title: CHO-K1 NoPUT Day3, biological rep1

city: Dublin

first: Berta

last: Capella Roca

address: The National Institute for Cellular Biotechnology, Dublin City University, Glasnevin

country: Ireland

hyb_protocol: Following fragmentation, 3.5 ug of ssDNA were hybridized for 16 h, 60 rpm at 45 C on GeneChip CHO Gene 2.0 ST array. The GeneChips were washed and stained in the GenChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip scanner.

data_processing: The data were analysed using the Transcriptome Analysis Console (TAC)

organism: Cricetulus griseus

source_name: CHO-K1 cultures in media without Putrescine

label_protocol: Biotinylated cRNA were prepared according to GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™Whole Transcript (WT) Expression Arrays from 300 ng total RNA.

growth_protocol: CHO-K1 suspension cells in 50 ml working volume in 250ml flasks (Corning) and maintained in an ISF1-X (Climo Shaker) Kuhner incubator

extract_protocol: A total of 4,000,000 cells were collected from the triplicate flasks grown with putrescine (+PUT) and without putrescine (NoPUT), and RNA was extracted using 1ml Trizol according to the manufacturer's instructions.

treatment_protocol: Triplicate CHO-K1 cultures were seeded at 200,000 cells/ml in 50 ml in SFM-F10 media (Capella Roca et al. 2019) supplemented with 1 mg/l putrescine (+PUT) and without putrescine (NoPUT) for three days

tag: cell line

value: Chinese Hamster Ovary cell line

tag: culture type

value: Suspension, 50 ml at 37 C, 170 rpm, 5 % CO2 and 80 % humidity

tag: treatment

value: starved for putrescine (growing in media without putrescine) for 3 days


title: EyeBank_cultured_human_corneal_epithelial_cells_+iHFL_001

status: Public on Dec 12 2019

type: RNA

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

description: Gene expression of passage 3 cells cultivated 7 days with iHFL (80% confluence)

hyb_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

scan_protocol: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: gPixNormIQR : The normalized Inter-quartile range of all of the inlier pixels per feature. The range is computed independently in each channel.

molecule: total RNA

organism: Homo sapiens

source_name: primary human epithelial corneal cell population

label_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x 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 Whole SurePrint G3 Human GE 8x60K (G4851A) 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.

growth_protocol:
Once the Descement membrane has been peeled, remaining corneas (stromas with their attached epithelial cells) are then incubated with dispase (2.5 mg/ml) overnight at 4°C. Using forceps, the epithelium is mechanically separated from the underlying stroma and treated with trypsin, which allows the human corneal epithelial cells (hCECs) to dissociate one from another. Once isolated, hCECs are seeded in tissues culture flasks together with feeder layer for expansion.
Cells are grown in DH medium (Dulbecco–Vogt modification of Eagle's medium with Ham's F12 in a 3:1 ratio supplemented with 5% FetalClone II serum, 5 μg/ml of insulin, 0.4 μg/ml of hydrocortisone, 10 ng/ml of epidermal growth factor, 10−10 M of cholera toxin, 100 IU/ml of penicillin, and 25 μg/ml of gentamycin) until they reach 75-95% confluence.

extract_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

treatment_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

tag: age

tag: Sex

value: female

tag: protocol

value: cultivated 7 days with iHFL


title: EyeBank_cultured_human_corneal_epithelial_cells_+i3T3_002

description: Gene expression of passage 3 cells cultivated 6 days with i3T3 (80% confluence)

value: cultivated 6 days with i3T3


title: CHO-K1 +PUT Day3, biological rep3

institute: National Institute for Cellular Biotechnology

label: biotin

source_name: CHO-K1 cultures in media with Putrescine

tag: cell type

value: in media with putrescine collected at day 3


title: CHO-K1 +PUT Day3, biological rep2


title: CHO-K1 NoPUT Day3, biological rep3


title: CHO-K1 +PUT Day3, biological rep1


title: EyeBank_cultured_human_corneal_epithelial_cells_006

description: Gene expression of passage 3 cells cultivated 14 days without feeder layer (80% confluence)

value: cultivated 14 days without feeder layer


title: Bisulfite-Seq: P1113_Naive

type: SRA

city: Beijing

first: Sijin

last: Cheng

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

country: China

institute: Peking University

description: processed data file: Naive.filt.DMR.bed.gz

library_source: genomic

data_processing:
kallisto was used to quantify the abundances of transcripts.
DESeq2 was used to conduct differential gene expression analysis
Bismark was used to align sequencing data from Bisulfite-Seq data to human reference genome.
MethPipe was used to quantify the methylation level.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts calculated by kallisto; differentially methylated region (DMR) for each CD8 T cell subset

