title: Aorta of ApoE KO mice1, Gpnmb vaccine


title: Spt4-FRB_DMSO_NET-seq

status: Public on Sep 27 2021

type: SRA

city: Oxford

first: Ulku

last: Uzun

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Library strategy: NET-seq
Single-end FASTQ files were processed using usegalaxy.org and RStudio. Reads were groomed using FASTQ groomer for Sanger & Illumina 1.8 + (Blankenberg et al., 2010). Adapter sequence ATCTCGTATGCCGTCTTC were trimmed and reads < 15 nt were discarded using Clip function. Reads were aligned to a combined fasta file of S.cerevisiae and S.pombe genomes using Bowtie for Illumina (Langmead, 2011). SAM files were converted to BAM files using SAM-to-BAM (Li, 2011).
Using RStudio/Bioconductor packages, multiply aligned reads were filtered, and reads were narrowed to the 3’ends. For spike-in normalisation, counts table was created for S.pombe genes using RStudio/Bioconductor. The estimateSizeFactors function in the DEseq2/RStudio package was applied to calculate the relative amounts of S.pombe reads (i.e. normalisation ratio) in each sample (Love, Huber, and Anders 2014). NET-seq data were calibrated by dividing S.cerevisiae reads by the normalisation ratios.
genome build: SacCer3 (R64) and ASM294v2
processed data file: normalised bigwig file for positive strand
processed data file: normalised bigwig file for negative strand

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD (30°C, 160 rpm) from OD600 0.2 to 0.65.

extract_protocol:
Cells were filtered and flash frozen in liquid nitrogen. 4 parts of the frozen S.cerevisiae pellet were spiked-in with one part of frozen S.pombe (containing a FLAG-tagged Rpb9) pellet (4:1 by weight). The combined pellet was lysed, and immunoprecipitation of the FLAG-tagged proteins was performed at 4°C as described in (Fischl et al., 2017). RNA was isolated with Qiagen miRNA kit according to the manufacturer’s instructions.
The isolated RNA was adapter ligated, fragmented, reverse transcribed, circularized, barcoded, and amplified as described in (Fischl et al., 2017).

tag: genotype

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; SPT4-FRB-eGFP; RPB3-3xFLAG

tag: treatment

value: Rapamycin (1mg/ml final in DMSO) addition 140 min prior to cell harvest

tag: extracted molecule

value: native RNA


title: 48H_DCA-240_Rep3

status: Public on May 04 2021

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

country: France

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2
HtSeqCount was used for counting genes with default parameters
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied with the 9h BHISG value as a reference for reporting the expression data of 14, 24 and 48h BHISG with Deoxycholate at 120µM and 240µM.
Genome_build: Clostridioides difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts and Normalized Counts (9H, 14H, 24H and 48H BHISG with and withoutDeoxycholate 120µM and 240µM), Normalized Counts , Statistics (FC, pvalue, Significant)

organism: Clostridioides difficile

source_name: Wild type strain 630

growth_protocol: Strains were grown aerobically in BHISG at 37°C for 9H, 14H, 24H and 48 H with 120µM, 240µM and without Deoxycholate

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

tag: strain

value: wild type

value: BHISG DCA-240

tag: time


title: 178-A031846

status: Public on Nov 23 2021

city: Basel

first: Jasmin

last: Haslbauer

address: Schönbeinstrasse 40

country: Switzerland

institute: Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland

data_processing:
Alignment: four demultiplexed FASTQ files per well in the assay sequenced with the HTG EdgeSeq Parser (version 5.0.535.3181) see HTG EdgeSeq System User Manual (RUO).
Post sequencing quality control: POS% ≥ 28% as failure; Read depth ≤ 750,000 as failure; RSD ≤ 0.094 as failure .
Normalization: No pre-filtering is applied to the data prior to analysis. The DESeq2 (package version 1.14.1)model corrects for library size using the median ratio method from Anders and Huber (2010).
Dispersions are estimated with the Cox Reid-adjusted profile likelihood method developed by McCarthy et al. (2012).  Log2 fold change is estimated via Tikhonov/ridge regularization with a zero-centered normal prior distribution with variance calculated using the observed distribution of maximum likelihood coefficients (see DESeq2 documentation for details).
Supplementary_files_format_and_content: Excel file containing tables of raw, QC raw, log2 CPM (counts per million), and median normalized data.

organism: Homo sapiens

source_name: COVID-19_lymph node

extract_protocol:
HTG uses an extraction free technology that involves resuspending crude sample in Lysis Buffer.  The sample is then treated with Proteinase K and stored or used.
HTG EdgeSeq library construction is defined in the HTG EdgeSeq System User Manual (RUO)

tag: group

tag: tissue

value: lymph node


title: 48H_DCA-240_Rep2


title: Aorta of ApoE KO mice2, control vaccine

status: Public on Oct 22 2021

city: Los Angeles

first: Masayoshi

last: Suda

state: CA

address: 8700 Beverly Blvd.

department: Medicine

country: USA

institute: Cedars Sinai Medical Center

data_processing:
these libraries were analyzed on a NextSeq500 with a NextSeq 500/550 High Output Kit v2 (Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCm38/mm10) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM), and expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Aorta

extract_protocol:
Total RNA was isolated from tissue samples with an RNeasy Mini Kit (Qiagen, 74104) and its quality was assessed by using the Agilent 2100 Bioanalyzer with the Agilent RNA6000 pico Kit (Agilent Technologies).
The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was employed to construct four libraries according to the specifications of the manufacturer.

treatment_protocol: We fed the HFD to ApoE KO mice from 4 weeks of age, administered Gpnmb vaccine or control vaccine at 8 weeks of age, and analyzed these mice at 16 weeks.

value: Aorta

tag: age

value: ApoE -/-

value: control vaccine


title: Aorta of ApoE KO mice3, control vaccine


title: 48H_DCA-120_Rep2

value: BHISG DCA-120


title: 48H_DCA-120_Rep3


title: 48H_BHISG_Rep3

value: BHISG


title: 48H_DCA-240_Rep1


title: 24H_DCA-240_Rep2


title: 48H_DCA-120_Rep1


title: 48H_BHISG_Rep2


title: 24H_DCA-120_Rep3


title: 24H_DCA-240_Rep3


title: 24H_DCA-240_Rep1


title: 48H_BHISG_Rep1


title: 24H_DCA-120_Rep1


title: 24H_BHISG_Rep2


title: 24H_BHISG_Rep3


title: 24H_BHISG_Rep1


title: Deox4-cy5_WT4-cy3

status: Public on Aug 01 2021

type: RNA

description: Biological replicate 4 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BY.

source_name: 48H Biofilm with Deoxycholate

label_protocol: 5 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E Wt with and without deoxycholate Biofilm 48H

extract_protocol: Total RNA was extracted using QIAgen RNAeasy kit.

value: C630E Mullany

source_name: 48H Biofilm


title: 14H_DCA-240_Rep1


title: 14H_DCA-240_Rep3


title: 24H_DCA-120_Rep2


title: 14H_DCA-120_Rep3


title: Deox2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: 14H_DCA-120_Rep1


title: 14H_BHISG_Rep3


title: 14H_DCA-120_Rep2


title: 14H_BHISG_Rep1


title: 14H_BHISG_Rep2


title: Deox3-cy3_WT3-cy5

description: Biological replicate 3 of 4.


title: 9H_DCA-240_Rep2


title: Deox1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: 9H_DCA-240_Rep3


title: 9H_DCA-240_Rep1


title: 9H_DCA-120_Rep1


title: 9H_BHISG_Rep3


title: 9H_DCA-120_Rep3


title: 9H_DCA-120_Rep2


title: 9H_BHISG_Rep2


title: H889 hSCLC PROX1 input

status: Public on May 01 2021

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
Reads were mapped to hg39 assembly using bowtie2
Low quality reads were filtered using samtools
Removed duplicates using picard
Bigwig files contain ChIP signal normalized to 10M reads
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq signal in bigwig format

molecule: genomic DNA

source_name: H889 hSCLC PROX1

growth_protocol: Cells were maintained in RPMI-1640 media (ThermoFisher Scientific, 11875135) supplemented with 5% heat deactivated fetal bovine serum (Sigma Aldrich) without antibiotics at 37 °C in a humidified atmosphere containing 5% CO2 and 95% air.

extract_protocol:
Cells (~7 x107 cells) in the exponential growth phase were fixed and nuclear extract were prepared. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with 10 μg antibody.
Libraries were constructed by using the NEBNext® ChIP-Seq Library Prep Master Mix (NEB,E6240) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, E7335S, Index Primers Set 2, E7500S) with Agencourt AMPure XP magnetic beads (Beckman coulter, A63881) exactly as per manufacturer’s instructions.

treatment_protocol: no treatment

tag: tissue/cell line

tag: tissue/cell type

value: Small cell lung cancer cell line

tag: passage

tag: antibody


title: H889 hSCLC NKX2-1 ChIP

source_name: H889 hSCLC NKX2-1

value: rabbit anti-TTF1 (NKX2-1) (10 mg; Sigma-Millipore 07 601; RRID:AB_310743)


title: H889 hSCLC NKX2-1 input


title: 14H_DCA-240_Rep2


title: H889 hSCLC PROX1 ChIP

value: rabbit anti-PROX1 (10 mg; Proteintech 11067-2-AP; RRID:AB_2268804)


title: H2107 hSCLC PROX1 ChIP

source_name: H2107 hSCLC PROX1


title: H2107 hSCLC NKX2-1 ChIP

source_name: H2107 hSCLC NKX2-1


title: H2107 hSCLC NKX2-PROX1 Input

source_name: H2107 hSCLC NKX2-PROX1


title: H128 hSCLC PROX1 ChIP

source_name: H128 hSCLC PROX1


title: H128 hSCLC NKX2-1 Input

source_name: H128 hSCLC NKX2-1


title: LX44 hPDX H3K27ac input

source_name: LX44 hPDX

value: JHU-LX44-SCLC PDX

value: Small cell lung cancer PDX flank


title: H128 hSCLC NKX2-1 ChIP


title: LX48 hPDX H3K27ac ChIP

source_name: LX48 hPDX

value: JHU-LX48-SCLC PDX

value: H3K27ac (Abcam, Ab4729)


