title: SAMPLE 84: Patient3.Pre_Replicate2

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

description:
ChipNumber: Chip11
Batch number: 4
OriginalSampleNumbers: 34

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using the Beadarray package

source_name: Breast tumour

label_protocol: 100-ng RNA per patient was amplified and biotinylated using Illumina® TotalPrep RNA Amplification Kit (Ambion) and quantified on a Bioanalyser 2100.

extract_protocol: Paired biopsies were taken at diagnosis and at surgery; half of the tissue was immediately frozen in liquid nitrogen and stored at −196°C. Frozen sections were removed, sectioned and stained with haematoxylin and eosin to assess tumour content. Approximately 100-mg tissue from pre- and post-treatment biopsies from 27 patients who completed everolimus treatment were placed in RNAlater® ICE (Ambion, Warrington, United Kingdom) overnight at −20°C prior to RNA extraction using the RNeasy Mini Kit, including RNase-Free DNase treatment (Qiagen, Crawley, United Kingdom). Aliquots of RNA were analysed by electrophoresis and quantified on a Bioanalyser 2100 (G2938c, Agilent Technologies, Stockport, United Kingdom).

treatment_protocol: Women recruited were to receive 5 mg of everolimus pre-operative treatment daily for 14 days prior to primary surgery

value: Breast tumour

value: ER+

value: PR-


title: SAMPLE 72: Patient25.Pre_Replicate2

status: Public on Aug 30 2018

type: RNA

country: United Kingdom

description:
ChipNumber: Chip8
Batch number: 3
OriginalSampleNumbers: 22

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: gender

value: Female

value: PR+


title: SAMPLE 82: Patient3.Post_Replicate2

description:
ChipNumber: Chip3
Batch number: 2
OriginalSampleNumbers: 6


title: SAMPLE 78: Patient29.Post_Replicate2

description:
ChipNumber: Chip15
Batch number: 5
OriginalSampleNumbers: 47


title: SAMPLE 74: Patient28.Post_Replicate2

description:
ChipNumber: Chip18
Batch number: 5
OriginalSampleNumbers: 59


title: SAMPLE 87: Patient31.Pre_Replicate1

description:
ChipNumber: Chip6
Batch number: 2
OriginalSampleNumbers: 25


title: SAMPLE 85: Patient31.Post_Replicate1

description:
ChipNumber: Chip13
Batch number: 4
OriginalSampleNumbers: 49


title: SAMPLE 77: Patient29.Post_Replicate1

description:
ChipNumber: Chip13
Batch number: 4
OriginalSampleNumbers: 47


title: SAMPLE 73: Patient28.Post_Replicate1

description:
ChipNumber: Chip17
Batch number: 5
OriginalSampleNumbers: 59


title: SAMPLE 79: Patient29.Pre_Replicate1

description:
ChipNumber: Chip6
Batch number: 2
OriginalSampleNumbers: 24


title: SAMPLE 69: Patient25.Post_Replicate1

description:
ChipNumber: Chip14
Batch number: 4
OriginalSampleNumbers: 52


title: SAMPLE 86: Patient31.Post_Replicate2

description:
ChipNumber: Chip15
Batch number: 5
OriginalSampleNumbers: 49


title: SAMPLE 71: Patient25.Pre_Replicate1

description:
ChipNumber: Chip6
Batch number: 2
OriginalSampleNumbers: 22


title: SAMPLE 68: Patient24.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 21


title: SAMPLE 83: Patient3.Pre_Replicate1

description:
ChipNumber: Chip9
Batch number: 3
OriginalSampleNumbers: 34


title: SAMPLE 80: Patient29.Pre_Replicate2

description:
ChipNumber: Chip8
Batch number: 3
OriginalSampleNumbers: 24


title: SAMPLE 76: Patient28.Pre_Replicate2

description:
ChipNumber: Chip8
Batch number: 3
OriginalSampleNumbers: 23


title: SAMPLE 75: Patient28.Pre_Replicate1

description:
ChipNumber: Chip6
Batch number: 2
OriginalSampleNumbers: 23


title: SAMPLE 66: Patient24.Post_Replicate2

description:
ChipNumber: Chip16
Batch number: 5
OriginalSampleNumbers: 58


title: SAMPLE 81: Patient3.Post_Replicate1

description:
ChipNumber: Chip1
Batch number: 1
OriginalSampleNumbers: 6


title: SAMPLE 67: Patient24.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 21


title: SAMPLE 70: Patient25.Post_Replicate2

description:
ChipNumber: Chip16
Batch number: 5
OriginalSampleNumbers: 52


title: SAMPLE 63: Patient23.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 20


title: SAMPLE 61: Patient23.Post_Replicate1

description:
ChipNumber: Chip13
Batch number: 4
OriginalSampleNumbers: 46


title: SAMPLE 65: Patient24.Post_Replicate1

description:
ChipNumber: Chip14
Batch number: 4
OriginalSampleNumbers: 58


title: SAMPLE 62: Patient23.Post_Replicate2

description:
ChipNumber: Chip15
Batch number: 5
OriginalSampleNumbers: 46


title: SAMPLE 60: Patient22.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 19


title: SAMPLE 64: Patient23.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 20


title: SAMPLE 59: Patient22.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 19


title: SAMPLE 55: Patient21.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 18


title: SAMPLE 54: Patient21.Post_Replicate2

description:
ChipNumber: Chip15
Batch number: 5
OriginalSampleNumbers: 44


title: SAMPLE 58: Patient22.Post_Replicate2

description:
ChipNumber: Chip15
Batch number: 5
OriginalSampleNumbers: 45


title: SAMPLE 56: Patient21.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 18


title: SAMPLE 53: Patient21.Post_Replicate1

description:
ChipNumber: Chip13
Batch number: 4
OriginalSampleNumbers: 44


title: SAMPLE 48: Patient19.Post_Replicate2

description:
ChipNumber: Chip12
Batch number: 4
OriginalSampleNumbers: 43


title: SAMPLE 51: Patient20.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 17


title: SAMPLE 52: Patient20.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 17


title: SAMPLE 43: Patient16.Post_Replicate1

description:
ChipNumber: Chip10
Batch number: 3
OriginalSampleNumbers: 41


title: SAMPLE 45: Patient16.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 15


title: Tbet+iTregPDL1 gene replicate3

city: Hamilton

first: Eric

middle: W

last: Dahlstrom

state: MT

address: 903 S. 4th St

department: RTB

country: USA

institute: NIAID, NIH

description: Sorted CD4+Tbet+FoxP3- cells expanded in the presence of anti-CD3, antiCD28, rmIL2 and rhTGF-b1 and PDL-1 fc for 3 days followed by expansion with IL-2 and TGF-b1 for additional 4 days.

hyb_protocol: Affymetrix (WT) Array hybridization protocol

scan_protocol: Data were collected using Affymetrix AGCC software.

data_processing: The Partek Genomics Suite software using RMA algorithm was used.The normalized expression values are log2-scaled.

organism: Mus musculus

source_name: T cells

label_protocol: Affymetrix (WT)  terminal labelling kit

growth_protocol: Sorted CD4+Tbet+FoxP3- cells expanded in the presence of anti-CD3, antiCD28, rmIL2 and rhTGF-b1 for 3 days in the presence or absence of PDL1 followed by expansion with IL-2 and TGF-b1 for additional 4 days.

extract_protocol: RNA extracted with RNAeasy kit from Qiagen and reverse transcribed with Ambion WT expression kit

value: spleen


title: SAMPLE 46: Patient16.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 15


title: SAMPLE 57: Patient22.Post_Replicate1

description:
ChipNumber: Chip13
Batch number: 4
OriginalSampleNumbers: 45


title: SAMPLE 38: Patient14.Pre_Replicate2

description:
ChipNumber: Chip18
Batch number: 5
OriginalSampleNumbers: 62


title: SAMPLE 44: Patient16.Post_Replicate2

description:
ChipNumber: Chip12
Batch number: 4
OriginalSampleNumbers: 41


title: SAMPLE 49: Patient19.Pre_Replicate1

description:
ChipNumber: Chip5
Batch number: 2
OriginalSampleNumbers: 16


title: SAMPLE 39: Patient15.Post_Replicate1

description:
ChipNumber: Chip1
Batch number: 1
OriginalSampleNumbers: 4


title: Tbet+iTregPDL1 gene replicate 2


title: Tbet+iTregPDL1 gene replicate 1


title: SAMPLE 41: Patient15.Pre_Replicate1

description:
ChipNumber: Chip2
Batch number: 1
OriginalSampleNumbers: 14


title: Tbet+iTreg gene replicate 2

description: Sorted CD4+Tbet+FoxP3- cells expanded in the presence of anti-CD3, antiCD28, rmIL2 and rhTGF-b1 for 3 days followed by expansion with IL-2 and TGF-b1 for additional 4 days.


