title: Liver_Ifnar-/-_Control [MS0779]

status: Public on May 08 2019

city: London

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Raw paired-end RNA-seq data was subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long, and leading and trailing bases below quality 25. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness, including unpaired reads, resulting from Trimmomatic, using option -U. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalised using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalised log2 gene expression values. Further quality control was performed using principal component analysis, boxplots, histograms and density plots.
Raw_counts_Toxoplasma_WT_IFNR_KO_4tissues.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
DESeq_normalised_counts_Toxoplasma_WT_IFNR_KO_4tissues.xlsx: Normalised counts generated using the DESeq method to remove the library-specific artefacts
DESeq_VSTlog2_normalised_values_Toxoplasma_WT_IFNR_KO_4tissues.xlsx: Log2 expression values generated from normalised counts using variance stabilizing transformation in DESeq2
Genome_build: Mus musculus genome Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: Excel files containing raw counts, DESeq2 normalized counts, and DESeq2 log2 expression values

organism: Mus musculus

extract_protocol:
Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion). Tissues were collected in TRI-Reagent (Sigma-Aldrich). Total RNA was extracted using the RiboPure™ Kit (Ambion).
Total/globin-reduced RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Quality and integrity of the tagged libraries were initially assessed with the HT DNA HiSens Reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer). Tagged libraries were then sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent). Libraries were normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

tag: mouse model

value: Toxoplasma gondii

tag: mouse strain

tag: condition

value: Control

tag: infection protocol

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female Ifnar1-/-, Ifngr1-/- and Ifnar1-/-Ifngr1-/- mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 6 post infection, whole blood, spleen, liver and lung samples were collected from individual mice using uninfected mice as controls.

tag: mouse genotype/variation

value: Ifnar-/-

value: Whole liver


title: Liver_Ifngr-/-_Control [MS0783]

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

value: Ifngr-/-

tag: tissue


title: Liver_Ifnar-/-_Control [MS0778]


title: Liver_Ifnar-/-_Control [MS0780]


title: Liver_WT_Control [MS0773]

value: WT


title: Liver_Ifnar-/- x Ifngr-/-_Control [MS0775]

source_name: Liver_Ifnar-/- x Ifngr-/-_Control

value: Ifnar-/- x Ifngr-/-


title: Liver_Ifngr-/-_Control [MS0782]


title: Liver_Ifngr-/-_Case [MS0768]

value: Disease


title: Liver_Ifngr-/-_Control [MS0781]


title: Liver_Ifngr-/-_Case [MS0771]


title: Liver_Ifngr-/-_Case [MS0767]


title: Liver_Ifnar-/-_Case [MS0765]


title: Liver_Ifnar-/-_Case [MS0766]


title: Liver_Ifnar-/-_Case [MS0764]


title: Liver_Ifngr-/-_Case [MS0769]


title: Liver_Ifnar-/- x Ifngr-/-_Control [MS0776]


title: Liver_Ifnar-/- x Ifngr-/-_Control [MS0777]


title: Liver_Ifnar-/-_Case [MS0763]


title: Liver_Ifnar-/- x Ifngr-/-_Case [MS0761]

source_name: Liver_Ifnar-/- x Ifngr-/-_Case


title: Liver_Ifnar-/- x Ifngr-/-_Case [MS0760]


title: Liver_WT_Control [MS0774]


title: Liver_Ifnar-/-_Case [MS0762]


title: Rattus_norvegicus_D28_Liver_CCl4_treated_1

status: Public on May 09 2019

type: RNA

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

country: Japan

institute: Chemicals Evaluation and Research Institute Japan

description: Gene expression on day 28 after CCl4 treatment

hyb_protocol: 0.6 ug 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 25x Agilent fragmentation buffer and 10x Agilent blocking agent 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 SurePrint G3 Rat GE 8x60K Microarray Toxplus ver.2 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 61 x 21.6 mm, Scan resolution 3 um, 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: 045522_D_F_20130222) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: five-week-old male F344/NSlc rats were purchased from Japan SLC, Inc. (Hamamatsu, Japan) and acclimatized to a basal diet (CRF-1; Oriental Yeast Co., Ltd., Tokyo, Japan) and tap water ad libitum for one week. They were housed in plastic cages with paper chip bedding in a barrier-maintained animal room on a 12 h light-dark cycle and conditioned at 23 ± 2°C with a relative humidity of 55 ± 15%.

extract_protocol: Total RNA was purified with an miRNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: Animals were fed a basal diet (untreated controls) or treated with DEN (4 mg/5 mL/kg body weight, dissolved in saline) or CCl4 (100 mg/5 mL/kg body weight, dissolved in corn oil) daily by gavage for 28  or 84 days.

tag: strain

value: F344 rat

value: Liver

tag: gender

value: male

tag: timepoint/treatment

value: day 28 after CCl4 treatment


title: Liver_Ifnar-/- x Ifngr-/-_Case [MS0759]


title: Liver_Ifnar-/- x Ifngr-/-_Case [MS0758]


title: Liver_WT_Case [MS0757]


title: Liver_Ifngr-/-_Case [MS0770]


title: Liver_WT_Control [MS0772]


title: CP06

city: Torun

first: CHANDRA

middle: SHEKHAR

last: PAREEK

state: Kuj. Pom.

address: ul. Wilenska 4

department: Centre for Modern Interdisciplinary Technologies

country: Poland

institute: Nicolaus Copernicus University

description:
young bull
fpkm calculated using cufflinks

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UMD cattle genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
fpkm calculated using cufflinks
Genome_build: UMD Bos Taurus plus y-chromosome
Supplementary_files_format_and_content: tab-delimited text files with option of excel file format, include RPKM values for each Sample ...

organism: Bos taurus

source_name: Pituitary gland tissue

extract_protocol:
Total RNA isolation from bovine pituitary gland tissues of three cattle breeds were harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Hereford

tag: age

value: Pituitary gland tissue


title: Liver_WT_Case [MS0753]


title: Spleen_Ifngr-/-_Control [MS0814]

value: Whole spleen


title: Liver_WT_Case [MS0755]


title: Liver_WT_Case [MS0754]


title: Spleen_Ifnar-/-_Control [MS0811]


title: Spleen_WT_Control [MS0804]


title: Spleen_Ifnar-/- x Ifngr-/-_Control [MS0807]

source_name: Spleen_Ifnar-/- x Ifngr-/-_Control


title: Spleen_Ifngr-/-_Case [MS0799]


title: Spleen_Ifngr-/-_Control [MS0812]


title: Spleen_Ifngr-/-_Case [MS0800]


title: Spleen_Ifnar-/-_Control [MS0809]


title: Spleen_Ifnar-/-_Control [MS0810]


title: Spleen_Ifnar-/- x Ifngr-/-_Control [MS0806]


title: Spleen_Ifnar-/-_Case [MS0797]


title: Spleen_Ifnar-/-_Case [MS0795]


title: Spleen_Ifnar-/-_Case [MS0794]


title: Spleen_Ifngr-/-_Case [MS0802]


title: Spleen_Ifngr-/-_Case [MS0801]


title: Spleen_WT_Control [MS0805]


title: Spleen_Ifnar-/- x Ifngr-/-_Control [MS0808]


title: Spleen_Ifnar-/- x Ifngr-/-_Case [MS0792]

source_name: Spleen_Ifnar-/- x Ifngr-/-_Case


title: Liver_WT_Case [MS0756]


title: Spleen_Ifngr-/-_Case [MS0798]


title: Spleen_Ifnar-/-_Case [MS0793]


title: Spleen_Ifnar-/- x Ifngr-/-_Case [MS0791]


title: Spleen_Ifnar-/-_Case [MS0796]


title: Spleen_WT_Case [MS0786]


title: Spleen_Ifnar-/- x Ifngr-/-_Case [MS0790]


title: Spleen_WT_Case [MS0788]


title: Spleen_Ifnar-/- x Ifngr-/-_Case [MS0789]


title: Spleen_WT_Case [MS0787]


title: Spleen_WT_Case [MS0785]


title: Spleen_Ifngr-/-_Control [MS0813]


title: Spleen_WT_Control [MS0803]


title: Blood_Ifnar-/- x Ifngr-/-_Control [MS0746]

source_name: Blood_Ifnar-/- x Ifngr-/-_Control

value: Whole blood


title: Blood_Ifnar-/- x Ifngr-/-_Control [MS0745]

value: Toxoplasma gondii


title: Blood_WT_Control [MS0743]

value: Control


title: Blood_Ifngr-/-_Case [MS0740]

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female Ifnar1-/-, Ifngr1-/- and Ifnar1-/-Ifngr1-/- mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 6 post infection, whole blood, spleen, liver and lung samples were collected from individual mice using uninfected mice as controls.


title: Blood_Ifngr-/-_Control [MS0752]


title: Blood_Ifngr-/-_Case [MS0738]


title: Blood_Ifngr-/-_Case [MS0739]


title: Blood_WT_Control [MS0742]


title: Blood_Ifnar-/-_Case [MS0732]

value: Ifnar-/-


title: Spleen_WT_Case [MS0784]


title: Blood_Ifnar-/-_Case [MS0734]


title: Blood_Ifnar-/-_Control [MS0749]


title: Blood_Ifngr-/-_Control [MS0751]


title: Blood_Ifnar-/- x Ifngr-/-_Case [MS0730]

source_name: Blood_Ifnar-/- x Ifngr-/-_Case


title: Blood_WT_Control [MS0741]


title: Blood_Ifnar-/- x Ifngr-/-_Case [MS0727]


title: Blood_Ifnar-/- x Ifngr-/-_Control [MS0744]


title: Blood_Ifnar-/-_Case [MS0735]


title: Blood_WT_Case [MS0725]


title: Blood_Ifnar-/-_Control [MS0747]


title: Blood_WT_Case [MS0724]


title: Blood_Ifngr-/-_Case [MS0737]


title: Blood_WT_Case [MS0726]


title: Blood_Ifngr-/-_Case [MS0736]


title: Blood_Ifnar-/-_Control [MS0748]


title: Blood_Ifngr-/-_Control [MS0750]


title: Blood_WT_Case [MS0722]


title: Lung_Ifngr-/-_Control [MS0721]

value: Whole lung


title: Blood_WT_Case [MS0723]


title: Blood_Ifnar-/- x Ifngr-/-_Case [MS0728]


title: Blood_Ifnar-/-_Case [MS0731]


title: Lung_Ifnar-/-_Control [MS0717]


title: Lung_Ifngr-/-_Control [MS0720]

value: Ifngr-/-


title: Lung_Ifnar-/-_Control [MS0718]


title: Lung_Ifnar-/-_Control [MS0716]


title: Lung_WT_Control [MS0711]

value: WT


title: Lung_Ifnar-/- x Ifngr-/-_Control [MS0714]

source_name: Lung_Ifnar-/- x Ifngr-/-_Control

value: Ifnar-/- x Ifngr-/-


title: Lung_Ifnar-/- x Ifngr-/-_Control [MS0713]


