title: blood_475


title: blood_478

status: Public on Aug 07 2019

type: SRA

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19  genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for each sample with raw reads count summarised to genebody region.

molecule: genomic DNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: plasma

tag: training/validation group

value: Training


title: blood_500


title: blood_483


title: blood_477


title: blood_472


title: blood_471


title: blood_469


title: blood_468


title: blood_466


title: blood_470


title: blood_465


title: blood_463


title: blood_462


title: blood_464


title: blood_460


title: blood_455


title: blood_461


title: blood_480


title: blood_484


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title: blood_458


title: blood_482


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title: blood_431


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title: blood_347


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title: blood_324


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title: blood_334


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title: blood_308


title: blood_303


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title: blood_297


title: blood_295


title: blood_296


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title: blood_288


title: blood_287


title: blood_282


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title: blood_300


title: blood_281


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title: blood_278


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title: blood_265


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title: blood_263


title: blood_299


title: blood_294


title: blood_262


title: blood_298


title: blood_260


title: blood_256


title: blood_279


title: blood_259


title: blood_254


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title: blood_252


title: blood_273


title: blood_250


title: blood_251


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title: blood_269


title: blood_241


title: blood_257


title: blood_237


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title: blood_236


title: blood_227


title: blood_228


title: blood_233


title: blood_225


title: blood_240


title: blood_234


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title: blood_226


title: blood_223


title: blood_222


title: blood_220


title: blood_221


title: blood_231


title: blood_219


title: blood_217


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title: blood_216


title: blood_214


title: blood_213


title: blood_235


title: blood_211


title: blood_212


title: blood_210


title: blood_207


title: blood_224


title: blood_206


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title: blood_203


title: blood_208


title: blood_204


title: blood_199


title: blood_200


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title: blood_201


title: blood_209


title: blood_196


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title: blood_184


title: blood_191


title: blood_182


title: blood_181


title: blood_183


title: blood_180


title: blood_179


title: blood_198


title: blood_178


title: blood_197


title: blood_177


title: blood_174


title: blood_176


title: blood_175


title: blood_170


title: blood_169


title: blood_167


title: blood_168


title: blood_164


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title: blood_162


title: blood_171


title: blood_157


title: blood_158


title: blood_155


title: blood_154


title: blood_153


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title: blood_172


title: blood_173


title: blood_151


title: blood_150


title: blood_285


title: blood_148


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title: blood_145


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title: blood_142


title: blood_143


title: blood_141


title: blood_140


title: blood_138


title: blood_137


title: blood_136


title: blood_139


title: blood_135


title: blood_156


title: blood_133


title: blood_132


title: blood_130


title: blood_131


title: blood_129


title: blood_126


title: blood_127


title: blood_125


title: blood_123


title: blood_146


title: blood_121


title: blood_124


title: blood_119


title: blood_122


title: blood_120


title: blood_118


title: blood_114


title: blood_117


title: blood_113


title: blood_134


title: blood_110


title: blood_112


title: blood_106


title: blood_109


title: blood_108


title: blood_105


title: blood_107


title: blood_128


title: blood_102


title: blood_103


title: blood_101


title: blood_99


title: blood_100


title: blood_98


title: blood_116


title: blood_95


title: blood_96


title: blood_115


title: blood_97


title: blood_94


title: blood_92


title: blood_88


title: blood_91


title: blood_90


title: blood_86


title: blood_89


title: blood_85


title: blood_83


title: blood_82


title: blood_104


title: blood_80


title: blood_79


title: blood_76


title: blood_71


title: blood_77


title: blood_70


title: blood_93


title: blood_69


title: blood_67


title: blood_66


title: blood_62


title: blood_63


title: blood_59


title: blood_60


title: blood_84


title: blood_54


title: blood_57


title: blood_56


title: blood_68


title: blood_53


title: blood_78


title: blood_50


title: blood_51


title: blood_73


title: blood_47


title: blood_49


title: blood_52


title: blood_46


title: blood_45


title: blood_44


title: blood_64


title: blood_61


title: blood_40


title: blood_42


title: blood_43


title: blood_41


title: blood_37


title: blood_39


title: blood_55


title: blood_34


title: blood_36


title: blood_38


title: blood_33


title: blood_28


title: blood_31


title: blood_48


title: blood_30


title: blood_26


title: blood_32


title: blood_27


title: blood_25


title: blood_19


title: blood_21


title: blood_20


title: blood_18


title: blood_15


title: blood_23


title: blood_17


title: blood_14


title: blood_13


title: blood_9


title: blood_11


title: blood_10


title: blood_8


title: blood_12


title: blood_7


title: blood_6


title: blood_5


title: blood_4


title: blood_2


title: blood_3


title: blood_1


title: blood_160


title: NMIBC_X870877

status: Public on Dec 01 2018

type: RNA

city: Beijing

first: HUANG

last: CHEN

address: Yinghuadongjie 2#, Chaoyang District, Beijing

department: Department of Etiology and Carcinogenesis

country: China

institute: China-Japan Friendship Hospital

description: gene expression in non-muscle invasive bladder cancers

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

source_name: cancer tissues from patient with non-muscle invasive bladder cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, CA, USA), and those allocated for microarray detection were purified with an RNeasy kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: All samples were snap-frozen in RNA laterand stored at -80°C before RNA preparation and microarray examination. No additional treatment was applied.

value: frozen bladder cancer tissue

tag: gender

value: male

tag: age (years)

tag: tumor stage


title: MIBC_X760427

description: gene expression in muscle invasive bladder cancers

source_name: cancer tissues from patient with muscle invasive bladder cancer


title: MIBC_X764674


title: NMIBC_X767311

value: ta


title: NMIBC_X765188


title: MIBC_X776774


title: MIBC_X777126

value: female


title: NMIBC_X780028


title: MIBC_X864247


title: NMIBC_X771047


title: NMIBC_X768523


title: NMIBC_X752947


title: NMIBC_X756057


title: MIBC_X783943


title: MIBC_X855190


title: NMIBC_X765416


title: NMIBC_X753008


title: MIBC_X759809


title: NMIBC_X858988

description: gene expression in nonmuscle-invasive bladder cancers


title: MIBC_X815599


title: MIBC_X756505


title: NMIBC_X759118


title: MIBC_X735817


title: MIBC_X712686


title: NMIBC_X822167


title: NMIBC_X766538


title: NMIBC_X751461


title: MIBC_X761608


title: NMIBC_X818708


title: 451Lu_10x_singlecell_parental

status: Public on Jul 01 2018

city: Cold Spring Harbor

first: Molly

last: Hammell

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
The Cell Ranger Single Cell Software Suite 1.3.1 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting using the Illumina BCL files as input.
Genome_build: hg19 1.2.0
Supplementary_files_format_and_content: CellRanger generates BAM files which contain raw reads for single-cell RNAseq, including cell identity, UMI information, and gemgroup id (referred to in guide barcode filenames). Gene-barcode matrices are the UMI-collapsed counts of these reads, representing counts of molecules per cell as determined and filtered by cellranger..matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

source_name: Melanoma cell line

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium with 10% Fetal Bovine serum and 1% Pencillin-Streptavadin. Cells were grown to ~80% confluency in 10cm culture dishes and split every 2-3 days.