title: Tbet+iTreg gene replicate 3


title: SAMPLE 40: Patient15.Post_Replicate2

description:
ChipNumber: Chip3
Batch number: 2
OriginalSampleNumbers: 4


title: Tbet+iTreg gene replicate 1


title: SAMPLE 37: Patient14.Pre_Replicate1

description:
ChipNumber: Chip17
Batch number: 5
OriginalSampleNumbers: 62


title: SAMPLE 47: Patient19.Post_Replicate1

description:
ChipNumber: Chip10
Batch number: 3
OriginalSampleNumbers: 43


title: SAMPLE 50: Patient19.Pre_Replicate2

description:
ChipNumber: Chip7
Batch number: 3
OriginalSampleNumbers: 16


title: SAMPLE 42: Patient15.Pre_Replicate2

description:
ChipNumber: Chip4
Batch number: 2
OriginalSampleNumbers: 14


title: SAMPLE 88: Patient31.Pre_Replicate2

description:
ChipNumber: Chip8
Batch number: 3
OriginalSampleNumbers: 25


title: SAMPLE 35: Patient14.Post_Replicate1

description:
ChipNumber: Chip17
Batch number: 5
OriginalSampleNumbers: 63


title: Menin_Utx_dKO

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

description: gene expression in Menin_Utx_dKO_CD8T cells

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner (G2600D) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software 11.5.1.1 (protocol GE1_1105_Oct12) using default parameters

source_name: splenic naïve CD8 T cell

label_protocol: 100 ng of total RNA was amplifies and labeled using Low Input Quick Amp Labeling Kit, One-Color

growth_protocol: Naïve CD8 T (CD44lowCD62Lhigh) cells were prepared using a Naïve CD8+ T cell Isolation kit (cat#130-096-543; Miltenyi Biotec).  Naïve CD8 T cells (1.5 × 106) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, H57-597; BioLegend) and anti-CD28 mAb (1 μg/ml, 37.5; BioLegend) for two days in the presence of IL-2 (10 ng/ml, Pepro Tech).  Next, the cells were transferred to a new plate and further cultured in the presence of IL-2 (10 ng/ml) for three days.

extract_protocol: Total RNA was isolated with PureLink RNA Mini Kit (lifetechnologies) according to the manufacture's protocol

tag: strain

tag: genotype/variaion


title: SAMPLE 36: Patient14.Post_Replicate2

description:
ChipNumber: Chip18
Batch number: 5
OriginalSampleNumbers: 63


title: 4003_Cont

type: SRA

city: New Haven

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

library_source: transcriptomic

data_processing:
RNA-seq analysis was performed using Partek flow (v6.6)
RNA-seq reads were trimmed and mapped to the hg19 genome reference using STAR (2.5.0e). Aligned reads were quantified to the gene level using Partek's E/M algorithm and gene annotation from Ensembl release 75. Gene-level quantitations were normalized by dividing the gene counts by the total number of reads, following by addition of a small offset (0.001). The offset was added to enable log2 transformation and the value of the offset was determined by exploring the data distribution.
Differential expression was assessed by fitting Partek's log-normal model with shrinkage (comparable in performance to limma-trend). Genes having geometric mean below value of 1.0 were filtered out from the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with gene expression matrix

source_name: Blood Tregs

growth_protocol: anti-CD3 and CD28 in the absence or presence of additional NaCl (40mM) in complete RPMI media for four days

extract_protocol:
Isolate PBMCs from whole blood and sorted CD4+CD25hi CD127neg CD45RO+Tregs by FACS
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: Control

tag: subject#

tag: age


title: 4003_NaCl

value: NaCl


title: SAMPLE 34: Patient12.Pre_Replicate2

description:
ChipNumber: Chip11
Batch number: 4
OriginalSampleNumbers: 36


title: SAMPLE 33: Patient12.Pre_Replicate1

description:
ChipNumber: Chip9
Batch number: 3
OriginalSampleNumbers: 36


title: 4092_NaCl


title: SAMPLE 29: Patient11.Pre_Replicate1

description:
ChipNumber: Chip2
Batch number: 1
OriginalSampleNumbers: 13


title: SAMPLE 30: Patient11.Pre_Replicate2

description:
ChipNumber: Chip4
Batch number: 2
OriginalSampleNumbers: 13


title: Utx_KO

description: gene expression in Utx_KO_CD8T cells


title: WT

description: gene expression in WT_CD8T cells

value: wild type


title: 4092_Cont


title: SAMPLE 32: Patient12.Post_Replicate2

description:
ChipNumber: Chip18
Batch number: 5
OriginalSampleNumbers: 55


title: SAMPLE 24: Patient10.Post_Replicate2

description:
ChipNumber: Chip16
Batch number: 5
OriginalSampleNumbers: 56


title: SAMPLE 26: Patient10.Pre_Replicate2

description:
ChipNumber: Chip11
Batch number: 4
OriginalSampleNumbers: 33


title: Keratinocytes of EKO mouse biological rep1

city: Louisville

first: Bing

last: Li

state: Kentucky

address: 505 S Hancock St

department: Microbiology and Immunology

institute: University of Louisville

description: Gene expression data from keratinocytes of KO1 mice treated with DMBA/TPA

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Mouse 430 2.0 arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level, followed by a one-way ANOVA.

source_name: Keratinocytes of EKO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Plus Reagent Kit

extract_protocol: Directions for extraction and purifying total RNA from keratinocytes by the PureLink RNA Mini Kit are according to the manufacturer's instructions.

treatment_protocol: Wild type(WT) mice and E-FABP deficient(EKO) mice were treated with DMBA/TPA according to procotoal for 5 months.

tag: genotype

value: E-FABP deficient (EKO)

tag: cell type

value: keratinocytes


title: SAMPLE 31: Patient12.Post_Replicate1

description:
ChipNumber: Chip17
Batch number: 5
OriginalSampleNumbers: 55


title: SAMPLE 28: Patient11.Post_Replicate2

description:
ChipNumber: Chip12
Batch number: 4
OriginalSampleNumbers: 40


title: Keratinocytes of EKO mouse biological rep2

description: Gene expression data from keratinocytes of KO2 mice treated with DMBA/TPA


title: SAMPLE 21: Patient9.Pre_Replicate1

description:
ChipNumber: Chip6
Batch number: 2
OriginalSampleNumbers: 28


title: SAMPLE 25: Patient10.Pre_Replicate1

description:
ChipNumber: Chip9
Batch number: 3
OriginalSampleNumbers: 33


title: Keratinocytes of EKO mouse biological rep3

description: Gene expression data from keratinocytes of KO3 mice treated with DMBA/TPA


title: SAMPLE 23: Patient10.Post_Replicate1

description:
ChipNumber: Chip14
Batch number: 4
OriginalSampleNumbers: 56


title: SAMPLE 22: Patient9.Pre_Replicate2

description:
ChipNumber: Chip8
Batch number: 3
OriginalSampleNumbers: 28


title: Menin_KO

description: gene expression in Menin_KO_CD8T cells


title: Keratinocytes of WT mouse biological rep2

description: Gene expression data from keratinocytes of WT2 mice treated with DMBA/TPA

source_name: Keratinocytes of WT mouse


title: Keratinocytes of WT mouse biological rep3

description: Gene expression data from keratinocytes of WT3 mice treated with DMBA/TPA


title: Keratinocytes of WT mouse biological rep1

description: Gene expression data from keratinocytes of WT1 mice treated with DMBA/TPA


title: SAMPLE 20: Patient9.Post_Replicate2

description:
ChipNumber: Chip12
Batch number: 4
OriginalSampleNumbers: 39


title: SAMPLE 27: Patient11.Post_Replicate1

description:
ChipNumber: Chip10
Batch number: 3
OriginalSampleNumbers: 40


title: 4716_NaCl


title: SAMPLE 19: Patient9.Post_Replicate1

description:
ChipNumber: Chip10
Batch number: 3
OriginalSampleNumbers: 39


title: 4715_Cont


title: 4716_Cont


title: 4715_NaCl


title: 4064_NaCl


title: 4064_Cont


title: SAMPLE 18: Patient8.Pre_Replicate2

description:
ChipNumber: Chip11
Batch number: 4
OriginalSampleNumbers: 31


title: 3905_Th1

growth_protocol: anti-CD3 and CD28 in the absence or presence of IL-12 (20ng/ml) in complete RPMI media for four days


title: 3905_Cont


title: 3906_Th1


title: SAMPLE 15: Patient8.Post_Replicate1

description:
ChipNumber: Chip1
Batch number: 1
OriginalSampleNumbers: 5


title: 3877_Th1


title: 3849_Th1


title: 3877_Cont


title: SUM44_LTED_B_3

city: Pittsburgh

first: Kevin

last: Levine

state: Pennsylvania

address: 204 Craft Ave

institute: University of Pittsburgh

data_processing:
Raw sequence data were mapped to hg38 genome (ensembl release version 82) and gene counts were quantified with Salmon (version 0.6.0)
Genome_build: hg38

extract_protocol:
RNA was isolated using Illustra RNAspin Mini Kit
TruSeq Stranded Total RNA Library Prep Kit was used for library preparation according to Illumina standard protocols

treatment_protocol: Parental and LTED MM134 and SUM44 cells were seeded in triplicates in 6-well plates. Parental cells were hormone deprived for three days before cell collection. For hormone deprivation, cells were washed twice daily for 3 days. For each wash, cells were rinsed twice with serum-free IMEM and then cultured in IMEM + 10% CSS. A minimum 1-hour interval was kept between two washes.

