D07


title: 5500254131233090312330_E04


title: 5500254131233090312334_F05


title: 5500254131233090312334_B05


title: 5500254131233090312330_B05


title: 5500254131233090312334_E10


title: 5500254131233090312334_C01


title: 5500254131233090312330_F02


title: 5500254131233090312334_C04


title: 5500254131233090312330_F07


title: 5500254131233090312330_F08


title: 5500254131233090312334_D07


title: 5500254131233090312334_F03


title: 5500254131233090312334_B04


title: 5500254131233090312334_H09


title: 5500254131233090312330_H03


title: 5500254131233090312330_A03


title: 5500254131233090312334_G05


title: 5500254131233090312334_E09


title: 5500254131233090312334_H08


title: 5500254131233090312330_A04


title: 5500254131233090312330_H02


title: 5500254131233090312330_F06


title: 5500254131233090312334_D03


title: 5500254131233090312334_G08


title: 5500254131233090312334_A01


title: 5500254131233090312330_D03


title: 5500254131233090312334_F09


title: 5500254131233090312334_G02


title: 5500254131233090312334_A09


title: 5500254131233090312334_D04


title: 5500254131233090312330_C05


title: 5500254131233090312334_A06


title: 5500254131233090312334_G03


title: 5500254131233090312334_D11


title: 5500254131233090312330_F03


title: 5500254131233090312334_C08


title: 5500254131233090312330_G04


title: 5500254131233090312334_F04


title: 5500254131233090312330_F01


title: CD157-_CD200-_#3

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

institute: Kyorin University School of Medicine

description:
Gene expression of CD157-CD200- ECs derived from mouse liver
liver ECs, CD157-, CD200-, replicate3

hyb_protocol: The hybridization and washing were performed using Gene Expression Hybridization kit (Agilent)  and Gene Epression Wash Buffers Pack(Agilent) following manufacturer's instruction.

scan_protocol: Feature Extraction Software (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software(Agilent).

source_name: liver ECs, CD157-, CD200-

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 2 ug cDNA using SureTag Complete DNA Labeling Kit(Agilent).

extract_protocol: The RNA was extracted using RNAeasy mini kit (Qiagen) and used for microarray analysis after being amplified using Ovation Pico WTA System V2 (NuGEN).

value: liver

value: EC

tag: cell population


title: 5500254131233090312334_D10


title: 5500254131233090312330_A06


title: 5500254131233090312330_B08


title: CD157-_CD200+_#3

description:
Gene expression of CD157-CD200+ ECs derived from mouse liver
liver ECs, CD157-, CD200+, replicate3

source_name: liver ECs, CD157-, CD200+


title: 5500254131233090312330_E08


title: CD157+_CD200+_#3

description:
Gene expression of CD157+CD200+ ECs derived from mouse liver
liver ECs, CD157+, CD200+, replicate3

source_name: liver ECs, CD157+, CD200+


title: 5500254131233090312330_E05


title: 5500254131233090312330_A02


title: CBE-/- (1) RNA-Seq replicate 2

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

data_processing:
The sequencing reads were mapped to Mus musculus reference genome (mm9) using TopHat with default settings.
Gene expression levels (FPKM) were computed using Cufflinks with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample generated by Cufflinks.

source_name: Pro-B cell line

growth_protocol: Pro-B cell lines were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol)

extract_protocol:
RNA was extracted with RNeasy Plus Mini Kit (#74134 , Qiagen) for RNA-Seq.
RNA libraries were make with Illumina Truseq stranded mRNA sample preparation kit following the manufacturer’s recommended procedure. Quality control of the libraries were performed using Fragment Analyzer. The resulting libraries were pooled together. The pooled library concentration is further quantified using KAPA library quantification qPCR kit and sequenced on Illumina NextSeq 500 using a Highoutput 75 cycle sequencing kit targeting 20-30 million single read 75 bp reads.

treatment_protocol: Pro-B cell lines were grown without any treatment.

tag: strain

value: Pro-B cell line

tag: genotype


title: CBE-/- (2) RNA-Seq replicate 2

tag: tissue


title: Eµ-/- RNA-Seq replicate 2


title: CBE-/- (1) RNA-Seq replicate 1


title: WT RNA-Seq replicate 2

value: Wild type


title: Eµ-/- RNA-Seq replicate 1

value: Bone marrow


title: CBE-/- (2) RNA-Seq replicate 1


title: WT RNA-Seq replicate 1


title: mouse_c_v5

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description: laser-capture-microdissected villus epithelium, fifth quintile mouse c

data_processing:
bcl2fastq2 v2.19 for demultiplexing
kallisto 0.43.0 for index creation: kallisto index -i Mus_musculus.GRCm38.rel90.cdna.filtered.idx Mus_musculus.GRCm38.rel90.cdna.filtered.fa.gz
kallisto 0.43.0 for pseudoalignment: kallisto quant -i path_to_index/Mus_musculus.GRCm38.rel90.cdna.filtered.idx -o path_to_output/  -b 100 path_to_fastq/Sample.fastq.gz
QC with Fastqc and qc and alignemnt analysis in Multiqc
Genome_build: Genome_build: Ensembl Mus_musculus.GRCm38.rel90, filtered in BiomaRt to only include source=="ensembl_havana"
Supplementary_files_format_and_content: Tab Separated Values, kallisto 0.43.0 pseudoalignment output