extract_protocol: A 10X Genomics Chromium machine was used to capture 3,000-4,000 single cells and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer. A Chromium Single Cell 3' Library and Gel Bead Kit V2 (PN-120237), Chromium Single Cell 3' Chip Kit V2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used with a 10x Genomics Chromium for Single-Cell Library Preparation Instrument, per the manufacturer's specifications and manuals and then sequenced paired-end 150 bp on HiSeq 4000 to a depth of 90000 UMI per cell.

treatment_protocol: For drug treatment, 1uM of drug was added to above mentioned media. Media with drug was prepared fresh every 10 days to ensure that the drug was active

tag: cell line

tag: treatment

value: Parental - no Treatment


title: 451Lu_10x_singlecell_resistant

value: Resistant - Cultured in 1uM PLX-4720


title: Beta 9hrs-1

status: Public on Dec 22 2017

city: Aachen

first: Mathias

middle: W.

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

country: Germany

institute: RWTH Áachen University

description: Gene expression after type I interferon stimulation

hyb_protocol: cRNA fragmentation, hybridization and washing steps were also carried-out exactly as recommended: ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this approach, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

organism: Mus musculus

source_name: Immortalized intestinal epithelial cells (Schwerk et al., PLoS One, 2013)

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Immortalized intestinal epithelial cells (IEC) (Schwerk et al., PLoS One, 2013) were cultured at 37°C, 5% CO2, 95% RH. IECs were were seeded at a cell density of 2x10^5 cells/ml on transwell cell culture inserts (pore size 0.4um, Costar). The cells were allowed to grow for 21 days in order to attain polarisation and complete confluency. The cell culture medium was changed every 3 days. Transepithelial resistance (TEER values) was measured using a Voltohmeter (EVOM, World Precision instruments) to determine barrier integrity. To determine basal resistance transwell inserts without cells was used.

extract_protocol: RNA was isolated using Trizol according to the mansufacturer's protocol.

treatment_protocol: IECs were left untreated (medium) or stimulated with 500U/ml IFN-β (Pulverer, Rand et al. 2010) or 20ng/ml IFN-λ2 (Peprotech) in IEC medium for 9 hours prior to RNA isolation (Trizol).

tag: cell type

value: intestinal epithelial cell line (Schwerk et al., PLoS One, 2013)

tag: stimulus

value: IFN I (beta) 500 U/mL 9 hours


title: Beta 9hrs-2


title: Lambda 9hrs-2

description: Gene expression after type III interferon stimulation

value: IFN III (lambda) 20 ng/mL 9 hours


title: Patient 24 Severe psoriasis skin

status: Public on Feb 19 2017

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

description: Patient 24

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor) and adjusted for batch effect.

label: biotin

source_name: Lesional_skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer’s protocol.

tag: treatement

value: pre-treatment

tag: disease state

value: Severe psoriasis skin


title: Patient 28 Normal skin

description: Patient 28

source_name: Non_lesional_skin biopsy

value: Normal skin


title: MIBC_X791193


title: Beta 9hrs-3


title: Patient 21 Severe psoriasis skin

description: Patient 21


title: Patient 20 Severe psoriasis skin

description: Patient 20


title: Control-2

description: Gene expression without stimulation


title: Patient 22 Severe psoriasis skin

description: Patient 22


title: Lambda 9hrs-1


title: Patient 32 Normal skin

description: Patient 32


title: Patient 33 Normal skin

description: Patient 33


title: Patient 30 Normal skin

description: Patient 30


title: Patient 29 Normal skin

description: Patient 29


title: Patient 25 Severe psoriasis skin

description: Patient 25


title: Patient 18 Severe psoriasis skin

description: Patient 18


title: Patient 31 Normal skin

description: Patient 31


title: Patient 27 Severe psoriasis skin

description: Patient 27


title: Control-3

description: Gene expression without stimulation


title: Lambda 9hrs-3


title: Patient 23 Severe psoriasis skin

description: Patient 23


title: Patient 19 Severe psoriasis skin

description: Patient 19


title: RBM10 (RRM1-ZnF)

status: Public on Aug 15 2017

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on an microarray scanner at 5 micron resolution (Axon Instruments GenePix 4000B). Images were quantified using Imagene 3.0.

data_processing: The experiment was represented with a matrix where rows correspond to probes and columns are the intensities of the Cy5-labeled RNA from the GST-RDBP pulldown assay. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

organism: synthetic construct

source_name: Pulldown RNA labeled with Cy3

label_protocol: Manufacturer's recommended protocol (Kreatech).

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.

tag: protocol

value: GST-tagged RNA-binding protein pulldown

tag: rna binding protein


title: Patient 26 Severe psoriasis skin

description: Patient 26


title: RBM10 (RRM1-ZnF-RRM2)

source_name: Pulldown RNA labeled with Cy5


title: Patient 16 Severe psoriasis skin

description: Patient 16


title: Patient 14 Mild psoriasis skin

description: Patient 14

value: Mild psoriasis skin


title: Patient 2 Mild psoriasis skin

description: Patient 2


title: Patient 5 Mild psoriasis skin

description: Patient 5


title: Patient 15 Severe psoriasis skin

description: Patient 15


title: Patient 10 Mild psoriasis skin

description: Patient 10


title: Patient 7 Mild psoriasis skin

description: Patient 7


title: Patient 4 Mild psoriasis skin

description: Patient 4


title: Patient 12 Mild psoriasis skin

description: Patient 12


title: Patient 9 Mild psoriasis skin

description: Patient 9


title: Patient 1 Mild psoriasis skin

description: Patient 1


title: Patient 3 Mild psoriasis skin

description: Patient 3


title: Patient 17 Severe psoriasis skin

description: Patient 17


title: RDBP

status: Public on Aug 31 2017

type: other

molecule: other

value: RDBP


title: Patient 8 Mild psoriasis skin

description: Patient 8


title: Patient 6 Mild psoriasis skin

description: Patient 6


title: Patient 11 Mild psoriasis skin

description: Patient 11


title: Patient 13 Mild psoriasis skin

description: Patient 13


title: Donor4 TF HIV-1 infected (GFP positive) cells + P. stercorea

status: Public on Feb 08 2017

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

description: Gene expression data from Donor4 LPMC infected with TF HIV-1 (GFP positive)

hyb_protocol: Each sample was hybridized to a GeneChip Human Gene 2.0 ST array.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multi-Array Average) normalization was performed

source_name: Donor4, G261_GFP_Pos-Ps

label_protocol: Total RNA was converted to cDNA with the GeneChip WT Pico Kit (Affymetrix) and amplified by 13 PCR cycles. In vitro transcription was performed using the same kit to generate cRNA.   The cRNA was again converted to ss-cDNA in a second cycle.  The cDNA was then fragmented and end-labeled with biotin.