molecule: genomic DNA

source_name: Naïve T cells isolated from colorectal cancer patient

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using HISTOPAQUE-1077 (Sigma-Aldrich) solution according to the manufacturer’s instructions. Briefly, 3 mL of fresh peripheral blood was collected prior to surgery in EDTA anticoagulant tubes and subsequently layered onto HISTOPAQUE-1077. After centrifugation, lymphocyte cells remained at the plasma-HISTOPAQUE-1077 interface and were carefully transferred to a new tube and washed twice with 1x PBS (Invitrogen). These lymphocytes were re-suspended with FACS buffer (PBS supplemented with 1% fetal bovine serum (FBS, Invitrogen)). Tumors and adjacent normal tissues were cut into approximately 1-mm3 pieces in the RPMI-1640 medium (Invitrogen), and mechanically dissociated and enzymatically digested with MACS Tumor Dissociation Kit (Miltenyi Biotec) for 30 min on a rotor at 37 °C, according to the manufacturer’s instruction. The dissociated cells were subsequently passed through a 70-µm cell-strainer (BD) and centrifuged at 400g for 10 min. The cell pellets were suspended in red blood cell lysis buffer (Solarbio) and incubated on ice for 2 min to lyse red blood cells. After washing twice with PBS (Invitrogen), the cell pellets were re-suspended in FACS buffer. The following fluorescent-labeled antibodies were used: BV711 anti-CD3 (BC96; 1:100—#300450), APC anti-CD8 (RPA-T8; 1:100—#301048), BV421 anti-CD45RA (HI100; 1:100—#47-0458-42), BV421 anti-CD45RO (HI100; 1:100—#47-0458-42), BV421 anti-CCR7 (HI100; 1:100—#47-0458-42), PE anti-CD39 (eBioA1; 1:100—#17-0399-42), FITC anti-CD103 (B-Ly7 and Ber-ACT8; 1:100—#12-1038-42) (all from eBioscience). Cell surface staining was performed in FACS buffer. Stained cells were acquired on the FACS AriaII (all BD Biosciences) for cell sorting. Data were analyzed with FlowJo software (Treestar).  1000 cells of different subtypes including naïve and TEM CD8+ T cells from PBMC, tumor-reactive CD8+ T cells, two clusters of tumor bystander CD8+ T cells were enriched by gating 7AAD−CD3+CD8+CD45RO-CD45RA+CCR7+, 7AAD−CD3+CD8+CD45RO+CD45RA-CCR7-, 7AAD−CD3+CD8+CD103+CD39+, 7AAD−CD3+CD8+CD103+CD39-, and 7AAD−CD3+CD8+CD103-CD39-, respectively, and sorted into 0.2 ml tubes(Axygen) chilled to 4 °C, prepared with lysis buffer with 1 μl 10 mM dNTP mix (Invitrogen), 1 μl 10 μM Oligo dT primer, 1.9 μl 1% Triton X-100 (Sigma), and 0.1 μl 40 U μl−1 RNase Inhibitor (Takara).
Transcriptome amplifications were performed according to Smart-Seq2 protocol with modification of reagent amount and PCR cycle numbers. The amplified cDNA products were purified with Agencourt XP DNA beads, and the concentration of each sample was quantified by Qubit HsDNA kits. Libraries were constructed and amplified using the TruePrep DNA Library Prep Kit V2 for Illumina. The libraries were then purified with Agencourt XP DNA beads and anaylsed by fragment analyser for quality assessment. Purified libraries were analysed by an Illumina Hiseq 4000 sequencer with 150-bp pair-end reads. Whole-genome bisulfite-seq was performed according to a previously published protocol (45). Briefly, 1000 cells were sorted into lysis buffer by FACS; DNA was released after proteinase treatment at 50?°C and then subjected to bisulfite conversion. After bead-based purification, DNA was complemented with the biotinylated random primer Bio-P5-N9 (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 100 units of Klenow polymerase (3’ to 5’ exo-). This random priming was repeated seven times in total. Second strands were synthesized using another random primer, P7-N9 (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’), and final libraries were generated after 7 to 9 cycles of PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

tag: subject status/id

value: colorectal cancer patient P1113

tag: tissue/position

value: Colon sigmoideum

value: Naive T cells


title: CHO-K1 NoPUT Day3, biological rep2


title: Bisulfite-Seq: P1120_DP

description: processed data file: DP.filt.DMR.bed.gz

source_name: CD103+ CD39+ (DP) T cells isolated from colorectal cancer patient

value: colorectal cancer patient P1120

value: male

value: Rectum

value: CD103+ CD39+ (DP) T cells


title: Bisulfite-Seq: P1112_DN

description: processed data file: DN.filt.DMR.bed.gz

source_name: CD103- CD39- (DN) T cells isolated from colorectal cancer patient

value: colorectal cancer patient P1112

value: CD103- CD39- (DN) T cells


title: Bisulfite-Seq: P1112_SP

description: processed data file: SP.filt.DMR.bed.gz

source_name: CD103+ CD39- (SP) T cells isolated from colorectal cancer patient

value: CD103+ CD39- (SP) T cells


title: Bisulfite-Seq: P1112_DP

description: processed data file: DP.filt.DMR.bed.gz


title: Bisulfite-Seq: P1112_Naive


title: Bisulfite-Seq: P1112_EM

description: processed data file: EM.filt.DMR.bed.gz

source_name: Effector Memory (EM) T cells isolated from colorectal cancer patient