source_name: villus epithelium fragment

extract_protocol:
Tissue blocks for microdissection were obtained from 8-12 week-old male C57BL/6 mice. The proximal Jejunum was briefly washed in cold PBS and embedded and frozen in OCT without fixation. 8μm thick sections were cut from the frozen block, mounted on polyethylene- naphthalate membrane-coated glass slides (Zeiss, A4151909081000), air-dried for 1m at room temperature, washed in 70% ethanol (30s), incubated in water (Sigma-Aldrich, W4502, 30s), stained with HistoGene Staining Solution (ThermoFisher Scientific, KIT0401, 20s), washed vigorously in water for a total of 30s. The stained sections were dehydrated with subsequent 30s incubations in 70%,95% and 100% ethanol and air dried for 3m before microdissection. Tissue sections were microdissected on a UV laser-based PALM Microbeam (Zeiss). The system makes use of a pulsed UV laser that cuts the tissue at indicated marks with minimal damage to surrounding cells; the cutting was performed with the following parameters: PALM 20X lens, cut energy 48 (1-100), cut focus 65 (1-100). Tissue fragments were catapulted and collected in 0.2ml adhesive cap tubes (Zeiss, A4151909191000) with these settings: LPC energy 67 (1-100), LPC focus 67 (1-100). The capturing success was visually confirmed by focusing the PALM on the targeted adhesive cap after the collection session. 8-10 Villi above 500µm length selected for microdissection for each of three mice, their epithelium was divided into 5 segments of equal length and isolated.  A total of 30’000-45’000 μm2 of villus epithelium area was collected for each of the five villus zones per mouse.
Library preparation for microdissected tissues was performed based on a previously published protocol (https://doi.org/10.1126/science.aan2399) with minor modifications. Specifically, we resuspended microdissected fragments in 9.5μl H2O and 1μl of 10x reaction buffer of the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634888) in the adhesive cap of the collection tubes. Tissue lysis was achieved by incubation for 5m at room temperature; the lysed samples were flash frozen until library preparation. The RNA was amplified with the SMART-Seq v4 kit according to the manufacturer’s instructions and by using 15 PCR cycles for the cDNA amplification step. 1ng of the amplified cDNA was converted into sequencing library with the Nextera XT DNA Library kit (Illumina, FC-131-1024). The quality control of the resulting libraries was performed with an Agilent High Sensitivity D1000 ScreenTape System (Agilent, 5067- 5584). Libraries that passed quality control were loaded with a concentration of 1.8pM on 75 cycle high output flow cells (Illumina, FC-404-2005) and sequenced on a NextSeq 500 (Illumina) with the following cycle distribution: 8bp index 1, 8bp index 2, 38bp read 1, 38bp read 2.

value: villus epithelium

tag: localization

value: proximal jejunum

tag: villus axis quintile

tag: mouse id

value: c


title: CD157+_CD200+_#2

description:
Gene expression of CD157+CD200+ ECs derived from mouse liver
liver ECs, CD157+, CD200+, replicate2

tag: cell type


title: CD157-_CD200+_#2

description:
Gene expression of CD157-CD200+ ECs derived from mouse liver
liver ECs, CD157-, CD200+, replicate2


title: SP_8w_#3

description:
Gene expression of EC-SP derived from mouse liver
liver ECs, SP, 8w, replicate 3

source_name: liver ECs, SP, 8w

value: SP


title: CD157-_CD200+_#1

description:
Gene expression of CD157-CD200+ ECs derived from mouse liver
liver ECs, CD157-, CD200+, replicate1


title: mouse_c_v3

description: laser-capture-microdissected villus epithelium, third quintile mouse c


title: mouse_c_v4

description: laser-capture-microdissected villus epithelium, fourth quintile mouse c


title: CD157+_CD200+_#1

description:
Gene expression of CD157+CD200+ ECs derived from mouse liver
liver ECs, CD157+, CD200+, replicate1


title: CD157-_CD200-_#2

description:
Gene expression of CD157-CD200- ECs derived from mouse liver
liver ECs, CD157-, CD200-, replicate2


title: MP_8w_#1

description:
Gene expression of EC-MP derived from liver ECs
liver ECs, MP, 8w, replicate 1

source_name: liver ECs, MP, 8w

value: MP


title: SP_8w_#1

description:
Gene expression of EC-SP derived from mouse liver
liver ECs, SP, 8w, replicate 1


title: MP_8w_#2

description:
Gene expression of EC-MP derived from liver ECs
liver ECs, MP, 8w, replicate 2


title: mouse_b_v5

description: laser-capture-microdissected villus epithelium, fifth quintile mouse b

value: b


title: mouse_c_v1

description: laser-capture-microdissected villus epithelium, first quintile mouse c


title: mouse_b_v2

description: laser-capture-microdissected villus epithelium, second quintile mouse b


title: mouse_b_v4

description: laser-capture-microdissected villus epithelium, fourth quintile mouse b


title: mouse_b_v1

description: laser-capture-microdissected villus epithelium, first quintile mouse b


title: mouse_b_v3

description: laser-capture-microdissected villus epithelium, third quintile mouse b


title: SP_8w_#2

description:
Gene expression of EC-SP derived from mouse liver
liver ECs, SP, 8w, replicate 2


title: CD157-_CD200-_#1

description:
Gene expression of CD157-CD200- ECs derived from mouse liver
liver ECs, CD157-, CD200-, replicate1


title: MP_8w_#3

description:
Gene expression of EC-MP derived from liver ECs
liver ECs, MP, 8w, replicate 3


title: mouse_c_v2

description: laser-capture-microdissected villus epithelium, second quintile mouse c


title: mouse_a_v4

description: laser-capture-microdissected villus epithelium, fourth quintile mouse a

value: a


title: mouse_a_v1

description: laser-capture-microdissected villus epithelium, first quintile mouse a


title: mouse_a_v5

description: laser-capture-microdissected villus epithelium, fifth quintile mouse a


title: mouse_a_v2

description: laser-capture-microdissected villus epithelium, second quintile mouse a


title: mouse_a_v3

description: laser-capture-microdissected villus epithelium, third quintile mouse a


title: WT_0h_rep3

city: Bunkyo-ku

first: Masato

last: Saito

department: Graduate School of Science, Department of Biological Sciences

institute: The University of Tokyo

description: Col 6-day-old cotyledons

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = AraGene-1_0-st
program-name = Expression Console
program-version = 1.3.0.187
program-company = Affymetrix

organism: Arabidopsis thaliana

source_name: Arabidopsis cotyledons without VISUAL culture

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seeds were grown with MS liquid medium at 22ºC under the continuous light conditions for 6 days.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with Rneasy Micro Kit (QIAGEN).

treatment_protocol: Cotyledons were cultured with the induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), and bikinin (10 μM) for 0 h or 72 h.

value: Cotyledons from 6-day-old plants

value: WT (Col)

tag: treatment

value: without VISUAL culture

tag: time


title: WT_72h_rep2

description: Col 6-day-old cotyledons were cultured for 72 h in VISUAL

source_name: Arabidopsis cotyledons cultured for 72 h in VISUAL

value: cultured for 72 h in VISUAL


title: bes1-3_0h_rep3

description: bes1-3 6-day-old cotyledons

value: bes1-3 (T-DNA insertion)


title: bes1-1_72h_rep3

description: bes1-1 6-day-old cotyledons were cultured for 72 h in VISUAL

value: bes1-1 (T-DNA insertion)


title: KAP1_ChIP-seq_R1

city: Bath

first: Keith

middle: W

last: Vance

address: Claverton Down

department: Department of Biology and Biochemistry

institute: University of Bath

data_processing:
Reads were trimmed with Trimmomatic (v 0.36) with the options: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Trimmed reads were aligned to the mm10 reference geneome with the  reference genome with the Burrows-Wheeler Aligner, bwa (v0.3.75)  (Li H. and Durbin) with the command  bwa mem mm10 <pair_1.fq> <pair_2.fq>
The aligned reads were filtered to exclude reads with a MAPQ alignment quality <20. Furthermore, we excluded reads aligning to blacklisted regions identified by the ENCODE consortium.
MACS2 version 2.1.1.20160309 was used to identify genomic regions bound by KAP1. We further filtered the aligned reads to retain only those with length 150 and called peaks relative to the input controls using the options ' --gsize=1.87e9 --qvalue=0.01 -B --keep-dup auto'.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated by MACS2 version 2.1.1.20160309  and values record the pileup values

source_name: Neuroblastoma cells

growth_protocol: N2A cells were grown in DMEM supplemented with 10% foetal bovine serum.