title: LX44 hPDX H3K27ac ChIP


title: LX22 hPDX H3K27ac input

source_name: LX22 hPDX

value: JHU-LX22-SCLC PDX


title: 9H_BHISG_Rep1

value: wild type


title: H128 hSCLC PROX1 Input


title: LX48 hPDX H3K27ac input


title: H889 hSCLC H3K27ac ChIP

source_name: H889 hSCLC


title: H69 hSCLC H3K27ac ChIP

source_name: H69 hSCLC


title: H526 SCLC H3K27ac Input

source_name: H526 SCLC


title: LX22 hPDX H3K27ac ChIP


title: H69 hSCLC H3K27ac Input


title: H526 SCLC H3K27ac ChIP


title: H524 hSCLC H3K27ac ChIP

source_name: H524 hSCLC


title: LX110 hPDX H3K27ac ChIP

source_name: LX110 hPDX

value: JHU-LX110-SCLC PDX


title: H510 hSCLC H3K27ac Input

source_name: H510 hSCLC


title: H378 SCLC H3K27ac ChIP

source_name: H378 SCLC


title: LX110 hPDX H3K27ac input


title: H2171 hSCLC H3K27ac Input

source_name: H2171 hSCLC


title: H524 hSCLC H3K27ac Input


title: H378 SCLC H3K27ac Input


title: H510 hSCLC H3K27ac ChIP


title: H889 hSCLC H3K27ac input


title: H211 SCLC H3K27ac Input

source_name: H211 SCLC


title: H211 SCLC H3K27ac ChIP


title: H2107 hSCLC H3K27ac Input

source_name: H2107 hSCLC


title: H2171 hSCLC H3K27ac ChIP


title: H1048 SCLC H3K27ac Input

source_name: H1048 SCLC


title: H1092 SCLC H3K27ac ChIP

source_name: H1092 SCLC


title: H1092 SCLC H3K27ac Input


title: H82 hSCLC H3K27ac ChIP

source_name: H82 hSCLC


title: H2107 hSCLC H3K27ac ChIP


title: H889 hSCLC FOXA2 Input

source_name: H889 hSCLC FOXA2


title: H1048 SCLC H3K27ac ChIP


title: H889 hSCLC FOXA2 ChIP

value: rabbit anti-FOXA2 (Cell Signaling Technology #3143; RRID:AB_2104878)


title: DIS380003-V7

status: Public on Mar 22 2021

city: Vancouver

first: Don

middle: D

last: Sin

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia

data_processing:
RNA-seq reads were mapped and quantified to the GENCODE genome reference (assembly GRCh37, release 31) using Salmon (0.13.1)
Number of reads mapped to each transcript were summarized to gene level using R package Tximport (1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with number of reads for every gene and every sample

source_name: Bronchial epithelial cells

extract_protocol:
RNA was extracted from cytological brush specimens stored in QIAzol RNA lysis buffer (QIAGEN, Stockach, Germany) using the RNeasy Plus kit (QIAGEN) according to the manufacturer’s instructions. Sample quality control was performed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA)
For qualifying samples, libraries were prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs, Ipswich, MA, USA)

tag: subject

value: SAL/FLU

tag: timepoint

value: post-treatment


title: DIS380003-V3

value: pre-treatment

value: Current-smoker


title: DIS380001-V3

value: Ex-smoker


title: DIS380002-V7


title: DIS320084-V7

value: FOR/BUD


title: DIS320080-V3


title: DIS320085-V3

value: FOR


title: DIS320079-V3


title: DIS320084-V3


title: DIS320080-V7


title: DIS320074-V3


title: DIS320074-V7


title: DIS320077-V7


title: DIS320071-V3


title: DIS320076-V3

value: Not randomized


title: DIS320077-V3


title: DIS320071-V7


title: DIS320070-V3


title: DIS320070-V7


title: DIS320085-V7


title: DIS320069-V7


title: DIS320067-V3


title: DIS380002-V3


title: DIS320067-V7


title: DIS320066-V3


title: DIS320063-V7


title: DIS320069-V3


title: DIS320066-V7


title: DIS320063-V3


title: DIS320062-V7


title: DIS320057-V7


title: DIS320057-V3


title: DIS320056-V7


title: DIS320055-V7


title: DIS320055-V3


title: DIS320054-V7


title: DIS320054-V3


title: DIS320053-V7


title: DIS320051-V7


title: DIS320060-V3


title: DIS320062-V3


title: DIS320050-V3


title: DIS320044-V7


title: DIS320041-V7


title: DIS320049-V3


title: DIS320045-V3


title: DIS320047-V7


title: DIS320047-V3


title: DIS320040-V7


title: DIS320051-V3


title: DIS320053-V3


title: DIS320049-V7


title: DIS320040-V3


title: DIS320043-V7


title: DIS320043-V3


title: DIS320044-V3


title: DIS320037-V7


title: DIS320039-V3


title: DIS320050-V7


title: DIS320036-V7


title: DIS320045-V7


title: DIS320035-V3


title: DIS320036-V3


title: DIS320035-V7


title: DIS320033-V7


title: DIS320034-V3


title: DIS320034-V7


title: DIS320039-V7


title: DIS320030-V7


title: DIS320025-V3


title: DIS320027-V3


title: DIS320037-V3


title: DIS320032-V7


title: DIS320028-V3


title: DIS320031-V7


title: DIS320032-V3


title: DIS320031-V3


title: DIS320024-V3


title: DIS320028-V7


title: DIS320026-V3


title: DIS320027-V7


title: DIS320026-V7


title: DIS320019-V3


title: DIS320018-V7


title: DIS320020-V3


title: DIS320023-V3


title: DIS320018-V3


title: DIS320017-V7


title: DIS320024-V7


title: DIS320017-V3


title: DIS320033-V3


title: DIS320030-V3


title: DIS320016-V7


title: DIS320016-V3


title: DIS320019-V7


title: DIS320013-V7


title: DIS320014-V7


title: DIS320011-V3


title: DIS320008-V7


title: DIS320008-V3


title: DIS320013-V3


title: DIS320007-V3


title: DIS320014-V3


title: DIS320006-V7


title: DIS320009-V7


title: DIS320011-V7


title: DIS320005-V3


title: DIS320009-V3


title: DIS320006-V3


title: DIS320007-V7


title: DIS320004-V3


title: DIS320003-V7


title: DIS320002-V7


title: DIS320005-V7


title: DIS320001-V7


title: DIS320002-V3


title: DIS320001-V3


title: DIS320003-V3


title: BU-FTM-16

status: Public on Nov 11 2020

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
The single cell sequence preprocessing was performed using the standard10X Genomics Cell Ranger Single Cell Software Suite v.3.0.0.
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering and differential expression analyses were performed using Seurat v.3.1.
Genome_build: mm10
Supplementary_files_format_and_content: matrix files

source_name: cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P) (Cat#130-092-628, Myltenyi Biotec) at 37˚C in the gentleMACS™ Octo Dissociator with Heaters (Myltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat#130-096-733, Myltenyi Biotec) followed by the red blood cell lysis (Cat#130-094-183, Myltenyi Biotec) and dead cell removal (Cat#130-090-101, Myltenyi Biotec) according to the manufacturer’s instructions. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
Single-cell RNA-seq (scRNAseq) was performed on the isolated cortical samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3′ gene expression (3′ GEX) V3 kit, using a targeted input of ~ 6,000 to 9,000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina, San Diego, CA) targeting a depth of 25,000–50,000 reads per cell.

treatment_protocol: Mice were treated with tamoxifen at two months of age to induce TREM2 expression in microglia. The control mice were given vehicle (corn oil).

tag: background strain

value: 5xFAD+/-;TREM2-R47H+/+; Cx3cr1CreER/+

value: Induced


title: BU-FTM-24


title: BU-FTM-20


title: BU-FTM-12


title: BU-FTM-8


title: BU-FTM-4


title: BU-FTM-19

value: Control


title: BU-FTM-15


title: BU-FTM-11


title: BU-FTM-7


title: BU-FTM-23


title: BU-FTM-22

value: 5xFAD+/-;TREM2-WT+/+; Cx3cr1CreER/+


title: BU-FTM-10


title: BU-FTM-3


title: BU-FTM-2


title: BU-FTM-18


title: BU-FTM-14


title: BU-FTM-13


title: BU-FTM-21


title: BU-FTM-6


title: BU-FTM-17


title: BU-FTM-9


title: BU-FTM-5


title: GEX_BU-EFTM-20

treatment_protocol: Mice were treated with tamoxifen at birth to induce TREM2 expression in microglia. The control mice were given vehicle (corn oil).


title: GEX_BU-EFTM-16


title: GEX_BU-EFTM-24


title: GEX_BU-EFTM-8


title: GEX_BU-EFTM-19


title: GEX_BU-EFTM-15


title: GEX_BU-EFTM-12


title: GEX_BU-EFTM-4


title: BU-FTM-1


title: GEX_BU-EFTM-11


title: GEX_BU-EFTM-3


title: GEX_BU-EFTM-18


title: GEX_BU-EFTM-22


title: GEX_BU-EFTM-7


title: GEX_BU-EFTM-23


title: GEX_BU-EFTM-6


title: GEX_BU-EFTM-2


title: GEX_BU-EFTM-10


title: GEX_BU-EFTM-14


title: GEX_BU-EFTM-21


title: GEX_BU-EFTM-1


title: p65_sh rep2

status: Public on Oct 05 2020

city: Guangzhou

first: Ziyang

last: Wang

state: --- Select One ---

address: 58 Zhongshan 2nd Road

country: China

institute: Ziyang Wang, Doctor, The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Skewer (v0.2.2) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed.
The reads were mapped to the human (Homo sapiens) genome (version hg19) using STAR (v2.4.2a) software.
Expression estimation of gene and transcript was performed by using RSEM (V1.2.29) software. Then edgeR (v3.8.5) package in R was used to perform TMM (trimmed mean of M values) and CPM (count per million) normalization for the the gene expression. TMM is mainly used to normalize the depth of sequencing in different samples and estimate the expression level for each sample. CPM is used to normalize the amount of read count expression between samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM and CPM normalized values for each Sample ...

source_name: HCT116_p65 knockdown

extract_protocol:
Total RNA was extract using Trizol reagent. mRNA was extracted from total RNA using magnetic beads and used Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 cells were infected with shNC, TEX10 knockdown or p65 knockdown lentiviruses for 24 h, and then screened by puromycin for 3 days.

tag: cell line

tag: cell type

value: Human colorectal cell line

tag: genotype/variation

value: p65 knockdown


title: p65_sh rep1


title: GEX_BU-EFTM-13

tag: genotype

tag: treatment


title: shNC2 rep1

value: shNC


title: TEX10_sh rep3

source_name: HCT116_TEX10 knockdown

value: TEX10 knockdown


title: shNC2 rep2


title: shNC1 rep3


title: TEX10_sh rep2


title: GEX_BU-EFTM-9


title: TEX10_sh rep1


title: shNC1 rep1


title: GEX_BU-EFTM-17


title: shNC1 rep2


title: GEX_BU-EFTM-5


title: Tsix +/- day 0 (replicate 2)

status: Public on Jun 25 2020

city: Boston

first: Eric

last: Aeby

state: Massachusetts

address: 185 Cambridge Street

department: Department of Molecular Biology and Department of Genetics

institute: Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School

data_processing:
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using bowtie2 and novoalign
allele specific reads were called by custom script (Pinter et al., 2012)
Metagene analysis was done by deeptools2 (Ramirez et al., 2016) and custom python scripts
Strand-specific PRO-seq coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million with deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (fwd:watson, rev:crick strand) and RPKM normalized