value: Effector Memory (EM) T cells


title: Bisulfite-Seq: P1101_DN

description: processed data file: DN.filt.DMR.bed.gz

value: colorectal cancer patient P1101

value: Colon transversum


title: Bisulfite-Seq: P1101_DP

description: processed data file: DP.filt.DMR.bed.gz

value: female


title: Bisulfite-Seq: P1101_EM

description: processed data file: EM.filt.DMR.bed.gz


title: Bisulfite-Seq: P1120_Naive


title: Bisulfite-Seq: P1101_Naive


title: Bisulfite-Seq: P1031_DN

description: processed data file: DN.filt.DMR.bed.gz

value: colorectal cancer patient P1031


title: Bisulfite-Seq: P1031_SP

description: processed data file: SP.filt.DMR.bed.gz


title: Bisulfite-Seq: P1031_DP

description: processed data file: DP.filt.DMR.bed.gz


title: Bisulfite-Seq: P1031_Naive


title: Bisulfite-Seq: P1031_EM

description: processed data file: EM.filt.DMR.bed.gz


title: Bisulfite-Seq: P1030_SP

description: processed data file: SP.filt.DMR.bed.gz

value: colorectal cancer patient P1030


title: Bisulfite-Seq: P0929_DN

description: processed data file: DN.filt.DMR.bed.gz

value: colorectal cancer patient P0929

value: Right colon


title: Bisulfite-Seq: P1030_DP

description: processed data file: DP.filt.DMR.bed.gz


title: Bisulfite-Seq: P1030_Naive


title: Bisulfite-Seq: P0929_DP

description: processed data file: DP.filt.DMR.bed.gz


title: Bisulfite-Seq: P0929_SP

description: processed data file: SP.filt.DMR.bed.gz


title: Bisulfite-Seq: P1030_DN

description: processed data file: DN.filt.DMR.bed.gz


title: Bisulfite-Seq: P0929_EM

description: processed data file: EM.filt.DMR.bed.gz


title: RNA-seq: P1120_DN

description: processed data file: CD8Tcell_raw_counts.csv.gz

library_source: transcriptomic

molecule: polyA RNA


title: RNA-seq: P1120_EM


title: RNA-seq: P1120_SP


title: RNA-seq: P1120_Naive


title: RNA-seq: P1113_DN

value: colorectal cancer patient P1113

value: Colon sigmoideum


title: RNA-seq: P1120_DP

value: colorectal cancer patient P1120


title: Bisulfite-Seq: P0929_Naive

value: male

value: Naive T cells


title: Bisulfite-Seq: P1101_SP

description: processed data file: SP.filt.DMR.bed.gz


title: RNA-seq: P1113_SP


title: RNA-seq: P1113_DP

value: CD103+ CD39+ (DP) T cells


title: RNA-seq: P1113_EM


title: RNA-seq: P1112_SP

value: colorectal cancer patient P1112

value: Rectum


title: RNA-seq: P1112_DN

value: CD103- CD39- (DN) T cells


title: RNA-seq: P1112_DP


title: RNA-seq: P1112_EM

value: Effector Memory (EM) T cells


title: RNA-seq: P1112_Naive


title: RNA-seq: P1101_DN

value: colorectal cancer patient P1101


title: Bisulfite-Seq: P1030_EM

description: processed data file: EM.filt.DMR.bed.gz


title: RNA-seq: P1101_SP

value: Colon transversum

value: CD103+ CD39- (SP) T cells


title: RNA-seq: P1101_Naive

value: female


title: RNA-seq: P1101_EM


title: RNA-seq: P1031_SP

value: colorectal cancer patient P1031


title: RNA-seq: P1031_DP


title: RNA-seq: P1101_DP


title: RNA-seq: P1030_DN

value: colorectal cancer patient P1030


title: RNA-seq: P1030_DP


title: RNA-seq: P1113_Naive


title: RNA-seq: P0929_DP

value: colorectal cancer patient P0929

value: Right colon


title: RNA-seq: P1030_EM


title: RNA-seq: P0929_DN


title: RNA-seq: P0929_SP


title: RNA-seq: P0929_EM


title: RNA-seq: P1030_SP


title: RNA-seq: P0929_Naive


title: RNA-seq: P1030_Naive


title: Regenerative

city: New York

first: Denise

last: Gay

address: 550 1st avenue

country: USA

institute: NYU langone

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices.

organism: Mus musculus

source_name: Skin wound dermis at wound day 18

extract_protocol:
At wound day 18, wound tissue was collected and incubated in 5U/ml Dispase (StemCell Technologies) at 37oC for 10 minutes to separate dermis from epidermis. Epidermis was examined for wound size (area) and hair placodes to distinguish phenotypes. Dermis from 6-8 wounds of each phenotype was combined, dermal cells released by collagenase treatment (Worthington Labs), filtered and dead cells and debris removed using the MACS Live-Dead kit (Miltenyi).
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

treatment_protocol: Adult 6-to-7 week old C57Bl/6j mice received 1.2x1.2 cm2 full thickness excision wounds on the lower back under isoflurane anesthesia. Animals received analgesic buprenorphine prior to surgery and 8 and 24 hours later to ameliorate pain. Wounds were completely reepithilialized by wound day 14-15. At wound day 18, animals were euthanized and tissue collected.

tag: strain

tag: source

value: Skin dermis

value: Dermal cells of skin wound

value: 6-7 weeks old, adult


title: WaGa no treatment

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

country: Germany

institute: DKZF

data_processing:
The Cell Ranger Single Cell Software Suite version 2.1.1 (http://10xgenomics.com/) was used  with default settings to align cDNA reads of each sample separately to the hg19 human reference genome. Afterwards, WaGa cells without treatment and WaGa cells under treatment were combined using the cellranger aggr function. For quality control in R, cells with less than 1000 UMI  counts, less than 1000 genes or expressing more than 10% mitochondrial genes were removed  from analyses. Furthermore, cells with more than 5000 genes or more than 30000 UMIs were considered as outliers and discarded. In total, 10816 cells were left. The Seurat R package was used for normalization and  biological analysis (Butler et al., 2018)
Genome_build: hg19
Supplementary_files_format_and_content: The combined, normalized and filtered expression count matrix of WaGa cells under treatment and control WaGa cells without treatment

source_name: Merkel cell carcinoma

growth_protocol: WaGa cells were maintained RPMI culturing medium

extract_protocol:
Since WaGa cells are growing in suspension no isolation step was required and cells were  directly single cell barcoded using the 10x Genomics 3’ Chromium v2.0 platform
Library preparation was performed according to  the 10x Genomics protocol and the library afterwards sequenced on an Illumina HiSeq 4000  (Illumina)

treatment_protocol: no treatment

value: WaGa

tag: agent

value: no treatment


title: FK106169

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St

department: Medicine

institute: Indiana University

description: RNAseq_Microdissected Breast Adipose Tissue

data_processing:
Sequences were obtained using the HiSeq 3000/4000 PE Cluster Kit and sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control.
All sequenced libraries were mapped to the human genome (UCSC hg38) using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”
The reads distribution across the genome was assessed using bamutils (from ngsutils)
Uniquely mapped sequencing reads were assigned to hg38refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10”.
Quality control of sequencing and mapping results was summarized using MultiQC.Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept. The data was normalized using TMM (trimmed mean of M values) method.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited excel files ( one for the microdissected human breast epithelium, one for the microdissected human breast stroma and one for the microdissected human breast adipose tissue) include three spreadsheets, each one for one microdissected tissue comaprtment include Log2CPM and raw data for each Sample

source_name: Breast tissue

growth_protocol: The breast tissue cores are collected by using a needle biopsy needle (Hologic, Marlborough, MA). The skin is cleaned, then numbed with lidocaine. The physician nicks the skin with a scalpel, usually in the upper-outer quadrant of the breast, and the needle is inserted into this incision. From this single incision, five sample cores are removed from the breast (approximately 200mg). A nurse/surgeon’s assistant holds pressure on the incision for 10 full minutes, then applies a pressure bandage. An ice pack is immediately placed on the breast. Within 10 min from collection the tissue cores are fresh frozen in liquid nitrogen

extract_protocol:
RNA from microdissected the epithelial compartment was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD), while total RNA from the microdissected stroma and adipose tissue was extracted using RNeasy Mini kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. Then 10 nanograms of RNA per sample were used to prepare a dual-indexed strand-specific cDNA library using Clontech SMARTer RNA Pico Kit v2. The resulting libraries were assessed for their quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer.