growth_protocol: Complete DMEM with 10% FBS and 1% PSG

extract_protocol: Qiagen RNAease micro kit, according to manufacturer's instructions

treatment_protocol: Spinoculation of TF HIV-1 and w/wo P. stercorea

tag: donor

value: Lamina Propria Mononuclear Cells (LPMCs)

value: TF HIV-1 infected cells + P. stercorea

tag: gfp status

value: GFP positive


title: Donor4 Mock infected + P. stercorea

description: Gene expression data from Donor4 LPMC uninfected + P. stercorea

source_name: Donor4, G261_Mock-Ps

value: Mock infected cells + P. stercorea


title: Donor4 TF HIV-1 treated bystander (GFP negative) cells

description: Gene expression data from Donor4 LPMC bystanders (GFP negative)

source_name: Donor4, G261_GFP_Neg

value: TF HIV-1 treated bystander cells

value: GFP negative


title: Donor4 Mock infected

description: Gene expression data from Donor4 LPMC uninfected

source_name: Donor4, G261_Mock

value: Mock infected cells


title: Donor4 TF HIV-1 treated bystander (GFP negative) cells + P. stercorea

description: Gene expression data from Donor4 LPMC bystanders (GFP negative) exposed to P. stercorea

source_name: Donor4, G261_GFP_Neg-Ps

value: TF HIV-1 treated bystander cells + P. stercorea


title: Donor3 TF HIV-1 treated bystander (GFP negative) cells + P. stercorea

description: Gene expression data from Donor3 LPMC bystanders (GFP negative) exposed to P. stercorea

source_name: Donor3, G247_GFP_Neg-Ps


title: Donor3 Mock infected

description: Gene expression data from Donor3 LPMC uninfected

source_name: Donor3, G247_Mock


title: Donor3 TF HIV-1 infected (GFP positive) cells + P. stercorea

description: Gene expression data from Donor3 LPMC infected with TF HIV-1 (GFP positive)

source_name: Donor3, G247_GFP_Pos-Ps


title: Donor2 TF HIV-1 treated bystander (GFP negative) cells + P. stercorea

description: Gene expression data from Donor2 LPMC bystanders (GFP negative) exposed to P. stercorea

source_name: Donor2, G201_GFP_Neg-Ps


title: Donor3 TF HIV-1 infected (GFP positive) cells

description: Gene expression data from Donor3 LPMC infected with TF HIV-1 (GFP positive) + P. stercorea

source_name: Donor3, G247_GFP_Pos

value: TF HIV-1 infected cells


title: Donor1 TF HIV-1 infected (GFP positive) cells + P. stercorea

description: Gene expression data from Donor1 LPMC infected with TF HIV-1 (GFP positive)

source_name: Donor1, G234_GFP_Pos-Ps


title: Donor2 TF HIV-1 treated bystander (GFP negative) cells

description: Gene expression data from Donor2 LPMC bystanders (GFP negative)

source_name: Donor2, G201_GFP_Neg


title: Donor2 TF HIV-1 infected (GFP positive) cells + P. stercorea

description: Gene expression data from Donor2 LPMC infected with TF HIV-1 (GFP positive)

source_name: Donor2, G201_GFP_Pos-Ps


title: Donor1 TF HIV-1 treated bystander (GFP negative) cells

description: Gene expression data from Donor1 LPMC bystanders (GFP negative)

source_name: Donor1, G234_GFP_Neg


title: Donor1 Mock infected

description: Gene expression data from Donor1 LPMC uninfected

source_name: Donor1, G234_Mock


title: Donor2 TF HIV-1 infected (GFP positive) cells

description: Gene expression data from Donor2 LPMC infected with TF HIV-1 (GFP positive) + P. stercorea

source_name: Donor2, G201_GFP_Pos


title: Donor2 Mock infected + P. stercorea

description: Gene expression data from Donor2 LPMC uninfected + P. stercorea

source_name: Donor2, G201_Mock-Ps


title: Donor3 Mock infected + P. stercorea

description: Gene expression data from Donor3 LPMC uninfected + P. stercorea

source_name: Donor3, G247_Mock-Ps


title: Donor1 TF HIV-1 treated bystander (GFP negative) cells + P. stercorea

description: Gene expression data from Donor1 LPMC bystanders (GFP negative) exposed to P. stercorea

source_name: Donor1, G234_GFP_Neg-Ps


title: Donor1 Mock infected + P. stercorea

description: Gene expression data from Donor1 LPMC uninfected + P. stercorea

source_name: Donor1, G234_Mock-Ps


title: EMC43x1a1_EP_1

status: Public on Aug 01 2016

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  mapped to hg19 genome using bowtie TopHat
Counts per gene was obtained using HTseq counts and normalized using edgeR package in R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include matrix of normalized log counts per million for each sample

source_name: pancreas

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

value: pancreas


title: EMC827_EP_3


title: EMC29o1a5periMet_EP_3


title: EMCT2x1a2_EP_1


title: EMC43x1a1_EP_3


title: EMCT2x1a2_EP_2


title: EMCT2x1a2_EP_3


title: EMC827_EP_2


title: EMC43x1a1_EP_2


title: EMC2095_EP_3


title: Donor1 TF HIV-1 infected (GFP positive) cells

description: Gene expression data from Donor1 LPMC infected with TF HIV-1 (GFP positive) + P. stercorea

source_name: Donor1, G234_GFP_Pos


title: EMC827_EP_1


title: EMC2095_EP_2


title: EMC226x4b5_EP_3


title: EMC2095_EP_1


title: EMC810o1a1_EP_3


title: EMC810o1a1_EP_1


title: EMC29o1a5periMet_EP_1


title: EMC29o1a5periMet_EP_2


title: smed-mbnl-like-2

data_processing: The experiments were represented with a matrix where rows correspond to probes and columns are the intensities of the Cy3- or Cy5-labeled RNA from the pulldown assay. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