extract_protocol: Approximately 2x10^7 N2A cells per ChIP were double cross-linked, first using 2 mM disuccinimidyl glutarate (DSG) for 45 min at room temperature, followed by 1% formaldehyde for 15 min at room temperature. 5 ug anti-KAP1 (ab10483, Abcam) antibody was used for IP. Chromatin was sheared to approximately 200 bp using a Bioruptor Pico (Diagenode) and ChIP DNA and matched input DNA from two independent KAP1 ChIP experiments were sequenced on an Illumina HiSeq 4000 (150 bp paired-end sequencing).

tag: cell line

value: Neuro-2A cells

tag: chip antibody

value: anti-KAP1 (ab10483, Abcam)


title: Input_Chromatin_R2


title: WT_72h_rep1


title: bes1-3_72h_rep1

description: bes1-3 6-day-old cotyledons were cultured for 72 h in VISUAL


title: bes1-1_72h_rep1


title: bes1-3_72h_rep2


title: WT_72h_rep3


title: bes1-1_72h_rep2


title: WT_0h_rep2

description: Col 6-day-old cotyledons


title: WT_0h_rep1

description: Col 6-day-old cotyledons


title: bes1-3_72h_rep3


title: bes1-3_0h_rep1

description: bes1-3 6-day-old cotyledons


title: Input_Chromatin_R1


title: MFM223

city: Nashville

first: Yan

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: HG19
Supplementary_files_format_and_content: Read Count Table

source_name: TNBC cell line

growth_protocol: Cell culture explained in https://www.jci.org/articles/view/45014

extract_protocol:
Sub-confluent cells (1-2 x10^6) were harvested and sRNA isolated (mirVana, Thermo Fisher) using standard spin protocol.
Libraries were prepared using the TruSeq Small RNA sample preparation kit (Illumina, San Diego, CA). The sRNA protocol specifically ligates RNA adapters to mature miRNAs harboring a 5’-phosphate and 3’-hydroxyl group as a result of enzymatic cleavage by RNase III processing enzymes, e.g. Dicer. In the first step, RNA adapters were ligated onto each end of the sRNA, and reverse transcription was used to create single-stranded cDNA. This cDNA was then PCR amplified for 18 cycles with a universal primer and a second primer containing one of 20 uniquely indexed tags to allow multiplexing. Size-selection of the cDNA constructs was performed using a 3% gel cassette on the Pippin Prep (Sage Sciences, Beverly, MA) to include only mature miRNAs and other sRNAs in the 5–40 bp size range and to remove adapter-adapter products. The resulting cDNA libraries then underwent a quality check on the Agilent Bioanalyzer HS DNA assay (Agilent, Santa Clara, CA) to confirm the final library size and on the Agilent Mx3005P quantitative PCR machine using the KAPA library quantification kit (Illumina, San Diego, CA) to determine concentration. A 2 nM stock was created, and samples were pooled by molarity for equimolar multiplexing. From the pool, 10 pM of the pool was loaded into each well of the flow cell on the Illumina cBot for cluster generation. The flow cell was then loaded and sequenced on the Illumina HiSeq 3000 to obtain at least 15 million single end (1x50 bp) reads per sample.


title: MDAMB468


title: SW527


title: MDAMB453


title: bes1-1_0h_rep3

description: bes1-1 6-day-old cotyledons


title: MDAMB231


title: MDAMB436


title: SUM185


title: bes1-1_0h_rep2

description: bes1-1 6-day-old cotyledons


title: KAP1_ChIP-seq_R2


title: bes1-3_0h_rep2

description: bes1-3 6-day-old cotyledons


title: HCC38


title: MDAMB157


title: HS578T


title: SUM159


title: bes1-1_0h_rep1

description: bes1-1 6-day-old cotyledons


title: HCC70


title: HDQP1


title: HCC1937


title: HCC1806


title: HCC1599


title: HCC1187


title: HCC1143


title: HCC1395


title: DU4475


title: CAL51


title: CAL851


title: CAL148


title: CAL120


title: BT549


title: MCB_treated_2

city: Houston

first: Achuth

last: Padmanabhan

state: TX

address: BCM-Michael DeBakey Center Room: BCMM-M527 Mail Stop: BCM130

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
CLC Genomics Workbench ver 10.0l.1
RNAseq workflow
Genome_build: Human NCBI GRCh38.p7
Supplementary_files_format_and_content: Tab deliminated with TPM as transcript expression

growth_protocol: RPMI plus 10% FBS

extract_protocol:
RNAeasy Kits from Qiagen
Standard Illumina RNAseq protocol

treatment_protocol: Treated with either  NSC632839 or MCB613 (6um) for 6 hours

value: breast cancer cell line

value: SRC stimulator


title: MCB_treated_1


title: NSC_treated_2

value: DUB inhibitor


title: NSC_treated_1


title: EpiSC_day14_rep3 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day14 replicate 3

hyb_protocol: miRNA expression profiling was performed using SurePrint mouse miRNA microarray technology, release 18 (G4872A, Agilent Technologies) at the FUGU Centre for Genomics (Finland, Helsinky). Briefly, 10 ng of miRNA was labelled and hybridized using the miRNA microarray system with miRNA complete labelling and Hyb kit version 3.0 (Agilent Technologies) by following manufacturer’s instructions.

scan_protocol: The arrays were scanned on a G2565CA microarray scanner and the features were extracted using Agilent Feature Extraction 12.0.07 software

extract_protocol: RNA samples were harvested in RNA later (Ambion) and RNA was extracted with the miRVana miRNA isolation kit (Ambion).

value: EpiSC

value: control cells

tag: time (day of isolation)

value: day 14


title: EpiSC_day9_rep3 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day9 replicate 3

source_name: EpiSC at day9

label_protocol: miRNA expression profiling was performed using SurePrint mouse miRNA microarray technology, release 18 (G4872A, Agilent Technologies) at the FUGU Centre for Genomics (Finland, Helsinky). Briefly, 10 ng of miRNA was labelled and hybridized using the miRNA microarray system with miRNA complete labelling and Hyb kit version 3.0 (Agilent Technologies) by following manufacturer’s instructions.

value: day 9


title: EpiSC_day14_rep2 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day14 replicate 2


title: EpiSC_day14_rep1 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day14 replicate 1


title: A549-3D-5-3

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description: Gene expression profile of A549 cells cultivated for 5 days in 3D cell culture.

hyb_protocol: Target samples were hybridized to Human HuGene 1.0 ST microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method (option GSB.adjust set to FALSE), for probe set summarization the robust methods from the affyPLM package were used. For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the microarray oligo-probes and annotation to Ensembl version 75.