treatment_protocol: laser micodissection is used to separate the three breast tissue compartments: epithelium, stroma and adipose tissue

tag: tissue compartment

value: Adipose Tissue

tag: study cohort

value: Healthy Control


title: WaGa treated with the HDAC inhibitor domatinostat

treatment_protocol: For treatment with the HDAC inhibitor domatinostat (4SC AG, Planegg-Martinsried,  Germany), cells were seeded in 6-well plates at a concentration of 1x10 6  cells/ml.  Domatinostat was dissolved in DMSO (PanReac AppliChem, Darmstadt, Germany).


title: Fibrotic


title: FK105568


title: RNA-seq: P1031_EM

value: Colon sigmoideum


title: FK104334


title: FK106715


title: RNA-seq: P1031_DN

value: CD103- CD39- (DN) T cells


title: FK105868


title: FK106154


title: FK105179


title: FK107267


title: FK105810

value: Susceptible


title: FK106505


title: FK105092


title: FK105134


title: FK104358


title: SK105868

description: RNAseq_Microdissected Breast Stroma

value: Stroma


title: SK107073

description: RNAseq_Microdissected Breast Stroma


title: SK105568

description: RNAseq_Microdissected Breast Stroma


title: SK105969

description: RNAseq_Microdissected Breast Stroma


title: SK106836

description: RNAseq_Microdissected Breast Stroma


title: RNA-seq: P1031_Naive

value: Naive T cells


title: SK105805

description: RNAseq_Microdissected Breast Stroma


title: SK105179

description: RNAseq_Microdissected Breast Stroma


title: SK106154

description: RNAseq_Microdissected Breast Stroma


title: FK102687


title: SK104334

description: RNAseq_Microdissected Breast Stroma


title: SK107267

description: RNAseq_Microdissected Breast Stroma


title: FK105891


title: SK106715

description: RNAseq_Microdissected Breast Stroma


title: SMETB07-509

description: RNAseq_Microdissected Breast Stroma


title: SK104374

description: RNAseq_Microdissected Breast Stroma


title: SK102492

description: RNAseq_Microdissected Breast Stroma


title: FK105450


title: SK102687

description: RNAseq_Microdissected Breast Stroma


title: SK105891

description: RNAseq_Microdissected Breast Stroma


title: SK105810

description: RNAseq_Microdissected Breast Stroma


title: SK105092

description: RNAseq_Microdissected Breast Stroma


title: SK104358

description: RNAseq_Microdissected Breast Stroma


title: SK105134

description: RNAseq_Microdissected Breast Stroma


title: SK106505

description: RNAseq_Microdissected Breast Stroma


title: K107073

description: RNAseq_Microdissected Breast Epithelium

value: Epithelium (TDLU)


title: SK106169

description: RNAseq_Microdissected Breast Stroma


title: SK100899

description: RNAseq_Microdissected Breast Stroma


title: K105568

description: RNAseq_Microdissected Breast Epithelium


title: K106997

description: RNAseq_Microdissected Breast Epithelium


title: K106169

description: RNAseq_Microdissected Breast Epithelium


title: K105969

description: RNAseq_Microdissected Breast Epithelium


title: K106836

description: RNAseq_Microdissected Breast Epithelium


title: K104334

description: RNAseq_Microdissected Breast Epithelium


title: SK105450

description: RNAseq_Microdissected Breast Stroma


title: K100899

description: RNAseq_Microdissected Breast Epithelium


title: K105868

description: RNAseq_Microdissected Breast Epithelium


title: K106154

description: RNAseq_Microdissected Breast Epithelium


title: K105179

description: RNAseq_Microdissected Breast Epithelium


title: K105891

description: RNAseq_Microdissected Breast Epithelium


title: K104374

description: RNAseq_Microdissected Breast Epithelium


title: K105450

description: RNAseq_Microdissected Breast Epithelium


title: K102687

description: RNAseq_Microdissected Breast Epithelium


title: K107267

description: RNAseq_Microdissected Breast Epithelium


title: K105810

description: RNAseq_Microdissected Breast Epithelium


title: METB07-509

description: RNAseq_Microdissected Breast Epithelium


title: K102492

description: RNAseq_Microdissected Breast Epithelium


title: K105134

description: RNAseq_Microdissected Breast Epithelium


title: K106505

description: RNAseq_Microdissected Breast Epithelium


title: VSC00015_Tp4_SKN06549

city: Pittsburgh

first: Anna

middle: J

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to Chlorocebus sabaeus (ChlSab1.1) using STAR spliced read aligner
Count read using HT-seq using ChlSab1.1.87 as reference
Normalization (TMM), quantitation (FPKM).
Genome_build: ChlSab1.1
Supplementary_files_format_and_content: FPKM

organism: Chlorocebus sabaeus

source_name: whole blood of juvenile male vervet monkey from the Caribbean island of St. Kitts

extract_protocol:
Total blood RNA was extracted from PaxGene Blood RNA tubes (Preanalytix) using PAXgene Blood RNA Kit (Qiagen).
For cDNA library creation, we used TruSeq Stranded RNA protocol using 100 ng of RNA with RiboZero and Globin treatment (Illumina). We generated 120 bp-long paired-end sequencing reads using high output flow cell lines on HiSeq 4000 sequencer (Illumina).