title: Lung_Ifnar-/- x Ifngr-/-_Control [MS0715]


title: Lung_Ifngr-/-_Case [MS0709]

value: Disease


title: Lung_Ifngr-/-_Case [MS0708]


title: Lung_WT_Control [MS0712]


title: Lung_WT_Control [MS0710]


title: Lung_Ifnar-/-_Case [MS0704]


title: Lung_Ifngr-/-_Case [MS0705]


title: Lung_Ifnar-/-_Case [MS0703]


title: Lung_Ifngr-/-_Case [MS0707]


title: Lung_Ifnar-/- x Ifngr-/-_Case [MS0700]

source_name: Lung_Ifnar-/- x Ifngr-/-_Case


title: Lung_Ifnar-/-_Case [MS0699]


title: Lung_Ifnar-/-_Case [MS0701]


title: Lung_Ifnar-/- x Ifngr-/-_Case [MS0698]


title: Lung_Ifngr-/-_Control [MS0719]


title: Lung_Ifnar-/- x Ifngr-/-_Case [MS0697]


title: Lung_Ifnar-/- x Ifngr-/-_Case [MS0696]


title: Lung_WT_Case [MS0695]


title: Lung_WT_Case [MS0693]


title: Lung_WT_Case [MS0694]


title: Lung_Ifngr-/-_Case [MS0706]


title: Lung_Ifnar-/-_Case [MS0702]


title: Lung_WT_Case [MS0692]


title: Lung_WT_Case [MS0691]


title: Blood_HDM [Chris_G_A5_39_WB11_9B_S221_L008]

data_processing:
Raw paired-end RNA-seq data was subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long, and leading and trailing bases below quality 25. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness, including unpaired reads, resulting from Trimmomatic, using option -U. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalised using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalised log2 gene expression values. Further quality control was performed using principal component analysis, boxplots, histograms and density plots.
Raw_counts_Test_HDM_model_BAL_Blood.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
DESeq_normalised_counts_Test_HDM_model_BAL_Blood.xlsx: Normalised counts generated using the DESeq method to remove the library-specific artefacts
DESeq_VSTlog2_normalised_values_Test_HDM_model_BAL_Blood.xlsx: Log2 expression values generated from normalised counts using variance stabilizing transformation in DESeq2
Genome_build: Mus musculus genome Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: Excel files containing raw counts, DESeq2 normalized counts, and DESeq2 log2 expression values

extract_protocol:
BAL Cell pellets were obtained from pooled lavage fluid, washed once in PBS and lysed in 350 μl RLT buffer. Lysates were passed through QIAshredder columns (QIAGEN). RNA was extracted using the RNeasy mini kit as per manufacturer’s instructions, including on-column DNase I digestion (both QIAGEN). Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the MagMAX™ Blood RNA isolation Kit (Thermo Fisher). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion).
Total/globin-reduced RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Quality and integrity of the tagged libraries were initially assessed with the HT DNA HiSens Reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer). Tagged libraries were then sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent). Libraries were normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

value: House dust mite (HDM) allergy

value: For HDM allergy induction via mucosal exposure, female C57BL/6/J mice were administered 25 μg HDM (Greer) in 25 μl PBS or 25 μl PBS control intranasally under isofluorane anaesthesia 5 days per week for 3 weeks. Whole blood and bronchoalveolar lavage (BAL) samples were collected from individual HDM and PBS control treated mice 24 hours after final allergen challenge. For BAL, airways were flushed 3 times with 1 ml of chilled 5 mM EDTA (Invitrogen, Thermo Fisher) in PBS via a tracheal cannula, before resting mice with 1 ml EDTA/PBS in the lungs for 5 minutes and lavaging a further 3 times with 1 ml EDTA/PBS.


title: Blood_HDM [Chris_G_A5_27_WB11_8B_S218_L008]


title: Blood_HDM [Chris_G_A5_26_WB10_8B_S217_L008]


title: Blood_Control [Chris_G_A5_25_WB11_3B_S216_L008]


title: Blood_HDM [Chris_G_A5_38_WB11_6B_S220_L008]


title: BAL_HDM [Chris_G_A4_22_WB17_5_S214_L007]

value: Bronchoalveolar lavage


title: BAL_HDM [Chris_G_A4_10_WB17_4_S211_L007]


title: Blood_Control [Chris_G_A4_23_WB10_3B_S215_L007]


title: Blood_Control [Chris_G_A4_12_WB11_1B_S213_L007]


title: BAL_HDM [Chris_G_A3_21_WB17_2_S210_L006]


title: Blood_HDM [Chris_G_A5_37_WB10_5B_S219_L008]


title: Blood_Control [Chris_G_A4_11_WB10_1B_S212_L007]


title: BAL_HDM [Chris_G_A3_9_WB17_1_S207_L006]


title: BAL_Control [Chris_G_A3_8_WB11_15_S206_L006]


title: BAL_Control [Chris_G_A3_7_WB11_13_S205_L006]


title: BAL_Control [Chris_G_A3_19_WB11_14_S208_L006]


title: HDM_allergy_Disease_whole lung [MS0416]

data_processing:
Raw paired-end RNA-seq data was subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long, and leading and trailing bases below quality 25. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness, including unpaired reads, resulting from Trimmomatic, using option -U. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalised using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalised log2 gene expression values. Further quality control was performed using principal component analysis, boxplots, histograms and density plots.
Raw_counts_Lung_6_module_generation.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
DESeq_normalised_counts_Lung_6_module_generation.xlsx: Normalised counts generated using the DESeq method to remove the library-specific artefacts
DESeq_VSTlog2_normalised_values_Lung_6_module_generation.xlsx: Log2 expression values generated from normalised counts using variance stabilizing transformation in DESeq2
Genome_build: Mus musculus genome Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: Excel files containing raw counts, DESeq2 normalized counts, and DESeq2 log2 expression values

extract_protocol:
Tissues were collected in TRI-Reagent (Sigma-Aldrich) (for Toxoplasma gondii samples –tissues were collected and samples were stored in RNAlater (Ambion), and then transferred to TRI-Reagent). Total RNA was extracted using the RiboPure™ Kit (Ambion).
Total RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Quality and integrity of the tagged libraries were initially assessed with the HT DNA HiSens Reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer). Tagged libraries were then sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent). Libraries were normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

value: Female C57BL/6/J mice were sensitized with 10 mg HDM (Greer) and 2 mg Imject Alum in 200 ml PBS or Alum alone as control by intraperitoneal injections on days 0 and 14, followed by intratracheal challenge with 10 mg HDM in 20 ml of PBS or PBS on days 21 and 24. Lung samples were collected from individual HDM and PBS control treated mice on day 25.

tag: mouse number


title: HDM_allergy_Disease_whole lung [MS0415]


title: HDM_allergy_Disease_whole lung [MS0414]


title: HDM_allergy_Disease_whole lung [MS0411]


title: HDM_allergy_Disease_whole lung [MS0412]


title: HDM_allergy_Disease_whole lung [MS0410]


title: HDM_allergy_Disease_whole lung [MS0409]


title: HDM_allergy_Disease_whole lung [MS0407]


title: HDM_allergy_Disease_whole lung [MS0413]


title: HDM_allergy_Disease_whole lung [MS0408]


title: HDM_allergy_Control_whole lung [MS0405]


title: HDM_allergy_Control_whole lung [MS0402]


title: BAL_Control [Chris_G_A2_18_WB11_12_S204_L005]


title: HDM_allergy_Control_whole lung [MS0404]


title: HDM_allergy_Control_whole lung [MS0398]


title: HDM_allergy_Control_whole lung [MS0403]


title: HDM_allergy_Control_whole lung [MS0400]


title: HDM_allergy_Control_whole lung [MS0399]


title: HDM_allergy_Control_whole lung [MS0406]


title: Candida_Disease_whole lung [MS0385]

value: Candida albicans

value: Candida albicans (clinical isolate SC5314) was cultured in yeast extract peptone dextrose medium at 37°C overnight, subcultured for a further 4 hours and resuspended in PBS immediately prior to infection. Female C57BL/6/J mice were infected intratrachealy with 1x105 Candida albicans diluted in 50 ml PBS. Lung samples were collected from individual mice on day 1 post infection, using uninfected C57BL/6/J mice as controls.


title: HDM_allergy_Control_whole lung [MS0397]


title: Candida_Disease_whole lung [MS0384]


title: Candida_Disease_whole lung [MS0386]


title: Candida_Disease_whole lung [MS0383]


title: Candida_Disease_whole lung [MS0382]


title: Candida_Disease_whole lung [MS0379]


title: Candida_Disease_whole lung [MS0380]


title: HDM_allergy_Control_whole lung [MS0401]


title: Candida_Control_whole lung [MS0373]


title: Candida_Control_whole lung [MS0375]


title: Candida_Control_whole lung [MS0372]


title: Candida_Disease_whole lung [MS0377]


title: Candida_Control_whole lung [MS0370]


title: Candida_Control_whole lung [MS0371]


title: Candida_Control_whole lung [MS0368]


title: Candida_Control_whole lung [MS0369]


title: Candida_Control_whole lung [MS0367]


title: Candida_Control_whole lung [MS0366]


title: Candida_Control_whole lung [MS0365]


title: Bps_acute_Disease_whole lung [MS0303]

value: Burkholderia pseudomallei - acute

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.


title: Bps_acute_Disease_whole lung [MS0299]


title: Bps_acute_Disease_whole lung [MS0298]


title: Bps_acute_Control_whole lung [MS0293]


title: Bps_acute_Control_whole lung [MS0292]


title: Bps_acute_Disease_whole lung [MS0304]


title: Bps_acute_Disease_whole lung [MS0300]


title: Bps_acute_Control_whole lung [MS0290]


title: Bps_acute_Control_whole lung [MS0295]


title: Bps_acute_Control_whole lung [MS0294]


title: Bps_acute_Control_whole lung [MS0287]


title: Bps_acute_Control_whole lung [MS0288]


title: Bps_acute_Control_whole lung [MS0289]


title: Bps_acute_Control_whole lung [MS0291]


title: Candida_Control_whole lung [MS0374]


title: Bps_acute_Control_whole lung [MS0286]


title: RSV_Disease_whole lung [MS0344]

value: Respiratory syncytial virus (RSV)

value: Plaque-purified human RSV A2 strain originally obtained from the ATCC was grown to high titer (≥107 focus-forming units per ml) in Hep-2 cells, snap frozen, and assayed for infectivity prior to use. Female C57BL/6/J mice (MRC NIMR) were infected i.n. with 1x106 FFU of RSV diluted in 100ml PBS. Control uninfected mice received PBS only. Lung samples were collected from individual mice on day 2 post infection.