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: Cells were either cultivated as monolayer in standard 12 well plates (PAA) or in the later described 3D system. As medium DMEM low glucose (Lonza) supplemented with 10% fetal calf serum (FCS) (Sigma-Aldrich, Munich, Germany) and 100 U/ml penicillin, 100 mg/ml streptomycin solution, 2 mM L-Glutamine (PAA) was used. 3D culture: Spheroids were grown in the Gravity-PLUS microtissue culture system (InSphero AG, Zurich, Switzerland), as follows: 2,500 tumour cells from subconfluently grown cells in 2D (A549, COLO699) were seeded into the hanging drop plates. Therefore, the 2D grown cells were detached with accutase (PAA) for five minutes at 37°C. After dilution with media cells counted and seeded in 40 µl drops at a density of 2500 cells/drop.  Both, cells and microtissues were cultivated at 37 °C in a humidified 5 % CO2-containing atmosphere.

extract_protocol: Total cell RNA was extracted using the TRIZOL protocol, and RNA quantity and integrity determined by optical density measurements and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively. Two hundred and fifty ng of high quality RNA was processed using the Ambion Affymetrix GeneChip WT Expression Kit.

tag: culture

tag: culture duration

tag: passage


title: Colo699-3D-1

description: Gene expression profile of Colo699 cells cultivated for 10 days in 3D cell culture.


title: A549-3D-5-1


title: Sample_CCE9710

city: Freiburg

first: Marta

middle: Joana Costa

last: Jordão

address: Breisacher strasse 64

department: Neuropathology

country: Germany

institute: Uniklinikum Freiburg

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were checked for their quality and consequently trimmed for adaptor sequence and masked for  low-quality sequence by using FastQC version 0.11.5 and Trimmomatic version 0.36
Reads were aligned to the GRCm38.87 genome assembly using STAR version 2.5.3a
Counting of reads was performed with htseq-count version 0.9.1
Genome_build: GRCm38.87
Supplementary_files_format_and_content: tab-delimited text files include raw transcript values for each sample

source_name: Cx3cr1CreER:R26-Tomato mice in which all resident macrophages express the endogenous tomato signal while peripheral immune cells do not.

extract_protocol:
Total RNA was extracted from FACS-sorted cells stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Olfactory bulb

tag: vsv-infection

value: Infected

value: Infiltrating monocytes

tag: phenotypic markers


title: BT20

last: Guo


title: EpiSC_day9_rep1 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day9 replicate 1


title: DA_day14_rep3 (miRNA)

description:
Primary cells
small-RNA
DA cells at day14 replicate 3

source_name: DA cells at day14

value: DA cells

value: DA induction


title: Sample_CCE9711

tag: strain


title: Sample_CCE9709

value: CD45hi activated microglia

value: Ly6G-CD45highCD11b+Tomato+ cells


title: A549-3D-2

description: Gene expression profile of A549 cells cultivated for 10 days in 3D cell culture.


title: Sample_CCE9708


title: Sample_CCE9707


title: Colo699-3D-2


title: Sample_CCE9706

value: Microglia

value: Ly6G-CD45lowCD11b+Tomato+ cells


title: A549-3D-3


title: A549-3D-5-2


title: Sample_CCE9704


title: Sample_CCE9705


title: Colo699-2D-2

description: Gene expression profile of Colo699 cells cultivated for 5 days in 2D cell culture.


title: Sample_CCE9712


title: Sample_CCE9703

value: Non-infected


title: DA_day14_rep1 (miRNA)

description:
Primary cells
small-RNA
DA cells at day14 replicate 1


title: DA_day9_rep2 (miRNA)

description:
Primary cells
small-RNA
DA cells at day9 replicate 2

source_name: DA cells at day9


title: A549-2D-3

description: Gene expression profile of A549 cells cultivated for 5 days in 2D cell culture.


title: Sample_CCE9702


title: Sample_CCE9701


title: A549-2D-1


title: DA_day9_rep1 (miRNA)

description:
Primary cells
small-RNA
DA cells at day9 replicate 1


title: Colo699-3D-3


title: Colo699-2D-3


title: EpiSC_day5_rep3 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day5 (before DA induction) replicate 3

source_name: EpiSC at day5 (before DA induction)

value: before DA induction

value: day 5


title: EpiSC_day5_rep1 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day5 (before DA induction) replicate 1


title: A549-3D-1


title: Colo699-2D-1


title: A549-2D-2


title: SAMPLE 232: saliva_Allergy

status: Public on Feb 06 2018

type: genomic

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

description: mononuclear cells gDNA sample from Allergy male individual

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

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

data_processing: Raw data analysis, QC, normalization, cell-count estimation and methylation β-values conversions were performed using the R-packages minfi and IMA. In brief, the raw Red/Green channel data from the 450K-llumina methylation array were read by the ‘read.450k.exp’ function, converted to methylation values by ‘preprocessRaw’ and subsequently normalized using ‘preprocessSWAN’, an implementation of the Subset-quantile Within Array Normalization (SWAN) normalization procedure. Principal component analysis and unsupervised clustering were used to check for sample outliers. All samples passed quality controls and were loaded into the R-package “IMA” for further processing/filtering. Samples having >75% of CpG sites with a detection p-value > 1e-05 were removed (all samples passed this filter). Cg-probes with a detection p-value greater than 0.01 in all samples and cg-probes on the X and Y chromosome were removed.