source_name: Pulldown RNA labeled with Cy5

tag: rna-binding protein

tag: channel


title: EMC1222x3c2_EP_2

tag: tissue


title: EMC226x4b5_EP_2


title: EMC810o1a1_EP_2


title: smed-mbnl-1 (isoform X1)

value: smed-mbnl-1 (isoform X1)


title: EMC828x1b1_EP_2


title: EMC7310_EP_3


title: EMC226x4b5_EP_1


title: smed-mbnl-like-1

source_name: Pulldown RNA labeled with Cy3


title: smed-mbnl-1 (isoform Xins)

value: smed-mbnl-1 (isoform Xins)


title: EMC828x1b1_EP_3


title: EMC1222x3c2_EP_3


title: EMC1222x3c2_EP_1


title: EMC7310_EP_1


title: EMC519x2a1_EP_2


title: EMC519x2a1_EP_1


title: EMC18128_EP_3


title: EMC18128_EP_2


title: EMC828x1b1_EP_1


title: EMC519x2a1_EP_3


title: EMC18128_EP_1


title: Donor3 TF HIV-1 treated bystander (GFP negative) cells

description: Gene expression data from Donor3 LPMC bystanders (GFP negative)

source_name: Donor3, G247_GFP_Neg


title: EMC226x4b5_EP


title: EMC828x3b1_EP


title: EMC1222x3b5_EP


title: EMC828x2a3_EP_2


title: EMC828x2a3_EP_1


title: EMC519_EP


title: EMC7310_EP


title: EMC29o1a5_EP


title: smed-bruli

value: smed-bruli


title: EMC1222x3a1_EP


title: EMC226x1a1_EP


title: EMC226x1a2_EP


title: EMC7310_EP_2


title: EMC1222o2a1_EP


title: EMC1222o2a2_EP


title: EMC226o1a5omMet_EP_1


title: EMC226_EP


title: EMC29o1a2_EP


title: EMC226o1a5omMet_EP_2


title: EMC41x1a3_EP


title: Donor4 TF HIV-1 infected (GFP positive) cells

description: Gene expression data from Donor4 LPMC infected with TF HIV-1 (GFP positive) + P. stercorea

source_name: Donor4, G261_GFP_Pos


title: EMC114x1a1_EP


title: EMC1222_EP


title: EMC1222x1a3_EP


title: EMC828x2a2_EP


title: EMC828x1b1_EP


title: EMC1229_EP


title: EMC41x2d2_EP


title: EMC2095_EP


title: EMC226o1a5_EP


title: EMC1222x1b1_EP


title: EMC514_EP


title: EMC18128_EP


title: EMCT2x2b1_LP


title: EMCT2x2b1_EP


title: EMC43x1a2_EP


title: EMC43x1a1_EP


title: RGC_P8_WT-3

status: Public on Jul 27 2016

city: Strasbourg

first: Frank

last: Pfrieger

address: 8 allée du Général Rouvillois

country: France

institute: Centre National de la Recherche Scientifique, University of Strasbourg

description: Retinal ganglion cells acutely isolated from P8 wildtype mice by immunopanning

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Alignment : Reads were mapped to mm10 assembly of mouse genome using Tophat2.0.10
Quantification : Gene expression was quantified using HTSeq v0.5.4p3 and annotations from Ensembl release 74
Normalization : Data normalization was performed with DESeq2 v1.0.19 Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts

source_name: Retinal ganglion cells

extract_protocol:
Total RNA was harvested immediately after immunopanning from retinal ganglion cells attached to the selection plate using a standard kit according to the manufacturer's instructions (RNeasy Plus Micro Kit, 74034, Qiagen).
Libraries suitable for high throughput DNA sequencing were created using TruSeq™ RNA Sample Preparation v2 Kit (Illumina).

tag: strain balb/cnctr-npc1m1n/j

value: homozygous


title: RGC_P8_NPC-1

description: Retinal ganglion cells acutely isolated from P8 NPC1-deficient mice by immunopanning

value: wildtype


title: RGC_P8_WT-4


title: RGC_P8_NPC-3


title: EMC3226_EP


title: RGC_P8_WT-2


title: RGC_P8_NPC-2


title: RGC_P8_NPC-4


title: RGC_P8_WT-1


title: Donor2 Mock infected

description: Gene expression data from Donor2 LPMC uninfected

source_name: Donor2, G201_Mock


title: 4T1 tumour cells, rep 1

status: Public on Jan 18 2016

city: Barcelona

first: Alexandra

last: Avgustinova

address: C/ Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

description: replicate 1

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Probes that were not expressed in any of the samples were removed before normalisation to avoid adding noise to the data.

source_name: 4T1 xenograft

label_protocol: Biotinylated cRNA were prepared using Ambion TotalPrep 96-RNA amplification kit for Illumina arrays

growth_protocol: 5 x 10^5 tumour cells were inoculated orthotopically into the 4th mammary fat pad of Ub-GFP Balb/c mice. Tumours were left to grow for 2-4 weeks, until they reached an average diameter of 10 mm.

extract_protocol: RNA was extracted with Trizol reagen in accordance with the manufacturer´s. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells were not treated

tag: sample type

value: 4T1 xenograft

tag: source strain

value: Balb/c

tag: host strain

value: Ub-GFP Balb/c

value: primary tumour

tag: Sex

value: female

tag: age

value: 6-8 weeks


title: 4T07 tumour cells, rep 1

description: replicate 1

source_name: 4T07 xenograft

value: 4T07 xenograft


title: 4T07 tumour cells, rep 2

description: replicate 2


title: Patient 53 Asian small plaque psoriasis non-lesional skin

status: Public on Jan 10 2016

scan_protocol: Hewlett-Packard GeneArray Scanner.

data_processing: GCRMA (using gcrma package from R/Bioconductor) and adjusted for batch effect. The expression data was combined with Western large psoriasis (GSE30999). Using a normalization based upon quantiles, the expression data was normalized based upon a specified normalization distribution of GSE30999 (see publication for GSE67853).

label: Biotin

source_name: skin biopsy, small psoriasis, non-lesional skin, pretreatment

label_protocol: GeneChip Affymetrix protocol.