tag: cell line

value: long-term estrogen-deprived (LTED)

tag: cell line type

value: Invasive lobular breast carcinoma


title: SAMPLE 16: Patient8.Post_Replicate2

description:
ChipNumber: Chip3
Batch number: 2
OriginalSampleNumbers: 5


title: SUM44_LTED_B_2


title: SAMPLE 14: Patient7.Pre_Replicate2

description:
ChipNumber: Chip8
Batch number: 3
OriginalSampleNumbers: 27


title: SAMPLE 11: Patient7.Post_Replicate1

description:
ChipNumber: Chip1
Batch number: 1
OriginalSampleNumbers: 7


title: SUM44_LTED_B_1


title: SAMPLE 13: Patient7.Pre_Replicate1

description:
ChipNumber: Chip6
Batch number: 2
OriginalSampleNumbers: 27


title: SAMPLE 17: Patient8.Pre_Replicate1

description:
ChipNumber: Chip9
Batch number: 3
OriginalSampleNumbers: 31


title: SAMPLE 12: Patient7.Post_Replicate2

description:
ChipNumber: Chip3
Batch number: 2
OriginalSampleNumbers: 7


title: SAMPLE 6: Patient4.Pre_Replicate2

description:
ChipNumber: Chip4
Batch number: 2
OriginalSampleNumbers: 10


title: 3906_Cont


title: SAMPLE 9: Patient6.Pre_Replicate1

description:
ChipNumber: Chip2
Batch number: 1
OriginalSampleNumbers: 12


title: SUM44_LTED_A_3


title: SAMPLE 4: Patient4.Post_Replicate2

description:
ChipNumber: Chip16
Batch number: 5
OriginalSampleNumbers: 53


title: SAMPLE 5: Patient4.Pre_Replicate1

description:
ChipNumber: Chip2
Batch number: 1
OriginalSampleNumbers: 10


title: SAMPLE 7: Patient6.Post_Replicate1

description:
ChipNumber: Chip17
Batch number: 5
OriginalSampleNumbers: 61


title: 3849_Cont


title: SUM44_LTED_A_2


title: SUM44_LTED_A_1


title: SAMPLE 2: Patient1.Pre_Replicate2

description:
ChipNumber: Chip11
Batch number: 4
OriginalSampleNumbers: 35


title: SAMPLE 10: Patient6.Pre_Replicate2

description:
ChipNumber: Chip4
Batch number: 2
OriginalSampleNumbers: 12


title: SAMPLE 3: Patient4.Post_Replicate1

description:
ChipNumber: Chip14
Batch number: 4
OriginalSampleNumbers: 53


title: SUM44F_parental_3

value: Parental


title: SUM44F_parental_2


title: SAMPLE 8: Patient6.Post_Replicate2

description:
ChipNumber: Chip18
Batch number: 5
OriginalSampleNumbers: 61


title: SAMPLE 1: Patient1.Pre_Replicate1

description:
ChipNumber: Chip9
Batch number: 3
OriginalSampleNumbers: 35


title: SUM44F_parental_1


title: THPR002B

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
quality trimmed with fqtrim (v 0.9.4) phred 30, min length 20
mapped with hisat2 (v 2.0.3)
counted mapped reads with featureCounts and Ensembl version 89 annotation
edgeR-robust DE analysis with genes filtered at rowSum cpm>1
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text file with raw read counts for each gene

source_name: endometrium

extract_protocol:
Qiagen rneasy kit
Illumina Tru-seq Stranded Ribo-zero

treatment_protocol: endometrial biopsies were flash-frozen in liquid nitrogen

value: endometrium

tag: phase

value: proliferative


title: THPR002D

value: mid-secretory


title: THPR001G


title: THPR002A


title: THPR002C


title: THPR001F


title: SUM44PE_parental_3


title: SUM44PE_parental_2


title: THPR001E


title: SUM44PE_parental_1


title: THPR001D


title: THPR001B


title: THPR001C


title: MM134_LTED_E_2


title: MM134_LTED_D_2


title: MM134_LTED_D_3


title: THPR001A


title: MM134_LTED_D_1


title: MM134_LTED_B_3


title: MM134_LTED_B_2


title: MM134_LTED_B_1


title: MM134_LTED_A_2


title: Non-foam intimal macrophages rep 3 (Bulk RNA-seq)

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

data_processing:
quality control: RSeQC version 2.3.
alignment: STAR version 2.0.4b.
quantification: Subread: featureCount version 1.4.5.
Genome_build: GRCm38 (Ensembl release 76)
Supplementary_files_format_and_content: Gene counts tables

source_name: Non-foam macrophages from intimal layer from Apoe -/- mouses aorta

extract_protocol:
The whole aorta (including the aortic sinus, arch, thoracic aorta and abdominal aorta) was carefully isolated, and the perivascular fat was removed. To remove the adventitia, the whole aorta was incubated with collagenase II (400U/ml)  with hyaluronidase (90 U/ml) at 37°C for 8 min, and then the adventitia was physically removed. The aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live foamy and non-foamy macrophages (PI-BODIPY493/503hiSSChiCD64+CD11b+, PI-BODIPY493/503loSSCloCD64+CD11b+) were sorted out using flow cytometry (BD FACSAria III). The sorted cells were quickly added to single cell lysis buffer.
The cDNA libraries were prepared from cell lysates in 10X Single-Cell Lysis Buffer (Takara-Clontech) containing 5% RNase inhibitor. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per the manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator with the following parameters: duty cycle, 10; intensity, 5; cycles/burst, 200; and time, 180 seconds. The cDNAs were blunt ended, supplemented with an A base at the 3’ end, and then ligated with Illumina sequencing adapters. The ligated fragments were amplified for 12 cycles using primers that incorporated unique index tags. The amplified fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

tag: mouse genotype

value: ApoE -/-

value: non-foam cells form intimal layer of aorta


title: MM134_LTED_A_3


title: Non-foam intimal macrophages rep 1 (Bulk RNA-seq)


title: Non-foam intimal macrophages rep 2 (Bulk RNA-seq)


title: Foam intimal macrophages rep 2 (Bulk RNA-seq)

source_name: Foam macrophages from intimal layer from Apoe -/- mouses aorta

value: foam cells form intimal layer of aorta


title: MM134_parental_3


title: MM134_LTED_A_1


title: KI rep2 (311-8)

city: Davis

first: Nadean

last: Brown

state: CA

address: 4407 Tupper Hall

department: Dept of Cell Biology and Human Anatomy

institute: University of California, Davis

data_processing:
Sequenced reads were trimmed and aligned to mm10 genome with Bowtie2
Transcripts were assembled and abundances estimated by Cufflinks (usegalaxy.org) using mm10 reference annotation; bias correction, multi-read correct; Cufflinks effective length correction
Assembled transcripts were analyzed for differential expression with CuffDiff (usegalaxy.org); geometric library normalization; pooled dispersion method; multi-read correct, Cufflinks effective length correction
Tabular file of differentially expressed transcripts was converted to .xlsx and sorted in excel by significance and fold change
Genome_build: mm10
Supplementary_files_format_and_content: .txt files include RPKM values, p-values and adjusted p-values (q-values) for each genotype

source_name: Retina

extract_protocol:
Pairs of E12.5 GFP+ optic cups were dissected and dissociated into single cell suspensions with TrypLE Select (Invitrogen, Cat:12563). Total RNA was extracted using RNeasy Micro Kit (Qiagen, Cat:74004). Samples were submitted to CCHMC Gene Expression for QC analysis with the Agilent Bioanalyzer.
Sequencing libraries were generated using the TruSeq RNA library kit (Illumina, RS-122-2001)

value: retina


title: MM134_parental_2


title: Foam intimal macrophages rep 1 (Bulk RNA-seq)


title: KI rep3 (311-10)


title: MM134_LTED_E_3


title: KI rep1 (311-5)


title: MM134_parental_1


title: MM134_LTED_E_1


title: MUT rep3 (466-11)

description:
E12_RNASEQ_HET_v_MUT
E12_RNASEQ_MUT_v_KI


title: MUT rep1 (466-3)


title: MUT rep2 (466-6)


title: HET rep3 (466-9)


title: HET rep2 (466-8)


title: HET rep1 (466-2)


title: Foam intimal macrophages rep 3 (Bulk RNA-seq)


title: 4027_P3_DP

molecule: polyA RNA

growth_protocol: PMA/Ionomycin (50ng/ml / 1000ng/ml) 4hr stimulation

extract_protocol:
Isolate PBMCs from whole blood and sorted CD4+CD25hi CD127neg Tregs by FACS
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: Treg

tag: cell subpopulation

value: DP


title: 4027_P5_IL10SP


title: 4027_P2_IFNGSP

value: IFNGSP


title: STAT1-deficient carrier challenged 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
total RNA bound to HA-tagged ribosomes
r951sStat1flxRpl22het17Group4

data_processing:
Sequence images were transformed to BCL files with the Illumina BaseCaller software and basecalls where then converted to fastq files using software CASAVA-v1.8.2
Sequences were aligned to the reference genome of Mus musculus (UCSC genome assembly version mm10).
Alignment was performed using the STAR  alignment software (Dobin et al., 2013) (version 2.3.0e) allowing 2 mismatches within 50 bases
Subsequently, conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting was conducted with SAMtools (Li et al., 2009) (version 0.1.18) and HTSeq (Anders et al., 2015) (version 0.6.1p1).
RPKM values were generated from raw counts using the method described and published by Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods. 2008 Jul 1;5(7):621-8.
Data was preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (Love et al., 2014) (version 1.8). Specifically, the data were normalized and tested for differentially expressed genes based on a generalized linear model likelihood ratio test assuming negative binomial data distribution. Candidate genes were filtered to a minimum of log2 1 fold change and FDR-corrected P < 0.05. Gene annotation was performed using Mus musculus entries from Ensembl (www.ensembl.org) via the biomaRt package (Durinck et al., 2005) (version 2.24.0).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM : tab-delimited text files include RPKM values for all the Samples
Supplementary_files_format_and_content: Candidate_Genelist  : tab-delimited files containing Candidate genes obtained from the comparison analysis of group STAT1-competent carrier challenged(DejaVu) vs STAT1-deficient carrier challenged (Stat1flx) with respective log2fold change values, adjusted p-values