label: Cy5 and Cy3

source_name: saliva, male, Allergy

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from PBMC pellets was extracted using Gentra Puregene Blood Kit (Qiagen, Hilden, Germany); genomic DNAfrom saliva was extracted using the Oragene PrepIT kit (DNA Genotek, Ottawa, Canada)

tag: allergy

value: Allergy

tag: gender

value: male

value: saliva

tag: batch


title: SAMPLE 230: saliva_Allergy

tag: tissue


title: SAMPLE 231: saliva_Allergy

description: cord blood gDNA sample from Allergy male individual


title: SAMPLE 227: saliva_Allergy


title: SAMPLE 228: saliva_Allergy

source_name: saliva, female, Allergy

value: female


title: SAMPLE 229: saliva_Allergy


title: SAMPLE 233: saliva_Allergy


title: SAMPLE 226: saliva_Allergy


title: SAMPLE 225: saliva_Allergy


title: SAMPLE 224: saliva_Allergy


title: SAMPLE 222: saliva_Allergy


title: SAMPLE 221: saliva_Allergy


title: EpiSC_day5_rep2 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day5 (before DA induction) replicate 2

value: EpiSC


title: SAMPLE 223: saliva_Allergy


title: SAMPLE 220: mononuclear cells_Control

source_name: mononuclear cells, female, Control

value: Control

value: mononuclear cells


title: SAMPLE 217: mononuclear cells_Control


title: SAMPLE 219: mononuclear cells_Control

source_name: mononuclear cells, male, Control


title: SAMPLE 218: mononuclear cells_Control


title: KO2

city: Shanghai

first: Gaoxiang

last: Ge

address: 320 Yue-Yang Rd

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

description: Gene expression in Th-POK-deficient mammary glands at lactation day 1

hyb_protocol: Slides were hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings. Dye channel: Green, Scan resolution=5μm, PMT 100%, 10% , 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Th-POK-deficient mammary gland at lactation day 1

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

extract_protocol: Total RNA was extracted from mammary glands using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: strain background

tag: genotype/variation

value: Th-POK-deficient

tag: developmental stage

value: lactation day 1

value: Mammary gland


title: SAMPLE 214: mononuclear cells_Control


title: SAMPLE 216: mononuclear cells_Control


title: KO3


title: WT4

description: Gene expression in wild-type mammary glands at lactation day 1

source_name: Wild-type mammary gland at lactation day 1

value: wild type


title: SAMPLE 211: mononuclear cells_Control


title: SAMPLE 210: mononuclear cells_Control


title: SAMPLE 212: mononuclear cells_Control


title: SAMPLE 213: mononuclear cells_Control


title: WT1


title: WT3


title: WT2


title: KO4


title: SAMPLE 209: mononuclear cells_Control


title: SAMPLE 208: mononuclear cells_Control


title: ALL cells from bone marrow

city: Olomouc

first: Petr

last: Vojta

address: Hnevotinska 5

department: Laboratory of experimental medicine

country: Czech Republic

institute: Palacky University

description: Reference genome control gDNA

hyb_protocol: According to Agilent Protocol: Agilent Oligonucleotide  Array-Based CGH for Genomic DNA Analysis Version 7.4

scan_protocol: Scanned on an Agilent SureScan Dx Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent CytoGenomics Version 4.0.3.12  was used for background subtraction, LOWESS normalization and classifying, editing, and annotating aberrations .

source_name: ALL cells

label_protocol: According to Agilentprotocol:  Agilent Oligonucleotide  Array-Based CGH for Genomic DNA Analysis Version 7.4

extract_protocol: gDNA extracted from bone marrow cells by DNeasy Blood & Tissue Kit Qiagen

value: ALL cells

tag: age

value: 8 years

value: bone marrow

source_name: Control

tag: sample type

value: Human Reference DNA

value: peripheral blood


title: SAMPLE 207: mononuclear cells_Control


title: SAMPLE 204: mononuclear cells_Control


title: SAMPLE 205: mononuclear cells_Control


title: SAMPLE 206: mononuclear cells_Control


title: KO1


title: SAMPLE 202: mononuclear cells_Control


title: SAMPLE 199: mononuclear cells_Control


title: SAMPLE 200: mononuclear cells_Control


title: SAMPLE 198: mononuclear cells_Control


title: SAMPLE 196: mononuclear cells_Control


title: SAMPLE 197: mononuclear cells_Control


title: SAMPLE 194: mononuclear cells_Control


title: SAMPLE 195: mononuclear cells_Control


title: SAMPLE 215: mononuclear cells_Control


title: SAMPLE 193: mononuclear cells_Control


title: SAMPLE 192: mononuclear cells_Control


title: SAMPLE 189: mononuclear cells_Control


title: SAMPLE 188: mononuclear cells_Control


title: SAMPLE 187: mononuclear cells_Control


title: SAMPLE 203: mononuclear cells_Control


title: SAMPLE 191: mononuclear cells_Control


title: SAMPLE 185: mononuclear cells_Control


title: SAMPLE 186: mononuclear cells_Control


title: SAMPLE 183: mononuclear cells_Control


title: SAMPLE 182: mononuclear cells_Control


title: SAMPLE 184: mononuclear cells_Control


title: SAMPLE 201: mononuclear cells_Control


title: SAMPLE 177: mononuclear cells_Allergy

source_name: mononuclear cells, female, Allergy


title: SAMPLE 175: mononuclear cells_Allergy

source_name: mononuclear cells, male, Allergy


title: SAMPLE 180: mononuclear cells_Control


title: SAMPLE 181: mononuclear cells_Control


title: SAMPLE 176: mononuclear cells_Allergy


title: SAMPLE 173: mononuclear cells_Allergy


title: SAMPLE 174: mononuclear cells_Allergy


title: SAMPLE 190: mononuclear cells_Control


title: SAMPLE 172: mononuclear cells_Allergy


title: SAMPLE 179: mononuclear cells_Allergy


title: SAMPLE 171: mononuclear cells_Allergy


title: SAMPLE 170: cord blood_Control

source_name: cord blood, female, Control

value: cord blood


title: SAMPLE 169: cord blood_Control

source_name: cord blood, male, Control


title: SAMPLE 168: cord blood_Control


title: SAMPLE 167: cord blood_Control


title: SAMPLE 166: cord blood_Control


title: SAMPLE 165: cord blood_Control


title: SAMPLE 162: cord blood_Control


title: SAMPLE 164: cord blood_Control


title: SAMPLE 163: cord blood_Control


title: SAMPLE 178: mononuclear cells_Allergy

value: Allergy


title: SAMPLE 160: cord blood_Control

value: male


title: SAMPLE 159: cord blood_Control


title: SAMPLE 158: cord blood_Control


title: SAMPLE 156: cord blood_Control


title: SAMPLE 157: cord blood_Control


title: SAMPLE 155: cord blood_Control


title: SAMPLE 153: cord blood_Control


title: SAMPLE 154: cord blood_Control


title: SAMPLE 151: cord blood_Control


title: SAMPLE 149: cord blood_Control


title: SAMPLE 150: cord blood_Control


title: SAMPLE 148: cord blood_Control


title: DA_day14_rep2 (miRNA)