value: psoriasis

tag: psoriasis subtype

value: Asian small plaque psoriasis

value: non-lesional skin

tag: treatment

value: pretreatment

tag: patient id


title: 4T07 tumour cells, rep 3

description: replicate 3


title: Patient 16 Asian small plaque psoriasis lesional skin

source_name: skin biopsy, small psoriasis, lesional skin, pretreatment

tag: disease state

value: lesional skin


title: Patient 46 Asian intermediate plaque psoriasis non-lesional skin

source_name: skin biopsy, intermediate psoriasis, non-lesional skin, pretreatment

value: Asian intermediate plaque psoriasis


title: 4T1 tumour cells, rep 3

description: replicate 3


title: Patient 59 Asian intermediate plaque psoriasis lesional skin

source_name: skin biopsy, intermediate psoriasis, lesional skin, pretreatment


title: 4T1 tumour cells, rep 2

description: replicate 2


title: Patient 59 Asian intermediate plaque psoriasis non-lesional skin


title: Patient 58 Asian small plaque psoriasis lesional skin


title: Patient 52 Asian small plaque psoriasis lesional skin


title: Patient 46 Asian intermediate plaque psoriasis lesional skin


title: Patient 47 Asian small plaque psoriasis non-lesional skin


title: Patient 50 Asian intermediate plaque psoriasis lesional skin


title: Patient 53 Asian small plaque psoriasis lesional skin


title: Patient 57 Asian small plaque psoriasis non-lesional skin


title: Patient 54 Asian intermediate plaque psoriasis non-lesional skin


title: Patient 52 Asian small plaque psoriasis non-lesional skin


title: Patient 25 Asian intermediate plaque psoriasis lesional skin


title: Patient 57 Asian small plaque psoriasis lesional skin


title: Patient 50 Asian intermediate plaque psoriasis non-lesional skin


title: Patient 58 Asian small plaque psoriasis non-lesional skin


title: Patient 6 Asian small plaque psoriasis lesional skin


title: Patient 54 Asian intermediate plaque psoriasis lesional skin


title: Patient 47 Asian small plaque psoriasis lesional skin


title: Patient 12 Asian intermediate plaque psoriasis non-lesional skin


title: Patient 24 Asian intermediate plaque psoriasis non-lesional skin


title: Patient 22 Asian intermediate plaque psoriasis non-lesional skin


title: Patient 24 Asian intermediate plaque psoriasis lesional skin


title: Patient 25 Asian intermediate plaque psoriasis non-lesional skin


title: EMC114_EP

value: pancreas


title: EMC29o1a1_EP


title: d56 PP_rep4

status: Public on May 22 2015

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 45ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Extracted microarray raw data were imported into Omics Explorer software v3.0 (Qlucore) under default import settings for Agilent One Color mRNA Microarrays. Accordingly, data processing steps were: 1) removal of control measurements, 2) log base 2 transformation, 3) normalization of non-control values by shifting to 75 Percentile, 4) averaging of values from on-chip replicates (quadruplicates), 5) baseline transformation to the median. Note, that initially, one additional group consisting of 4 samples have been imported into Qlucore Omics Explorer. Finally, these 4 samples have been exchanged by 4 newly generated samples. However, baseline transformation in Qlucore Omics Explorer software (see step 5) is based on all samples (including the 4 samples that were finally removed, not considered anymore and not contained in this submission).

label: Alexa Fluor 555

source_name: d56 PP_rep4

label_protocol: 4-8 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification). The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies). Prior to the reverse transcription reaction, 1µl of a 1:50000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) were added to each total RNA sample.

extract_protocol: C57Bl/6N mice were housed under SPF conditions and  used at indicated ages. For 6- and 11-days-old samples one litter was pooled for each sample. For older mice 2-3 mice per sample were used. Small intestines were taken out, Peyer's patches were removed for 28- and 56-days-old mice. Tissue was digested with Liberase TM/DNAse and put on a 40/70% Percoll gradient. Peyer's patches, mLNs and thymi were pressed trough a mesh.  CD4+TCRb+CD8a-CD45+DAPI- cells were sort purified (FACS Aria, BD) from the leukocyte suspension and purity was assessed. 0.5e5-2e5 sorted cells were used to extract RNA using  the RNeasy Micro Kit (Qiagen) with the protocol for 1e5 cells.

tag: cell type

value: CD4 T cells

tag: strain


title: d56 LP_rep4

source_name: d56 LP_rep4


title: d56 mLN_rep3

source_name: d56 mLN_rep3


title: hs TRIM56

status: Public on Sep 14 2015

description:
RNCMPT00494
raw data in channel 2 of file A94_2.D.txt

data_processing: The experiment was represented with a matrix where rows correspond to probes and columns are the intensities of the Cy5- or Cy3-labeled RNA from the GST-RBP pulldown assay. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