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium or differentiated accordingly

extract_protocol:
Total RNA was isolated using TRIzol extraction,biotin-labeled RNA was enriched using strepatividing pulldown
Library preparation is combined to PROseq experiment (three individual streptavidin enrichment steps) and was performed as described in (Kwak et al. 2013 and Mahat et al. 2016); Strand-specific RNA sequencing, multiplexed

treatment_protocol: Nuclei were isolated, permeabilized for nuclear run-on. Nascent transcripts were labeled with Biotin-11-ATP, Biotin-11-CTP, Biotin-11-GTP, Biotin-11-UTP

value: Tsix +/-

tag: developmental stage

value: undifferentiated ES cells

tag: Sex

value: female

tag: strain

value: C57BL/6J x CAST/EiJ hybrid


title: RSV_vehicle_7d_M_67

status: Public on Nov 19 2019

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins Dr

institute: NIBR

data_processing:
Reads were de-multiplexed with the Illumina pipeline. Raw reads were aligned to a reference FASTA file that contains a curated list of transcripts (RefSeq, transcripts as of 2013). Alignment was done with BWA (Burrows-Wheeler Aligner) and reads per million (RPM) values were created from the sequence alignment map (SAM) output file
Messenger RNAs less than 200 bp were eliminated from the analysis.
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCC.seq"
Supplementary_files_format_and_content: text file containing normalized (reads per million=RPM) expression values for genes 200 base pairs and longer

source_name: lung

growth_protocol: BALB/c mice were mock treated or infected with 5.5x10^5 RSV A2 with or without 3 mg/kg dexamethasone.  During scheduled takedowns on day 5 or 7, a left lung specific BAL performed by first tying off the upper right lobe (3x0.2 ml sterile saline). After BAL the upper right lobe was aseptically removed into a 1.7ml Eppendorf tube containing 0.4ml RNA later, weighed, and placed on ice.

extract_protocol:
RNA was extracted using Qiagen RNeasy 96 Universal Tissue Kit (Cat #74881), where samples were homogenized in QIAzol followed by Chloroform extraction and ethanol precipitation. Then the samples were then purified using the columns contained in the kit using the manufacturer's protocol.
500 ng total RNA was used to make Illumina libraries using the TruSeq stranded kit

value: BALB/c

tag: tissue

value: lung

tag: infection

value: RSV

tag: time point

value: 7 days


title: CD630_WT4-Cy3_sig544-cy5

status: Public on Aug 28 2020

description: Biological replicate 4 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

source_name: strain C630E grown 6h in TY (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E was grown for 6 hours in TY medium.

extract_protocol: Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.

value: C630E Mullany

source_name: sig54 mutant grown 6h in TY


title: Tsix +/- day 0 (replicate 1)


title: Hgw11 retina scRNA-seq

status: Public on May 07 2020

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description:
Single retinal cells from gestational week 11 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp

data_processing:
fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)

molecule: polyA RNA

source_name: Retinal Cells

extract_protocol: 10x Genomics 3' v2 Single Cell RNA-sequencing

value: dissociated retina

tag: cell source

value: primary tissue


title: Tsix +/- differentiation day 7 (replicate 1)

value: differentiation day 7


title: RSV_vehicle_7d_M_66

treatment_protocol: BALB/c mice were mock treated or infected with 5.5x10^5 RSV A2 with or without 3 mg/kg dexamethasone.  During scheduled takedowns on day 5 or 7, a left lung specific BAL performed by first tying off the upper right lobe (3x0.2 ml sterile saline). After BAL the upper right lobe was aseptically removed into a 1.7ml Eppendorf tube containing 0.4ml RNA later, weighed, and placed on ice.


title: Tsix +/- differentiation day 7 (replicate 2)


title: RSV_vehicle_5d_M_23

value: 5 days


title: RSV_vehicle_5d_M_20


title: mock_vehicle_7d_M_55

value: mock


title: RSV_dex_7d_M_76

value: Dexamethasone, 3 mg/kg


title: RSV_dex_7d_M_77


title: RSV_dex_5d_M_26


title: mock_vehicle_7d_M_53


title: mock_vehicle_5d_M_08


title: RSV_dex_7d_M_75


title: CD630_WT2-Cy3_sig542-cy5

description: Biological replicate 2 of 4.


title: mock_vehicle_5d_M_06


title: mock_vehicle_7d_M_52


title: CD630_WT1-Cy5_sig541-cy3

description: Biological replicate 1 of 4.


title: mock_vehicle_5d_M_04


title: Hgw9 retina scRNA-seq

description:
Single retinal cells from gestational week 9 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
Read 1: 98bp, Read 2: 26bp; i7:8bp


title: CD630_WT3-Cy5_sig543-cy3

description: Biological replicate 3 of 4.


title: RSV_dex_5d_M_30


title: RSV_vehicle_7d_M_65


title: RSV_dex_5d_M_32


title: HBEC_RSV

source_name: HBEC

growth_protocol: Airway epithelial cells were seeded in 24 well plates as follows: NCI-H292, passage 20, 250,000 cells/well;  A549, passage 12, 200,000 cells/well; human bronchial epithelial cells (HBECs), passage 4, 200,000 cells/well; small airway epithelial cells (SAECs), passage 4, 200,000 cells/well.  NCI-H292 and A549 cells were seeded in 500 ul RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  HBEC and SAEC cells were seeded in 500 ul BEBM + BEGM singlequots from Lonza or SABM + SAGM singlequots from Lonza, respectively.  The following day, compound dilutions were prepared in the same media with 0.2% DMSO and 250 ul with 2x compound was added to the approprate well.  For mock and viral infection, 250 ul of media alone or media containing RSV A2 MOI 1 was added to the appropriate wells for a total of 500 ul per well.  For ALI HBEC samples, HBECs that were cultured for 3 weeks at alir liquid interface (ALI) on transwell plates were infected with 10,000 or 50,000 pfu RSV.  Samples were collected at the indicated times by removing media, washing once with PBS and adding 300 ul RLT per well.

extract_protocol:
RNA was purified using RNeasy mini kits (Qiagen) according to the manufacturer’s protocol
one micrograms total RNA was used to make Illumina-compatible libraries using a custom protocol

value: HBEC

value: epithelial


title: RSV_vehicle_5d_M_21


title: HBEC_mock

treatment_protocol: Airway epithelial cells were seeded in 24 well plates as follows: NCI-H292, passage 20, 250,000 cells/well;  A549, passage 12, 200,000 cells/well; human bronchial epithelial cells (HBECs), passage 4, 200,000 cells/well; small airway epithelial cells (SAECs), passage 4, 200,000 cells/well.  NCI-H292 and A549 cells were seeded in 500 ul RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  HBEC and SAEC cells were seeded in 500 ul BEBM + BEGM singlequots from Lonza or SABM + SAGM singlequots from Lonza, respectively.  The following day, compound dilutions were prepared in the same media with 0.2% DMSO and 250 ul with 2x compound was added to the approprate well.  For mock and viral infection, 250 ul of media alone or media containing RSV A2 MOI 1 was added to the appropriate wells for a total of 500 ul per well.  For ALI HBEC samples, HBECs that were cultured for 3 weeks at alir liquid interface (ALI) on transwell plates were infected with 10,000 or 50,000 pfu RSV.  Samples were collected at the indicated times by removing media, washing once with PBS and adding 300 ul RLT per well.


title: H292_RSV


title: H292_mock


title: H292_RSV_Dex

value: Dexamethasone, 1 micromolar

value: 32 hours


title: A549_RSV


title: A549_mock


title: 32h_Dex_mock

growth_protocol: NCI-H292 cells between passage 20 and 24 were seeded into 96 well plates at 70,000 cells/well in RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  The following day, compound dilutions were prepared in the same RPMI 1% FBS media with 0.2% DMSO and 50 ul was added to the approprate well.  For mock and viral infection, 50 ul of RMPI 1% FBS media or media containing 100,000 pfu RSV A2 GFP was added to the appropriate wells for a total of 100 ul per well.  For EGF treatment, 50 ul of 80 ng/ml EGF was added to the appropriate wells for a total of 100 ul per well of 40 ng/ml EGF.


title: 32h_DMSO_mock

treatment_protocol: NCI-H292 cells between passage 20 and 24 were seeded into 96 well plates at 70,000 cells/well in RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  The following day, compound dilutions were prepared in the same RPMI 1% FBS media with 0.2% DMSO and 50 ul was added to the approprate well.  For mock and viral infection, 50 ul of RMPI 1% FBS media or media containing 100,000 pfu RSV A2 GFP was added to the appropriate wells for a total of 100 ul per well.  For EGF treatment, 50 ul of 80 ng/ml EGF was added to the appropriate wells for a total of 100 ul per well of 40 ng/ml EGF.

value: DMSO


title: E25

status: Public on Sep 09 2019

data_processing:
Illumina Casava1.7 software used for basecalling.
Only sequence with a minimum length of 30 were considered.
Sequences were mapped to their de novo Peptoclostridium difficile whole genome sequences using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b NO -v MEAN
Genome_build: Peptoclostridium difficile E1 (CAMD01) ; T20(CAMC01) ; T5 (CAMB01) ; E12 (CAMZ01) ; T14 (CANC01) ; E14 (CAMS01) ; T6 (CAMR01) ; E23 (CAMY01) ; T10 (CANB01) ; E15 (CAMM01) ; T11 (CAML01) ; E25 (CAMJ01) ; T15 (CAMK01) ; E16 (CAMH01) ; T61 (CAND01) ; E24 (CAMP01) ; T42 (CAMQ01)
Supplementary_files_format_and_content: Genes-count: Gene ID ; count
Supplementary_files_format_and_content: Couple-comparison: Organization (Class, Operon) ; Gene ID ; RNASeq (Coverage, Ratio) ; Gene Information (Orthologuous, Name, Product)

source_name: Wild type strain E25

growth_protocol: Strains were grown aerobically in TY 6h at 37°C

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols (Truseq non stranded RNA seq kit)

tag: strain type

value: Severe

value: wild type


title: 32h_Dex_RSV

value: lung


title: T10

source_name: Wild type strain T10

value: Control


title: T61

source_name: Wild type strain T61


title: T6

source_name: Wild type strain T6


title: E15

source_name: Wild type strain E15


title: E14

source_name: Wild type strain E14

value: Prevalent


title: E16

source_name: Wild type strain E16


title: E23

source_name: Wild type strain E23


title: E24

source_name: Wild type strain E24


title: 32h_DMSO_RSV

value: RSV


title: T15

source_name: Wild type strain T15


title: E12

source_name: Wild type strain E12


title: E1

source_name: Wild type strain E1


title: T5

source_name: Wild type strain T5


title: T42

source_name: Wild type strain T24


title: DMSO-3

status: Public on Aug 28 2019

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile R20291 whole genome sequence using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied to compare Deoxycholate to DMSO, Cholate to DMSO and Deoxycholate to Cholate
Genome_build: Peptoclostridium difficile R20291 (FN545816.1)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts, Normalized Counts, Statistics (FC, pvalue, significant)

source_name: strain R20291 Grown with DMSO

growth_protocol: Strains were grown anerobically in TY 10h at 37°C

extract_protocol:
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (MicrobExpress rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq non stranded RNA seq kit

tag: subsp.