description:
Primary cells
small-RNA
DA cells at day14 replicate 2

tag: cell type

value: DA cells

tag: treatment

value: DA induction

value: day 14


title: SAMPLE 152: cord blood_Control

value: Control

value: female


title: EpiSC_day9_rep2 (miRNA)

description:
Primary cells
small-RNA
EpiSC at day9 replicate 2

source_name: EpiSC at day9

value: EpiSC

value: control cells

tag: time (day of isolation)

value: day 9


title: SAMPLE 137: cord blood_Control


title: SAMPLE 146: cord blood_Control


title: SAMPLE 161: cord blood_Control


title: SAMPLE 140: cord blood_Control


title: SAMPLE 138: cord blood_Control


title: SAMPLE 142: cord blood_Control


title: SAMPLE 141: cord blood_Control


title: SAMPLE 136: cord blood_Control


title: SAMPLE 143: cord blood_Control


title: SAMPLE 147: cord blood_Control


title: SAMPLE 134: cord blood_Control


title: SAMPLE 133: cord blood_Control


title: SAMPLE 135: cord blood_Control


title: SAMPLE 130: cord blood_Control


title: SAMPLE 131: cord blood_Control


title: SAMPLE 132: cord blood_Control


title: SAMPLE 129: cord blood_Control


title: SAMPLE 127: cord blood_Allergy

source_name: cord blood, female, Allergy


title: SAMPLE 128: cord blood_Control


title: SAMPLE 144: cord blood_Control


title: SAMPLE 123: cord blood_Allergy


title: SAMPLE 125: cord blood_Allergy

source_name: cord blood, male, Allergy


title: SAMPLE 145: cord blood_Control


title: SAMPLE 126: cord blood_Allergy


title: SAMPLE 121: cord blood_Allergy


title: SAMPLE 139: cord blood_Control


title: SAMPLE 122: cord blood_Allergy


title: SAMPLE 119: cord blood_Allergy


title: SAMPLE 116: saliva_Allergy

value: saliva


title: SAMPLE 118: cord blood_Allergy


title: SAMPLE 120: cord blood_Allergy


title: SAMPLE 110: cord blood_Allergy


title: SAMPLE 108: mononuclear cells_Control

value: mononuclear cells


title: SAMPLE 117: cord blood_Control


title: SAMPLE 105: saliva_Allergy


title: SAMPLE 115: cord blood_Allergy


title: SAMPLE 112: mononuclear cells_Allergy


title: SAMPLE 113: saliva_Allergy


title: SAMPLE 106: mononuclear cells_Control


title: SAMPLE 111: saliva_Allergy


title: DA_day9_rep3 (miRNA)