title: RSV_Disease_whole lung [MS0343]


title: RSV_Disease_whole lung [MS0341]


title: RSV_Disease_whole lung [MS0340]


title: RSV_Disease_whole lung [MS0339]


title: RSV_Disease_whole lung [MS0338]


title: RSV_Disease_whole lung [MS0337]


title: Bps_acute_Disease_whole lung [MS0296]


title: RSV_Disease_whole lung [MS0335]


title: RSV_Disease_whole lung [MS0336]


title: RSV_Control_whole lung [MS0332]

value: Control


title: RSV_Control_whole lung [MS0334]


title: RSV_Control_whole lung [MS0330]


title: RSV_Control_whole lung [MS0331]


title: RSV_Control_whole lung [MS0329]


title: RSV_Control_whole lung [MS0326]


title: RSV_Control_whole lung [MS0325]


title: RSV_Control_whole lung [MS0328]


title: Influenza_Disease_whole lung [MS0320]

value: Influenza A virus

value: Influenza A/X-31 (H3N2) strain (a kind gift from Dr J. Skehel, MRC NIMR) was grown in the allantoic cavity of 10 day-embryonated hen’s eggs, stored at -80 °C and titrated on MDCK cells prior to infection. Female C57BL/6/J mice were infected intranasally with 8x103 TCID50 in 30 ml of PBS. Control uninfected mice received PBS only. Lung samples were collected from individual infected and control treated mice on day 6 post infection.


title: RSV_Control_whole lung [MS0333]

value: Whole lung


title: Influenza_Disease_whole lung [MS0317]


title: Influenza_Disease_whole lung [MS0321]


title: Influenza_Disease_whole lung [MS0324]


title: RSV_Control_whole lung [MS0327]


title: Influenza_Disease_whole lung [MS0318]


title: RSV_Disease_whole lung [MS0342]


title: Influenza_Disease_whole lung [MS0316]


title: Influenza_Disease_whole lung [MS0315]


title: Blood_Ifnar-/-_Case [MS0733]

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female Ifnar1-/-, Ifngr1-/- and Ifnar1-/-Ifngr1-/- mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 6 post infection, whole blood, spleen, liver and lung samples were collected from individual mice using uninfected mice as controls.

value: Ifnar-/-

value: Whole blood


title: Influenza_Control_whole lung [MS0314]


title: Influenza_Disease_whole lung [MS0319]

value: Disease


title: Influenza_Control_whole lung [MS0308]


title: Influenza_Control_whole lung [MS0310]


title: Influenza_Control_whole lung [MS0309]


title: Influenza_Control_whole lung [MS0312]


title: Influenza_Control_whole lung [MS0313]


title: Influenza_Control_whole lung [MS0311]


title: Influenza_Control_whole lung [MS0306]


title: Influenza_Control_whole lung [MS0305]


title: Toxoplasma_Disease_whole lung [MS0430]

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.


title: Toxoplasma_Disease_whole lung [MS0432]


title: Blood_Ifnar-/- x Ifngr-/-_Case [MS0729]

value: Ifnar-/- x Ifngr-/-


title: Toxoplasma_Disease_whole lung [MS0431]


title: Toxoplasma_Disease_whole lung [MS0433]


title: Toxoplasma_Disease_whole lung [MS0429]


title: Toxoplasma_Disease_whole lung [MS0428]


title: Toxoplasma_Control_whole lung [MS0424]


title: Toxoplasma_Control_whole lung [MS0426]


title: Toxoplasma_Control_whole lung [MS0425]


title: Toxoplasma_Control_whole lung [MS0423]


title: Toxoplasma_Control_whole lung [MS0422]


title: Toxoplasma_Disease_whole lung [MS0427]


title: Toxoplasma_Control_whole lung [MS0420]


title: Toxoplasma_Control_whole lung [MS0419]


title: Toxoplasma_Control_whole lung [MS0417]


title: Toxoplasma_Control_whole lung [MS0418]


title: Lung_HDM_CD4_total [GRA769A48]

data_processing:
Raw paired-end RNA-seq data was subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long, and leading and trailing bases below quality 25. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness, including unpaired reads, resulting from Trimmomatic, using option -U. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalised using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalised log2 gene expression values. Further quality control was performed using principal component analysis, boxplots, histograms and density plots.
Raw_counts_HDM_sorted_CD4_Tcells.xlsx:Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
DESeq_normalised_counts_HDM_sorted_CD4_Tcells.xlsx:Normalised counts generated using the DESeq method to remove the library-specific artefacts
DESeq_VSTlog2_normalised_values_HDM_sorted_CD4_Tcells.xlsx:Log2 expression values generated from normalised counts using variance stabilizing transformation in DESeq2
Genome_build: Mus musculus genome Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: Excel files containing raw counts, DESeq2 normalized counts, and DESeq2 log2 expression values

extract_protocol:
FACS sorted blood/lung cells were collected into TRI-Reagent LS (Sigma-Aldrich). Total RNA was extracted using the Purelink RNA microkit (Thermo Fisher).
Total RNA (30–500 pg) was used to prepare cDNA libraries using the NEBNext® Single Cell/Low Input RNA Library Prep Kit NEBNext® Multiplex Oligos for Illumina® #E6609 (New England BioLabs). Quality and integrity of the tagged libraries were initially assessed with the HT DNA HiSens Reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer). Tagged libraries were then sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent). Libraries were normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

value: House dust mite (HDM) allergy

value: Female C57BL/6/J mice (MRC NIMR) were sensitized with 10 mg HDM (Greer) and 2 mg Imject Alum (Thermo Scientific) in 200 ml PBS or Alum alone as control by i.p. injections on days 0 and 14, followed by i.t. challenge with 10 mg HDM in 20 ml of PBS or PBS on days 21 and 24 as described6. Whole blood and lung samples were collected from individual HDM and PBS control treated mice on day 25. For FACS sorting of T cells, pooled blood from 4-5 individual HDM or PBS treated mice was collected into heparin sodium (Wockhardt) at 10 to 30 international units per ml of blood. Peripheral blood mononuclear cells were isolated by density separation with Lympholyte®-Mammal (Cedarlane). Lung CD4+ T cells were enriched by positive selection (Miltenyi Biotech) from a corresponding pool of lungs. Blood and lung cells were stained with CD3 (145-2C11) APC, CD4 (RM4-5) eFluor450 and CD44 (IM7) PE (all from eBioscience) and CD3+CD4+, CD3+CD4+ CD44low and CD44high cells were sorted on MoFlo XDP (Beckman Coulter) and BD FACSAria™ Fusion (Beckton Dickinson) flow cytometers and 15,000 per population collected into TRI-Reagent LS (Sigma-Aldrich).

tag: cell type

tag: mouse id

value: Lung


title: Lung_HDM_CD44low [GRA769A46]

value: CD3+CD4+ CD44lo


title: Lung_HDM_CD44hi [GRA769A47]

value: CD3+CD4+ CD44hi


title: Influenza_Control_whole lung [MS0307]


title: Lung_HDM_CD4_total [GRA769A45]


title: Lung_HDM_CD44low [GRA769A43]


title: Lung_HDM_CD44hi [GRA769A41]


title: Lung_HDM_CD4_total [GRA769A42]


title: Lung_HDM_CD44hi [GRA769A44]


title: Lung_HDM_CD44low [GRA769A40]


title: Lung_HDM_CD4_total [GRA769A39]


title: Lung_HDM_CD44low [GRA769A37]


title: Lung_Control_CD4_total [GRA769A36]


title: Lung_Control_CD44low [GRA769A34]


title: Lung_Control_CD44hi [GRA769A35]


title: Lung_Control_CD44hi [GRA769A32]


title: Lung_Control_CD4_total [GRA769A33]


title: Lung_Control_CD44low [GRA769A31]


title: Toxoplasma_Control_whole lung [MS0421]


title: Lung_Control_CD44hi [GRA769A29]


title: Lung_Control_CD4_total [GRA769A30]


title: Blood_HDM_CD4_total [GRA769A24]

value: Blood


title: Lung_Control_CD44low [GRA769A28]

value: Control


title: Lung_Control_CD44hi [GRA769A26]


title: Blood_HDM_CD44low [GRA769A22]


title: Lung_Control_CD4_total [GRA769A27]


title: Blood_HDM_CD44hi [GRA769A20]


title: Lung_Control_CD44low [GRA769A25]


title: Blood_HDM_CD44hi [GRA769A23]


title: Blood_HDM_CD4_total [GRA769A21]


title: Blood_HDM_CD44low [GRA769A19]


title: Blood_HDM_CD44hi [GRA769A17]


title: Blood_HDM_CD4_total [GRA769A18]


title: Blood_HDM_CD44low [GRA769A16]


title: Lung_HDM_CD44hi [GRA769A38]


title: Blood_HDM_CD44hi [GRA769A14]


title: Blood_Control_CD44hi [GRA769A11]


title: Blood_Control_CD4_total [GRA769A12]


title: Blood_HDM_CD44low [GRA769A13]


title: Blood_Control_CD44hi [GRA769A8]


title: Blood_Control_CD44low [GRA769A10]


title: Blood_Control_CD44hi [GRA769A5]


title: Blood_Control_CD44low [GRA769A7]


title: Blood_Control_CD4_total [GRA769A6]


title: Blood_Control_CD44low [GRA769A1]


title: Blood_Control_CD44hi [GRA769A2]


title: Blood_Control_CD4_total [GRA769A3]


title: HDM_Disease_whole blood [MS0284]

data_processing:
Raw paired-end RNA-seq data was subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long, and leading and trailing bases below quality 25. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness, including unpaired reads, resulting from Trimmomatic, using option -U. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalised using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalised log2 gene expression values. Further quality control was performed using principal component analysis, boxplots, histograms and density plots.
Raw_counts_Blood_6_module_generation.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
DESeq_normalised_counts_Blood_6_module_generation.xlsx: Normalised counts generated using the DESeq method to remove the library-specific artefacts
DESeq_VSTlog2_normalised_values_Blood_6_module_generation.xlsx: Log2 expression values generated from normalised counts using variance stabilizing transformation in DESeq2
Genome_build: Mus musculus genome Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: Excel files containing raw counts, DESeq2 normalized counts, and DESeq2 log2 expression values

extract_protocol:
Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion).
Globin-reduced RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Quality and integrity of the tagged libraries were initially assessed with the HT DNA HiSens Reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer). Tagged libraries were then sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent). Libraries were normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

value: Female C57BL/6/J mice were sensitized with 10 mg HDM (Greer) and 2 mg Imject Alum in 200 ml PBS or Alum alone as control by intraperitoneal injections on days 0 and 14, followed by intratracheal challenge with 10 mg HDM in 20 ml of PBS or PBS on days 21 and 24. Lung samples were collected from individual HDM and PBS control treated mice on day 25.