tag: tissue

value: whole blood

tag: gender

value: male

tag: developmental stage

value: juvenile

tag: days after exposure to stressor

tag: animal


title: VSC00015_Tp2_SKN06072


title: VSC00015_Tp1_AAV07288


title: VSC00014_Tp2_SKN06059


title: VSC00014_Tp4_SKN06533


title: VSC00013_Tp2_SKN06046


title: K105805

description: RNAseq_Microdissected Breast Epithelium


title: VSC00014_Tp1_AAV07269


title: VSC00013_Tp4_SKN06517


title: K106715

description: RNAseq_Microdissected Breast Epithelium


title: VSC00012_Tp2_SKN06033


title: VSC00012_Tp4_SKN06501


title: VSC00011_Tp4_SKN06485


title: VSC00010_Tp4_SKN06469


title: VSC00011_Tp1_AAV07212


title: VSC00011_Tp2_SKN06020


title: VSC00010_Tp2_SKN06007


title: VSC00010_Tp1_AAV07193


title: K105092

description: RNAseq_Microdissected Breast Epithelium


title: VSC00009_Tp2_SKN05994


title: VSC00009_Tp4_SKN06453


title: VSC00008_Tp4_SKN06437


title: K104358

description: RNAseq_Microdissected Breast Epithelium


title: VSC00008_Tp2_SKN05981


title: VSC00009_Tp1_AAV07174


title: VSC00007_Tp2_SKN05968


title: VSC00007_Tp1_AAV07136


title: VSC00006_Tp4_SKN06405


title: VSC00006_Tp2_SKN05955


title: VSC00006_Tp1_AAV07117


title: VSC00005_Tp4_SKN06389


title: VSC00005_Tp2_SKN05942


title: VSC00005_Tp1_AAV07098


title: VSC00013_Tp1_AAV07250


title: VSC00004_Tp1_AAV07079


title: VSC00004_Tp2_SKN05929


title: VSC00004_Tp4_SKN06373


title: VSC00003_Tp4_SKN06357


title: VSC00003_Tp2_SKN05916


title: VSC00002_Tp1_AAV07041


title: VSC00002_Tp4_SKN06341


title: VSC00002_Tp2_SKN05903


title: VSC00001_Tp1_AAV07022


title: VSC00001_Tp2_SKN05890


title: VSC00008_Tp1_AAV07155


title: VSC00001_Tp4_SKN06325


title: VSC00007_Tp4_SKN06421


title: MP_14_fish_2A.M

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: single end protocol R2 used for 7N barcode + 8N UMI in fastq header

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Read count by homer (http://homer.salk.edu/homer/ngs/)
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: text files include mRNA molecule count values for each Sample

organism: Danio rerio

source_name: Total brain

extract_protocol:
10,000 cells from each sample were sorted into lysis/binding buffer (Life Technologies). mRNA was captured with 6.5ul of Dynabeads oligo(dT) (Life Technologies), washed, and eluted at 85C with 10ul of 10 mM Tris-HCl (pH7.5).
We used a derivation of the MARS-seq as described (Jaitin et al. Science 2014), developed for single cell MARS-seq to produce 3' exprssion libraries with a minimum of 3 replicates per sample.

value: WT

value: Brain

tag: selection markers

value: Thermo Fisher

tag: catalog #


title: MP_13_fish_1A.M

tag: age


title: MP_15_fish_3A.M


title: AB7153

description: paired-end (read2 used to read cell and molecule barcodes only)

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Single-cell libraries were prepared as previously described (Keren-Shaul, Nature Protocols, 2019). In brief, mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier (Keren-Shaul, Nature Protocols, 2019).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

value: Immune cells

tag: selection marker

tag: catalog#


title: AB5657

value: eGFP-mPEG

tag: cell type

value: mPEG-GFP


title: AB7155


title: AB3014


title: AB7154


title: no sgRNA 2

city: Jonesboro

first: Robert

middle: Colquhoun

last: Shields

state: Arkansas

address: Lab Science East

department: Biological Sciences

institute: Arkansas State University

description:
cDNA library
repeat 2 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: Counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus mutans

source_name: bacterial cells

growth_protocol: Bacterial cells used for extraction of RNA were grown in FMC medium (maltose as a carbohydrate source), in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ? 0.5)

extract_protocol:
Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C. Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

value: <delta>cas9 P23-gfp Pxyl-cas9Sm

tag: media

value: FMC-Maltose w/ 0.1% xylose

tag: growth point


title: no sgRNA 1

description:
cDNA library
repeat 1 of 3

tag: strain


title: no sgRNA 3

description:
cDNA library
repeat 3 of 3


title: VSC00003_Tp1_AAV07060


title: xylose 1

description:
cDNA library
repeat 1 of 3

value: <delta>cas9 P23-gfp sgRNA-gfp Pxyl-cas9Sm


title: control 2

description:
cDNA library
repeat 2 of 3

value: FMC-Maltose w/o xylose


title: control 3

description:
cDNA library
repeat 3 of 3


title: control 1

description:
cDNA library
repeat 1 of 3


title: xylose 3

description:
cDNA library
repeat 3 of 3


title: H9_200nM_romidepsin_rep1_pro

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: nascent RNA

data_processing:
Library strategy: PRO-seq
adapter trimming: cutadapt 1.8.1
FASTQ deduplication: fqdedup v0.1.0
FASTX trimming and reverse complementing: fastx_trimmer, fastx_reverse_complement 0.0.14. Note that the first 8 bases of the read are a UMI and need to be trimmed.
alignment: bowtie2 2.3.2
file manipulation: samtools 1.6
file manipulation: seqOutBias v1.1.3
Genome_build: hg38
Supplementary_files_format_and_content: stranded bigWig counts files

source_name: H9 cells

growth_protocol: H9 cell from ATCC and were were grown in RMPI-1640 with 10% FBS.