description:
Primary cells
small-RNA
DA cells at day9 replicate 3

source_name: DA cells at day9


title: SAMPLE 107: mononuclear cells_Control


title: SAMPLE 109: saliva_Control

source_name: saliva, female, Control


title: SAMPLE 104: mononuclear cells_Allergy


title: SAMPLE 124: cord blood_Allergy


title: SAMPLE 103: saliva_Allergy

source_name: saliva, male, Allergy


title: SAMPLE 101: mononuclear cells_Allergy


title: SAMPLE 100: cord blood_Allergy


title: SAMPLE 99: mononuclear cells_Control


title: SAMPLE 102: mononuclear cells_Allergy


title: SAMPLE 98: cord blood_Control


title: SAMPLE 95: saliva_Allergy


title: SAMPLE 96: saliva_Control


title: SAMPLE 97: cord blood_Control


title: SAMPLE 94: saliva_Allergy


title: SAMPLE 114: saliva_Allergy


title: SAMPLE 92: saliva_Allergy


title: SAMPLE 90: saliva_Allergy


title: SAMPLE 89: cord blood_Control


title: SAMPLE 91: mononuclear cells_Control


title: SAMPLE 93: mononuclear cells_Allergy


title: SAMPLE 85: mononuclear cells_Allergy


title: SAMPLE 88: mononuclear cells_Allergy


title: SAMPLE 86: saliva_Control


title: SAMPLE 84: cord blood_Control


title: SAMPLE 87: mononuclear cells_Control


title: SAMPLE 83: saliva_Control

source_name: saliva, male, Control


title: SAMPLE 78: saliva_Control


title: SAMPLE 79: mononuclear cells_Allergy


title: SAMPLE 82: mononuclear cells_Allergy


title: SAMPLE 76: saliva_Allergy

source_name: saliva, female, Allergy


title: SAMPLE 80: saliva_Control


title: SAMPLE 75: saliva_Allergy


title: SAMPLE 81: saliva_Allergy


title: SAMPLE 71: cord blood_Control


title: SAMPLE 77: mononuclear cells_Control

source_name: mononuclear cells, male, Control


title: SAMPLE 70: mononuclear cells_Control


title: SAMPLE 73: mononuclear cells_Allergy


title: SAMPLE 74: cord blood_Allergy


title: SAMPLE 68: cord blood_Control


title: SAMPLE 69: mononuclear cells_Control

source_name: mononuclear cells, female, Control


title: SAMPLE 67: mononuclear cells_Control


title: SAMPLE 61: saliva_Control


title: SAMPLE 64: saliva_Control


title: SAMPLE 66: mononuclear cells_Control


title: SAMPLE 63: mononuclear cells_Allergy


title: SAMPLE 65: cord blood_Control


title: SAMPLE 60: mononuclear cells_Control


title: SAMPLE 57: saliva_Control


title: SAMPLE 72: cord blood_Allergy


title: SAMPLE 58: cord blood_Allergy


title: SAMPLE 55: cord blood_Allergy


title: SAMPLE 54: mononuclear cells_Control


title: SAMPLE 52: saliva_Allergy


title: SAMPLE 53: cord blood_Control


title: SAMPLE 56: saliva_Allergy


title: SAMPLE 51: mononuclear cells_Control


title: SAMPLE 50: saliva_Control


title: SAMPLE 48: cord blood_Allergy


title: SAMPLE 46: mononuclear cells_Control


title: SAMPLE 45: cord blood_Control


title: SAMPLE 47: mononuclear cells_Control


title: SAMPLE 44: cord blood_Allergy


title: SAMPLE 49: cord blood_Control


title: SAMPLE 41: mononuclear cells_Allergy


title: SAMPLE 43: mononuclear cells_Control


title: SAMPLE 38: saliva_Allergy


title: SAMPLE 59: cord blood_Allergy


title: SAMPLE 40: mononuclear cells_Control


title: SAMPLE 62: mononuclear cells_Allergy


title: SAMPLE 36: saliva_Control


title: SAMPLE 33: saliva_Allergy


title: SAMPLE 32: saliva_Allergy


title: SAMPLE 35: saliva_Control


title: SAMPLE 31: cord blood_Control


title: SAMPLE 34: cord blood_Allergy


title: SAMPLE 28: saliva_Control


title: SAMPLE 37: saliva_Allergy


title: SAMPLE 29: cord blood_Allergy


title: SAMPLE 25: cord blood_Allergy


title: SAMPLE 24: mononuclear cells_Allergy


title: SAMPLE 30: saliva_Control


title: SAMPLE 23: cord blood_Allergy


title: SAMPLE 22: cord blood_Control


title: SAMPLE 21: saliva_Allergy


title: SAMPLE 26: mononuclear cells_Control


title: SAMPLE 27: cord blood_Allergy


title: SAMPLE 17: mononuclear cells_Allergy


title: SAMPLE 19: saliva_Control


title: SAMPLE 20: cord blood_Allergy


title: SAMPLE 18: saliva_Control


title: SAMPLE 42: mononuclear cells_Allergy


title: SAMPLE 16: mononuclear cells_Allergy


title: SAMPLE 39: mononuclear cells_Control


title: SAMPLE 10: cord blood_Allergy


title: SAMPLE 12: cord blood_Allergy


title: SAMPLE 11: cord blood_Control

description: cord blood gDNA sample from Control female individual


title: SAMPLE 15: cord blood_Allergy


title: SAMPLE 13: cord blood_Control

description: cord blood gDNA sample from Control male individual


title: SAMPLE 14: mononuclear cells_Allergy


title: SAMPLE 4: mononuclear cells_Allergy


title: SAMPLE 7: cord blood_Control


title: SAMPLE 9: saliva_Control

description: saliva gDNA sample from Control male individual


title: SAMPLE 6: saliva_Control

description: saliva gDNA sample from Control female individual


title: SAMPLE 8: cord blood_Allergy


title: SAMPLE 2: saliva_Control


title: SAMPLE 1: mononuclear cells_Allergy


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 9904796235_R06C02

city: North Ryde

first: Peter

middle: Laurence

last: Molloy

state: NSW

address: 11 Julis Ave

department: Health and Biosecurity

country: Australia

institute: CSIRO

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

data_processing: Data was normalized using Bioconductor package 'wateRmelon'. Bioconductor package 'Harman' was used for batch correction. The raw data are available in the .idat files and in the file "signal_intensities_369samples.csv". The batch corrected and normalized beta values are available in the file "processed_369samples.csv" on the series record.

source_name: Neonatal blood spot,Control supplement

extract_protocol: Genomic DNA was extracted from 3x3mm dried blood spot punches using GenSolve technology followed by purification using the QIAamp DNA micro kit and an additional ethanol precipitation step

value: Female

value: neonatal blood spot


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 9904796235_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 9904796235_R05C02

source_name: Neonatal blood spot,Fish oil supplement


title: Genomic DNA from dried neonatal blood spot punches_DHA 9904796235_R04C02

value: Male


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 9904796235_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 9904796235_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886039_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 9904796235_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886039_R04C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886039_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886039_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886039_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886039_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886039_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886039_R06C01


title: SAMPLE 5: saliva_Control


title: SAMPLE 3: cord blood_Control


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886039_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 9904796235_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 9904796235_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10003886039_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833106_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833106_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833106_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833106_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886039_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833106_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10003886039_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R02C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833106_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833095_R05C02


title: Normal control 5

city: London

first: Marco

last: Mura

state: Ontario

address: 800 Commissioners Road East E6-203

department: Medicine

country: Canada

institute: Western University

description: Gene expression data from normal control

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

scan_protocol: Microarray was performed with Genechip Human Gene 1.0 ST on an Affymetrix Genechip Scanner 3000 and Genechip Fluidics Station 450

data_processing:
Affymetrix CEL files were imported into Partek software (Partek) and probe-level data were pre-processed. This included robust multi-array average (Rma) background correction and data normalization, which was performed across all arrays using quantile normalization. Background-adjusted, normalized values were then compiled, or summarized, using the median polish technique, to generate a single measure of expression. As an exploratory data analysis, Principal Component Analysis (PCA) mapping and F Ratio analysis (signal-to-noise ratio) were also performed.
The q value, which represents the minimal false discovery ratio (FDR) at which an individual hypothesis test may be called significant, was used to identify differentially expressed genes between the group with severe PH and the group without PH. The q value was computed with SAM (Significant analysis of Microarray) software. The additional criterion for gene selection was a fold change of at least 1.5.

source_name: Lung sample from normal tissue

label_protocol: cDNA was synthesized from 4 ug of RNA with high capacity cDNA Reverse Transcription kits (Applied Byosystems). cDNA-synthesis was carried out on a PTC-100 Programmable Thermal controller (MJ Research). RNA was qualified by RNA nano chips on an Agilent 2100 Bilanalyzer (Agilent Technologies.

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

treatment_protocol: Fresh frozen lung tissue specimens were obtained from the recipient organs of Pulmonary Fibrosis patients undergoing lung transplantation. Specimens were obtained as soon as the first recipient lung was taken out, snap frozen in liquid nitrogen, and stored at -80ºC

tag: disease state

value: Normal control

value: Lung


title: Normal control 2


title: Normal control 11


title: Mixed IPF-NSIP patient 5

description: Gene expression data from mixed IPF-NSIP patient

source_name: Lung sample from recipient organ

value: Mixed IPF-NSIP


title: Normal control 6


title: Normal control 8


title: Mixed IPF-NSIP patient 4


title: Normal control 3


title: Normal control 9


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833095_R04C02


title: Mixed IPF-NSIP patient 2


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833095_R02C02


title: Normal control 4


title: Normal control 10


title: Normal control 7


title: Normal control 1


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833095_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833095_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833080_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R03C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R06C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833080_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833080_R04C02


title: Mixed IPF-NSIP patient 1


title: Non-specific interstitial pneumonia patient 6

description: Gene expression data from NSIP patient

value: Non-specific interstitial pneumonia


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833080_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833080_R02C01