source_name: brain

extract_protocol:
Brains were isolated and stored in RNAlater solution (Thermofisher) at -80° C until further processing. Frozen tissue was transferred in Supplemented Homogenization Buffer (HB-S) and lysed with tissue lyser (Qiagen). After lysis of the tissues and before immunopurification, a small fraction of lysate of each sample (input) was set aside and total RNA was extracted with TRIzol (Sigma) reagent followed by the RNeasy plus Micro Kit’s procedure (Qiagen). After immunopurification of the ribosome-associated RNAs, RNA quality was assessed on a 2100 BioAnalyzer (Agilent) and RNA amounts were quantified using the Qubit 2.0 Fluorometer (Life Technologies). The RNA integrity value (RIN) of the samples selected to be sequenced ranged between 7 and 9.2.
RNA-samples were prepared using "TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat. No. RS-122-2301, RS-122-2302, and RS-122-2303) according to the manufacturer's protocol (Illumina). Samples were sequenced using the HiSeq 2000 (Illumina) (SE, 50 bp, ca. 30 Mio reads/sample)

value: Stat1fl/fl x Rpl22HA/+

tag: intracranial neonatal infection

value: rLCMV-Cre carrier

tag: intravenous infection

value: challenged with LCMVwt


title: STAT1-deficient carrier challenged 2

description:
total RNA bound to HA-tagged ribosomes
r951sStat1flxRpl22het16Group4


title: STAT1-deficient carrier challenged 1

description:
total RNA bound to HA-tagged ribosomes
r951sStat1flxRpl22het15Group4


title: STAT1-deficient carrier challenged 4

description:
total RNA bound to HA-tagged ribosomes
r951sStat1flxRpl22het18Group4


title: Prostate adenocarcinoma

city: Cleveland

first: Shiv

middle: Shankar

last: Verma

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

description:
Transgenic mice supplemented with vehicle G2
TRAMP tumor

hyb_protocol: As described by Affymetrix. Standard protocol.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 and GeneChip Operating Software acquired raw fluorescence data.

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each gene, and p-values are computed from the theoretical t-distribution. gene with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

The file probesets_with_fold-change_differences.txt.gz contains ~9K probe sets identified with log2fold-changes greater than 0.5.

source_name: primary prostate cancer

label_protocol: Microarray assay was performed using  core facality of Case western Reserve University (CWRU), started from 0.5 µg total RNA samples that were first subject to dephosphorylation reaction to remove 5’ phosphate groups of miRNA molecules. Then an oligonucleotide adapter was added to 3’ end of sample (3’OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contains a tag segment for capturing fluorescent dye during a later Cy3 dye staining process.

extract_protocol: Total RNA was extracted from frozen mouse prostate tissue specimen isolated by TRIzol (Invitrogen Corporation). The quality and quantity of RNA for quality control (QC) was assessed by NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE). RNA quality was evaluated with Agilent’s RNA 2100 Bioanalyzer with 28S/18S ratios and RIN determined by 2100 Expert Software (Santa Clara, CA). The final RNA samples were selected which passed the RIN number 7 or above and were pooled for microarray experiment.

tag: background strain

value: TRAMP transgenic


title: 4026_P5_IL10SP

tag: tissue


title: 4026_P6_DN

value: DN


title: STAT1-competent carrier challenged 4

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22het24Group3

value: Stat1+/+ x Rpl22HA/+


title: STAT1-competent carrier challenged 3

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22het9Group3


title: STAT1-competent carrier challenged 5

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22het25Group3


title: 4026_P3_DP


title: 4026_P2_IFNGSP


title: 4023_P6_DN


title: STAT1-competent carrier challenged 2

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22het6Group3


title: HI.2774.001.Index_4.JQ11

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

library_source: genomic

data_processing:
Illumina Casava software used for basecalling
Reads were sorted using SAMtools v1.2, transformed in FASTQ files using BEDTools v2.17 and trimmed using Trim Galore! v0.4.0
Reads were aligned using Bismark v0.14.5 (44) and indexed with SAMtools v1.2.
The methylKit package (version 0.9.4)  (Altuna Akalin, (2012). " Genome Biology , 13:R87)  was used for data processing and analysis  (1 CpGs minimum per tile, 10x reads per sample and  ≥20% average differences between groups of replicates)
Genome_build: Rnor 5.0
Supplementary_files_format_and_content: textl file including tthe output of methylKit for hypermethylated and hypomethylated regions between control and treatment for each generation

molecule: genomic DNA

organism: Rattus norvegicus

source_name: epididymal sperm

extract_protocol:
At PND 90 the male rats for F1, F2 and F3 generations were anesthetized by isofurane and euthanized by cardiac puncture. Fresh right caudal epididymis was placed in a 35 mm Petri dish with prewarmed Gibco®Media-199 without phenol red (Life Technologies), 0.5% fatty acid-free BSA (Fraction V; Sigma-Aldrich,St.), nicked scalpel several times and then incubated for 10 min in a humidified 5% CO2 incubator at 37°C to allow sperm to diffuse.
500 ng of DNA (PureLink genomic DNA kit Invitrogen) were used for RRBS libraries (H. Gu et al. Nature protocols 6, 468, (2001)) using the gel-free technique. The bisulfite conversion and subsequent clean-up were done by using the EpiTect bisulfite kit (Qiagen). Libraries PCR was realized with PfuTurbo Cx hotstart DNA polymerase (Agilent Technologies).

treatment_protocol: Five-week-old female rats (F0) were exposed by gavage (1 mL/100g body weight) with corn oil (Control group) or the POPs Arctic mixture (POPs group; 500 µg/kg body weight) thrice weekly for 5 weeks. The gavage continued through mating until parturition.

value: Sprague-Dawley

tag: generation

value: epididymal sperm

tag: treatment

value: organochlorines


title: HI.2774.001.Index_5.JQ12

tag: strain


title: 4027_P6_DN


title: HI.2774.001.Index_2.JQ10


title: 4023_P5_IL10SP


title: HI.2763.008.Index_12.JQ9


title: STAT1-competent carrier non-challenged 5

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22Het29Group2

value: non challenged


title: 4023_P3_DP


title: Normal prostate gland

description:
Non-transgenic mice supplemented with vehicle G1
Non transgenic mice

source_name: Normal prostate gland

value: wildtype


title: 4023_P2_IFNGSP


title: HI.2763.008.Index_7.JQ8


title: HI.2763.008.Index_6.JQ7


title: 4022_P6_DN


title: STAT1-competent carrier non-challenged 7

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22Het31Group2


title: STAT1-competent carrier non-challenged 3

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22hetC3Group2


title: STAT1-competent carrier challenged 1

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22het2Group3


title: 4022_P3_DP


title: HI.2774.001.Index_7.JQ5

value: control


title: HI.2774.001.Index_6.JQ4


title: STAT1-competent carrier non-challenged 2

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22hetC2Group2


title: HI.2774.001.Index_12.JQ6


title: STAT1-competent carrier non-challenged 1

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22hetC1Group2


title: STAT1-competent carrier non-challenged 6

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22Het30Group2


title: 4022_P2_IFNGSP


title: HI.2763.008.Index_5.JQ3


title: 4019_P6_DN


title: STAT1-competent carrier non-challenged 4

description:
total RNA bound to HA-tagged ribosomes
r951sRpl22hetC4Group2


title: Intestine_goldfishfood_goldfishbiome_rep4

city: Waterloo

first: Paul

last: Craig

state: ON

address: 200 University Ave West

department: Biology

country: Canada

institute: University of Waterloo

description: Gene expression 14 days after antibiotic treatment, biome change, and diet change in D. rerio intestine

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

scan_protocol: Slides were scanned immediately after washing on SureScan Microarray Scanner G2600D using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw fluorescent   data   files   were   converted   to   normalized   expression   indices   using   the RMAalgorithm   in   GeneSpring   GX   (Agilent   Technologies).

organism: Danio rerio

source_name: intestine

label_protocol: A total  of  500  ng  of  total  RNA  was  labeled  following  the  explicit  instructions  of  the  one-color  microarray  based  gene  expression analysis with low input quick Amp labeling protocol (Agilent Technologies).

growth_protocol: Prior to experimentation all zebrafish were housed in aquaria with reciculating water kept at 25 C and a 12h:12h day:night cycle. Goldfish were kept in a separate reciculating system at 25 C and a 12h:12h day:night cycle. All animals were fed daily.

extract_protocol: Total  RNA  was  extracted  from  frozen  intestinal  samples using  Trizol  reagent  following the  manufacturer’s  instructions  (Invitrogen).  Purity  and  integrity  of  the  extracted  RNA was  validated  on  a  2100  Bioanalyzer  Instrument  (Agilent  Technologies)

treatment_protocol: Zebrafish were treated with anitbiotics (except wild types) for 7 days. The water was changed daily and fresh anitbiotics added. The temperature and day:night cycle were maintained. After 7 days, the water was changed and animals allowed to recover for 1 day. Subsequently, animals were implanted with either zebrafish microbiomes or goldfish microbiomes.  The animals were then fed daily either zebrafish food or goldfish food for 14 days. The five treatment groups were housed seperatley to prevent contamination.