value: strain

value: Wild type


title: DMSO-2


title: T20

source_name: Wild type strain T20


title: Chol-2

source_name: strain R20291 Grown with 5 mM Cholate


title: DMSO-1


title: Chol-3


title: DMSO-0


title: Chol-0


title: T11

source_name: Wild type strain T11


title: Deox-3

source_name: strain R20291 Grown with 0.5 mM Deoxycholate


title: Deox-2


title: Chol-1


title: T14

source_name: Wild type strain T14


title: E16

status: Public on May 22 2019

description:
10x_E16
10x Genomics single cell RNAseq
E16 mouse single retinal cells from 10x Genomics Chromium Single Cell
PolyA RNA
processed data file: 10x_aggregate.mtx
processed data file: genes.tsv
processed data file: barcodes.tsv

data_processing:
Smart-seq: Fastq files were aligned to mm10 using Hisat and processed to bam files using samtools; mapped reads were assigned using Cuffquant and libraries normalized using Cuffnorm.
10x: Demux and generation of fastq files using default parameters from Cellranger v1.2.1 mkfastq; Alignment of .fastq files using Cellranger v1.2.1 count with refdata-cellranger-mm10 v1.2.0 as a reference index; count matrices were manually aggregated and used as input to Monocle2 single cell RNAseq framework.
Genome_build: Smart-seq: mm10 (GRCm38)
Genome_build: 10x: mm10 (refdata-cellranger-mm10 v1.2.0)
Supplementary_files_format_and_content: SmartSeq_aggregate.mtx: Expression Data of aggregate Smart-Seq cells.
Supplementary_files_format_and_content: SmartSeq_genes.tsv: Gene features of aggregate Smart-Seq cells.
Supplementary_files_format_and_content: SmartSeq_cells.tsv: Cell Features of aggregate Smart-Seq cells.
Supplementary_files_format_and_content: 10x_aggregate.mtx: Expression Data of aggregate 10x Samples.
Supplementary_files_format_and_content: genes.tsv: Gene features of aggregate 10x Samples.
Supplementary_files_format_and_content: barcodes.tsv: Cell Features of aggregate 10x Samples.

source_name: Retinal Cells

extract_protocol: Adapted Smart-seq2 protocol or 10x Genomics Chromium single cell system with v2 Chemistry.

treatment_protocol: None - wildtype animals.

value: Retinal cell

tag: age

tag: strain/background

value: Wildtype


title: Deox-1


title: H48D240_rep2

status: Public on Apr 05 2019

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2
HtSeqCount was used for counting genes with default parameters
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied with the 48h BHISG value as a reference for reporting the expression data of 48h BHISG with Deoxycholate 240µM.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts and Normalized Counts (48H BHISG with and withoutDeoxycholate 240µM), Normalized Counts, Statistics (FC, pvalue, Significant)

source_name: Wild type strain 630_H48D240

growth_protocol: Strains were grown aerobically in BHISG at 37°C for 48 H

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols; Truseq stranded RNA seq kit

tag: growth condition

value: aerobically in BHISG at 37°C for 48hrs with 240 µM Deoxycholate


title: H48D240_rep3


title: H48BHISG_rep1

source_name: Wild type strain 630_H48BHISG

value: aerobically in BHISG at 37°C for 48hrs


title: H48BHISG_rep3


title: E14_rep2

description:
10x_E14_rep2
10x Genomics single cell RNAseq
E14 mouse single retinal cells from 10x Genomics Chromium Single Cell
PolyA RNA
processed data file: 10x_aggregate.mtx
processed data file: genes.tsv
processed data file: barcodes.tsv


title: HP_2

status: Public on Jan 08 2019

first: Wanpen

last: Vongpatanasin

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015).
Aligned reads were quantified using featurecount (v1.4.6) (Liao et al., 2014) per gene ID against Gencode version 10 (Mudge and Harrow, 2015).
Differential gene expression analysis was done using the R package DEseq2 (v 1.6.3).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and FPKM values for all samples.

extract_protocol:
Total RNA was extracted from gastrocnemius muscle 12wks after treatment, using TRIzol (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All experiments were performed using 20-24 week-old C57BL6 male mice obtained from UT Southwestern breeding core. Mice in the high Pi (HP) group were fed with diet containing 2.0% inorganic Pi (2.3% total Pi), TD08020, Envigo Teklad Diets, Madison, WI) for 12 weeks. Mice in the control group (NP) were fed with diet containing 0.6% inorganic Pi (0.9% total Pi, TD160114) for 12 weeks. Other mineral contents of the 2 diets are the same (0.3% magnesium, 1.9% calcium, 1.8% potassium, and 0.9% sodium).

value: gastrocnemius

tag: background strain

tag: diet

value: high phosphate

tag: diet time

value: 12 weeks


title: NP_3

value: normal phosphate


title: E14_rep1

description:
10x_E14_rep1
10x Genomics single cell RNAseq
E14 mouse single retinal cells from 10x Genomics Chromium Single Cell
PolyA RNA
processed data file: 10x_aggregate.mtx
processed data file: genes.tsv
processed data file: barcodes.tsv

tag: cell type

tag: genotype/variation


title: HP_1


title: NP_2


title: HP_3


title: H48BHISG_rep2


title: H48D240_rep1


title: Deox-0

tag: genotype


title: NP_1


title: Tumor_OV170

status: Public on Oct 04 2018

type: genomic

city: Gothenburg

first: Hanna

last: Engqvist

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

description: Genomic DNA was extracted from primary ovarian carcinomas was genotyped using Infinum Omni 2.5-8 v1.3 Genotyping BeadChips (Illumina)

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: GenomeStudio software version 2011.1.

label: cy3 and cy5

source_name: Primary invasive ovarian carcinomas

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated from fresh frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification.

value: Primary invasive ovarian carcinoma

tag: figo stage

value: I


title: Tumor_OV346


title: Tumor_OV364


title: Tumor_OV387


title: Tumor_OV336

value: II


title: SinR4-cy5_WT4-cy3

status: Public on Dec 25 2018

description: Biological replicate 4 of 4.

source_name: sinR mutant grown 7h TY

growth_protocol: C.difficile strain C630E WT and sinR mutant were grown in TY

value: C630E Mullany sinR::erm

source_name: WT grown 7h TY

value: C630E Mullany


title: Tumor_OV389

description: Paired-end strand-specific RNA libraries

data_processing:
Quality control of FASTQ files using FastQC
Removal of adapter sequences using TrimGalore wrapper script
FASTQ files were mapped to the human reference genome hg19 using the STAR aligner and the resulting BAM-file was name-sorted
Raw read counts were calculated using htseq-count in htseq
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file "OV106-391_counts.txt" is given in text format

extract_protocol:
Total RNA was extracted from the tumor samples using the RNeasy Lipid Tissue Mini Kit (Qiagen), followed by RNA concentration and integrity assessment using Nanodrop ND1000 (Nanodrop Technologies) in combination with QuBit (ThermoFisher Scientific) and the RNA 6000 Nano LabChip Kit with Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. Samples with an RNA integrity number (RIN) of 6 or higher were used for sequencing.
Illumina TruSeq strand-specific RNA libraries (Ribosomal depletion using RiboZero human) containing 125 bp pair-end reads were obtained for each sample on a HiSeq2000 sequencer (Illumina). Paired-end sequencing was used.

value: early-stage primary invasive ovarian carcinoma

tag: histotype

value: EC


title: Tumor_OV391

tag: tissue

value: HGSC


title: SinR2-cy3_WT2-cy5

description: Biological replicate 2 of 4.

extract_protocol: Total RNA was extracted using QIAgen RNAeasy kit.


title: Biofilm4-cy3_Planktonic4-cy5

description: Biological replicate 4 of 4.

source_name: Biofilm in Bioreactor

growth_protocol: C.difficile strain C630E Biofilm in Bioreactor and in Planktonic growth at 24H in TY

tag: strain

source_name: Planktonic grown 24h TY


title: SinR3-cy5_WT3-cy3

description: Biological replicate 3 of 4.


title: SinR1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: Tumor_OV340


title: Muscle stem cells cultured in 10% FBS and 100 ng/mL oncostatin M for 3 days

status: Public on Dec 01 2018

hyb_protocol: Fifteen micrograms of cRNA was hybridized to Affymetrix MOE_430_2 arrays, and arrays were washed and stained using an Affymetrix FS4500 fluidics station

scan_protocol: GeneChips were scanned using The Affymetrix GC3000 scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

label: biotin

source_name: MuSCs_10% FBS and 100 ng/mL oncostatin M for 3 days

label_protocol: Twenty nanograms of total RNA was prepared for array analysis using Affymetrix 3’ IVT Express amplification reagents

growth_protocol: Mouse muscle stem cells were purified essentially as previously described (Cosgrove et al., 2014) using a FACS Aria 2, routinely yielding >95% CD34+α7 integrin+ cells from a single round of sorting.

extract_protocol: Total RNA was prepared with Qiagen RNeasy kits according to Qiagen's instructions

treatment_protocol: Muscle stem cells were cultured in 10% FBS plus or minus 100 ng/mL oncostatin M for 3 days

tag: strain background

value: wildtype

value: 8 weeks

value: muscle

value: cultured muscle stem cells (MuSC)

tag: culture condition


title: Tumor_OV380

value: MC


title: Tumor_OV384


title: Biofilm2-cy3_Planktonic2-cy5

description: Biological replicate 2 of 4.


title: Muscle stem cells cultured in 10% FBS for 3 days

source_name: MuSCs_10% FBS for 3 days

value: 10% FBS for 3 days


title: Tumor_OV385


title: Tumor_OV376


title: Biofilm1-cy5_Planktonic1-cy3

description: Biological replicate 1 of 4.