title: HDM_Disease_whole blood [MS0285]


title: HDM_Disease_whole blood [MS0281]


title: Blood_HDM_CD4_total [GRA769A15]


title: HDM_Disease_whole blood [MS0280]


title: HDM_Control_whole blood [MS0274]


title: HDM_Disease_whole blood [MS0277]


title: HDM_Disease_whole blood [MS0278]


title: HDM_Disease_whole blood [MS0279]


title: HDM_Control_whole blood [MS0272]


title: HDM_Control_whole blood [MS0270]


title: Blood_Control_CD44low [GRA769A4]


title: HDM_Control_whole blood [MS0273]


title: Blood_Control_CD4_total [GRA769A9]


title: HDM_Control_whole blood [MS0271]


title: HDM_Control_whole blood [MS0269]


title: HDM_Disease_whole blood [MS0282]


title: HDM_Disease_whole blood [MS0283]


title: HDM_Control_whole blood [MS0267]


title: Candida_Disease_whole blood [MS0255]

value: Candida albicans

value: Candida albicans (clinical isolate SC5314) was cultured in yeast extract peptone dextrose medium at 37°C overnight, subcultured for a further 4 hours and resuspended in PBS immediately prior to infection. Female C57BL/6/J mice were infected intratrachealy with 1x105 Candida albicans diluted in 50 ml PBS. Lung samples were collected from individual mice on day 1 post infection, using uninfected C57BL/6/J mice as controls.


title: Candida_Disease_whole blood [MS0254]


title: Candida_Disease_whole blood [MS0251]


title: Candida_Disease_whole blood [MS0250]


title: Candida_Disease_whole blood [MS0249]


title: Candida_Control_whole blood [MS0244]


title: HDM_Disease_whole blood [MS0276]


title: Candida_Control_whole blood [MS0243]


title: Candida_Control_whole blood [MS0242]


title: Candida_Control_whole blood [MS0241]


title: Candida_Control_whole blood [MS0239]


title: Candida_Control_whole blood [MS0238]


title: Candida_Control_whole blood [MS0237]


title: Candida_Control_whole blood [MS0240]


title: Bps_acute_Disease_whole blood [MS025]

value: Burkholderia pseudomallei - acute

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.


title: HDM_Control_whole blood [MS0275]


title: Bps_acute_Disease_whole blood [MS026]


title: HDM_Control_whole blood [MS0268]


title: Bps_acute_Disease_whole blood [MS029]


title: Bps_acute_Disease_whole blood [MS0629]


title: Bps_acute_Disease_whole blood [MS027]


title: Bps_acute_Disease_whole blood [MS03]


title: Candida_Disease_whole blood [MS0253]


title: Bps_acute_Disease_whole blood [MS0628]


title: Bps_acute_Control_whole blood [MS031]


title: HDM_Control_whole blood [MS0266]


title: Candida_Control_whole blood [MS0245]


title: Bps_acute_Disease_whole blood [MS02]


title: Bps_acute_Control_whole blood [MS020]


title: Bps_acute_Control_whole blood [MS0624]


title: RSV_Disease_whole blood [MS0176]

value: Respiratory syncytial virus (RSV)

value: Plaque-purified human RSV A2 strain originally obtained from the ATCC was grown to high titer (≥107 focus-forming units per ml) in Hep-2 cells, snap frozen, and assayed for infectivity prior to use. Female C57BL/6/J mice (MRC NIMR) were infected i.n. with 1x106 FFU of RSV diluted in 100ml PBS. Control uninfected mice received PBS only. Lung samples were collected from individual mice on day 2 post infection.


title: RSV_Disease_whole blood [MS0175]

value: Disease

value: Whole blood


title: Candida_Control_whole blood [MS0236]


title: RSV_Disease_whole blood [MS0172]


title: RSV_Disease_whole blood [MS0174]


title: RSV_Disease_whole blood [MS0171]


title: RSV_Disease_whole blood [MS0169]


title: RSV_Disease_whole blood [MS0173]


title: RSV_Disease_whole blood [MS0170]


title: RSV_Disease_whole blood [MS0168]


title: RSV_Control_whole blood [MS0162]


title: RSV_Control_whole blood [MS0163]


title: RSV_Control_whole blood [MS0164]


title: RSV_Control_whole blood [MS0161]


title: RSV_Control_whole blood [MS0165]


title: RSV_Control_whole blood [MS0166]


title: Bps_acute_Control_whole blood [MS0627]


title: Bps_acute_Control_whole blood [MS04]


title: Bps_acute_Control_whole blood [MS05]


title: RSV_Control_whole blood [MS0160]


title: Bps_acute_Control_whole blood [MS01]


title: RSV_Disease_whole blood [MS0167]


title: Influenza_Control_whole blood [MS081]

value: Influenza A virus

value: Influenza A/X-31 (H3N2) strain (a kind gift from Dr J. Skehel, MRC NIMR) was grown in the allantoic cavity of 10 day-embryonated hen’s eggs, stored at -80 °C and titrated on MDCK cells prior to infection. Female C57BL/6/J mice were infected intranasally with 8x103 TCID50 in 30 ml of PBS. Control uninfected mice received PBS only. Lung samples were collected from individual infected and control treated mice on day 6 post infection.


title: Influenza_Disease_whole blood [MS083]


title: Influenza_Disease_whole blood [MS092]


title: RSV_Control_whole blood [MS0159]


title: RSV_Control_whole blood [MS0158]


title: Influenza_Control_whole blood [MS079]


title: Influenza_Disease_whole blood [MS089]


title: Influenza_Disease_whole blood [MS085]


title: Influenza_Disease_whole blood [MS088]


title: RSV_Control_whole blood [MS0157]


title: Influenza_Disease_whole blood [MS087]


title: Influenza_Disease_whole blood [MS084]


title: Influenza_Disease_whole blood [MS086]


title: Influenza_Control_whole blood [MS078]


title: Influenza_Control_whole blood [MS077]


title: Influenza_Control_whole blood [MS074]


title: Influenza_Control_whole blood [MS076]


title: Toxoplasma_Disease_whole blood [MS0232]

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.


title: Toxoplasma_Disease_whole blood [MS0231]


title: Toxoplasma_Disease_whole blood [MS0229]


title: Toxoplasma_Disease_whole blood [MS0228]


title: Toxoplasma_Disease_whole blood [MS0226]


title: Toxoplasma_Disease_whole blood [MS0230]


title: Toxoplasma_Disease_whole blood [MS0227]


title: Influenza_Control_whole blood [MS082]


title: Influenza_Control_whole blood [MS080]


title: Influenza_Control_whole blood [MS073]


title: Toxoplasma_Control_whole blood [MS0222]


title: Toxoplasma_Control_whole blood [MS0223]


title: Toxoplasma_Control_whole blood [MS0224]


title: Toxoplasma_Control_whole blood [MS0225]


title: Toxoplasma_Control_whole blood [MS0220]


title: Toxoplasma_Control_whole blood [MS0221]


title: Influenza_Control_whole blood [MS075]


title: Toxoplasma_Control_whole blood [MS0219]


title: Bps_chronic_Disease_whole blood [MS045]

data_processing:
Raw paired-end RNA-seq data was subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long, and leading and trailing bases below quality 25. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness, including unpaired reads, resulting from Trimmomatic, using option -U. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalised using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalised log2 gene expression values. Further quality control was performed using principal component analysis, boxplots, histograms and density plots.
Raw_counts_Blood_4_module_testing.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
DESeq_normalised_counts_Blood_4_module_testing.xlsx: Normalised counts generated using the DESeq method to remove the library-specific artefacts
DESeq_VSTlog2_normalised_values_Blood_4_module_testing.xlsx: Log2 expression values generated from normalised counts using variance stabilizing transformation in DESeq2
Genome_build: Mus musculus genome Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: Excel files containing raw counts, DESeq2 normalized counts, and DESeq2 log2 expression values

value: Burkholderia pseudomallei - chronic

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 100 colony forming units (chronic model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Whole blood samples were collected from individual infected and control treated mice on days on days 27, 39, 49, 65 and 90 post infection.


title: Bps_chronic_Disease_whole blood [MS041]


title: Bps_chronic_Disease_whole blood [MS051]


title: Toxoplasma_Control_whole blood [MS0216]


title: Bps_chronic_Disease_whole blood [MS052]


title: Bps_chronic_Disease_whole blood [MS044]


title: Bps_chronic_Disease_whole blood [MS040]


title: Toxoplasma_Control_whole blood [MS0217]


title: Bps_chronic_Disease_whole blood [MS038]


title: Bps_chronic_Disease_whole blood [MS037]


title: Toxoplasma_Control_whole blood [MS0218]


title: Bps_chronic_Disease_whole blood [MS06]


title: Bps_chronic_Disease_whole blood [MS043]


title: Bps_chronic_Disease_whole blood [MS09]


title: Bps_chronic_Disease_whole blood [MS014]


title: Bps_chronic_Disease_whole blood [MS013]


title: Bps_chronic_Disease_whole blood [MS011]


title: Bps_chronic_Disease_whole blood [MS016]


title: Bps_chronic_Control_whole blood [MS042]


title: Bps_chronic_Control_whole blood [MS035]


title: Bps_chronic_Disease_whole blood [MS034]


title: Bps_chronic_Control_whole blood [MS032]


title: Bps_chronic_Control_whole blood [MS033]


title: Bps_chronic_Control_whole blood [MS050]


title: Bps_chronic_Control_whole blood [MS046]


title: Bps_chronic_Control_whole blood [MS049]


title: Bps_chronic_Control_whole blood [MS048]


title: Bps_chronic_Control_whole blood [MS039]


title: Bps_chronic_Control_whole blood [MS047]


title: Bps_chronic_Control_whole blood [MS036]


title: Bps_chronic_Control_whole blood [MS015]


title: Bps_chronic_Control_whole blood [MS012]


title: Listeria_Disease_whole blood [MS0112]

value: Listeria monocytogenes

value: Listeria monocytogenes was originally obtained from Drs. H. Rogers, K. Murphy, and E. Unanue, DNAX Research Institute, USA. Bacteria were grown in BHI broth to mid-log phase as determined by OD560 and cryopreserved in 20% glycerol/PBS at -80°C. Female C57BL/6 mice were infected by intravenous injection of 5x103 CFU of Listeria monocytogenes derived from cryopreserved stocks diluted in 200 ml of PBS. Control uninfected mice received PBS only. Whole blood samples were collected from individual infected and control treated mice on day 3 post infection.