value: antibiotic treated (7 days), goldfish biome replaced, fed goldfish food (14 days)

value: intestine

tag: gender

value: female

value: Adult


title: Intestine_goldfishfood_goldfishbiome_rep1


title: Intestine_goldfishfood_goldfishbiome_rep3


title: Intestine_goldfishfood_goldfishbiome_rep2


title: 4022_P5_IL10SP

value: blood

value: Treg

tag: subject#


title: 4019_P3_DP

value: DP

tag: age


title: HI.2763.008.Index_2.JQ1


title: HI.2763.008.Index_4.JQ2


title: 4019_P2_IFNGSP

value: IFNGSP


title: Intestine_goldfishfood_zebrafishbiome__rep3

description: Gene expression 14 days after antibiotic treatment, biome replacement, and diet change in D. rerio intestine

value: antibiotic treated (7 days), zebrafish biome replaced, fed goldfish food (14 days)


title: Intestine_goldfishfood_zebrafishbiome__rep2


title: HI.2774.003.Index_5.F4L

description:
processed data file: DMS1_hyper.perbase.20.percent.txt
processed data file: DMS1_hypo.perbase.20.percent.txt
processed data file: DMS2_hyper.perbase.20.percent.txt
processed data file: DMS2_hypo.perbase.20.percent.txt
processed data file: DMS3_hyper.perbase.20.percent.txt
processed data file: DMS3_hypo.perbase.20.percent.txt

data_processing:
Illumina Casava software used for basecalling.
Reads were sorted using SAMtools v1.2, transformed in FASTQ files using BEDTools v2.17 and trimmed using Trim Galore! v0.4.0.
Reads were aligned using Bismark v0.14.5 (44) and indexed with SAMtools v1.2.
The methylKit package (version 0.9.4) (Altuna Akalin, (2012). Genome Biology, 13:R87) was used for data processing and analysis (1 CpGs minimum per tile, 10x reads per sample and ≥20% average differences between groups of replicates).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: *.perbase.20.percent.txt: Tab-delimited text files include the output of methylKit for hypermethylated and hypomethylated regions between control and treatment for each generation.


title: HI.2774.003.Index_2.F4J


title: HI.2774.002.Index_12.F4I


title: Intestine_zebrafishfood_goldfishbiome_rep4

description: Gene expression 14 days after antibiotic treatment, biome change, and no diet change in D. rerio intestine

value: antibiotic treated (7 days), goldfish biome replaced, fed zebrafish food (14 days)


title: BT-474 Tam2

city: Helsinki

first: Susanne

last: Hultsch

address: Tukholmankatu 8

department: FIMM, HiLife

country: Finland

institute: University of Helsinki

description: Tamoxifen resistant BT-474; BT-474 (ATCC) cells were continuously treated with 1uM 4-OH-tamoxifen for eight to twelve months.

data_processing:
Basecalls performed using standard Illumina base-caller
RNA-seq reads were pre-processed using Trimmomatics v0.32 with the following configurations ILLUMINACLIP:TruSeqAdapters-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Pre-processed RNA-seq reads were aligned to the hg38 genome assembly (EnsEMBL v80 or v82) using the STAR per-sample 2-pass mapping strategy. STAR v2.3.0e aligner was used with the following configurations --outSAMattributes All --outSAMunmapped Within. The STAR indexes were build from primary assembly sequences and by taking into account transcript annotations.
PCR duplicates were marked with the MarkDuplicates tool of PICARD v1.63 with the following configurations CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT
Patient sample data (GSE58708 dataset) has been reanalyzed as described above
Counts and Counts per Megabase of library size (CPM) values were calculated using subreadR, limma, and edgeR as implemented in the statistical environment R (v.3.3.0). Data from the listed breast cancer cell lines were combined with patient sample data (GSE58708 dataset), normalized using the TMM function, and adjusted for an effect associated with the experiments using the function removeBatchEffect.
Genome_build: hg38 genome assembly, EnsEMBL v80 or v82
Supplementary_files_format_and_content: Tab-delimited text file (.txt). Columns: 1) EnsEMBL gene id, 2) Gene name, 3) raw count value, 4) non-batch adjusted log2 CPM value, and 5) batch adjusted log2 CPM value

source_name: mammary gland

growth_protocol: Human breast cancer cell lines MCF-7 (HTB-22, ATCC), T-47D (HTB-133, ATCC), ZR-75-1 (CRL-1500, ATCC) and BT-474 (HTB-20, ATCC) were obtained from the American Type Culture Collection. The cells were grown in DMEM with L-Glutamine (MCF-7 and BT-474, PAN Biotech, Aidenbach, Germany) or RPMI-1640 with L-Glutamine (ZR-75-1 and T-47D, PAN Biotech) supplemented with 10 % FCS (Gibco, Life Technologies, Carlsbad, CA) and 1 % penicillin/streptomycin (Gibco). Culture media for T-47D, MCF-7 and BT-474 additionally contained 0,1 % bovine insulin (Sigma. St. Louis, MO). The tamoxifen-resistant cell lines (MCF-7 Tam1, T-47D Tam1 & Tam2, ZR-75-1 Tam1 & Tam2, BT-474 Tam1 & Tam2) were derived from the parental cell lines by continuous exposure to 4-OH-tamoxifen (Sigma, 1 μM in ethanol) for 8–12 months. Culture media was replaced every 2–3 days. All cells were incubated at 37 °C with 5 % CO2and passaged when ca 80 % confluent.

extract_protocol:
total RNA was isolated using miRNeasy kit (Qiagen) and its quality was controlled by using the Agilent Bioanalyzer with the RNApico chip (Agilent). Qubit RNA-kit (Life Technologies) was used to quantitate RNA amount per sample.
The strand-specific paired-end RNA-sequencing library was prepared then with ScriptSeq™ Complete kit for human/mouse/rat (Illumina). The library preparation included the ribodepletion of rRNA from 1µm of total RNA and generation of double stranded cDNA by revers transcription with random hexamers for generation of cDNA. SPRI beads (Agencourt AMPure XP) were used to purify the libraries and to remove fragments less than 200 bp in length. The mean fragment size ranged from 300 to 400 nucleotides. The library quality was evaluated on the High Sensitivity chip by Agilent Bioanalyzer (Agilent).
Ribo depletion RNA-Seq

treatment_protocol: see above

tag: vendor

value: tamoxifen-resistant derivative of cell line from ATCC


title: 4019_P5_IL10SP

tag: cell type


title: HI.2774.002.Index_7.F4H

value: Sprague-Dawley


title: BT-474

value: Cell line from ATCC


title: Intestine_zebrafishfood_goldfishbiome_rep3


title: Intestine_goldfishfood_zebrafishbiome_rep1


title: ZR-75-1 Tam2

description: Tamoxifen resistant ZR-75-1; ZR-75-1 (ATCC) cells were continuously treated with 1uM 4-OH-tamoxifen for eight to twelve months.


title: BT-474 Tam1


title: Intestine_zebrafishfood_goldfishbiome_rep1


title: Intestine_zebrafishfood_goldfishbiome_rep2


title: Intestine_zebrafishfood_zebrafishbiome_rep3

description: Gene expression 14 days after antibiotic treatment, biome replacement, and no diet change in D. rerio intestine

value: antibiotic treated (7 days), zebrafish biome replaced, fed zebrafish food (14 days)


title: Intestine_zebrafishfood_zebrafishbiome_rep4


title: HI.2774.003.Index_12.F4F

value: epididymal sperm


title: HI.2774.003.Index_7.F4E


title: T-47D Tam2

description: Tamoxifen resistant T-47D; T-47D (ATCC) cells were continuously treated with 1uM 4-OH-tamoxifen for eight to twelve months.


title: HI.2774.003.Index_6.F4D


title: ZR-75-1


title: HI.2774.003.Index_4.F4K

value: organochlorines


title: Intestine_zebrafishfood_zebrafishbiome_rep2


title: T-47D Tam1


title: Intestine_wildtype_Control_rep3

description: Gene expression 14 days after no antibiotic treatment, biome or diet change in D. rerio intestine

value: wild type zebrafish (21 days)


title: T-47D


title: MCF-7


title: Intestine_wildtype_Control_rep2


title: ZR-75-1 Tam1


title: tma64∆/tma20∆ 69F

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of 68F. Wig files composed of combination of two biological replicates (68F and 69F).

data_processing:
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). Reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all 4 of these alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome or disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer.


title: MCF-7 Tam1

description: Tamoxifen resistant MCF-7; MCF-7 (ATCC) cells were continuously treated with 1uM 4-OH-tamoxifen for eight to twelve months.


title: HI.2774.003.Index_8.F3L


title: HI.2774.003.Index_3.F3K


title: HI.2774.002.Index_2.F4A

value: control


title: HI.2774.002.Index_5.F4C


title: tma64∆/tma22∆ 71F

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of 70F. Wig files composed of combination of two biological replicates (70F and 71F).


title: tma64∆/tma22∆ 70F

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of 71F. Wig files composed of combination of two biological replicates (70F and 71F).


title: Intestine_wildtype_Control_rep1

value: intestine


title: HI.2774.002.Index_6.F4G


title: HI.2774.003.Index_1.F3J


title: tma64∆/tma20∆ 68F

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of 69F. Wig files composed of combination of two biological replicates (68F and 69F).


title: Intestine_wildtype_Control_rep4

value: female


title: Intestine_zebrafishfood_zebrafishbiome_rep1

value: Adult


title: HI.2774.002.Index_11.F3I


title: HI.2774.002.Index_4.F4B


title: HI.2774.002.Index_9.F3G


title: HI.2774.003.Index_11.F3F


title: HI.2774.003.Index_10.F3E


title: HI.2774.003.Index_9.F3D


title: Intestine_goldfishfood_zebrafishbiome__rep4


title: wild type DJY09_1

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY10_1. Wig files composed of combination of two biological replicates (DJY09_1 and DJY10_1).

value: wild-type (BY4741)


title: wild type DJY10_1

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY09_1. Wig files composed of combination of two biological replicates (DJY09_1 and DJY10_1).