title: Tumor_OV377


title: Tumor_OV373

value: CCC


title: Tumor_OV375


title: Tumor_OV155


title: Freshly isolated muscle stem cells

source_name: Freshly isolated_MuSCs

value: Freshly isolated muscle stem cells (MuSC)

value: none (freshly isolated)


title: Tumor_OV368


title: Tumor_OV315

value: Primary invasive ovarian carcinoma


title: Tumor_OV390

value: I


title: Tumor_OV388

value: II


title: Tumor_OV387


title: Tumor_OV365


title: Tumor_OV364

value: Metastasis


title: Biofilm3-cy5_Planktonic3-cy3

description: Biological replicate 3 of 4.

value: C630E Mullany


title: Tumor_OV366

value: early-stage primary invasive ovarian carcinoma


title: Tumor_OV362


title: Tumor_OV358


title: Tumor_OV378


title: Tumor_OV383


title: Tumor_OV372

value: EC


title: Tumor_OV352


title: Tumor_OV348

value: HGSC


title: Tumor_OV326


title: Tumor_OV370


title: Tumor_OV344


title: Tumor_OV363


title: Tumor_OV360


title: Tumor_OV382


title: Tumor_OV343


title: Tumor_OV342


title: Tumor_OV353

value: LGSC


title: Tumor_OV359


title: Tumor_OV356


title: Tumor_OV357


title: Tumor_OV355


title: Tumor_OV371


title: Tumor_OV339


title: Tumor_OV349


title: Tumor_OV340


title: Tumor_OV347


title: Tumor_OV332


title: Tumor_OV338


title: Tumor_OV345


title: Tumor_OV337


title: Tumor_OV333


title: Tumor_OV331


title: Tumor_OV341


title: Tumor_OV327


title: Tumor_OV329


title: Tumor_OV326


title: Tumor_OV328


title: Tumor_OV325


title: Tumor_OV324


title: Tumor_OV336


title: Tumor_OV323


title: Tumor_OV314


title: Tumor_OV313


title: Tumor_OV318


title: Tumor_OV315


title: Tumor_OV335


title: Tumor_OV321


title: Tumor_OV317


title: Tumor_OV312


title: Tumor_OV310


title: Tumor_OV311


title: Tumor_OV309


title: Tumor_OV305


title: Tumor_OV308


title: Tumor_OV307


title: Tumor_OV306


title: Tumor_OV304


title: Tumor_OV207


title: Tumor_OV303


title: Tumor_OV206


title: Tumor_OV301


title: Tumor_OV205


title: Tumor_OV202


title: Tumor_OV204


title: Tumor_OV188


title: Tumor_OV203


title: Tumor_OV177


title: Tumor_OV172


title: Tumor_OV178


title: Tumor_OV185


title: Tumor_OV152


title: Tumor_OV155


title: Tumor_OV162


title: Tumor_OV169


title: Tumor_OV201


title: Tumor_OV135


title: GFP_positive_Endothelial_Cells

status: Public on Apr 19 2018

description: mapped reads per kilobase transcript per million mapped reads per sample

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the transcriptome file with bwa v .0.5.9 with default parameters, converted to .bam format by samtools 0.1.19
Reads aligning to each transcript were counted with samtools v.0.1.19 idxstats,
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCC.seq.fa"
Supplementary_files_format_and_content: the total number of mapped reads and the length of each transcript was used to convert the read counts for each transcript in each sample to RPKM

source_name: Mesenteric Endothelial Cells

extract_protocol:
Total RNA from sorted cells was isolated by TRIzol Reagent (Thermo Scientific) according to manufacturer’s instructions and purified by Qiagen RNeasy columns.
two nanograms of total RNA was used to make Illumina-compatible sequencing libraries with NuGen Ultra Low RNAseq librar prep kit, and the libraries were sequenced using 50 bp single reads on an Illumina HiSeq 1000

treatment_protocol: The Gpr68 eGFP reporter mice were sacrificed with CO2 and the bladders were dissected out and cut into small pieces with micro scissors in PBS. The tissues were digested with 12.5 mg/mL collagenase IV (Gibco) and 10 U/mL papain (Worthington) at 37 ºC for 1 h. The suspension was triturated with fire-polished glass pipettes and then spun down to collect the cell pellet. After washing the pellet twice with PBS, the cells were suspended in FACS buffer. The cells were stained with CD31-APC and CD45-APC-Cy7 (BD Biosciences) for 20 min at 4 ºC in the dark, and stained with PI before sorting. We sorted the cells that are CD31+ CD45- GFP+ and CD31+ CD45- GFP- into two 1.5 mL tubes each containing 1ml Trizol (Thermo Scientific)

value: FVB/N

value: Mesenteric Endothelial Cells

tag: treatment

value: untreated


title: Tumor_OV151


title: P1WT2treated_HNGJVAFXX_CTTGTA

status: Public on Apr 03 2018

city: Bentley

first: Irina

last: Kuznetsova

state: Western Australia

address: Building 304, Kent Street

country: Australia

institute: Curtin University

data_processing:
Alignmnet with HISAT2 2.0.5
Alignments were filtered to retain only properly paired, primary alignments with SAMtools 1.5
Read pairs that aligned to the mitochondria were realigned to the mitochondrial genome sequence with with HISAT2 2.0.5 (--no-spliced-alignment)
Gene-level counts were produced with featureCounts 1.5.1 (--largestOverlap -s 2)
Differential expression analysis was performed with DESeq2 1.16.1 (padj<0.05 considered significant)
GO for control samples were achived with goseq 1.28.0, R package
Statistics against mitochondrial genome positions were calculated with pysamstats 1.0.1 Python utility (pysamstats –fasta –type variation_strand)
Quantification of pseudouridylation was performed as described by Antonicka et al.2017
Genome_build: mm10

source_name: WT2 CMC treated

growth_protocol: Total RNA isolated from hearts

extract_protocol: standart TruSeq library preparation

treatment_protocol: Total heart RNA was isolated and cytoplasmic rRNA depletion was performed using a Ribo-Zero rRNA removal kit (Illumina). CMC (N-cyclohexyl-N’-(2-morpholinoethyl)carbodiimide methop-toluenesulfonate; Santa- Cruz Biotechnology) modification was performed as described by Antonicka et.al. (Antonicka et al., 2017).

value: heart

value: Wild type


title: P1WT3treated_HNGJVAFXX_AGTCAA

source_name: WT3 CMC treated


title: Tumor_OV163

value: CCC


title: Tumor_OV106

value: MC


title: P1KO3treated_HNGJVAFXX_CCGTCC

source_name: KO3 CMC treated

value: PTCD1 knockout


title: Tumor_OV131


title: GFP_negative_Endothelial_Cells


title: P1KO2treated_HNGJVAFXX_ATGTCA

source_name: KO2 CMC terated


title: P1WT2control_HNGJVAFXX_GCCAAT

source_name: WT2 control


title: Tumor_OV170


title: P1WT1control_HNGJVAFXX_ACAGTG

source_name: WT1 control


title: P1WT3control_HNGJVAFXX_GATCTG

source_name: WT3 control


title: P1KO1treated_HNGJVAFXX_AGTTCC

source_name: KO1 CMC treated


title: P1KO2control_HNGJVAFXX_CTGATC

source_name: KO2 control


title: P1KO1control_HNGJVAFXX_ACTTGA

source_name: KO1 control


title: OVCA_NKDD_supernatant

status: Public on Feb 01 2018

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the transcriptome file with bwa v .0.5.9 with default parameters, converted to .bam format by samtools 0.1.19
Reads aligning to each transcript were counted with samtools v.0.1.19 idxstats,
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "human_refgu_ERCC.txt"
Supplementary_files_format_and_content: the total number of mapped reads per sample was used to convert the read counts for each transcript in each sample to RPM
Supplementary_files_format_and_content: mapped reads per million mapped reads per sample

source_name: OVCA (Ovarian Cancer Cell Line)

growth_protocol: NK cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) and supplemented with 10 ng/ml human IL-2 (Peprotech).  Generation of NK cell conditioned tissue culture supernatants: NK cells cultured in IL-2 were incubated with 250 ng/ml PDGF-DD (R&D Systems) in 24-well plates for 16h in the presence of 1 μg/ml IgG1 (NKDD+IgG supernatant) or blocking anti-NKp44 3.43.14 mAb (NKDD+αNKp44 supernatant). After 16h, supernatants were pooled, centrifuged and filtered to remove cellular debris, and then stored at -80°C until further use.

extract_protocol:
Total RNA was isolated using Trizol followed by Qiagen RNAeasy columns.
500 ng total RNA was used to make Illumina libraries using the TruSeq Stranded Total RNA library prep kit. Libraries were sequenced on an Illumina HiSeq 1000, single-end 50 bp run, to a sequencing depth of between 28 million and 60 million mapped reads per sample.

treatment_protocol: NK cell stimulations: NK cells were stimulated with 250 ng/ml PDGF-DD or PMA + ionomycin (PMA/i) for 8h or left unstimulated in 24-well plates prior to RNA isolation. Cancer cell-line treatments: Cancer cell-lines (Meljuso, Colo38, MCF7 and OVCA) were cultured in RPMI supplemented with 10% bovine calf serum (complete medium) or with NK cell-conditioned tissue culture supernatant (NKDD+IgG or NKDD+αNKp44) diluted 1:2 in complete medium for 48h before RNA isolation.