title: Non-specific interstitial pneumonia patient 10

description: Gene expression data from NSIP patient


title: Idiopathic pulmonary fibrosis patient 22

description: Gene expression data from IPF patient

value: Idiopathic pulmonary fibrosis


title: Idiopathic pulmonary fibrosis patient 17

description: Gene expression data from IPF patient


title: Non-specific interstitial pneumonia patient 1

description: Gene expression data from NSIP patient


title: Idiopathic pulmonary fibrosis patient 21

description: Gene expression data from IPF patient


title: Non-specific interstitial pneumonia patient 4

description: Gene expression data from NSIP patient


title: Non-specific interstitial pneumonia patient 5

description: Gene expression data from NSIP patient


title: Idiopathic pulmonary fibrosis patient 12

description: Gene expression data from IPF patient


title: Non-specific interstitial pneumonia patient 3

description: Gene expression data from NSIP patient


title: Non-specific interstitial pneumonia patient 7

description: Gene expression data from NSIP patient


title: Idiopathic pulmonary fibrosis patient 15

description: Gene expression data from IPF patient


title: Mixed IPF-NSIP patient 3


title: Idiopathic pulmonary fibrosis patient 16

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 19

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 18

description: Gene expression data from IPF patient


title: Non-specific interstitial pneumonia patient 9

description: Gene expression data from NSIP patient


title: Idiopathic pulmonary fibrosis patient 14

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833063_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833080_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833063_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R04C02


title: Idiopathic pulmonary fibrosis patient 11

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R03C02


title: Idiopathic pulmonary fibrosis patient 20

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833063_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833063_R06C01


title: Non-specific interstitial pneumonia patient 2

description: Gene expression data from NSIP patient


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R05C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R04C01


title: Non-specific interstitial pneumonia patient 8

description: Gene expression data from NSIP patient


title: Idiopathic pulmonary fibrosis patient 13

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833063_R01C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R02C01


title: Idiopathic pulmonary fibrosis patient 9

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R04C02


title: Idiopathic pulmonary fibrosis patient 10

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 8

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833034_R03C02


title: Idiopathic pulmonary fibrosis patient 1

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 5

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 7

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 2

description: Gene expression data from IPF patient


title: Idiopathic pulmonary fibrosis patient 6

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833095_R05C01


title: Idiopathic pulmonary fibrosis patient 3

description: Gene expression data from IPF patient


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R02C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833034_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833063_R03C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R06C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833034_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833034_R04C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R03C01


title: U266_Normoxia_24h_cell2

city: Shinjyuku

first: Tomohiro

last: Umezu

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® human Gene 2.0 ST Array, and washed according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

scan_protocol: GeneChips were and stained, and scanned by Scanner 3000 7G system according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

data_processing: The data were analyzed with Command Console Software ver. 3.2 and Expression Console Software ver. 1.3.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Multiple Myeloma-derived cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA.

growth_protocol: Parental cells (RPMI8226, KMS-11, U266, IM-9) and HR cells (RPMi8226-HR, KMS-11-HR, U266-HR, IM-9-HR) were seeded at a density of 5 × 10^5 cells/ml, and cultured for 24 hours under normoxia conditions (20% O2) and hypoxic conditions (1% O2, 5% CO2, 94% N2) in a humidified gas-sorted hypoxic incubator (MCO-5M, Sanyo, Osaka, Japan), respectively.

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

tag: cell line

value: Multiple Myeloma-derived cell line

tag: condition

value: normoxia (20% O2)


title: IM-9-HR_Hypoxia_24h_cell2

source_name: hypoxia-resistant-Multiple Myeloma-derived subl line

value: IM-9 (hypoxia-resistant)

value: hypoxia (1% O2)


title: IM-9_Normoxia_24h_cell2


title: U266-HR_Hypoxia_24h_cell1

value: U266 (hypoxia-resistant)

value: hypoxia-resistant-Multiple Myeloma-derived subl line


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833034_R02C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833034_R01C01


title: IM-9-HR_Hypoxia_24h_cell1


title: U266-HR_Hypoxia_24h_cell2


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833094_R04C02


title: Th0 Blimp1 rep2

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

description: processed data file: RNAseq_Blimp1RV_poholek.txt

data_processing:
Raw sequencing data were decoded and demultiplexed with CASAVA 1.8.2 to generate FastQ files, mapped onto the mouse genome build mm9 using Tophat2.0.8 and gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.2. All downstream statistical analyses were performed with Partek Genomics Suite 6.6.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNAseq_Blimp1RV_poholek.txt: Tab-delimited text file includes RPKM values.

source_name: CD4 T cell

growth_protocol:
Cell isolation: Cells from spleen and lymph node were obtained by mechanical disruption and sort purified for naïve phenotype: CD4+ CD44lo CD62L+ CD25neg.
In vitro protocol: All cells were stimulated in RPMI medium with 10% FCS, 2mM glutamine, 100 IU/ml penicillin, 0.1mg/ml streptomycin, 20mM HEPES buffer pH 7.2-7.5, and 2mM β-mercaptoethanol. Cells were activated by plate-bound α-CD3 and α-CD28 (10ug/ml) for 3 days under neutral conditions, α-IL-4 (10ug/ml) and α-IFNg (10ug/ml).

extract_protocol:
Approximately 0.5e6 cells were isolated by sorting GFP+ cells from three independent biological replicates of CD4 T cells transduced with Empty Vector or Blimp-1 expressing retrovirus. Total RNA was prepared by using mirVana miRNA Isolation Kit (AM1560, ABI).
A fraction of total RNA (2 μg) was processed into mRNA-seq library by using TruSeq RNA sample prep kit (FC-122-1001, Illumina). The libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 (Illumina).

treatment_protocol: RV transduction: Blimp-1 cDNA was cloned into MigR1 expression vector that uses GFP as a selection marker. Sorted naïve CD4+ T cells from WT were cultured in the presence of plate-bound α-CD3 (10ug/ml), α-CD28 (10ug/ml) with α-IFN-γ (10ug/ml) and α-IL-4 for 36 hrs, then transduced with control (empty vector, MigR1), or Blimp-1 expressing retrovirus and cultured for two days. Cells were sorted for RNA isolation (GFP+).

tag: strain/background

value: WT

value: Th0 activated T cells

tag: transduction


title: Th0 Blimp1 rep3


title: Idiopathic pulmonary fibrosis patient 4

description: Gene expression data from IPF patient


title: Th0 Blimp1 rep1


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R03C02


title: IM-9_Normoxia_24h_cell1


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R06C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R05C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R01C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833094_R06C01


title: Th0 MigR1 rep3

value: empty vector


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R05C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833094_R04C01


title: U266_Normoxia_24h_cell1


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833094_R02C01

value: Female


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833085_R06C02

value: neonatal blood spot


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833094_R01C01


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833094_R03C01

value: Male


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833085_R05C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833085_R03C02


title: Genomic DNA from dried neonatal blood spot punches_CONTROL 10005833085_R04C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833085_R02C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833085_R01C02


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833085_R06C01


title: Genomic DNA from dried neonatal blood spot punches_DHA 10005833085_R05C01


title: KMS-11-HR_Hypoxia_24h_cell2

value: KMS-11 (hypoxia-resistant)