title: HI.2774.001.Index_1.F2JII


title: HI.2774.001.Index_3.F2K


title: HI.2774.002.Index_1.F3A


title: tma64∆/tma22∆ sui1-L96P DJY08_4

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY07_4. Wig files composed of combination of two biological replicates (DJY07_4 and DJY08_4).

value: tma64-delta/tma22-delta sui1-L96P


title: HI.2774.002.Index_3.F3B


title: HI.2774.002.Index_10.F3H


title: PMM rep1

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

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

organism: Sus scrofa

source_name: PMM

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

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

tag: breed

value: Qinyu Pig

value: 178 days old

value: psoas major muscle (PMM)


title: PMM rep3


title: LDM rep3

source_name: LDM

value: longissimus dorsi muscle (LDM)


title: tma64∆/tma22∆ sui1-L96P DJY07_4

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY08_4. Wig files composed of combination of two biological replicates (DJY07_4 and DJY08_4).


title: LDM rep2


title: EMSC (Sp-AC/d2-CSF/d7)

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

institute: University of Macao

description: EMSC spheroids underwent storage for 2 days in ambient condition (room temperature) and then re-plated in cerebrospinal fluids and cultured in Normothermia condition for 7 days.

data_processing: RNA was extracted from cells harvested under various conditions by using RNAeasy mini kit (Qiagen) and cDNA libraries were synthesized and processed by using HumanHT-12 v4 Expression BeadChip. Further analysis was performed using the BeadStudio Data Analysis software (Illumina) and Excel. The microarray dataset was normalized and filtered to remove probes with detection P value > 0.01 in at least 50% of the samples. Two normalization methods were utilized to analyze the dataset on the basis of their biological relevance. First, the average probe intensity of all biological and technical replicates was used to compare the test and control groups for their gene expression profiles. Second, the probe intensity of analyzed genes in the control sample EMSC was used as a baseline to identify the expression of the genes in the test samples. Pathway enrichment was assessed using a hypergeometric test against gene sets collected from Msigdb covering pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Biocarta, Reactome and the Gene Ontology (GO) terms. In order to control the false discovery rate, we set statistical significance at P = 0.001 as the cutoff for a pathway enrichment test.

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: We attempted to recapitulate the above in vivo observations of EMSC transdifferentiation into neural cells in vitro. AC-d2 EMSCsp were re-plated in a 12-well plate to form a monolayer in the MSC medium at 0.5 ml/well, and the attached cells spread well with over 95% viability as we reported [31]. The culture medium was then either refreshed with the same medium or replaced with pooled CSF collected from the EAE-induced monkeys, and the cells were cultured for 14 days (Fig. 5A). The cells in CSF gradually transformed into neural-like cells with outgrowing fibers from some cell bodies, whereas all the cells in the MSC medium retained the typical MSC phenotype (Fig. 5B).

extract_protocol: we used the Qiagen RNA easy kit(Cat.No.74136) to extract the RNA follow its manunal book.

treatment_protocol: To elucidate the dynamic changes of the transcriptomic profile of EMSC cultured in CSF, we conducted microarray on EMSC, EMSCsp-AC/d2, and EMSCsp-AC/d2 re-plated and cultured in CSF for 7 days (EMSCsp-AC/d2-CSF/d7). Pairwise comparisons of the transcriptomic profiles of the three samples reveal a total of 7,480 differentially expressed genes by more than 2-fold across all the comparisons (Fig. 6A). Particularly, when comparing EMSCsp-AC/d2-CSF/d7 to EMSC, we obtained 1,879 up-regulated and 1,456 down-regulated genes (Table S1).

value: ESC-derived mesenchymal stem cell spheres


title: EMSC

description: Embryonic stem cell (Envy) derived mesenchymal stem cells (EMSC) cultivated in the normal cell culture condition (Normothermia).


title: HI.2774.001.Index_8.F2L

description:
processed data file: DMS1_hyper.perbase.20.percent.txt
processed data file: DMS1_hypo.perbase.20.percent.txt
processed data file: DMS2_hyper.perbase.20.percent.txt
processed data file: DMS2_hypo.perbase.20.percent.txt
processed data file: DMS3_hyper.perbase.20.percent.txt
processed data file: DMS3_hypo.perbase.20.percent.txt

value: Sprague-Dawley


title: HI.2774.002.Index_8.F3C


title: PMM rep2


title: EMSC (Sp-AC/d2)

description: EMSC spheroids underwent storage for 2 days in ambient condition (room temperature)


title: tma64∆/tma22∆/SUI1 DJY07_3

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY08_3. Wig files composed of combination of two biological replicates (DJY07_3 and DJY08_3).


title: HI.2763.008.Index_10.F2H


title: tma64∆/tma22∆/SUI1 DJY08_3

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY07_3. Wig files composed of combination of two biological replicates (DJY07_3 and DJY08_3).


title: HI.2763.008.Index_11.F2I


title: HI.2763.008.Index_9.F2G


title: HI.2774.001.Index_11.F2F


title: HI.2774.001.Index_10.F2E


title: HI.2774.001.Index_9.F2D


title: Tbet+iTregPDL1 exon replicate 2

description: Sorted CD4+Tbet+FoxP3- cells expanded in the presence of anti-CD3, antiCD28, rmIL2 and rhTGF-b1 and PDL-1 fc for 3 days followed by expansion with IL-2 and TGF-b1 for additional 4 days.

data_processing: The Partek Genomics Suite software using RMA algorithm was used.The normalized expression values are log2-scaled.

source_name: T cells

extract_protocol: RNA extracted with RNAeasy kit from Qiagen and reverse transcribed with Ambion WT expression kit

value: spleen


title: SUI1 DJY08_1

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY07_1. Wig files composed of combination of two biological replicates (DJY07_1 and DJY08_1).


title: sui1-L96P DJY08_2

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY07_2. Wig files composed of combination of two biological replicates (DJY07_2 and DJY08_2).


title: Tbet+iTreg exon replicate 1

description: Sorted CD4+Tbet+FoxP3- cells expanded in the presence of anti-CD3, antiCD28, rmIL2 and rhTGF-b1 for 3 days followed by expansion with IL-2 and TGF-b1 for additional 4 days.


title: Tbet+iTregPDL1 exon replicate 1


title: C9223

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software.
Reads were mapped to the reference genome (bosTau7) using the software package Tophat (version: 2.0.13).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
The number of reads that mapped to each annotated gene in the bovine GTF file was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Cow genome assembly: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files including gene Ensembl ID and number of mapped reads.

organism: Bos taurus

source_name: Mammary gland

extract_protocol:
Total RNA was extracted from mammary tissue using the RNeasy Plus Universal Mini Kit (Qiagen, Valencia, CA) and RNA concentration was determined using a NanoDrop instrument (ND-2000, ThermoFisher Scientific, Waltham, MA). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
RNA-Seq library was constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations. Libraries were sequenced on the Illumina HiSeq3000 platform at the University of Florida Biotechnology Center.

value: Mammary gland

value: Holstein

value: ID:9223 TRT:CL


title: H9203

value: ID:9203 TRT:HT


title: H9196

value: ID:9196 TRT:HT


title: Tbet+iTregPDL1 exon replicate3

city: Hamilton

first: Eric

last: Dahlstrom

address: 903 S. 4th St

institute: NIAID, NIH


title: H9204

value: ID:9204 TRT:HT


title: C9214

value: ID:9214 TRT:CL


title: Tbet+iTreg exon replicate 2


title: LDM rep1


title: Tbet+iTreg exon replicate 3


title: HI.2763.008.Index_8.F2C

value: epididymal sperm

value: control


title: TCS

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

data_processing:
Basecalling were performed by Illumina GA Pipeline v1.5
raw reads were filtered to generate clean data
clean reads were aligned against genome by  SOAP a l i g n e r /SOAP2（Li, 2009）
Reads per kilobase transcriptome per million mapped reads(RPKM) was used to analyze the expression of genes
Genome_build: Reference Genome Sequence is NZ_CM001015.1; NZ_CM001016.1; NZ_CM001017.1; NZ_CM001018.1; NZ_CM001019.1
Supplementary_files_format_and_content: text files include RPKM values for each Sample .

organism: Streptomyces clavuligerus

source_name: mycelium

growth_protocol: the total RNA of Streptomyces clavuligeruswas extracted from cultures incubated at 25ºC for 72 h in fermentation mediumand were then treated with RNase-free DNase I (Invitrogen) twice according to the recommended protocols.

extract_protocol:
the mycelia were ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA
The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).

tag: genotype

value: TCS mutant strain

value: TCS


title: HI.2763.008.Index_1.F2A


title: C9202

value: ID:9202 TRT:CL


title: SUI1 DJY07_1

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY08_1. Wig files composed of combination of two biological replicates (DJY07_1 and DJY08_1).


title: sui1-L96P DJY07_2

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of DJY08_2. Wig files composed of combination of two biological replicates (DJY07_2 and DJY08_2).


title: HI.2763.008.Index_3.F2B


title: F613

value: wildtype


title: 5H2 Fab-anti-NHBA

type: protein

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

country: Italy

institute: GSK Vaccines

description:
purified fragment antigen binding
n/a

hyb_protocol: Protein array was first blocked 60 min in Blocking Buffer (Block it, Arrayit Sunnyvale, CA 94085, USA). The array was then incubated 1h a room temperature with huFab 5H2 diluted 1:2000 for anti-human IgG-specific analysis. After washing with 0.1% Tween 20 in PBS buffer (PBST), array was incubated with an AlexaFluor®647-labelled anti-human IgG, fab specific secondary antibody (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slide was washed again as before, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a Powerscanner (Tecan Trading AG, Switzerland) and the 16-bit images were generated with Powerscanner software at 10 µm per pixel resolution.