value: tumor cell

value: sup from NK cells stimulated with 250 ng/ml PDGF-DD in RPMI + 10% BCS

tag: cell line

value: OVCA (Ovarian Cancer Cell Line)


title: OVCA_media

value: RPMI + 10% BCS


title: P1WT1treated_HNGJVAFXX_GGCTAC

source_name: WT1 CMC treated


title: OVCA_negative_supernatant

value: control sup, RPMI + 10% BCS + 250ng/ml PDGF-DD


title: Meljuso_NKDD_supernatant

source_name: Meljuso (Melanoma Cell Line)

value: Meljuso (Melanoma Cell Line)


title: MCF_NKDD_supernatant

source_name: MCF (Breast Cancer Cell Line)

value: MCF (Breast Cancer Cell Line)


title: P1KO3control_HNGJVAFXX_TAGCTT

source_name: KO3 control


title: Meljuso_media


title: MCF_negative_supernatant


title: MCF_media


title: COLO38_negative_supernatant

source_name: COLO38 (Melanoma Cell Line)

value: COLO38 (Melanoma Cell Line)


title: D5_NK_PDGF_DD

source_name: Donor 5

value: primary NK cells

value: 8h stimulation with 250ng/ml PDGF-DD (R&D Systems)


title: D5_NK_PMA_ionomycin

value: 8h stimulation with PMA/ionomcyin


title: D5_NK_IL_2_media


title: COLO38_media


title: D4_NK_PDGF_DD_2

source_name: Donor 4


title: D4_NK_PMA_ionomycin


title: D4_NK_PDGF_DD


title: D3_NK_PMA_ionomycin

source_name: Donor 3


title: D4_NK_PMA_ionomycin_2


title: D3_NK_IL_2_media


title: D4_NK_IL_2_media_2


title: AF1_NK_PMA_ionomycin

source_name: Donor AF3


title: D4_NK_IL_2_media


title: D3_NK_PDGF_DD


title: AF1_NK_PDGF_DD

source_name: Donor AF2


title: Meljuso_negative_supernatant


title: COLO38_NKDD_supernatant


title: AF1_NK_IL_2_media

source_name: Donor AF1


title: Tfam (L/L) rep3

status: Public on Jan 29 2018

description:
55263 wt
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv

data_processing:
HISAT2 version 2.0.4 (hisat2 -p 8 –dat) was used to perform alignment of paired-end reads to the Mus Musculus reference genome (GRCm38). The output files were sorted and indexed with SAMtools version 1.3.1
StringTie version 1.2.4  (stringtie -p 18 -e -B) was applied to estimate transcripts abundance
prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) Python version 2.7.6 was used to extract raw counts
DESeq2 R package version 3.3.2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: gene_count_matrix_tfam_strain.csv (Raw counts)
DESeq2_results_tfam_strain.csv (DESeq2 results)

source_name: heart

extract_protocol: standard TruSeq library preparation

value: Tfam (L/L)

tag: age


title: Tfam (L/L) rep1

description:
55257 wt
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Tfam (L/L) rep2

description:
55259 wt
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Tfam (L/L, cre) rep5

description:
55265 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv

value: Tfam (L/L, cre)


title: Tfam (L/L, cre) rep4

description:
55261 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Tfam (L/L, cre) rep1

description:
55251 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Tfam (L/L, cre) rep3

description:
55255 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Mterf4 (L/L) rep3

status: Public on Nov 14 2017

data_processing:
HISAT2 version 2.0.4 (hisat2 -p 8 –dat) was used to perform alignment of paired-end reads to the Mus Musculus reference genome (GRCm38). The output files were sorted and indexed with SAMtools version 1.3.1
StringTie version 1.2.4  (stringtie -p 18 -e -B) was applied to estimate transcripts abundance
prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) Python version 2.7.6 was used to extract raw counts
DESeq2 R package version 3.3.2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 results

extract_protocol:
Total RNA isolated from hearts
standard TruSeq library preparation

value: Mterf4 (L/L)


title: Mterf4 (L/L) rep4


title: Tfam (L/L, cre) rep2

description:
55253 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Mterf4 (L/L) rep5


title: Mterf4 (L/L) rep1


title: Mterf4 (L/L, cre) rep1

value: Mterf4 (L/L, cre)


title: Mterf4 (L/L, cre) rep3


title: Polrmt (L/L) rep4

value: Polrmt (L/L)


title: Polrmt (L/L) rep2


title: Polrmt (L/L) rep3


title: Polrmt (L/L, cre) rep4

value: Polrmt (L/L, cre)


title: Polrmt (L/L, cre) rep3


title: ILC1 donor 1 medium

description: immune subset

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Human 1.0 ST Array in the GeneChip Hypridization Oven 640 for 18hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Sation 450

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

data_processing: Data were processed using the AffySTExpressionFileCreator function of GenePattern from the Broad Institute using quantile normalization and background correction. Data were analzyed using Multiplot Studio from the Broad Institute.

source_name: tonsil

label_protocol: Biotyinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

growth_protocol: CD3-CD19-NKp44+CD103+ ILC1 sorted from enriched tonsilar CD56+ cells were expanded in IL-2 (10 ng/ml, Peprotech) for 10 days prior to PDGF-DD stimulation.

extract_protocol: Qiagen RNAeasy Plus Micro kit was used to extract RNA from freshly sorted human myeloid cell subsets.

treatment_protocol: Tonsil ICL1 were stimulated with or without 250 ng/ml PDGF-DD (R&D systems) for 16h prior to RNA isolation

tag: agent


title: ILC1 donor 2 + PDGF-DD

description: immune subset

value: 50 ng/ml PDGF-DD


title: Polrmt (L/L, cre) rep2


title: Mterf4 (L/L, cre) rep2


title: Mterf4 (L/L) rep2


title: ILC1 donor 1 + PDGF-DD

description: immune subset


title: Polrmt (L/L, cre) rep1


title: Twinkle (L/L) rep2

value: Twinkle (L/L)


title: Twinkle (L/L) rep5


title: Twinkle (L/L) rep3


title: Twinkle (L/L, cre) rep3

value: Twinkle (L/L, cre)


title: Twinkle (L/L) rep1


title: Twinkle (L/L) rep4


title: Polrmt (L/L) rep1


title: Twinkle (L/L, cre) rep2


title: Lrpprc (L/L) rep1

value: Lrpprc (L/L)


title: Lrpprc (L/L) rep2


title: Twinkle (L/L, cre) rep1


title: Lrpprc (L/L, cre) rep4

value: Lrpprc (L/L, cre)


title: Lrpprc (L/L, cre) rep1


title: Phage-P4_13_rep3

status: Public on Jul 07 2017

description:
Phage RNA recovered after 13min post infection
processed data file: Phage-infect-P4_T3.5-T13_statistics.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced were mapped to Pseudomonas aeruginosa PAK whole genome sequence or Phage P4 sequence complemented by the manually annotated ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 13M value as a reference for reporting the expression data of 0M.
Genome_build: Pseudomonas aeruginosa PAK (KK037225.1), Pseudomonas phage PAK_P4 (NC_022986)
Supplementary_files_format_and_content: Genome annotation (Gene ID), Raw Counts (0M, 13M), Normalized Counts (0M, 13M), Statistics (FC, pvalue, significant)

organism: Pseudomonas phage PAK_P4

source_name: Pseudomonas phage PAK P4

growth_protocol: Pseudomonas cells were grown in LB supplemented with 10mM MgCl2 at 37°C until OD600nm   ̴ 0,3

extract_protocol:
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (Ribo-Zero rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols using the Truseq stranded RNA seq kit.

treatment_protocol: Synchronous infection with bacteriophage PAK_P4 for 0min, 3,5min or 13min (MOI = 50) and halted by rapid cooling in diluted phenol

tag: subsp.

value: phage PAK

tag: time point

value: 13 min post infection


title: Lrpprc (L/L) rep4


title: Lrpprc (L/L) rep3


title: Phage-P4_3.5_rep2

description:
Phage RNA recovered after 3.5min post infection
processed data file: Phage-infect-P4_T3.5-T13_statistics.xls

value: 3.5 min post infection


title: Lrpprc (L/L, cre)rep2


title: Phage-P4_3.5_rep1


title: Host-P4_13_rep2

description:
Host RNA recovered after 13min post infection
processed data file: Host-infect-P4_T0-T13_statistics.xls

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAK

value: Host PAK

value: PAK


title: Phage-P4_13_rep2


title: Phage-P4_3.5_rep3


title: Host-P4_13_rep3


title: Phage-P4_13_rep1


title: Host-P4_13_rep1


title: Host-P4_0_rep2

description:
Host RNA recovered after 0min post infection
processed data file: Host-infect-P4_T0-T13_statistics.xls

value: 0 min post infection


title: Host-P4_0_rep3


title: d_3_2

status: Public on May 19 2017

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the transcriptome file with bwa v .0.5.9 with default parameters, converted to .bam format by samtools 0.1.19
Reads aligning to each transcript were counted with samtools v.0.1.19 idxstats,
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCCRefseq.fa"
Supplementary_files_format_and_content: the total number of mapped reads and the length of each transcript was used to convert the read counts for each transcript in each sample to RPKM

source_name: Cardiotoxin injury, TA muscle

extract_protocol:
Total RNA from each muscle sample was isolated by TRIzol Reagent (Thermo Scientific 15596026) according to manufacturer’s instructions and purified by Qiagen RNeasy columns.
one microgram of total RNA was used to make Illumina-compatible sequencing libraries, and the libraries were sequenced using 50 bp single reads on an Illumina HiSeq 1000

treatment_protocol: For cardiotoxin (CTX) injection, CTX from Naja mossambica mossambica (Sigma C9759) was dissolved in normal saline (0.9% w/v of NaCl) to make a 10 μM working solution, and was aliquoted and stored at -20°C. After anesthesia of the mouse with isoflurane (1.5%-2% in oxygen), the anterior aspect of the adult mouse hindlimb (8- to 10-week-old C57BL/6) was sterilized with 70% ethanol, shaved to expose the skin, and approximately 50 μL of CTX solution was injected into the midbelly of the tibialis anterior (TA) muscle using a 0.3ml U100 BD insulin syringe.

value: 10 uM Naja mossambica mossambica (Sigma C9759) cardiotoxin

tag: Sex

value: female

value: tibialis anterior (TA) muscle


title: Lrpprc (L/L, cre) rep3


title: d_3_3


title: d_3_1


title: Uninjured_3

source_name: Uninjured, TA muscle

value: untreated


title: Uninjured_2


title: SigB1-cy3_WT1-cy5

description: Biological replicate 1 of 4.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

source_name: sigB mutant grown 10h TY

growth_protocol: C.difficile strain C630E WT and sigB mutant were grown in TY

value: C630E Mullany

source_name: WT grown 10h TY

value: WT


title: SigB4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: WT2

status: Public on Mar 07 2017

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile R20291 whole genome sequence using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the WT as a reference
Genome_build: Peptoclostridium difficile R20291 (FN545816.1)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts (∆tcdR, WT), Normalized Counts (∆tcdR, WT), Statistics (FC, pvalue, significant)

source_name: Wild type strain R20291

growth_protocol: Strains were grown aerobically in TY 18h at 37°C

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

value: strain

value: wild type


title: Host-P4_0_rep1


title: SigB2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: tcdR2

source_name: Mutant tcdR of strain R20291

value: Mutant tcdR


title: tcdR1


title: Tumor_OV346

source_name: Primary invasive ovarian carcinomas

value: early-stage primary invasive ovarian carcinoma

value: I

value: HGSC


title: WT1


title: Uninjured_1


title: 630E-14H_rep1

status: Public on Sep 28 2016

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 6 h value as a reference for reporting the expression data of 14 and 24 h.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts (630, 630Derm, 630E, 6H, 14H, 24H), Normalized Counts (630, 630Derm, 630E, 6H, 14H, 24H), Statistics (FC, pvalue, significant)

source_name: Erythromycin-sensitive strain 630E

growth_protocol: Strains were grown aerobically in TY at 37°C for 6, 14 and 24 H)

tag: strain provider

value: Rood laboratory

tag: phenotype

value: Erythromycin-sensitive


title: 630E-24H_rep2


title: 630E-24H_rep1


title: 630E-6H_rep2


title: 630E-14H_rep2


title: ILC1 donor 2 medium

description: immune subset

tag: cell type


title: cardiac_tissue_Lina3

status: Public on Apr 27 2017

description: gene expression of cardiac tissue from a high fat diet fed with DPP-4 inhibitor administration mice