tag: protocol

value: GST-tagged RNA-binding protein pulldown

tag: rna binding protein

value: hs TRIM56


title: d28 LP_rep4

source_name: d28 LP_rep4


title: d28 LP_rep2

source_name: d28 LP_rep2


title: d56 PP_rep3

source_name: d56 PP_rep3


title: dm MEI-P26

description:
RNCMPT00454
raw data in channel 2 of file A74_2.D.txt

source_name: Pulldown RNA labeled with Cy5

value: dm MEI-P26


title: d6 mLN_rep1

source_name: d6 mLN_rep1


title: d56 mLN_rep1

source_name: d56 mLN_rep1


title: ce LIN-41

description:
RNCMPT00493
raw data in channel 1 of file A94_2.D.txt

source_name: Pulldown RNA labeled with Cy3

value: ce LIN-41


title: d56 LP_rep1

source_name: d56 LP_rep1


title: d56 mLN_rep4

source_name: d56 mLN_rep4


title: d6 mLN_rep3

source_name: d6 mLN_rep3


title: d56 PP_rep1

source_name: d56 PP_rep1


title: d6 mLN_rep2

source_name: d6 mLN_rep2


title: d28 LP_rep3

source_name: d28 LP_rep3


title: d56 LP_rep2

source_name: d56 LP_rep2


title: d28 LP_rep1

source_name: d28 LP_rep1


title: d6 mLN_rep4

source_name: d6 mLN_rep4


title: d56 LP_rep3

source_name: d56 LP_rep3


title: d56 mLN_rep2

source_name: d56 mLN_rep2


title: d56 PP_rep2

source_name: d56 PP_rep2


title: d11 SI_rep4

source_name: d11 SI_rep4


title: ce NCL-1

description:
RNCMPT00490
raw data in channel 2 of file A92_2.D.txt

source_name: Pulldown RNA labeled with Cy5

value: ce NCL-1


title: Patient 35 Asian intermediate plaque psoriasis lesional skin

source_name: skin biopsy, intermediate psoriasis, lesional skin, pretreatment


title: dm BRAT

description:
RNCMPT00452
raw data in channel 2 of file A73_2.D.txt

value: dm BRAT


title: d6 Th_rep4

source_name: d6 Th_rep4


title: hs TRIM71

description:
RNCMPT00453
raw data in channel 1 of file A74_2.D.txt

source_name: Pulldown RNA labeled with Cy3

value: hs TRIM71


title: d11 SI_rep1

source_name: d11 SI_rep1


title: dm WECH

description:
RNCMPT00455
raw data in channel 1 of file A75_2.D.txt

value: dm WECH


title: d6 SI_rep4

source_name: d6 SI_rep4


title: d6 SI_rep1

source_name: d6 SI_rep1


title: d6 Th_rep3

source_name: d6 Th_rep3


title: d6 Th_rep2

source_name: d6 Th_rep2


title: d6 SI_rep3

source_name: d6 SI_rep3


title: d11 SI_rep2

source_name: d11 SI_rep2


title: d6 Th_rep1

source_name: d6 Th_rep1


title: d11 SI_rep3

source_name: d11 SI_rep3


title: SPI1_rep4

status: Public on Sep 01 2014

hyb_protocol: cRNA fragmentation, hybridization and washing steps were also carried-out exactly as recommended: “One-Color Microarray-Based Gene Expression Analysis Protocol V5.7”.

data_processing: Data extraction was performed with the “Feature Extraction Software V10.7.3.1” by using the recommended default extraction protocol file: GE1_107_Sep09.xml. Processed intensity values of the green channel (“gProcessedSignal” or “gPS”) were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This scaling factor was calculated by dividing a “reference 75th Percentile value” (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray (“Array i” in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold was defined as 1% of the reference 75th Percentile value (= 15). All of those normalized gPS values that fell below this intensity border, were substituted by the respective surrogate value of 15.

source_name: IEC from neonate mice infected with SPI1 mutant S. Typhimurium (ΔinvC) at the age of 1 day obtained at day 4 p.i. biological replicate 4

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the “Quick Amp Labeling kit, one color” (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: IECs were prepared as described recently (Lotz et al., J. Exp Med. 2006). In brief, mouse intestinal tissue was incubated for 10 min at 37°C in 0.3 M EDTA. shaken vigorously and epithelial cells were separated from the underlying tissue and immune cells by repeated sedimentation at 1 x g at 4°C. Flow cytometric analysis revealed less than 5% and 1% of CD45+ cells in IEC preparations from adult and suckling mice, respectively.

extract_protocol: RNA was isolated using TRIzol (Invitrogen, Darmstadt, Germany) according to the manufacturer’s protocol.

tag: infection

value: delta invC S. Typhimurium SPI1 mutant


title: SPI1_rep2

source_name: IEC from neonate mice infected with SPI1 mutant S. Typhimurium (ΔinvC) at the age of 1 day obtained at day 4 p.i. biological replicate 2


title: SPI1_rep1

source_name: IEC from neonate mice infected with SPI1 mutant S. Typhimurium (ΔinvC) at the age of 1 day obtained at day 4 p.i. biological replicate 1


title: d6 SI_rep2

source_name: d6 SI_rep2


title: co_rep2

source_name: IEC obtained from 5-day-old healthy mice, biological replicate 2


title: wt_rep1

source_name: IEC from neonate mice infected with S. Typhimurium wildtype at the age of 1 day obtained at day 4 p.i. biological replicate 1

value: S. Typhimurium wt


title: wt_rep3

source_name: IEC from neonate mice infected with S. Typhimurium wildtype at the age of 1 day obtained at day 4 p.i. biological replicate 3


title: co_rep3

source_name: IEC obtained from 5-day-old healthy mice, biological replicate 3


title: SPI1_rep3

source_name: IEC from neonate mice infected with SPI1 mutant S. Typhimurium (ΔinvC) at the age of 1 day obtained at day 4 p.i. biological replicate 3


title: co_rep1

source_name: IEC obtained from 5-day-old healthy mice, biological replicate 1


title: wt_rep2

source_name: IEC from neonate mice infected with S. Typhimurium wildtype at the age of 1 day obtained at day 4 p.i. biological replicate 2


title: co_rep4

source_name: IEC obtained from 5-day-old healthy mice, biological replicate 4


title: Tlr4_rep4

status: Public on Aug 23 2014

source_name: IEC isolated from healthy 28-day-old Tlr4 KO mice, biological replicate 4

growth_protocol: IECs were prepared as described recently (Lotz et al., J. Exp Med. 2006). In brief, mouse intestinal tissue was incubated for 10 min at 37°C in 0.3 M EDTA. shaken vigorously and epithelial cells were separated from the underlying tissue and immune cells by repeated sedimentation at 1 x g at 4°C. Flow cytometric analysis revealed less than 5% of CD45+ cells in IEC preparations.

tag: genotype

value: Tlr4 KO


title: Trif_rep2

source_name: IEC isolated from healthy 28-day-old Trif LPS/LPS mice, biological replicate 2

value: Trif mut


title: Tlr3_rep3

source_name: IEC isolated from healthy 28-day-oldTlr3 KO mice, biological replicate 3

value: Tlr3 KO


title: Tlr3_rep2

source_name: IEC isolated from healthy 28-day-oldTlr3 KO mice, biological replicate 2


title: MyD88_rep4

source_name: IEC isolated from healthy 28-day-old MyD88 KO mice, biological replicate 4

value: MyD88 KO


title: Trif_rep1

source_name: IEC isolated from healthy 28-day-old Trif LPS/LPS mice, biological replicate 1


title: Tlr3_rep1

source_name: IEC isolated from healthy 28-day-oldTlr3 KO mice, biological replicate 1


title: wt_rep3

source_name: IEC isolated from healthy 28-day-old wildtype mice, biological replicate 3

value: wt


title: MyD88_rep3

source_name: IEC isolated from healthy 28-day-old MyD88 KO mice, biological replicate 3


title: wt_rep1

source_name: IEC isolated from healthy 28-day-old wildtype mice, biological replicate 1


title: wt_rep4

source_name: IEC from neonate mice infected with S. Typhimurium wildtype at the age of 1 day obtained at day 4 p.i. biological replicate 4


title: Trif_rep3

source_name: IEC isolated from healthy 28-day-old Trif LPS/LPS mice, biological replicate 3


title: Tlr3_rep4

source_name: IEC isolated from healthy 28-day-oldTlr3 KO mice, biological replicate 4


title: wt_rep4

source_name: IEC isolated from healthy 28-day-old wildtype mice, biological replicate 4