title: Bps_chronic_Control_whole blood [MS010]

value: Control


title: Bps_chronic_Control_whole blood [MS07]


title: Listeria_Disease_whole blood [MS0109]


title: Listeria_Disease_whole blood [MS0107]


title: Listeria_Disease_whole blood [MS0103]


title: Listeria_Disease_whole blood [MS0106]


title: Listeria_Disease_whole blood [MS0105]


title: Listeria_Disease_whole blood [MS0104]


title: Listeria_Disease_whole blood [MS0111]


title: Listeria_Disease_whole blood [MS0110]


title: Listeria_Disease_whole blood [MS0108]


title: Listeria_Control_whole blood [MS0101]


title: Listeria_Control_whole blood [MS099]


title: Listeria_Control_whole blood [MS0102]


title: Listeria_Control_whole blood [MS0100]


title: Listeria_Control_whole blood [MS096]


title: Listeria_Control_whole blood [MS095]


title: Listeria_Control_whole blood [MS097]


title: Listeria_Control_whole blood [MS098]


title: MCMV_Disease_whole blood [MS0132]

value: Murine cytomegalovirus (mCMV)

value: Smith strain mCMV originally obtained from the ATCC was prepared in salivary glands from BALB/c mice and purified over a sorbital gradient. Female C57BL/6 mice were infected intraperitoneally with 3x104 FFU of mCMV8. Whole blood samples were collected from individual mice on day 2 post infection, using uninfected C57BL/6 mice as controls.


title: Listeria_Control_whole blood [MS093]


title: Bps_chronic_Control_whole blood [MS08]


title: MCMV_Disease_whole blood [MS0129]


title: Listeria_Control_whole blood [MS094]


title: MCMV_Disease_whole blood [MS0128]


title: MCMV_Disease_whole blood [MS0131]


title: MCMV_Disease_whole blood [MS0130]


title: MCMV_Disease_whole blood [MS0124]


title: MCMV_Disease_whole blood [MS0125]


title: MCMV_Disease_whole blood [MS0127]


title: MCMV_Disease_whole blood [MS0126]


title: MCMV_Disease_whole blood [MS0123]


title: MCMV_Control_whole blood [MS0122]


title: MCMV_Control_whole blood [MS0119]


title: MCMV_Control_whole blood [MS0121]


title: MCMV_Control_whole blood [MS0116]


title: MCMV_Control_whole blood [MS0117]


title: MCMV_Control_whole blood [MS0118]


title: MCMV_Control_whole blood [MS0115]


title: Malaria_Disease_whole blood [MS0155]

value: Plasmodium chabaudi chabaudi AS

value: The cloned Plasmodium chabaudi chabaudi AS line was originally obtained from David Walliker, University of Edinburgh, UK. Female C57BL/6/J mice housed under reverse light conditions were infected by intraperitoneal injection of 105 infected red blood cells derived from cryopreserved stocks. Whole blood samples were collected from individual mice on day 6 post infection, using uninfected C57BL/6/J mice as controls.


title: MCMV_Control_whole blood [MS0114]


title: MCMV_Control_whole blood [MS0113]


title: Malaria_Disease_whole blood [MS0156]


title: Malaria_Disease_whole blood [MS0154]


title: Malaria_Disease_whole blood [MS0153]


title: Malaria_Disease_whole blood [MS0152]


title: Malaria_Disease_whole blood [MS0149]


title: Malaria_Disease_whole blood [MS0148]


title: Malaria_Disease_whole blood [MS0150]


title: Malaria_Disease_whole blood [MS0151]


title: Malaria_Disease_whole blood [MS0145]


title: Malaria_Disease_whole blood [MS0147]


title: Malaria_Disease_whole blood [MS0146]


title: MCMV_Control_whole blood [MS0120]


title: Bps_acute_Control_whole blood [MS028]

value: Burkholderia pseudomallei - acute

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.


title: Malaria_Control_whole blood [MS0143]


title: Malaria_Disease_whole blood [MS0144]

value: Disease


title: Malaria_Control_whole blood [MS0650]

value: Whole blood


title: Malaria_Control_whole blood [MS0140]


title: Malaria_Control_whole blood [MS0142]


title: RAW15_Cebpb+Isoproterenol_B

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

country: USA

institute: UCLA

data_processing:
Illumina HiSeq Control Software 3.4.0 used for basecalling
STAR 2.5.3a used for alignment
STAR 2.5.3a used for normalized abundance measurement
Genome_build: GRCm38 GencodeM15
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed CPM values for each Sample

growth_protocol: RAW 264.7 cells were grown in DMEM with high glucose, Glutamax, and pyruvate (Gibco, #10569044), with 10% FBS for 2 days before being seeded at 0.25 x 10^6 cells per well in 2mL in 6-well plates (Corning, #353046).

extract_protocol:
Culture media was aspirated from adherent cells, RLT lysis buffer (supplemented with beta-mercaptoethanol) was added to wells to lyse cells, and lysates were processed with Qiagen Rneasy Mini Kit, utilizing qiashredder tubes for homogenization and on-column DNAse
Lexogen QuantSeq 3' FWD

treatment_protocol: Following 18-24 hours incubation after seeding, cells were transfected with siRNA at a concentration of 25nM, using Lipofectamine RNAiMAX transfection reagent (Thermo Fisher, #13778075). Following 24 hours of transfection, cells were then stimulated with isoproterenol.

tag: experiment #

tag: replicate

tag: sirna

value: Cebpb siRNA (Thermo Fisher, #s63860)

tag: agent

value: Isoproterenol (Sigma, ##I2760)


title: Malaria_Control_whole blood [MS0137]

tag: mouse model


title: Malaria_Control_whole blood [MS0135]

tag: condition


title: Malaria_Control_whole blood [MS0139]

tag: infection protocol


title: RAW14_Cebpb+Isoproterenol_A


title: Malaria_Control_whole blood [MS0138]


title: Malaria_Control_whole blood [MS0133]


title: Malaria_Control_whole blood [MS0136]


title: RAW14_NegCon+Isoproterenol_A

value: Control siRNA (Thermo Fisher, #4390843)


title: RAW15_Cebpb_A


title: Malaria_Control_whole blood [MS0141]


title: RAW14_Cebpb+Isoproterenol_B


title: RAW15_NegCon+Isoproterenol_A


title: RAW15_Cebpb_B


title: RAW14_Cebpb_A


title: RAW15_NegCon_B


title: RAW14_Cebpb_B


title: RAW14_NegCon_B


title: RAW15_NegCon+Isoproterenol_B


title: RAW14_NegCon_A


title: RAW15_NegCon_A


title: Malaria_Control_whole blood [MS0134]


title: RAW14_NegCon+Isoproterenol_B


title: 011317-F1-GV3

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.6
HiSAT2 alignment to NCBI GRCm38.p4 (Mus Musculus) assembly
Trimming 8 bases from 5' end of unaligned reads (from first alignment); alignment of trimmed reads
Merging accepted_hits.bam from three alignment step (samtools merge)
featureCounts (Subread 1.5.1)
DESeq2 1.16.1
Genome_build: GRCm38.p4 (Mus Musculus)
Supplementary_files_format_and_content: read_count.txt (Per-gene read count, tab-delimited)

source_name: B6xD2 F1 GV oocytes

growth_protocol: Female mice of B6, D2, and B6xD2 F1 genotypes were obtained from Jackson Laboratories at 7 weeks age and used from 8 to 12 weeks age. Both GV and MII oocytes were collected into room temperature HEPES-buffered M2 media. During GV oocyte collection, M2 medium was supplemented with 0.225M 3-Isobutyl-1-methylxanthine (IBMX) (Sigma: I7018) to prevent GVBD. Immediately after collection, MII or GV oocytes isolated from a single mother were pooled, constituting a single biological replicate. The zonae pellucidae were removed by treating in acidified Tyrode’s buffer (TYRODE 1910) for approximately 30 sec followed by immediate washing through M2 media for 1 min.

extract_protocol:
RNA was extracted from pools of GV or MII oocytes (n=9-20) collected from a single mother, using the ARCTURUS PicoPure RNA Isolation kit (ThermoFisher #12204-01). Per the protocol oocytes were heat treated in 20 μL PicoPure extraction buffer at 40oC for 30 minutes and then processed immediately or stored at -80oC. During the RNA isolation, the optional DNase treatment was done for 15 minutes at RT (Qiagen #79254). Isolated RNA was eluted into 11 μl of the PicoPure elution buffer and was immediately used or stored at -80oC.
Five microliters of the isolated RNA was processed and amplified with SPIA technology using the Ovation RNAseq System V2 (NUGEN #7102-32). Libraries were purified using a Qiagen MinElute Cleanup Kit (Qiagen #28204) and eluted into 22 μl of the provided elution buffer. Purified library concentrations were quantified on a Nanodrop (Thermo Fisher NanoDrop Lite) or Biodrop (uLite) and stored at -80oC. Approximately 1μg of SPIA library sample was diluted into 1X TE for a total volume of 130 μL and was fragmented to an average fragment length of 300 bp on a Covaris shearer. 20 μl of each fragmented SPIA library were then mixed with 14 μl H2O, 4 μl 10X S1 nuclease buffer, and 2 μl S1 nuclease for a 40 μL total reaction volume that was incubated for 30 minutes at RT (Promega # M5761). Starting with an additional bead purification, SPIA libraries were taken through the Ovation Ultralow System V2 1-16 (Nugen #0344-32). Samples were randomized for barcode ligation. Library amplification proceeded for 12 cycles. After the last bead purification, amplified-barcoded libraries were eluted in 30 μL of 1X TE. The first batch of libraries were sequenced on an Illumina HiSeq 2500 system; these libraries were loaded at 65% of standard concentration with PhiX library added up to 10% of the input. The second batch of libraries was sequenced on the HiSeq 4000 system where the input was not decreased and PhiX was loaded only to the standard 1%.
50bp single-end RNAseq

value: B6xD2 F1

tag: Stage

value: GV

tag: batch


title: 011317-D2-GV2

source_name: D2 GV oocytes

tag: strain


title: 011317-D2-MII2

source_name: D2 MII oocytes

value: MII


title: 011317-B6-MII1

source_name: B6 MII oocytes


title: 011317-B6-MII3


title: 011317-B6-MII2


title: 011317-B6-GV2

source_name: B6 GV oocytes


title: 011317-B6-GV1


title: 011017-F1-GV2


title: 011017-D2-MII1


title: 011017-F1-MII1

source_name: B6xD2 F1 MII oocytes


title: 011017-F1-MII2


title: 011017-D2-GV1


title: 011017-F1-GV1


title: ChIP-seq_HAP1_BCL7B_ARID1A_r1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
ChIP-seq for ARID1A IP in HAP1 cell line with BCL7B KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv

library_source: genomic

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair
Supplementary_files_format_and_content: csv file contains read counts for each sample in each regulatory element

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 cell line

growth_protocol: HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.