treatment_protocol: A final concentration of 200nM romidepsin was added for 60 minutes

tag: cell line

value: embryonic stem cells

tag: treatment

value: 60 minutes 200nM romidepsin


title: H9_200nM_romidepsin_rep3_pro

description: nascent RNA


title: H9_200nM_romidepsin_rep2_pro

description: nascent RNA


title: H9_DMSO_rep2_pro

description: nascent RNA

value: control


title: RNAseq_IMR90_alpha-amanitin_1hour

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq
76-bp or 50-bp reads were aligned to the human genome (hg19) using Bowtie2 (version 2.2.9).
Redundant reads were removed by picard (version 2.7.1). Low quality read (MapQ < 10) were also removed.
ChIP-seq peaks were defined by HOMER software (version 4.8.3) using the option “-center -style factor -F 1 -P 0.0001 -fdr 0.05” for RNA Pol II and TP53, while the alternative option “-center -style histone -F 2 -P 0.0001 -fdr 0.05” was used for other proteins. Input samples were used for the control of peak calling.
ChIP-seq score of more than 7-fold compared to the Input were removed from the bigwig file.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file were generated using bedGraphToBigWig (version 4)
RNA-seq of RNAseq_IMR90_Control_noEU, RNAseq_IMR90_EU_1hr, RNAseq_IMR90_Triptolide_5min and RNAseq_IMR90_alpha-amanitin_1hour
Sequenced reads were aligned to the human genome (hg19) using the STAR program (v2.5.2)
Reads assigned to exons were estimated by the RSEM program (v1.2.31) )
RNA-seq score of CCL20, MMp1, IER3 and TRIB1 genes were compared with the nascent RNA levels obtained from RT-qPCR result. Entire RNA-seq score were normalized by the linear regression slopes obtained from comparison.
Genome_build: hg19
Supplementary_files_format_and_content: normalized bedGraph score were converted to bigwig using bedGraphToBigWig (version 4)

source_name: IMR90 cells

growth_protocol: Normal diploid IMR90 human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.15% sodium bicarbonate, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1 ´ MEM non-essential amino acids. BJ human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
In situ Hi-C was performed as previously described (Rao et al., 2014, Cell). ChIP-seq was performed as previously described (Aird et al., 2017 JCB).  RNA was extracted from IMR90 cells using RNeasy Mini kit (Qiagen).  RNA-seq was carried out as previously described with modifications (Tanizawa et al. 2017 NSMB).
For in situ Hi-C, sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc). ChIP-seq was carried out as described previously (Iwasaki et al. 2015).  Approximately 1 ng ChIP DNA was subjected to the illumine library construction using NEBNext Ultra DNA library prep kit (New England Biolabs).  Adaptor-ligated DNA was PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.  For RNA-seq, Poly (A) RNA was purified using NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs), and sequence libraries were constructed using NEBNext mRNA Library prep Master mix for Illumina (New England Biolabs).  Adaptor-ligated DNAs were PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.
in situ Hi-C/ ChIP-seq/ RNA-seq

treatment_protocol: pBABE-puro plasmids carrying H-rasV12 were used for retrovirus packaging, and virus infection was performed.  H-rasV12-expressing cells were cultured in medium containing 1 µg/ml puromycin for 7 days to obtain OIS cells. pTRIPZ plasmids containing NCAPH2 shRNAs (#1, V3THS_326285; #2, V3THS_326286; #3, V3THS_326290, Dharmacon) were used for CAP-H2 knockdown.  Lentivirus was prepared using ViraPower kit (Thermo Fisher Scientifc) according to the manufacturer’s protocol.  Doxycycline (1μg/ml) was added to culture medium every 48 hours after lentiviral transfection for shRNA expression. OIS cells were further infected with lentivirus encoding one of the three shRNA constructs (#1, #2, and #3) against NCAPH2 and harvested 3 days after the lentivirus infection.

tag: relevant information for chip_antibody

tag: genptype/ variation

value: wild type/ OIS

tag: passage

value: Lung fibroblasts

tag: karyotype

value: Normal diploid


title: H9_DMSO_rep3_pro

description: nascent RNA


title: RNAseq_IMR90_EU_1hr


title: ChIPseq_IMR90_CAPH2_alpha-amanitin_1hour

value: Rabbit polyclonal anti-CAP-H2 (Bethyl Laboratories, A302-275A, lot #A2)

value: Validated by RNAi & western blot


title: RNAseq_IMR90_Triptolide_5min


title: RNAseq_IMR90_Control_noEU


title: ChIPseq_IMR90_CAPH2_Triptolide_30min


title: mic_human5.M

source_name: Brain cortex

tag: tissue

value: Brain

tag: source

value: BioLegend


title: ChIPseq_IMR90_CAPH2_Triptolide_5min


title: xylose 2

description:
cDNA library
repeat 2 of 3


title: ChIPseq_IMR90_CAPH2_alpha-amanitin_30min


title: ChIPseq_IMR90_SMC2_OIS

value: Rabbit polyclonal anti-SMC2 (Bethyl Laboratories, A300-058A), lot #A3)

value: Validated by western blot


title: mic_human4.M

tag: selection markers


title: mic_human6.M

tag: catalog #


title: ChIPseq_IMR90_CAPH2_Control_noEU


title: mic_human3.M

tag: age


title: VSC00012_Tp1_AAV07231

value: whole blood

tag: gender

value: male

tag: developmental stage

value: juvenile

tag: days after exposure to stressor

tag: animal


title: mic_human1.M


title: mic_human2.M


title: Tumor 3

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
We performed 76 nt paired-end sequencing using an Illumina NextSeq500 platform.
Illumina Casava software was used for basecalling.
The short-read sequences  were mapped to the mouse reference genome (GRCm38.82) by the splice junction aligner TopHat V2.1.0.
The number of reads mapped to each gene based on the TxDb. Mmusculus gene ensembls were counted, reported and annotated using the Rsamtools, GenomicFeatures, GenomicAlignments packages.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Tab-delimited text files include log2 count per million values for each Sample

source_name: MSC tumor PDGFRA + KSHV

growth_protocol: The isolated mouse MSC cells were infected with rKSHV.219, MOI of 3, in the presence of polybrene (8 ug/ml) for 1 hour. 2 days later, puromycin was added to the culture to select and expand the infected cells. All murine cells were cultured in MEM alpha media: supplemented with 20% heat inactivated fetal bovine serum (FBS) (MSC media); or KS-like growth medium (KS media)

extract_protocol:
RNA was isolated and purified using the RNeasy mini kit (Qiagen). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
mRNA from cell lines and tumor samples were processed for directional mRNA-seq library construction using the Preparation Kit according to the manufacturer's protocol.