title: Tlr4_rep3

source_name: IEC isolated from healthy 28-day-old Tlr4 KO mice, biological replicate 3


title: wt_rep2

source_name: IEC isolated from healthy 28-day-old wildtype mice, biological replicate 2


title: MyD88_rep2

source_name: IEC isolated from healthy 28-day-old MyD88 KO mice, biological replicate 2


title: MyD88_rep1

source_name: IEC isolated from healthy 28-day-old MyD88 KO mice, biological replicate 1


title: Tlr4_rep2

source_name: IEC isolated from healthy 28-day-old Tlr4 KO mice, biological replicate 2


title: Trif_rep4

source_name: IEC isolated from healthy 28-day-old Trif LPS/LPS mice, biological replicate 4


title: Tlr4_rep1

source_name: IEC isolated from healthy 28-day-old Tlr4 KO mice, biological replicate 1


title: BRAT

status: Public on Mar 30 2015

data_processing: The experiment was represented with a matrix where rows correspond to probes and columns are the intensities of the Cy5-labeled RNA from the GST-BRAT pulldown assay. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

source_name: Pulldown RNA labeled with Cy5

value: BRAT

tag: channel


title: RNCMPT00067

status: Public on May 10 2013

data_processing: Each batch of experiments was represented with a matrix where rows correspond to probes and columns are the pulldown intensities of the RBPs in that batch. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all the experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).