extract_protocol:
ChIPmentation was carried out as described (Schmidl et al, Nature Methods 2015). Cells were washed once with PBS and fixed with 1% paraformaldehyde in up to 1ml PBS for 10 min at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 g for 10min at 4 C, washed twice with cold PBS supplemented with 1 mM phenylmethyl sulfonyl fluoride (PMSF). The pellet was lysed in sonication buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 0.25% SDS, 1uL protease inhibitors (Sigma) and 1 mM PMSF) and sonicated with a Covaris S220 sonicator to a range of 200-700 bp. Lysates were centrifuged at full speed for 5min at 4 C, and the supernatant transferred to a new tube. The lysate was then brought to RIPA buffer conditions (final concentration: 10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1uL protease inhibitors (Sigma) and 1 mMPMSF) to a volume of 200 ml per IP. For each immunoprecipitation, 10 ml magnetic Protein A (Life Technologies) were washed twice and resuspended in PBS supplemented with 0.1% BSA. The antibody was added and bound to the beads by rotating 2 h at 4 C. Used antibodies were H3K4me1 (0.5 mg per IP, Diagenode pAb-194-050), H3K27ac (1 mg per IP, Diagenode pAB-196-050) and H3K27me3 (1 mg per IP, Millipore 07-499). For control libraries, an IP with 2.5 mg of a nonspecific IgG rabbit antibody was used. Blocked antibody-conjugated beads were then placed on a magnet, supernatant was removed and the sonicated lysate was added to the beads followed by incubation for 3-4 h at 4 C on a rotator. Beads were washed subsequently with RIPA (twice), RIPA-500 (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS and 0.1% DOC) (twice) and RIPA-LiCl (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 250mM LiCl, 1% Triton X-100, 0.5% DOC and 0.5% NP40) (twice). Beads were washed once with cold Tris-Cl pH 8.0, to remove detergent, salts and EDTA. Beads were washed once more with cold Tris-Cl pH 8.0.
DNA was purified with SPRI AMPure XP beads (sample-to-beads ratio 1:2) or Qiagen MinElute columns. One microlitre of each library was amplified in a 10-ml qPCR reaction containing 0.15 mM primers, 1uL SYBR Green and 5 ml Kapa HiFi HotStart ReadyMix (Kapa Biosystems), to estimate the optimum number of enrichment cycles with the following programme: 72 oC for 5min, 98 oC for 30 s, 24 cycles of 98 oC for 10 s, 63 oC for 30 s and 72 oC for 30 s, and a final elongation at 72 oC for 1min. Kapa HiFi HotStart ReadyMix was incubated at 98 oC for 45 s before preparation of all PCR reactions (qPCR and final enrichment PCR). Final enrichment of the libraries was performed in a 50-ml reaction using 0.75 mM primers and 25 ml Kapa HiFi HotStart ReadyMix. Libraries were amplified for N+1 cycles, where N is equal to the rounded-up Cq value determined in the qPCR reaction. Enriched libraries were purified using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200-400 bp. Library preparation was performed using custom Nextera primers as described for ATAC-seq. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform and the 50-bp single-end configuration.

tag: library

value: ChIP-seq

tag: cell line

tag: ip

tag: knockout


title: ChIP-seq_HAP1_SMARCC1_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with SMARCC1 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv

value: Input


title: ChIP-seq_HAP1_SMARCC2_ARID1A_r1

description:
ChIP-seq for ARID1A IP in HAP1 cell line with SMARCC2 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_BCL7B_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with BCL7B KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_ARID1B_ARID1A_r1

description:
ChIP-seq for ARID1A IP in HAP1 cell line with ARID1B KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_ARID1A_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with ARID1A KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_SMARCC1_ARID1A_r1

description:
ChIP-seq for ARID1A IP in HAP1 cell line with SMARCC1 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_SMARCA2_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with SMARCA2 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_SMARCA4_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with SMARCA4 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: Hi-C

city: Memphis

first: Jinghui

last: Zhang

state: TN

address: 262 Danny Thomas PL, Mail stop 1135

institute: St. Jude Children's Research Hospital

description:
The Nalm6 cell line was established from the peripheral blood of a 19-year-old man with acute lymphoblastic leukemia (ALL) in relapse in 1976.
3 independent sequencing runs on different dates.

data_processing:
The reads were mapped to hg19 and processed using Juicer v1.5 with default parameters. The data matrices were further extracted from .hic files with the dump function from juicer tools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Nalm6_HiC_inter.hic

source_name: B cell precursor leukemia

growth_protocol: Nalm6 cell line was cultured under recommended conditions to about 80% confluence.

extract_protocol: Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature, then digested with 125 units of MboI, and labeled by biotinylated nucleotides and proximity-ligated. After reverse crosslinking, ligated DNA was purified and sheared to 300-500 bp, then ligation junctions were pulled down with streptavidin beads and prepared as general Illumina library. The Hi-C sample underwent 76-cycles paired-end sequencing on the Illumina HiSeq 4000.

value: B cell precursor leukemia cell line


title: ChIP-seq_HAP1_ARID1A_ARID1A_r1

description:
ChIP-seq for ARID1A IP in HAP1 cell line with ARID1A KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_SMARCA4_ARID1A_r1

description:
ChIP-seq for ARID1A IP in HAP1 cell line with SMARCA4 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_SMARCA2_ARID1A_r1

description:
ChIP-seq for ARID1A IP in HAP1 cell line with SMARCA2 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_ARID1B_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with ARID1B KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_SMARCC2_Input_r1

description:
ChIP-seq for Input IP in HAP1 cell line with SMARCC2 KO, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: RAW15_Cebpb+Isoproterenol_A


title: HDM_allergy_Disease [3998676008_D]

description:
raw data file: MRC57.txt
Disease samples from House dust mite (HDM) allergy infection model

hyb_protocol: 1.5 µg cRNA was then hybridized to Mouse WG-6 v2.0 bead chips (Illumina) according to the manufacturer’s protocols.

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray data was processed in GeneSpring GX v14.8 (Agilent Technologies). Flags were used to filter out the probe sets that did not result in a ‘present’ call in at least 10% of the samples, with the ‘present’ lower cut-off of 0.99. Signal values were then set to a threshold level of 10, log2 transformed, and per-chip normalised using 75th percentile shift algorithm. Next, per-gene normalisation was applied by dividing each messenger RNA transcript by the median intensity of all the samples. Next, transcripts were filtered to select the most variable probes: those that had a minimum of 1.5-fold expression change compared with the median intensity across all samples, in greater than 10% of all samples.

label: biotin

label_protocol: cRNA was prepared from 200 ng tissue total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). Quality was checked using an RNA 6000 Nano kit (Agilent) using a BioAnalyzer 2100 (Agilent). Biotinylated cRNA samples were randomized.

extract_protocol: Tissues were collected in TRI-Reagent (Sigma-Aldrich) (for Toxoplasma gondii samples –tissues were collected and samples were stored in RNAlater (Ambion), and then transferred to TRI-Reagent). Total RNA was extracted using the RiboPure™ Kit (Ambion).

tag: mouse strain

value: House dust mite (HDM) allergy

value: Female C57BL/6/J mice were sensitized with 10 mg HDM (Greer) and 2 mg Imject Alum in 200 ml PBS or Alum alone as control by intraperitoneal injections on days 0 and 14, followed by intratracheal challenge with 10 mg HDM in 20 ml of PBS or PBS on days 21 and 24. Lung samples were collected from individual HDM and PBS control treated mice on day 25.

tag: tissue

value: lung


title: HDM_allergy_Control [3998676008_C]

description:
raw data file: MRC57.txt
Control samples from House dust mite (HDM) allergy infection model

value: Control


title: HDM_allergy_Control [3998676008_B]


title: HDM_allergy_Control [3998594013_C]


title: HDM_allergy_Disease [3998676008_F]


title: HDM_allergy_Control [3998594004_A]


title: HDM_allergy_Control [3998594004_F]


title: HDM_allergy_Disease [3998594013_D]


title: HDM_allergy_Disease [3998594038_F]


title: HDM_allergy_Disease [3998594013_B]


title: Candida_Disease [3999575059_B]

description:
raw data file: MRC56.txt
Disease samples from Candida albicans infection model

value: Candida albicans

value: Candida albicans (clinical isolate SC5314) was cultured in yeast extract peptone dextrose medium at 37°C overnight, subcultured for a further 4 hours and resuspended in PBS immediately prior to infection. Female C57BL/6/J mice were infected intratrachealy with 1x105 Candida albicans diluted in 50 ml PBS. Lung samples were collected from individual mice on day 1 post infection, using uninfected C57BL/6/J mice as controls.


title: HDM_allergy_Control [3998830010_A]


title: HDM_allergy_Control [3998594013_F]


title: HDM_allergy_Disease [3998830010_C]

value: Disease


title: Candida_Control [3999575059_C]

description:
raw data file: MRC56.txt
Control samples from Candida albicans infection model


title: Candida_Control [3999575059_D]


title: HDM_allergy_Disease [3998830010_E]


title: Candida_Disease [3999575059_A]


title: Candida_Control [3999575041_F]


title: HDM_allergy_Control [3998594038_B]


title: HDM_allergy_Disease [3998594004_D]


title: HDM_allergy_Control [3998594038_E]


title: HDM_allergy_Control [3998830010_D]


title: HDM_allergy_Disease [3998594038_D]


title: Candida_Disease [3999575041_C]


title: HDM_allergy_Disease [3998594004_E]


title: Candida_Disease [3999575041_E]


title: Candida_Control [3999575041_D]


title: Candida_Control [3999575041_A]


title: Candida_Disease [3999575059_F]


title: Candida_Disease [3999575056_E]


title: Candida_Disease [3999575056_D]


title: Candida_Disease [3999575065_D]


title: Candida_Disease [3999575065_B]


title: RSV_Disease [8697771013_B]

description:
raw data file: MRC29.txt
Disease samples from Respiratory syncytial virus (RSV) infection model

value: Respiratory syncytial virus (RSV)

value: Plaque-purified human RSV A2 strain originally obtained from the ATCC was grown to high titer (≥107 focus-forming units per ml) in Hep-2 cells, snap frozen, and assayed for infectivity prior to use. Female C57BL/6/J mice (MRC NIMR) were infected i.n. with 1x106 FFU of RSV diluted in 100ml PBS. Control uninfected mice received PBS only. Lung samples were collected from individual mice on day 2 post infection.


title: Candida_Control [3999575065_E]


title: RSV_Disease [8650489022_B]


title: Candida_Control [3999575065_F]


title: Candida_Control [3999575056_B]


title: RSV_Disease [8650489034_D]


title: RSV_Disease [8650489049_C]


title: RSV_Disease [8697771046_F]


title: RSV_Disease [8697771066_C]


title: RSV_Disease [8650489036_C]


title: RSV_Disease [8650489030_F]


title: RSV_Control [8697771046_A]

description:
raw data file: MRC29.txt
Control samples from Respiratory syncytial virus (RSV) infection model


title: RSV_Disease [8697771057_E]


title: RSV_Control [8650489012_F]


title: Candida_Control [3999575056_A]


title: RSV_Control [8650489036_E]


title: RSV_Disease [8650489012_A]


title: RSV_Control [8697771057_C]


title: RSV_Control [8650489034_B]


title: RSV_Control [8650489095_B]


title: Candida_Control [3999575056_C]


title: RSV_Control [8650489022_A]


title: RSV_Control [8697771013_F]


title: RSV_Control [8650489049_D]


title: RSV_Control [8650489030_C]


title: Influenza_Disease [8784170050_D]

description:
raw data file: MRC24.txt
Disease samples from Influenza A virus infection model

value: Influenza A virus

value: Influenza A/X-31 (H3N2) strain (a kind gift from Dr J. Skehel, MRC NIMR) was grown in the allantoic cavity of 10 day-embryonated hen’s eggs, stored at -80 °C and titrated on MDCK cells prior to infection. Female C57BL/6/J mice were infected intranasally with 8x103 TCID50 in 30 ml of PBS. Control uninfected mice received PBS only. Lung samples were collected from individual infected and control treated mice on day 6 post infection.