treatment_protocol: Virus infection was performed according to the method used in a previous study, with minor modifications (see associated publication).

value: KS-like growth medium


title: Tumor 7


title: Tumor 5


title: Tumor 6


title: Tumor 8


title: KSHV positive Pα(+)S MSCs in MEM alpha media 3

source_name: Mouse mesenchymal stem cells (MSCs) PDGFRA +

value: MSC media


title: Tumor 1


title: Tumor 4


title: H9_DMSO_rep1_pro

description: nascent RNA

tag: cell type

value: embryonic stem cells


title: KSHV positive Pα(+)S MSCs in MEM alpha media 2


title: Tumor 2


title: KSHV positive  Pα(+)S MSCs in KS media 3


title: KSHV positive Pα(+)S MSCs in MEM alpha media 1


title: KSHV positive  Pα(+)S MSCs in KS media 1


title: KSHV positive  Pα(+)S MSCs in KS media 2


title: KSHV positive Pα(+)S MSCs in MEM alpha media H3K4me3 ChIP rep3

data_processing:
ChIP-seq reads were analyzed following the AQUAS ChIP-seq bioinformatics pipeline using default parameters (Kundaje lab,  https://github.com/kundajelab/chipseq_pipeline).
FASTQ reads were aligned to the mouse mm9 genome using BWA v0.7.13 and duplicate reads were removed using Picard tools v1.126.
Peaks and signal tracks were generated using MACS2.1 and filtered for blacklist regions identified by ENCODE.
Bedtools v2.26.0 intersect was used to determine peak overlaps with Refseq genes +2.5kb upstream of TSS regions to identify H3K27me3 and H3K4me3 enriched genes.
NGS Plot v2.61 was used to generate density plots.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

extract_protocol:
KSHV MEM and KSHV KS cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Crosslinking was terminated by adding glycine to a final concentration of 0.125M. Cells were washed twice in ice-cold PBS and harvested by centrifugation. Every 2×107 cells were lysed in 5 ml ice-cold Farnham lysis buffer (5 mM PIPES [pH 8.0], 85 mM KCl, 0.5% NP-40) with protease inhibitors. The nuclei were spun down and resuspended in 1 ml RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, and 0.3% SDS in 1×PBS) with protease inhibitors. Chromatin was sheared to about 250 bp fragments with 10 cycles using a Bioruptor Pico sonication device (Diagenode).
The NEB Next Ultra II DNA Library Prep Kit for Illumina (cat. # E7645L) was used for preparing libraries with the manufacturer’s protocol and associated reagents.

tag: antibody


title: KSHV positive Pα(+)S MSCs in MEM alpha media H3K4me3 ChIP rep1


title: KSHV positive Pα(+)S MSCs in MEM alpha media H3K4me3 ChIP rep2


title: KSHV positive Pα(+)S MSCs in MEM alpha media H3K27me3 ChIP rep2


title: KSHV positive Pα(+)S MSCs in MEM alpha media H3K27me3 ChIP rep1


title: KSHV positive Pα(+)S MSCs in MEM alpha media ChIP input


title: KSHV positive Pα(+)S MSCs in MEM alpha media IgG ChIP

value: IgG


title: KSHV positive  Pα(+)S MSCs in KS media ChIP input


title: KSHV positive  Pα(+)S MSCs in KS media H3K27me3 ChIP rep3


title: KSHV positive  Pα(+)S MSCs in KS media H3K27me3 ChIP rep1


title: KSHV positive  Pα(+)S MSCs in KS media H3K27me3 ChIP rep2


title: KSHV positive  Pα(+)S MSCs in KS media H3K4me3 ChIP rep3


title: mic_Wild-24.M

tag: strain

value: Wild/France

value: Bio-Rad


title: KSHV positive  Pα(+)S MSCs in KS media H3K4me3 ChIP rep1

tag: treatment


title: KSHV positive Pα(+)S MSCs in MEM alpha media H3K27me3 ChIP rep3


title: mic_Wild-23.M


title: mic_Wild-25.M


title: mic_Wild-21.M


title: mic_Wild-22-CD45neg.M


title: Sample_6

city: New Haven

first: Richard

last: Flavell

address: 300 Cedar Street, TAC S-569

department: Department of Immunobiology

institute: Yale University

data_processing:
Drop-seq preprocessing was performed using DropSeq tools (https://anaconda.org/bioconda/dropseq_tools).
The alignment was peformed using STAR (2.6)
Bead synthesis error was detected using DetectBeadSynthesisErrors in DropSeq tools.
Read counts per cell were generated using BAMTagHistogram in DropSeq tools.
Visualization was done using ggplot2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped text file which includes gene-by-cell count matrix

source_name: Colon

extract_protocol:
Colons from 2 mice per genotype were dissected and flushed of fecal material. Tissue was opened longitudinally and further washed. Tissues were digested and single cell suspensions generated, and genotype samples pooled. Cells were then subjected to DropSeq.
RNA libraries were prepared for single sequencing using standard Illumina protocols

value: Hand2Cre C57BL/6 x SJL backcrossed to Il18f/f C57BL/6

value: Colon

tag: genotype

value: IL-18 Neuronal KO


title: mic_FVB_SPF-3.M

value: FVB


title: Sample_5

value: IL-18 WT


title: mic_FVB_SPF-1.M

value: Brain


title: MP_9_Bc_3A.M

value: BALB/cAnNCrl


title: MP_8_Bc_2A.M


title: MP_6_CD1_3A.M


title: MP_7_Bc_1A.M


title: KSHV positive  Pα(+)S MSCs in KS media H3K4me3 ChIP rep2


title: KSHV positive  Pα(+)S MSCs in KS media IgG ChIP


title: MP_5_CD1_2A.M


title: MP_4_CD1_1A.M


title: MP_1_B6_1A.M


title: MP_3_B6_1C.M


title: MP_2_B6_1B.M


title: AB4712

value: Immune cells

tag: selection marker

tag: catalog#


title: AB4713


title: AB4708


title: AB3010


title: AB3011


title: mic_FVB_SPF-2.M


title: AB3012


title: PIN 65 Normal

city: Dublin 9

first: Sandra

last: Roche

address: Glasnevin

institute: Dublin City University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HUGene 2.0ST . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was analysed using the Transcription Analysis console 4.0.2 using Affymetrix default analysis settings.