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 10×Blocking buffer and 25×Fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus sp.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Microarray Tissue Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were fed a high-fat diet or a normal chow for totally 8 weeks from 4 weeks age, and analyzed at 12 weeks of age. A DPP-4 inhibitor was administered within water at the concentration of 10 mg/kg/day for 8 weeks since 4 weeks of age.

value: cardiac tissue

tag: gender

value: male

tag: diet

value: high fat diet

value: DPP-4 inhibitor


title: 630E-6H_rep1


title: cardiac_tissue_HF2

description: gene expression of cardiac tissue from a high fat diet fed mice


title: cardiac_tissue_NC1

description: gene expression of cardiac tissue from a normal chow fed mice

value: normal chow


title: cardiac_tissue_HF3


title: 630∆erm-24H_rep1

source_name: Erythromycin-sensitive strain 630∆erm

value: Mullany laboratory


title: 630∆erm-14H_rep2


title: cardiac_tissue_HF1


title: SigB3-cy3_WT3-cy5

description: Biological replicate 3 of 4.

tag: genotype/variation


title: 630∆erm-14H_rep1


title: 630∆erm-6H_rep2


title: cardiac_tissue_NC2

tag: tissue


title: 630-24H_rep2

source_name: Wild type strain 630

tag: strain

value: wild-type strain 630

value: Erythromycin-resistant


title: 630-14H_rep1


title: 630∆erm-6H_rep1


title: cardiac_tissue_Lina4


title: Phage-P3_13_rep3

status: Public on Jul 20 2016

description:
Phage RNA recovered after 13min post infection
Phage-infect-P3_T3.5-T13_statistics.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced were mapped to Pseudomonas aeruginosa PAK whole genome sequence or Phage P3 sequence complemented by the manually annotated ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 13M value as a reference for reporting the expression data of 0M.
Genome_build: Pseudomonas aeruginosa PAK (KK037225.1)
Supplementary_files_format_and_content: Genome annotation (Gene ID), Raw Counts (0M, 13M), Normalized Counts (0M, 13M), Statistics (FC, pvalue, significant)

organism: Pseudomonas phage PAK_P3

source_name: Pseudomonas phage PAK P3

extract_protocol:
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (Ribo-Zero rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

treatment_protocol: Synchronous infection with bacteriophage PAK_P3 for 0min, 3,5min or 13min (MOI = 50) and halted by rapid cooling in diluted phenol

value: phage PAK

value: 13 min post infection


title: Phage-P3_13_rep2


title: cardiac_tissue_NC5


title: 630-24H_rep1


title: 630∆erm-24H_rep2


title: 630-14H_rep2


title: 630-6H_rep1


title: 630-6H_rep2


title: Phage-P3_3.5_rep2

description:
Phage RNA recovered after 3.5min post infection
Phage-infect-P3_T3.5-T13_statistics.xls

value: 3.5 min post infection


title: Phage-P3_3.5_rep1

description:
Phage RNA recovered after 3.5 min post infection
Phage-infect-P3_T3.5-T13_statistics.xls


title: Phage-P3_3.5_rep3


title: Host-P3_13_rep2

description:
Host RNA recovered after 13min post infection
Host-infect-P3_T0-T13_statistics.xls

value: Host PAK

value: PAK


title: Host-P3_13_rep1


title: Host-P3_0_rep2

description:
Host RNA recovered after 0min post infection
Host-infect-P3_T0-T13_statistics.xls

value: 0 min post infection


title: Phage-P3_13_rep1


title: Host-P3_0_rep1


title: Host-P3_0_rep3


title: Host-P3_13_rep3


title: 38h-01_Vivo

status: Public on Jan 31 2016

description:
Biological replicate 1 of 4.
raw data file: E_38H-01_CY3-300_CY5-470.gpr

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner

data_processing: Background correction: backgroundCorrect 'normexp', Normalization: normalizeWithinArrays 'loess', Correlation of spot duplicat: duplicateCorrelation, Adjust to linear method: lmFit, Statistical analysis: eBayes, decideTests 'global' 'BY'[statistical results provided as Series Supplementary file].

source_name: R20291 extracted after 38h in vivo growth

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark. DNA samples were labelled using the Bioprime plus array CGH indirect genomic labeling system (invitrogen)

growth_protocol: We did a 9 hours preculture of Clostridium difficile R20291 in Tryptone yeast extract (TY), we centrifuged and resuspended in PBS. Then we gave 5ml of this preparation to 6 mouses  per time point (C. difficile monoxenic mouse model). Finally mouse were sacrificed, according European rules, at different time 4, 6, 8, 14 and 38 hours after infection to collect the luminal and mucosa associated bacteria in the caeca.

extract_protocol: Total RNA extracted using RNAPro Blue (FastPrep) and following Qbiogen manufacturer's instructions

tag: strain background

value: wild type

source_name: R20291 grown 14H in PY (reference)


title: GNF4877_95

status: Public on Oct 22 2015

description: 48 hr stimulation

data_processing:
Illumina CASAVA pipeline v.1.8.2 was used for basecalling
Single end sequence reads were mapped to file of Refseq transcripts (NCBI RefSeq snapshot April/2/2013) with bwa v0.5.9 using default parameters
Samtools 0.1.19 was used to make .bam files, sort them, and count reads aligning to each transcript.  RPM was calculated using those counts and the number of mapped reads for each sample.
Genome_build: NCBI RefSeq snapshot April/2/2013
Supplementary_files_format_and_content: text file includes RPM values for each Sample

organism: Rattus norvegicus

source_name: islet cell

growth_protocol: Whole islets from Sprague Dawley rats were isolated followed by immediate hand picking to ensure removal of contaminating cell populations

extract_protocol:
Following quantification, dispersed islets were loaded into Fluidigm C1 IFC microfluidic chips according to manufacturer specifications (Fluidigm). Briefly, 60 µL of a 200 cell/µL mixture was combined with 40 µL of C1 suspension reagent. 5 µL was loaded into the 10-17 µm Fluidigm IFC using the mRNA Seq: Cell Load (1771x/1772x/1773x) protocol. After loading, the IFC was manually inspected to ensure single cell capture by phase contrast microscopy. Following inspection, cells were lysed according to Fluidigm's C1 protocol.
Reverse transcription, and PCR amplification were all performed on the IFC using the SMARTer Ultra Low RNA kit (Clontech) with the mRNA Seq: RT & Amp (1771x/1772x/1773x) protocol. cDNA was quantified by Pico Green assay (Life Technologies) and then normalized with C1 DNA dilution buffer to 0.1-0.3ng/µL.  Sequencing libraries were prepared with the Nextera XT DNA Sample Preparation Index Kit, (Illumina, PN FC-131-1002).  Sequencing libraries were run on an Illumina HiSeq 1000 sequencer using single 50 bp reads, one 96-well plate per lane.

treatment_protocol: After isolation, whole islets were cultured in RPMI1640 (Gibco) containing 10% FBS and 5.5mM glucose with either 0.1% DMSO or 3 µM GNF4877. After 48 hrs of culture, islets were trypsinized with 0.05% trypsin for 5 minutes at 37C into a single cell suspension and neutralized with media. Following dispersal, cells were passed through a 40 µm filter and quantified by ViCell (Beckman Coulter).

value: Sprague Dawley

value: pancreas

value: islet cell

value: 8 week male

tag: genotype


title: GNF4877_96

description: 48 hr stimulation


title: 4H-04_Vivo

description:
Biological replicate 2 of 4.
raw data file: B_4h-04_cy3-420_cy5-390.gpr

source_name: R20291 extracted after 4h in vivo growth


title: GNF4877_92

description: 48 hr stimulation


title: GNF4877_93

description: 48 hr stimulation


title: 8H-02_Vivo

description:
Biological replicate 2 of 4.
raw data file: B_8H-02_CY3-300_CY5-470.gpr

source_name: R20291 extracted after 8h in vivo growth


title: GNF4877_86

description: 48 hr stimulation


title: 8H-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: D_8h-06_cy3-430_cy5-370.gpr


title: GNF4877_9

description: 48 hr stimulation


title: 38h-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: G_38H-05_CY3-430_CY5-370.gpr


title: 8H-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: C_8h-05_cy3-420_cy5-370.gpr


title: 38h-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: H_38H-06_CY3-420_CY5-370.gpr


title: GNF4877_94

description: 48 hr stimulation


title: GNF4877_85

description: 48 hr stimulation


title: GNF4877_84

description: 48 hr stimulation


title: GNF4877_90

description: 48 hr stimulation


title: GNF4877_87

description: 48 hr stimulation


title: GNF4877_81

description: 48 hr stimulation


title: 6h-02_Vivo

description:
Biological replicate 1 of 4.
raw data file: E_6h-02_cy3-440_cy5-390.gpr

source_name: R20291 extracted after 6h in vivo growth


title: 6h-04_Vivo

description:
Biological replicate 2 of 4.
raw data file: F_6h-04_cy3-450_cy5-380.gpr


title: GNF4877_8

description: 48 hr stimulation


title: 6h-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: G_6h-05_cy3-310_cy5-470.gpr


title: GNF4877_80

description: 48 hr stimulation


title: 6h-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: H_6h-06_cy3-310_cy5-470.gpr


title: 4H-05_Vivo

description:
Biological replicate 3 of 4.
raw data file: C_4h-05_cy3-310_cy5-470.gpr


title: 38h-02_Vivo

description:
Biological replicate 2 of 4.
raw data file: F_38H-02_CY3-300_CY5-470.gpr


title: 8H-01_Vivo

description:
Biological replicate 1 of 4.
raw data file: A_8h-01_cy3-300_cy5-470.gpr


title: 4H-06_Vivo

description:
Biological replicate 4 of 4.
raw data file: D_4h-06_cy3-300_cy5-470.gpr


title: 4H-02_Vivo

description:
Biological replicate 1 of 4.
raw data file: A_4h-02_cy3-420_cy5-390.gpr