title: Influenza_Disease [8784170069_A]


title: Influenza_Disease [8762536150_F]


title: Influenza_Disease [8650489066_C]


title: Influenza_Disease [8650489024_A]


title: Influenza_Control [8784170066_B]

description:
raw data file: MRC24.txt
Control samples from Influenza A virus infection model


title: Influenza_Control [8650489056_A]


title: Influenza_Control [8784170050_E]


title: Bps_acute_Disease [7800220062_D]

description:
raw data file: MRC22.txt
Disease samples from Burkholderia pseudomallei - acute infection model

value: Burkholderia pseudomallei - acute

value: Burkholderia pseudomallei strain 576 originally isolated from a melioidosis patient was provided by Dr. T. Pitt (Health Protection Agency, London, UK). Female C57BL/6 mice were infected intranasally with 50 ml containing 2,500 colony forming units (acute model) of B. pseudomallei derived from cryopreserved stocks diluted in pyrogen-free saline. Control uninfected mice received 50 ml pyrogen-free saline only. Lung samples were collected from individual infected and control treated mice on day 3 post infection.


title: Influenza_Disease [8762536123_D]


title: Influenza_Control [8784170033_C]


title: Bps_acute_Disease [7800220076_F]


title: Bps_acute_Disease [7800220062_A]


title: Influenza_Control [8762536123_E]


title: Bps_acute_Disease [7800220070_F]


title: Bps_acute_Disease [7800220070_C]


title: Influenza_Disease [8650489056_B]


title: Bps_acute_Disease [7800220076_D]


title: Influenza_Control [8762536150_B]


title: Influenza_Disease [8650489056_F]


title: Bps_acute_Disease [7469653004_C]


title: Influenza_Control [8650489066_F]


title: Bps_acute_Disease [7469653004_D]


title: Influenza_Control [8650489056_D]


title: Influenza_Control [8650489024_D]


title: Bps_acute_Control [7800220070_B]

description:
raw data file: MRC22.txt
Control samples from Burkholderia pseudomallei - acute infection model


title: Bps_acute_Control [7509459088_B]


title: Bps_acute_Control [7800220052_E]


title: Bps_acute_Disease [7509459075_E]


title: Toxoplasma_Disease [5871841148_D]

description:
raw data file: Benaroya.txt
Disease samples from Toxoplasma gondii infection model

value: Toxoplasma gondii

value: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.


title: Influenza_Disease [8784170033_D]


title: Bps_acute_Control [7800220076_C]


title: Bps_acute_Control [7469653020_E]


title: Bps_acute_Control [7509459088_E]


title: Toxoplasma_Disease [5871841152_C]


title: Bps_acute_Control [7469653020_B]


title: Toxoplasma_Control [5871841148_E]

description:
raw data file: Benaroya.txt
Control samples from Toxoplasma gondii infection model


title: Toxoplasma_Disease [5871841151_A]


title: Toxoplasma_Disease [5871841147_F]


title: Toxoplasma_Control [5871841147_D]


title: Toxoplasma_Control [5871841147_B]


title: Bps_acute_Control [7509459088_D]


title: Toxoplasma_Control [5871841147_A]


title: Bps_acute_Control [7509459075_A]


title: Toxoplasma_Disease [5871841143_E]


title: Bps_acute_Control [7800220052_F]


title: Toxoplasma_Control [5871841144_D]


title: Toxoplasma_Control [5871841144_E]


title: Toxoplasma_Disease [5871841148_C]


title: Toxoplasma_Disease [5871841141_F]


title: Toxoplasma_Control [5871841141_D]


title: Toxoplasma_Control [5871841140_F]


title: Influenza_Disease [8784170066_E]


title: Toxoplasma_Control [5871841139_D]


title: Toxoplasma_Disease [5871841139_E]


title: Toxoplasma_Control [5871841139_A]


title: Toxoplasma_Disease [5871841140_B]


title: HDM_allergy_Control [3998594022_A]

description:
raw data file: MRC55.txt
Control samples from House dust mite (HDM) allergy infection model

label_protocol: cRNA was prepared from 200 ng globin-reduced blood RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). Quality was checked using an RNA 6000 Nano kit (Agilent) using a BioAnalyzer 2100 (Agilent). Biotinylated cRNA samples were randomized.

extract_protocol: Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion).

value: whole blood


title: Spleen_transformed_Bcell_myeloma-like_Rep4

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

description: Cells similar to transformed plasma cells or myeloma cells

hyb_protocol: Hybridization, washing and scanning of the GeneChip Mouse Gene 1.1 ST 16-Array Plate were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Affymetrix Expression console used following summarization: Plier, Norm.: Global Median

label: Biotin

source_name: B cell_transformed_MYC+BMI1+BCLXL+IRF4

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) were used together with the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Spleen cells from normal  untreated C57BL/6 mice were stimulated with LPS (25 microgram/ml) in vitro.

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

treatment_protocol: Cells were transduced with pools of retroviral particles on day 2 and 3 after LPS stimulation. Two different pools or retroviruses were used. Samples B13-1, B13-2 and  B13-3  were transduced with retroviral parrticles encoding MYC, BMI1 and BCLXL. Samples named P7- 1, P7-2, P7-3 and P7-4 were transduced with retroviral particles encoding MYC, BMI1, BCLXL and IRF4. After transduction, the cells were kept in culture between 6 - 12 weeks before extraction of RNA. Each sample are obtained from individual preparations of spleen cells, transduced with independent preparations of retroviruses. The samples B13-1, B13-2 and  B13-3 are three biological replicates. The samples  P7- 1, P7-2, P7-3 and P7-4 are four biological replicates.

tag: sample type


title: HDM_allergy_Disease [3998594022_F]

description:
raw data file: MRC55.txt
Disease samples from House dust mite (HDM) allergy infection model


title: HDM_allergy_Disease [3998594022_E]


title: HDM_allergy_Control [3999575038_D]


title: Spleen_transformed_Bcell_lymphoma-like_Rep3

description: Cells similar to transformed mature B cells or B-cell lymphoma cells

source_name: B cell_transformed_MYC+BMI1+BCLXL


title: HDM_allergy_Control [3999575038_C]


title: HDM_allergy_Disease [3999575038_B]


title: HDM_allergy_Control [3998594022_B]


title: Spleen_transformed_Bcell_myeloma-like_Rep3


title: adult_E2-12h.ERa_ChIPseq

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

data_processing:
ChIP-seq reads were filtered to retain only read pairs with mean base quality score >20.  ERa ChIP-seq samples were hard-clipped to 36nt.  SMC1a ChIP-seq samples were submitted to cutadapt v1.2.1 with parameters "-a AGATCGGAAGAG -O 5 q 0" to trim adapter, then filtered to retain only reads at least 30nt in length.
Trimmed & filtered ChIP-seq reads were mapped to mm10 via Bowtie allowing only uniquely-mapped hits (parameter "-m 1"), then coordinate-sorted and deduplicated via the Picard tool suite.
Normalized depth tracks for ChIP-seq data were generated by BEDTools genomeCoverageBed after extending all uniquely-mapped non-duplicate reads to average fragment size (150nt for ERa, 200nt for all others), then normalized to 15M (for ERa) or 20M (all others) and converted to bigWig format with UCSC utility bedGraphToBigWig.
genome build: mm10
processed data files format and content: ChIP-seq and RNA-seq normalized depth track in bigWig format

source_name: uterus

extract_protocol:
ChIP-seq: Frozen mouse tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
ChIP-seq: Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: Mice were either used at 21 days old or were ovariectomized at 10 weeks old, held for 10-14 days to allow endogenous hormones to clear. Mice were given a single intraperitoneal injection of 250 ng E2  dissolved in 0.1 ml of normal saline or 1 mg P4 dissolved in sesame oil. Control vehicle (V) animals were injected with 0.1 ml normal saline. Tissue samples  were collected 1, 2, 6, 8 12 or 24 hours after the injections.

value: uterus

tag: antibody

value: Santa Cruz SC-542


title: adult_E2-8h.ERa_ChIPseq


title: HDM_allergy_Control [3999575057_F]

value: House dust mite (HDM) allergy

value: Female C57BL/6/J mice were sensitized with 10 mg HDM (Greer) and 2 mg Imject Alum in 200 ml PBS or Alum alone as control by intraperitoneal injections on days 0 and 14, followed by intratracheal challenge with 10 mg HDM in 20 ml of PBS or PBS on days 21 and 24. Lung samples were collected from individual HDM and PBS control treated mice on day 25.


title: Spleen_transformed_Bcell_myeloma-like_Rep2


title: HDM_allergy_Control [3999575060_F]

value: Control


title: HDM_allergy_Disease [3999575057_D]


title: Spleen_transformed_Bcell_lymphoma-like_Rep2


title: HDM_allergy_Control [3999575060_B]


title: HDM_allergy_Control [3999575057_B]


title: HDM_allergy_Disease [3999575060_D]


title: Spleen_transformed_Bcell_lymphoma-like_Rep1


title: HDM_allergy_Disease [3999575038_A]


title: Candida_Disease [3999575042_F]

description:
raw data file: MRC54.txt
Disease samples from Candida albicans infection model

value: Candida albicans


title: HDM_allergy_Disease [3999575060_A]


title: Spleen_transformed_Bcell_myeloma-like_Rep1


title: HDM_allergy_Disease [3999575057_A]


title: Influenza_Control [8784170069_F]

value: lung


title: HDM_allergy_Control [3999575051_A]


title: normal RNAi, biological rep1

city: Shanghai

first: Kai

last: Xu

address: No.2901, Beidi Rd

country: China

institute: Shanghai academy of agricultural sciences

description: Gene expression data from leaves under normal condition

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 .