data_processing: Image was processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data was performed using in-house developed software and R scripts. For each sample, the mean fluorescence intensity (MFI) of 8 replicated spots was determined, after subtraction of the background value surrounding each spot.

molecule: protein

source_name: recombinant antibody

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol: Gene fragments corresponding to the heavy and light chains of the variable regions were synthesized by Geneart (Life Technologies) with Eco31I site flanking gene extremities. The 5H2 Fab was produced by transient transfection using Expi293 (Life Technologies) cells in suspension, according to the manufacturer’s protocol. Equal amounts (15 μg each/30 mL of transfection volume) of vector DNA encoding FabH and FabL chain were used to transfect Expi293 cells. The cells were incubated at 37°C with a humidified atmosphere of 8% CO2 in air on an orbital shaker rotating at 125 rpm. Cell culture supernatant was harvested after 36 and 72 h post transfection, clarified by centrifugation for 30 min at 4000 rpm and concentrated. The Fab was purified from the supernatant using a Strep Trap HP pre-packed column with StrepTactin Sepharose High Performance medium (GE Healthcare), followed by gel filtration chromatography on a Superdex 200 16/60 column (GE Healthcare). After purification, a cleavable C-terminal Strep tag II on the heavy chain was removed with TEV (tobacco etch virus) protease. Purity of the Fab was assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) after coomassie staining and its amount was quantified by absorbance at 280 nm.

tag: description

tag: subclass

value: fab


title: rat 7, at T2

status: Public on Aug 29 2018

city: Pont-à-Celles

first: Marie

last: Dagonnier

state: Hainaut

address: Place du Fichaux, 38

department: Stroke

country: Belgium

institute: The Florey Institutes for Neurosciences

description: gene expression data from SHR rat blood at 2 hours after MCA occlusion

hyb_protocol: Samples were randomly hybridized to the GeneChip® RatGene 1.0 ST arrays (Affymetrix, Santa Clara CA, USA; cat#9011730).

scan_protocol: GeneChips were scanned using the Fluidics control station (Affymetrix GeneChip Fluidics Station 450, Affymetrix, Santa Clara, CA, USA)

data_processing:
For gene expression, pairwise comparisons were made between neighboring time points of the experiment using linear models, and the resulting F-statistic was used to identify genes whose expression varied the most across the time course of the experiment. Models were constructed, and significance testing was performed using the R package limma
Genes with expression varying the most over time were ranked by p-value of the F statistic, with a cut-off of 5x10^-7

source_name: Blood

label_protocol: The Encore Biotine module (NuGen, San Carlos, CA, USA; cat#4200-12) was used for fragmentation and labelling. Gene hybridisation was performed using the Affymetrix GeneChip Expression 3’ Amplification Reagent Hybridisation Controls kit (Affymetrix, Santa Clara, CA, USA; cat#900454)

growth_protocol: Eight male 16 week old spontaneously hypertensive rats were maintained under standard housing conditions with a normal light/dark cycle with ad libitum access to normal rat chow and water for two weeks before stroke induction.

extract_protocol: RNA was prepared from the whole blood cell pellets using the PAXgene Blood RNA Kit (PreAnalytiX #762174, Qiagen).

treatment_protocol: Stroke was induced by thread occlusion of the middle cerebral artery (MCAo) using a silicon-coated thread which was maneuvered through the internal carotid until resistance was felt and a drop in cerebral blood flow noted on Laser Doppler; Whole blood (250µl) was drawn from the lateral tail vein (1ml syringe, 26G needle) into 500 international units of heparin (500IU, Pfizer) at 0 (immediately before anesthesia induction), 1, 2, 3, and 6 hours post MCA occlusion. The 24 hour sample was taken by heart puncture immediately following anesthetic overdose

tag: animal

value: rat 7

value: male

value: spontaneously hypertensive rats (SHR)

value: 16 weeks

value: Blood

value: MCA occlusion

tag: time

value: 2 hours


title: rat 8, at T0

description: gene expression data from SHR rat blood before MCA occlusion

value: rat 8

value: before MCA occlusion


title: rat 8, at T3

description: gene expression data from SHR rat blood at 3 hours after MCA occlusion

value: 3 hours


title: rat 7, at T6

description: gene expression data from SHR rat blood at 6 hours after MCA occlusion

value: 6 hours


title: rat 7, at T3


title: rat 6, at T24

description: gene expression data from SHR rat blood at 24 hours after MCA occlusion

value: rat 6

value: 24 hours


title: rat 5, at T24

value: rat 5


title: rat 5, at T0

value: control


title: rat 6, at T0


title: rat 8, at T2


title: rat 5, at T6


title: rat 8, at T24


title: rat 8, at T6


title: rat 7, at T24


title: rat 7, at T1

description: gene expression data from SHR rat blood at 1 hour after MCA occlusion

value: 1 hour


title: rat 7, at T0


title: rat 6, at T3


title: rat 4, at T3

value: rat 4


title: rat 5, at T3


title: rat 5, at T2


title: rat 6, at T2


title: rat 4, at T0


title: rat 8, at T1


title: rat 4, at T1


title: rat 4, at T2


title: rat 4, at T24


title: rat 5, at T1


title: rat 4, at T6


title: rat 6, at T6


title: rat 6, at T1


title: rat 3, at T24

value: rat 3


title: shFAKNE

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel files include readcount values for each sample

source_name: Myc-CaP prostate cancer cell line

growth_protocol: Myc-CaP cells stably transfected with shRNAs targeting FAK or negative control were cultured in DMEM (Biological Industries, Israel) supplemented with 10% heat-inactivated fetal bovine serum (Biological Industries, Israel), 0.1mM nonessential amino acids (Gibico) and 1% Penicillin-Streptomycin (Gibico) at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent. RNA purity was checked using the NanoPhotomete spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Myc-CaP cells stably transfected with shRNAs targeting FAK or negative control were treated with 10μM norepinephrine or vehicle for 24 hours.

value: FVB; Hi-Myc transgenic

value: norepinephrine

tag: transfection

value: shRNAs targeting FAK


title: shNCNE

value: shRNAs targeting negative control


title: rat 1, at T1

value: rat 1

value: male

value: spontaneously hypertensive rats (SHR)

value: 16 weeks

value: Blood

value: MCA occlusion


title: rat 2, at T6

value: rat 2

value: 6 hours


title: rat 3, at T3

value: 3 hours


title: rat 2, at T3


title: rat 3, at T1


title: rat 3, at T0

value: before MCA occlusion

value: control


title: rat 1, at T6


title: rat 1, at T24

value: 24 hours


title: rat 3, at T2

value: rat 3

value: 2 hours


title: rat 1, at T3


title: rat 1, at T0


title: shFAKctr

value: FVB; Hi-Myc transgenic

value: vehicle


title: shNCctr

value: shRNAs targeting negative control


title: EGPA N1106

first: Peter

middle: C.

last: Grayson

address: 10 Center Dr Building 10 6N216G

department: NIAMS

institute: NIH

description: Gene expression from patient with EGPA

hyb_protocol: Each verified cRNA sample was hybridized overnight onto the Affymetrix Human Gene 1.0 ST Array (each containing approximately 19,658 probe sets).

scan_protocol: Confocal laser scanning (Agilent) was performed to detect the streptavidin- labeled fluors.

data_processing: CEL files were processed with the SCANfast function from the SCAN.UPC Bioconductor package (v2.20.0) using the Brainarray (v22.0.0) hugene10sthsentrezgprobe as the probe summary package and adjusted with ComBat.

source_name: Nasal brushings

label_protocol: RNA was converted into double-stranded cDNA with the SuperScript II reverse transcriptase (Invitrogen) using an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, Boulder, CO). The ENZO Bioarray RNA transcript labeling kit (Affymetrix) was used for in vitro transcription of the purified double stranded cDNA. The biotin-labeled cRNA was purified using the RNeasy kit (Qiagen).

extract_protocol: Using a nasal speculum, brushings were obtained from the right inferior turbinate with a standard cytology brush (Medical Packaging Company, Camarillo, CA). Brushings were placed in RNA lysis buffer and frozen at −80C until use. RNA was isolated via Qiagen RNeasy Mini Kits per manufacturer’s protocol. The integrity and purity of RNA were assessed using an Agilent Bioanalyzer and spectrophotometric analysis, respectively. An average of 3μg of high-quality total RNA was obtained from each collection.