title: GNF4877_79

description: 48 hr stimulation


title: GNF4877_72

description: 48 hr stimulation


title: GNF4877_73

description: 48 hr stimulation


title: GNF4877_71

description: 48 hr stimulation


title: GNF4877_74

description: 48 hr stimulation


title: GNF4877_63

description: 48 hr stimulation


title: GNF4877_78

description: 48 hr stimulation


title: GNF4877_7

description: 48 hr stimulation


title: GNF4877_62

description: 48 hr stimulation


title: GNF4877_6

description: 48 hr stimulation


title: GNF4877_69

description: 48 hr stimulation


title: GNF4877_65

description: 48 hr stimulation


title: GNF4877_58

description: 48 hr stimulation


title: GNF4877_55

description: 48 hr stimulation


title: GNF4877_56

description: 48 hr stimulation


title: GNF4877_59

description: 48 hr stimulation


title: GNF4877_51

description: 48 hr stimulation


title: GNF4877_53

description: 48 hr stimulation


title: GNF4877_60

description: 48 hr stimulation


title: GNF4877_64

description: 48 hr stimulation


title: GNF4877_54

description: 48 hr stimulation


title: GNF4877_61

description: 48 hr stimulation


title: GNF4877_77

description: 48 hr stimulation


title: GNF4877_57

description: 48 hr stimulation


title: GNF4877_68

description: 48 hr stimulation


title: GNF4877_50

description: 48 hr stimulation


title: GNF4877_66

description: 48 hr stimulation


title: GNF4877_5

description: 48 hr stimulation


title: GNF4877_52

description: 48 hr stimulation


title: GNF4877_47

description: 48 hr stimulation


title: GNF4877_48

description: 48 hr stimulation


title: GNF4877_42

description: 48 hr stimulation


title: GNF4877_46

description: 48 hr stimulation


title: GNF4877_43

description: 48 hr stimulation


title: GNF4877_41

description: 48 hr stimulation


title: GNF4877_38

description: 48 hr stimulation


title: GNF4877_40

description: 48 hr stimulation


title: GNF4877_35

description: 48 hr stimulation


title: GNF4877_33

description: 48 hr stimulation


title: GNF4877_32

description: 48 hr stimulation


title: GNF4877_44

description: 48 hr stimulation


title: GNF4877_30

description: 48 hr stimulation


title: GNF4877_31

description: 48 hr stimulation


title: GNF4877_49

description: 48 hr stimulation


title: GNF4877_29

description: 48 hr stimulation


title: GNF4877_36

description: 48 hr stimulation


title: GNF4877_25

description: 48 hr stimulation


title: GNF4877_24

description: 48 hr stimulation


title: GNF4877_34

description: 48 hr stimulation


title: GNF4877_39

description: 48 hr stimulation


title: GNF4877_22

description: 48 hr stimulation


title: GNF4877_23

description: 48 hr stimulation


title: GNF4877_27

description: 48 hr stimulation


title: GNF4877_21

description: 48 hr stimulation


title: GNF4877_45

description: 48 hr stimulation


title: GNF4877_26

description: 48 hr stimulation


title: GNF4877_37

description: 48 hr stimulation


title: GNF4877_2

description: 48 hr stimulation


title: GNF4877_14

description: 48 hr stimulation


title: GNF4877_17

description: 48 hr stimulation


title: GNF4877_19

description: 48 hr stimulation


title: GNF4877_12

description: 48 hr stimulation


title: GNF4877_20

description: 48 hr stimulation


title: GNF4877_16

description: 48 hr stimulation


title: GNF4877_18

description: 48 hr stimulation


title: DMSO_92

description: 48 hr stimulation


title: DMSO_94

description: 48 hr stimulation


title: GNF4877_11

description: 48 hr stimulation


title: DMSO_9

description: 48 hr stimulation


title: GNF4877_13

description: 48 hr stimulation


title: GNF4877_15

description: 48 hr stimulation


title: DMSO_96

description: 48 hr stimulation


title: DMSO_88

description: 48 hr stimulation


title: GNF4877_10

description: 48 hr stimulation


title: DMSO_83

description: 48 hr stimulation


title: cardiac_tissue_Lina5

description: gene expression of cardiac tissue from a high fat diet fed with DPP-4 inhibitor administration mice

value: cardiac tissue

value: male

value: high fat diet


title: GNF4877_1

description: 48 hr stimulation


title: DMSO_91

description: 48 hr stimulation


title: DMSO_95

description: 48 hr stimulation


title: DMSO_85

description: 48 hr stimulation


title: DMSO_89

description: 48 hr stimulation


title: DMSO_81

description: 48 hr stimulation


title: DMSO_90

description: 48 hr stimulation


title: DMSO_78

description: 48 hr stimulation


title: DMSO_86

description: 48 hr stimulation


title: DMSO_87

description: 48 hr stimulation


title: DMSO_77

description: 48 hr stimulation


title: DMSO_76

description: 48 hr stimulation


title: DMSO_84

description: 48 hr stimulation


title: DMSO_74

description: 48 hr stimulation


title: DMSO_75

description: 48 hr stimulation


title: DMSO_72

description: 48 hr stimulation


title: DMSO_80

description: 48 hr stimulation


title: DMSO_82

description: 48 hr stimulation


title: DMSO_73

description: 48 hr stimulation


title: DMSO_71

description: 48 hr stimulation


title: DMSO_79

description: 48 hr stimulation


title: DMSO_7

description: 48 hr stimulation


title: DMSO_8

description: 48 hr stimulation


title: DMSO_69

description: 48 hr stimulation


title: DMSO_68

description: 48 hr stimulation


title: DMSO_67

description: 48 hr stimulation


title: DMSO_65

description: 48 hr stimulation


title: DMSO_66

description: 48 hr stimulation


title: DMSO_64

description: 48 hr stimulation


title: DMSO_63

description: 48 hr stimulation


title: DMSO_6

description: 48 hr stimulation


title: DMSO_62

description: 48 hr stimulation


title: DMSO_61

description: 48 hr stimulation


title: DMSO_60

description: 48 hr stimulation


title: DMSO_55

description: 48 hr stimulation


title: DMSO_58

description: 48 hr stimulation


title: DMSO_54

description: 48 hr stimulation


title: DMSO_52

description: 48 hr stimulation


title: DMSO_5

description: 48 hr stimulation


title: DMSO_51

description: 48 hr stimulation


title: DMSO_43

description: 48 hr stimulation


title: DMSO_46

description: 48 hr stimulation


title: DMSO_42

description: 48 hr stimulation


title: DMSO_48

description: 48 hr stimulation


title: DMSO_57

description: 48 hr stimulation


title: DMSO_45

description: 48 hr stimulation


title: DMSO_41

description: 48 hr stimulation


title: DMSO_38

description: 48 hr stimulation


title: DMSO_37

description: 48 hr stimulation


title: DMSO_59

description: 48 hr stimulation


title: DMSO_39

description: 48 hr stimulation


title: DMSO_49

description: 48 hr stimulation


title: DMSO_36

description: 48 hr stimulation


title: DMSO_4

description: 48 hr stimulation


title: DMSO_35

description: 48 hr stimulation


title: DMSO_30

description: 48 hr stimulation


title: DMSO_34

description: 48 hr stimulation


title: DMSO_29

description: 48 hr stimulation


title: DMSO_33

description: 48 hr stimulation


title: DMSO_47

description: 48 hr stimulation


title: DMSO_32

description: 48 hr stimulation


title: DMSO_3

description: 48 hr stimulation


title: DMSO_31

description: 48 hr stimulation


title: DMSO_21

description: 48 hr stimulation


title: DMSO_20

description: 48 hr stimulation


title: DMSO_19

description: 48 hr stimulation


title: DMSO_28

description: 48 hr stimulation


title: DMSO_16

description: 48 hr stimulation


title: DMSO_27

description: 48 hr stimulation


title: DMSO_26

description: 48 hr stimulation


title: DMSO_24

description: 48 hr stimulation


title: DMSO_23

description: 48 hr stimulation


title: DMSO_11

description: 48 hr stimulation


title: DMSO_22

description: 48 hr stimulation


title: DMSO_2

description: 48 hr stimulation


title: DMSO_10

description: 48 hr stimulation


title: DMSO_17

description: 48 hr stimulation


title: DMSO_15

description: 48 hr stimulation


title: DMSO_14

description: 48 hr stimulation


title: DMSO_12

description: 48 hr stimulation


title: DMSO_1

description: 48 hr stimulation


title: CD630_prdR1-Cy3_WT1-Cy5

status: Public on Oct 01 2015

description: Biological replicate 1 of 2.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

source_name: strain C630E grown 3.5h in TY with proline (reference)

growth_protocol: C. difficile strain C630E and the prdR mutant were grown in TY supplemented with 30 mM L-proline to an OD600 of 0.5-0.7.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy kit.

value: wild-type

tag: growth condition

value: Ty medium with proline

source_name: prdR mutant grown 4.25h in TY with proline

tag: background

value: prdR mutation


title: CD630_TY1-Cy3_TYP1-Cy5

description: Biological replicate 1 of 2.

source_name: strain C630E grown 4.2h in TY (reference)

growth_protocol: C. difficile strain C630E was grown in TY medium and TY medium with 30 mM of proline.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy extraction kit.

value: Ty medium

source_name: strain C630E grown 3.5h in TY with proline


title: CD630_TY2-Cy5_TYP2-Cy3

description: Biological replicate 2 of 2.


title: female,C3H/HeJ,strain, dorsal root ganglion tissue

status: Public on Feb 18 2015

description: Gene expression data from wildtype mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse MOE_430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: CEL files were processed using GCRMA in R (version 2.6.2 (2008-02-08)), using packages downloaded from Bioconductor

label_protocol: cDNA and amplified antisense RNA was made from 1.4 mg of pooled total RNA, using the Affymetrix Single Amplification protocol.

growth_protocol: DRGs were dissected from naïve 2-month-old mice of both sexes (n=3 mice/sex/strain) between 09:00–12:00 h

extract_protocol: Total RNA was isolated from tissues using Trizol (Invitrogen) followed by RNeasy (Qiagen, Valencia, CA).

treatment_protocol: wildtype mice

value: dorsal root ganglion

value: wildtype

value: female

tag: age

value: 2 months


title: female,SWR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SWR/J


title: female,P/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: P/J


title: female,SM/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SM/J


title: female,NON/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NON/LtJ


title: female,C58/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: female,A/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: A/J


title: female,NOD/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NOD/LtJ


title: female,PL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: PL/J


title: female,MRL/MpJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: MRL/MpJ


title: female,NZO/HILtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NZO/HILtJ


title: female,C57BR/cdJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: female,FVB/NJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: FVB/NJ


title: female,RIIIS/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: RIIIS/J


title: female,BUB/BnJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BUB/BnJ


title: female,KK/HIJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: KK/HIJ


title: female,SJL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: SJL/J


title: CD630_WT2-Cy3_prdR2-Cy5

description: Biological replicate 2 of 2.

value: wild-type

value: Ty medium with proline

value: prdR mutation