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Genespring 13.1.

organism: Oryza sativa

source_name: OsHMGB707 RNAi  rice leaves,normal conditions, replicate 1

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

growth_protocol: The seedlings were grown with the liquid culture solution in grow chamber with a 16h light (28℃)/8h dark(24℃) photoperiod.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer's instructions.

value: leaves

tag: genotype/variation

value: OsHMGB707 RNAi


title: HDM_allergy_Disease [3999575051_E]

value: Disease


title: Candida_Disease [3999575065_A]

value: Candida albicans (clinical isolate SC5314) was cultured in yeast extract peptone dextrose medium at 37°C overnight, subcultured for a further 4 hours and resuspended in PBS immediately prior to infection. Female C57BL/6/J mice were infected intratrachealy with 1x105 Candida albicans diluted in 50 ml PBS. Lung samples were collected from individual mice on day 1 post infection, using uninfected C57BL/6/J mice as controls.


title: normal RNAi, biological rep3

source_name: OsHMGB707 RNAi  rice leaves,normal conditions, replicate 3


title: normal RNAi, biological rep2

source_name: OsHMGB707 RNAi  rice leaves,normal conditions, replicate 2


title: HDM_allergy_Control [3999575051_F]


title: HDM_allergy_Disease [3999575051_D]


title: Candida_Control [3999575042_B]

description:
raw data file: MRC54.txt
Control samples from Candida albicans infection model


title: Candida_Disease [3999575042_C]


title: Candida_Control [3999575042_A]


title: normal wild type, bological rep1

source_name: wild-type rice leaves,normal conditions, replicate 1

value: wild type


title: normal wild type, bological rep2

source_name: wild-type rice leaves,normal conditions, replicate 2


title: normal overexression, biological rep1

source_name: OsHMGB707 overexpression rice leaves,normal conditions, replicate 1

value: OsHMGB707 overexpression


title: normal wild type, bological rep3

source_name: wild-type rice leaves,normal conditions, replicate 3


title: Candida_Disease [3999575039_B]


title: normal overexression, biological rep3

source_name: OsHMGB707 overexpression rice leaves,normal conditions, replicate 3


title: normal overexression, biological rep2

source_name: OsHMGB707 overexpression rice leaves,normal conditions, replicate 2


title: Candida_Disease [3999575039_F]


title: Candida_Control [3999575048_E]


title: Candida_Control [3999575039_D]


title: Candida_Control [3999575039_A]


title: Candida_Disease [3999575048_C]


title: Candida_Control [3999575039_C]


title: Candida_Disease [3999575039_E]


title: 124B BrTuB07 vs. 124R BrTuB07

city: Santa Monica

first: HSIAOWANG

last: CHEN

address: 2825 Santa Monica Blvd

department: Medicine

hyb_protocol: In comparison of expression between each breast tumor baseline sample prior to any treatment and to the same patient sample taken after 2-weeks of treatment with HER2-targeted therapy(run-in). 825 ng each of labeled individual Breast tumor baseline sample(cy3 label) and treatment run-in sample from the same patient were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent Microarray scanner (G2565CA) with extended dynamic range applied. Images were quantified using Agilent Feature Extraction Software version A.10.7 or version 11.0 refer to raw data file column.

data_processing:
Agilent Feature Extraction Software was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used  to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.2  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging.
In Rosetta analysis, setting for cluster Algoritm is list here and applies to both sample experiment and sequence.  Algorithm=Agglomerative, Algorithm parameters: Heuristic criteria=Average link, Similarity measure metric type=Cosine correlation.
In Rosetta analysis, setting for statistical cuts is list here to generate the cluster.  Thresholds=equal or bigger than 2 fold change with P-vaule equal or less than 0.01. Number of experiment cut is not applied.

source_name: 124B BrTuB07

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol.

value: Breast tumor baseline

source_name: 124R BrTuB07

value: after 2-weeks of treatments with HER2-targeted therapy

tag: er status (ihc staining results)

value: Neg

tag: pr_status (ihc staining results)

tag: treatment group

value: TCH

tag: drug response

value: RD


title: 125B BrTuB07 vs. 125R BrTuB07

source_name: 125B BrTuB07

source_name: 125R BrTuB07

value: TCTy


title: 120B BrTuB07 vs. 120R BrTuB07

source_name: 120B BrTuB07

source_name: 120R BrTuB07

value: Pos


title: Candida_Control [3999575048_F]

tag: mouse model

tag: condition

tag: infection protocol

value: whole blood


title: 121B BrTuB07 vs. 121R BrTuB07

source_name: 121B BrTuB07

source_name: 121R BrTuB07

value: TCHTy

value: PCR


title: 127B BrTuB07 vs. 127R BrTuB07

source_name: 127B BrTuB07

source_name: 127R BrTuB07


title: 122B BrTuB07 vs. 122R BrTuB07

source_name: 122B BrTuB07

source_name: 122R BrTuB07


title: 123B BrTuB07 vs. 123R BrTuB07

source_name: 123B BrTuB07

source_name: 123R BrTuB07


title: 128B BrTuB07 vs. 128R BrTuB07

source_name: 128B BrTuB07

source_name: 128R BrTuB07


title: 130B BrTuB07 vs. 130R BrTuB07

source_name: 130B BrTuB07

source_name: 130R BrTuB07


title: 119B BrTuB07 vs. 119R BrTuB07

source_name: 119B BrTuB07

source_name: 119R BrTuB07


title: Candida_Disease [3999575048_B]

value: Candida albicans


title: 116B BrTuB07 vs. 116R BrTuB07

source_name: 116B BrTuB07

source_name: 116R BrTuB07


title: Candida_Control [3999575058_E]

value: Control


title: Candida_Disease [3999575058_F]


title: Candida_Disease [3999575058_D]


title: Candida_Control [3999575058_C]


title: RSV_Disease [8784170068_F]

description:
raw data file: MRC17.txt
Disease samples from Respiratory syncytial virus (RSV) infection model

value: Respiratory syncytial virus (RSV)

value: Plaque-purified human RSV A2 strain originally obtained from the ATCC was grown to high titer (≥107 focus-forming units per ml) in Hep-2 cells, snap frozen, and assayed for infectivity prior to use. Female C57BL/6/J mice (MRC NIMR) were infected i.n. with 1x106 FFU of RSV diluted in 100ml PBS. Control uninfected mice received PBS only. Lung samples were collected from individual mice on day 2 post infection.


title: Candida_Control [3999575058_A]

value: Candida albicans (clinical isolate SC5314) was cultured in yeast extract peptone dextrose medium at 37°C overnight, subcultured for a further 4 hours and resuspended in PBS immediately prior to infection. Female C57BL/6/J mice were infected intratrachealy with 1x105 Candida albicans diluted in 50 ml PBS. Lung samples were collected from individual mice on day 1 post infection, using uninfected C57BL/6/J mice as controls.


title: 110B BrTuB07 vs. 110R BrTuB07

source_name: 110B BrTuB07

source_name: 110R BrTuB07


title: 104B BrTuB07 vs. 104R BrTuB07

source_name: 104B BrTuB07

source_name: 104R BrTuB07


title: RSV_Disease [8784170067_C]

value: Disease


title: 105B BrTuB07 vs. 105R BrTuB07

source_name: 105B BrTuB07

source_name: 105R BrTuB07


title: 114B BrTuB07 vs. 114R BrTuB07

source_name: 114B BrTuB07

source_name: 114R BrTuB07


title: 107B BrTuB07 vs. 107R BrTuB07

source_name: 107B BrTuB07

source_name: 107R BrTuB07


title: 115B BrTuB07 vs. 115R BrTuB07

source_name: 115B BrTuB07

source_name: 115R BrTuB07


title: 106B BrTuB07 vs. 106R BrTuB07

source_name: 106B BrTuB07

source_name: 106R BrTuB07


title: RSV_Control [8784170068_E]

description:
raw data file: MRC17.txt
Control samples from Respiratory syncytial virus (RSV) infection model


title: 111B BrTuB07 vs. 111R BrTuB07

source_name: 111B BrTuB07

source_name: 111R BrTuB07


title: RSV_Control [8784170067_A]


title: RSV_Disease [8784170057_E]


title: RSV_Disease [8784170048_C]


title: RSV_Control [8784170057_B]


title: Candida_Disease [3999575058_B]


title: RSV_Disease [8784170034_F]


title: 103B BrTuB07 vs. 103R BrTuB07

source_name: 103B BrTuB07

source_name: 103R BrTuB07


title: 100B BrTuB07 vs. 100R BrTuB07

source_name: 100B BrTuB07

source_name: 100R BrTuB07


title: RSV_Disease [8784170043_D]


title: 98B BrTuB07 vs. 98R BrTuB07

source_name: 98B BrTuB07

source_name: 98R BrTuB07


title: 97B BrTuB07 vs. 97R BrTuB07

source_name: 97B BrTuB07

source_name: 97R BrTuB07


title: 90B BrTuB07 vs. 90R BrTuB07

source_name: 90B BrTuB07

source_name: 90R BrTuB07


title: 101B BrTuB07 vs. 101R BrTuB07

source_name: 101B BrTuB07

source_name: 101R BrTuB07


title: 91B BrTuB07 vs. 91R BrTuB07

source_name: 91B BrTuB07

source_name: 91R BrTuB07


title: 89B BrTuB07 vs. 89R BrTuB07

source_name: 89B BrTuB07

source_name: 89R BrTuB07


title: RSV_Control [8784170043_C]


title: 85B BrTuB07 vs. 85R BrTuB07

source_name: 85B BrTuB07

source_name: 85R BrTuB07


title: RSV_Control [8762536125_D]


title: 79B BrTuB07 vs. 79R BrTuB07

source_name: 79B BrTuB07

source_name: 79R BrTuB07


title: RSV_Control [8762536102_E]


title: RSV_Control [8762536112_F]


title: RSV_Disease [8762536112_C]


title: RSV_Disease [8762536125_A]


title: RSV_Control [8762536110_D]


title: 83B BrTuB07 vs. 83R BrTuB07

source_name: 83B BrTuB07

source_name: 83R BrTuB07


title: 80B BrTuB07 vs. 80R BrTuB07

source_name: 80B BrTuB07

source_name: 80R BrTuB07


title: 81B BrTuB07 vs. 81R BrTuB07

source_name: 81B BrTuB07

source_name: 81R BrTuB07


title: RSV_Control [8762536112_B]


title: 78B BrTuB07 vs. 78R BrTuB07

source_name: 78B BrTuB07

source_name: 78R BrTuB07


title: 84B BrTuB07 vs. 84R BrTuB07

source_name: 84B BrTuB07

source_name: 84R BrTuB07


title: RSV_Disease [8762536102_B]


title: 77B BrTuB07 vs. 77R BrTuB07

source_name: 77B BrTuB07

source_name: 77R BrTuB07


title: Influenza_Disease [8784170101_C]

description:
raw data file: MRC06.txt
Disease samples from Influenza A virus infection model

value: Influenza A virus

value: Influenza A/X-31 (H3N2) strain (a kind gift from Dr J. Skehel, MRC NIMR) was grown in the allantoic cavity of 10 day-embryonated hen’s eggs, stored at -80 °C and titrated on MDCK cells prior to infection. Female C57BL/6/J mice were infected intranasally with 8x103 TCID50 in 30 ml of PBS. Control uninfected mice received PBS only. Lung samples were collected from individual infected and control treated mice on day 6 post infection.


title: RSV_Disease [8762536096_C]


title: RSV_Control [8762536102_A]