value: Nasal brushings

tag: disease

value: EGPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

value: Neg

tag: race

value: White

value: F

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: flares (number of relapses)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Former

tag: immune_meds (recorded at time of sample collection)

value: Azathioprine

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: EGPA N1104

description: Gene expression from patient with EGPA

tag: tissue

value: Severe

value: MPO

tag: age

tag: gender

value: Never


title: EGPA N1110

description: Gene expression from patient with EGPA

tag: disease

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Asian

value: M


title: EGPA N1103

description: Gene expression from patient with EGPA

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Methotrexate


title: EGPA N1102

description: Gene expression from patient with EGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca


title: EGPA N1101

description: Gene expression from patient with EGPA

tag: race

tag: ethnicity


title: EGPA N1107

description: Gene expression from patient with EGPA

tag: disease_duration (yrs)

tag: flares (number of relapses)

value: Mycophenolate mofetil


title: rat 2, at T2

tag: animal

value: rat 2

value: male

tag: strain

value: spontaneously hypertensive rats (SHR)

value: 16 weeks

value: Blood

tag: treatment

value: MCA occlusion

tag: time

value: 2 hours


title: EGPA N1105

description: Gene expression from patient with EGPA

tag: tissue

value: Nasal brushings

value: EGPA

value: Neg

value: White

value: F

value: non-Hisp

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)

value: Rituximab

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: rat 2, at T0

tag: gender

tag: age

value: before MCA occlusion

value: control


title: rat 2, at T1

value: 1 hour


title: rat 1, at T2

value: rat 1


title: GPA N1100

description: Gene expression from patient with GPA

tag: disease

value: GPA

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

value: Active

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: ActiveGPA

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: Severe

tag: anca

value: Never

value: N


title: rat 2, at T24

tag: animal

value: rat 2

value: male

tag: strain

value: spontaneously hypertensive rats (SHR)

value: 16 weeks

value: Blood

value: MCA occlusion

value: 24 hours


title: EGPA N1096

description: Gene expression from patient with EGPA

value: Nasal brushings

value: EGPA

value: MPO

tag: race

value: White

value: F

tag: ethnicity

value: non-Hisp

tag: disease_duration (yrs)

tag: flares (number of relapses)

value: Methotrexate


title: gRna_rlucPolyA: gonad RNA-seq

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description: RNA-seq

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version hg19 of the human genome or ce10 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Pairs were filtered out if they mapped to the same strand, to different chromosomes, or if the 5’end coordinate of the – strand read was less than or equal to the 5’end coordinate of the + strand read. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. C. elegans datasets were further filtered for reads from the rDNA loci as will as those mapping to regions corresponding to transgenic reporter constructs existing in the strains and corresponding to sequences used in the RNAi vectors.
bedGraph files were generated from replicate concatenated processed ATAC-seq reads .bed files using bedtools genomecov v2.23 (-scale 1/(library size - chrM reads/100000)) which were then converted to .bigWig files using the ENCODE program bedGraphToBigWig.
UMIs from RNA-seq reads were extracted with UNI-tools followed by read trimming with fastx_trimmer and mapping with STAR. Mapped files were deduplicated with UNI-tools and remapped with STAR to generate bam and bedGraph files
RNA-seq normalized bedGraph files were converted to bigWig format with bedGraphToBigWig and replicates were averaged using bamCompare from the deeptools suite.
RNA-seq count tables were generated using RSEM and differential expression determined using DESeq2
UMIs from ChIP-seq reads were extracted using UMI-tools followed by read trimming with fastx_trimmmer and mapping with Bowtie2.
Uniquely mapping ChIP-seq reads were converted to bed files of the full fragment lengths then to library normalized bigWig files using bamCoverage from the deepTools suite. BigWig files were then normalized to input controls using bamCompare from the deepTools suite with --ratio substract for worm and --ratio ratio for human
Windows around annotated transcription start sites were counted for intersections with full-paired-end-fragment ChIP-seq reads using bedtools intersect and windows containing significant signal determined using DESeq2
Genome_build: ce10, hg19
Supplementary_files_format_and_content: library-normalized bigWig files of processed ATAC-seq reads, mapped RNA-seq reads, and input-normalized ChIP-seq reads
Supplementary_files_format_and_content: Gene count tables for RNA-seq reads and promoter-window count tables for full-paired-end-fragment ChIP-seq reads

organism: Caenorhabditis elegans

source_name: worm gonads

growth_protocol: C. elegans strains were maintained on OP50 bacteria and NGM agar plates at 15ºC. Worms were transferred to fresh food once a week.

extract_protocol:
Synchronized L4 animals were washed 5 times in M9 buffer and collected on ice. RNA was isolated using RNeasy Plus Mini Kit (Qiagen). RNA was reverse transcribed using GoScript® Reverse Transcriptase kit (Promega).
Library preparation was done following standard Bioo Scientific protocol and NEXTflex® Rapid Directional qRNA-Seq™ Kit2 (Bioo Scientific). Libraries were sequnced using single end sequencing length of a 75 nucleotides on a HiSeq400 machine (Illumina).

tag: genotype/variation

tag: tissue

value: worm gonads

tag: passages/stage


title: KD_ASchange_40% replicate 1

city: Berkeley

first: Qingqing

last: Wang

address: 161 Koshland Hall, UC Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
testgroup2_0.6_1
processed data file: cufflinks_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt

data_processing:
RNA-seq reads were mapped with STAR 2.5.4b in the 2-pass mode with parameters specified here: https://github.com/qqwang-berkeley/JUM/wiki/0.b.-Input-files
Data were then analyzed with six alternative splicing differential analysis software tools. Versions of the tools and detailed commands are listed in SI Appendix, Table S2 of the publication.
ROC curves are compared among the predictions of differential alternative splicing from six tools. Ranking score for ROC curve plotting is defined and extracted from each software tool's output files as follows: 1-adjusted_pvalue for JUM, Cufflinks nd rMATS; the maximum value of E(dPSI) among local splicing variation junctions in an AS event for MAJIQ; the value of the Bayes factor for MISO; the probability value for Whippet.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *_vs_testgroup1.txt: Tab-delimited text format; Three columns: column 1 - Gene ID; 2 - Ranking score as the extent of whether the gene transcripts are predicted to be differentially alternatively spliced by the corresponding software tool; 3 - Label for the gene transcripts as truly differentially alternatively spliced or not in the simulation (1 means truly differentially alternatively spliced and 0 means not).
AS_genes_list.txt, non_AS_gene_list.txt: These two lists contain the ground truth for the simulated RNA-seq datasets, for which AS_gene_list.txt lists the 2,000 genes whose transcripts are alternatively spliced and non_AS_gene_list.txt shows the genes whose transcripts that are not alternatively spliced.

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol: Not provided.

tag: cell line

tag: sirna

value: PSI


title: control replicate 3

description:
testgroup1_3
none

value: Non-targeting


title: KD_ASchange_40% replicate 2

description:
testgroup2_0.6_2
processed data file: cufflinks_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt


title: KD_ASchange_60% replicate 1

description:
testgroup2_0.8_1
processed data file: cufflinks_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt


title: KD_ASchange_20% replicate 2

description:
testgroup2_0.4_2
processed data file: cufflinks_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt


title: KD_ASchange_20% replicate 1

description:
testgroup2_0.4_1
processed data file: cufflinks_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt


title: KD_ASchange_20% replicate 3

description:
testgroup2_0.4_3
processed data file: cufflinks_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.4_vs_testgroup1.txt


title: KD_ASchange_40% replicate 3

description:
testgroup2_0.6_3
processed data file: cufflinks_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.6_vs_testgroup1.txt


title: KD_ASchange_60% replicate 2

description:
testgroup2_0.8_2
processed data file: cufflinks_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt


title: EGPA N1094

description: Gene expression from patient with EGPA

tag: disease

value: Neg

tag: age

tag: gender

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

tag: bvas

tag: vdi

value: Never

tag: immune_meds (recorded at time of sample collection)

value: Azathioprine

tag: gc_or_immune (prednisone or any immune med at time of sample collection)

value: N


title: Control N1092

description: Gene expression from Control

value: Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

value: Healthy

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

tag: anca

tag: race


title: Control N1098

description: Gene expression from Control

tag: tissue

value: Sarcoidosis

tag: ethnicity

tag: disease_duration (yrs)

tag: flares (number of relapses)


title: Control N1082

description: Gene expression from Control

value: Nasal brushings

tag: disease

tag: age

value: Y


title: Control N1099

description: Gene expression from Control

tag: gender

value: M

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

value: Former


title: KD_ASchange_60% replicate 3

description:
testgroup2_0.8_3
processed data file: cufflinks_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: JUM_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: MAJIQ_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: MISO_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: rMATS_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt
processed data file: Whippet_output_gene_score_label_testgroup2-0.8_vs_testgroup1.txt

tag: cell line

tag: sirna


title: GPA N1088

description: Gene expression from patient with GPA

value: GPA

value: Inactive

value: InactiveGPA

value: Severe

value: White

tag: bvas

tag: vdi

tag: immune_meds (recorded at time of sample collection)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: Control N1081

description: Gene expression from Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: F

value: non-Hisp


title: GPA N1091

description: Gene expression from patient with GPA

tag: tissue

tag: anca

tag: race

tag: ethnicity

value: Never

value: Mycophenolate mofetil


title: EGPA N1095

description: Gene expression from patient with EGPA

tag: disease

value: EGPA

value: Neg

tag: age

tag: flares (number of relapses)

value: Azathioprine

value: N


title: GPA N1074

description: Gene expression from patient with GPA

value: Nasal brushings

value: Limited

tag: gender

tag: disease_duration (yrs)

tag: pga (physician global assessment - scale 0 to 10 with 10 meaning very active disease)

value: Methotrexate


title: Control N1097

description: Gene expression from Control

value: Control

value: Healthy

value: M

tag: bvas

tag: vdi


title: Control N1087

description: Gene expression from Control

value: Sarcoidosis

tag: immune_meds (recorded at time of sample collection)

tag: gc_or_immune (prednisone or any immune med at time of sample collection)


title: Control N1086

description: Gene expression from Control

tag: disease_activity (active means ongoing active nasal inflammation, inactive means a history of prior nasal inflammation, never means no history of nasal involvement)

tag: batch

value: AllergicRhinitis


title: EGPA N1108

description: Gene expression from patient with EGPA

tag: classification (c1 = healthy control; c2= sarcoidosis; c3 = allergic rhinitis; c4 = egpa)

tag: severity (severe = organ threatening manifestations (e.g. glomerulonephritis or alveolar hemorrhage). limited = non severe disease.)

value: White


title: control replicate 1

description:
testgroup1_1
none

tag: cell line

tag: sirna

value: Non-targeting


title: control replicate 2

description:
testgroup1_2
none