title: RNCMPT00053


title: RNCMPT00156

source_name: Pulldown RNA labeled with Cy3


title: RNCMPT00021


title: RNCMPT00070


title: RNCMPT00024


title: RNCMPT00160


title: RNCMPT00063


title: RNCMPT00159

value: RALY


title: RNCMPT00022

value: GST-tagged RNA-binding protein pulldown


title: RNCMPT00064


title: RNCMPT00158


title: RNCMPT00020


title: RNCMPT00161


title: RNCMPT00056


title: RNCMPT00155


title: RNCMPT00076

value: TARDBP


title: RNCMPT00157


title: RNCMPT00037


title: RNCMPT00154


title: RNCMPT00045


title: RNCMPT00153


title: RNCMPT00059


title: RNCMPT00150


title: RNCMPT00034


title: RNCMPT00054


title: RNCMPT00149


title: RNCMPT00152


title: RNCMPT00151


title: RNCMPT00012


title: RNCMPT00061


title: RNCMPT00144


title: RNCMPT00145

value: snf


title: RNCMPT00008


title: RNCMPT00060


title: RNCMPT00148


title: RNCMPT00010


title: RNCMPT00015


title: RNCMPT00058


title: RNCMPT00110


title: RNCMPT00146


title: RNCMPT00009


title: RNCMPT00105

value: pum


title: RNCMPT00139

value: pAbp


title: RNCMPT00090


title: RNCMPT00138

value: rin


title: RNCMPT00032

value: HuR


title: RNCMPT00078


title: RNCMPT00133

value: cpo


title: RNCMPT00137

value: mub


title: RNCMPT00046


title: RNCMPT00143


title: RNCMPT00096


title: RNCMPT00129


title: RNCMPT00132


title: RNCMPT00104


title: RNCMPT00136


title: RNCMPT00134


title: RNCMPT00127


title: RNCMPT00147


title: RNCMPT00131


title: RNCMPT00006


title: RNCMPT00028


title: RNCMPT00140

value: mod


title: RNCMPT00141


title: RNCMPT00007


title: RNCMPT00080


title: RNCMPT00103


title: RNCMPT00142


title: RNCMPT00069

value: sm


title: RNCMPT00273


title: RNCMPT00065


title: RNCMPT00272


title: RNCMPT00097

value: Lark


title: RNCMPT00109


title: RNCMPT00122


title: RNCMPT00102


title: RNCMPT00066


title: RNCMPT00093


title: RNCMPT00121

value: elav


title: RNCMPT00089


title: RNCMPT00035


title: RNCMPT00039


title: RNCMPT00082


title: RNCMPT00029


title: RNCMPT00052


title: RNCMPT00118

value: how


title: RNCMPT00100

value: msi


title: RNCMPT00126


title: RNCMPT00117


title: RNCMPT00120

value: fne


title: RNCMPT00088


title: RNCMPT00019


title: RNCMPT00124


title: RNCMPT00116


title: RNCMPT00031


title: RNCMPT00119

value: Sxl


title: RNCMPT00101

value: GST-tagged RNA-binding protein pulldown


title: RNCMPT00042


title: RNCMPT00123


title: RNCMPT00107


title: RNCMPT00114

value: aret


title: RNCMPT00011

value: papi


title: RNCMPT00095


title: RNCMPT00040


title: RNCMPT00003


title: RNCMPT00099


title: RNCMPT00106


title: RNCMPT00112


title: RNCMPT00284


title: RNCMPT00279


title: RNCMPT00291


title: RNCMPT00281

value: Syncrip


title: RNCMPT00083


title: RNCMPT00283


title: RNCMPT00282


title: RNCMPT00285


title: RNCMPT00289

value: Hnrnpr-Xt


title: RNCMPT00270


title: RNCMPT00113


title: RNCMPT00108


title: RNCMPT00287


title: RNCMPT00288

value: HNRNPR-Gg


title: RNCMPT00280


title: RNCMPT00111


title: RNCMPT00094


title: RNCMPT00278


title: RNCMPT00274

value: HuR


title: RNCMPT00263


title: RNCMPT00269

value: PTB


title: RNCMPT00265


title: RNCMPT00268


title: RNCMPT00051


title: RNCMPT00259


title: RNCMPT00258


title: RNCMPT00256


title: RNCMPT00253


title: RNCMPT00255


title: RNCMPT00262


title: RNCMPT00248


title: RNCMPT00234


title: RNCMPT00249


title: RNCMPT00237


title: RNCMPT00254


title: RNCMPT00235


title: RNCMPT00238


title: RNCMPT00240


title: RNCMPT00246


title: RNCMPT00257


title: RNCMPT00230


title: RNCMPT00229


title: RNCMPT00236


title: RNCMPT00241


title: RNCMPT00225


title: RNCMPT00224


title: RNCMPT00228


title: RNCMPT00251


title: RNCMPT00232


title: RNCMPT00226


title: RNCMPT00252


title: RNCMPT00239


title: RNCMPT00245

value: HNRNPAB


title: RNCMPT00223


title: RNCMPT00220


title: RNCMPT00218


title: RNCMPT00219


title: RNCMPT00217


title: RNCMPT00215


title: RNCMPT00216


title: RNCMPT00261


title: RNCMPT00212


title: RNCMPT00036


title: RNCMPT00203


title: RNCMPT00199


title: RNCMPT00205


title: RNCMPT00186


title: RNCMPT00084


title: RNCMPT00026

value: hnRNPK


title: RNCMPT00073


title: RNCMPT00013


title: RNCMPT00197


title: RNCMPT00086


title: RNCMPT00074


title: RNCMPT00200


title: RNCMPT00044


title: RNCMPT00185


title: RNCMPT00091

value: HNRNPL


title: RNCMPT00004


title: RNCMPT00025

value: HNRNPC


title: RNCMPT00202


title: RNCMPT00038


title: RNCMPT00184


title: RNCMPT00062


title: RNCMPT00047

value: QKI


title: RNCMPT00187


title: RNCMPT00209


title: RNCMPT00206


title: RNCMPT00057


title: RNCMPT00016


title: RNCMPT00014


title: RNCMPT00183


title: RNCMPT00079


title: RNCMPT00077


title: RNCMPT00023


title: RNCMPT00081


title: RNCMPT00179


title: RNCMPT00181


title: RNCMPT00043


title: RNCMPT00005


title: RNCMPT00068

value: shep


title: RNCMPT00072


title: RNCMPT00055


title: RNCMPT00174


title: RNCMPT00182


title: RNCMPT00173


title: RNCMPT00178

value: hnRNPLL


title: RNCMPT00085


title: RNCMPT00071

value: SNRPA


title: RNCMPT00171


title: RNCMPT00050


title: RNCMPT00049


title: RNCMPT00027

value: hnRNPL


title: RNCMPT00176

value: GST-tagged RNA-binding protein pulldown


title: RNCMPT00175


title: RNCMPT00033


title: RNCMPT00172


title: RNCMPT00180


title: RNCMPT00177

value: PSF


title: RNCMPT00170


title: RNCMPT00169


title: RNCMPT00075

value: STAR-PAP


title: RNCMPT00017


title: RNCMPT00018

value: FUS


title: RNCMPT00001


title: Double stranded DNA of vcrA (100ng)

status: Public on Jul 27 2010

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

institute: CNRS - Blaise Pascal University

description: Standard PCR product

hyb_protocol: For each hybridization experiment, labeled product were vacuum dried and resuspended in 3,3 µL of water. Then, the hybridization mix (Roche NimbleGen) was realized according to the manufacturer's protocols. The arrays were hybridized on a 4-bay NimbleGen Hybridization System (Roche NimbleGen) at 42°C for 16 hrs 30min. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Samples were scanned using a Scanner Innoscan 900AL (Innopsys, Carbonne, France) at 1 μm resolution. Individual array images were acquired independently using the same PMT gain (=2) for each image as recommended using the software Mapix® (Innopsys). Then, for each array image, raw expression data had been extracted using the NimbleScan software v2.5. (Roche NimbleGen) and feature intensities were exported as .pair files.

data_processing: Means of the six replicates of each probes were calculated, and selected as values used for the study.

organism: Dehalococcoides mccartyi VS

source_name: Synthetic gene

label_protocol: DNA products were labelled with ULS aRNA labelling kit as described in the Kreatech ULS labelling procedure (Kreatech Diagnostics).

value: VS

tag: origin

value: Dehalococcoides sp. VS

value: Double stranded DNA of vcrA (100ng)


title: Double stranded DNA of mmoC (100ng)

description: Standard PCR product

organism: Methylosinus trichosporium OB3b

value: Methylosinus trichosporium OB3b

tag: sample type

value: Double stranded DNA of mmoC (100ng)


title: Single stranded DNA of vcrA (50ng)

description: Asymetric PCR product

value: Single stranded DNA of vcrA (50ng)


title: Double stranded DNA of ahdA1c (100ng)

description: Standard PCR product

organism: Sphingomonas paucimobilis

value: EPA 505

value: Sphingomonas paucimobilis EPA 505

value: Double stranded DNA of ahdA1c (100ng)


title: Single stranded DNA of ahdA1c (50ng)

description: Asymetric PCR product

value: Single stranded DNA  of ahdA1c (50ng)


title: RNCMPT00167


title: Single stranded DNA of mmoC (50ng)

description: Asymetric PCR product

value: Single stranded DNA of mmoC (50ng)


title: RNCMPT00041


title: RNCMPT00163


title: RNCMPT00165


title: RNCMPT00087


title: RNCMPT00166


title: RNCMPT00002


title: RNCMPT00164


title: patient 112 after treatment (paired analysis)

status: Public on Aug 30 2011

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: patient 112 after treatment

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer

scan_protocol: Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing:
Probe intensities were extracted from Affymetrix CEL files and normalized using RMA and summarized at the transcript cluster level using the R/Bioconductor (http://bioconductor.org) oligo package.  Array quality control was performed to remove arrays that significantly differed in performance.  Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package.  Significance testing was performed using a moderated t-test, and comparisons of pre- (V0) and post-treatment (V1) individuals were performed using a moderated paired t-test.  Gene set analysis was performed using the MSigDB (http://www.pnas.org/content/102/43/15545.abstract) and libraries generated from the Halloran labs Pathogenesis Based Transcript (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets.  The PBTs represent the major biologic events in cellular graft rejection and were derived from experimental mouse kidney transplants, cultured cells and human kidney biopsies.  Gene sets were converted to HUGO gene symbols and analysis was executed using the limma romer function.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: post-treatment

label_protocol: Follow protocols of Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using QIAGEN PAXgene Blood RNA Kit (Catalog Number 762164, Qiagen, USA). Briefly, centrifuged the PAXgene Blood RNA tube, pellet was visibly dissolved by adding 350 μl buffer BR1 and vortexing.  The proteins was digested using 40 μl proteinase K  for 10 minutes at 55°C  with a shaker–incubator at 1000 rpm. Lysate was directly flowing through a PAXgene Shredder spin column.  After adding  350 μl ethanol (96–100%) into flowing through lysate,  the lysate-ethanol mix was transferred into a PAXgene RNA spin column, following a DNA digestion using DNAse I and several wash, total RNA was eluted and dissolved into RNAse free water (All Reagents and Columns are from Kit).

treatment_protocol: 2.5 ml of Patient’s whole blood was collected into one PAXgene RNA Tube (Catalog Number 762165, Qiagen, USA)  using standard venipuncture and storaged in -20c  for 24 hours, then transferred in -70c until use.

tag: tissue

value: blood

value: post intravenous immune globulin (IVIG) and rituximab desensitization

tag: individual

value: patient 112 after treatment


title: RNCMPT00162

value: GST-tagged RNA-binding protein pulldown


title: RNCMPT00168