source_name: Normal human tumour afjacent material

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Samples were snap frozen in liquid nitrogen once received from pathology department

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

tag: tissue source

value: Normal Adjacent


title: Kit KA 24h rep2

city: Dublin 2

first: David

last: Henshall

address: 123 Saint Stephen Green

institute: FutureNeuro centre, Royal College of Surgeons in Ireland

description: small RNAs

data_processing:
MiRNA sequencing data was uploaded to Chimira webserver (Vitsios and Enright, 2015) where the sequences were adapter trimmed, mapped against miRBase v21 hairpin sequences and count-based miRNA expression data were generated (Kozomara and Griffiths-Jones, 2014).
Supplementary_files_format_and_content: total_plain_counts.counts files contain numbers of reads mapped to each miRNA per sample; total_modification_counts.counts files contain number of reads carrying A/C/T/G/ADAR modification at different positions along each miRNA of each sample

source_name: hippocampal exosomes

growth_protocol: Mice used in these experiments were 6-9 weeks old male C57BL/6 from Harlan Laboratories (UK), inbred with a 12 h light-dark cycle at 21-23ﾟC and humidity of 40-60% with ad libitum access to food and water.

extract_protocol:
ultracentrifugation (UC) method of exosome extraction: The protocol was adapted from Perez-Gonzalez et al (Perez-Gonzalez et al., 2012). Hippocampi were dissected and stored at -80. When ready for isolation, placed in 1mL hibernate A (Biosciences) and cut into small pieces. Tissue was manually titurated with additional 8mL hibernate A further loosened by passing it through a 10ml plastic pipette to obtain a homogenous solution. The solution was centrifuged at 300g for 10 minutes; note: this and further centrifugations were carried at 4°C. Supernatant was passed through 40μm mesh filter and again through a 0.2μm syringe filter. The filtrate was centrifuged at 2000g for 10 minutes. Ice cold PBS was added and was centrifuged at 10000g for 30 minutes. The supernatant was pipetted to an ultracentrifuge tube (polyalamar, thin-walled tubes, Fisher Scientific) which was ultracentrifuged at 100000g (23200rpm on surespin360 rotor) for 70 minutes to pellet EEFs. The tube was inverted and EEFs re-suspended in PBS.
exosome precipitation solution (Kit) method of exosome extraction: This used the adapted exosome isolation protocol from above without the 100000g ultracentrifugation step. Briefly, 1ml cold PBS was used to cut brain tissue into smaller pieces and then was manually titurated with additional 1ml PBS. The solution like before were put through low speed centrifugations and also passed through two filters as above. Without additional PBS, after the 10000g centrifugation, the exosome precipitation solution provided in the ExoQuick kit for biofluids was used; for every 500µl of sample, 120µl of solution is added. This mix was incubated at 4°C for 30 minutes. The sample was spun at 13000rpm for 2 minutes at 4°C and then re-suspended in PBS.
RNA was extracted from the exosomes post RNase-treatment; Isolated exosomes resuspended in 100µl PBS volume were treated with 2µl (20µg) of RNase-A (Fisher Scientific). This was incubated at 37ﾟC for 10 min shaking at 450rpm. To stop the reaction, 20µl (400U) of RNase Inhibitor (Biosciences) was added and again this was incubated at 37ﾟC for 20 min shaking at 450rpm. RNA extraction was carried out similar to that above with 800μl Trizol LS (Qiagen) used to titurate the sample, and a chloroform-mediated phase separation and isopropanol-mediated precipitation. The RNA was reconstituted in 7-9μl RNase-free water at 60°C for 10 minutes, shaking at 800rpm.
After extraction of RNA, 5μl from each sample was used to construct small complementary DNA libraries using the Illumina TruSeq Small RNA library kit, with each sample barcoded for identification. Small amount of RNA input required slight modification in the protocol whereby all kit reagents were halved in order to prevent substantial adapter dimer formation. Libraries were size selected using a Pippin Prep (Sage Science) with 3% agarose dye free cassettes and size selection was validated using a 2100 High sensitivity DNA Bioanalyzer chip (Agilent 2100). The concentration of each library was determined using the HS-dsDNA kit for Qubit. The cDNA libraries already barcoded for identification of each sample were pooled and then sequenced

treatment_protocol: Induction of status epilepticus was achieved via microinjection of KA (Sigma-Aldrich) into the right amygdala, propagating seizures to the hippocampus through the perforant pathway. As previously described (Mouri et al., 2008) mice were anaesthetized using 3-5% isoflurane in oxygen. The mice were then placed in a mouse-adapted stereotaxic frame. After a midline scalp incision, three cortical electrodes for electroencephalogram (EEG) recording were fixed with the dental cement. These were surgically inserted above the ipsilateral and contralateral dorsal hippocampus and the frontal cortex. A guide cannula (coordinates from Bregma; AP = -0.94 mm, L = -2.85 mm) was fixed in place using dental cement. Mice were placed in an incubator at 26ﾟC to recover. An injection cannula was then guided in through the already placed guide cannula for injection of either 0.3µg in 0.2µl KA or PBS into the basolateral amygdala nucleus. This led to seizure onset within 5-10 minutes. After 40 minutes, mice were administered anti-convulsant 8 mg/kg midazolam (Roche) intraperitoneally (IP) to curtail the seizures (Diviney et al., 2015). The animals were then placed in a warm recovery chamber. After cardiac perfusion with PBS to remove blood components, mice were sacrificed at a number of different timepoints 4, 8, 24 h or 2 w for PBS-control and KA-treated

tag: tissue

value: hippocampus

tag: cellular component

value: exosomes

tag: exosome extraction method

value: ExoQuick kit

tag: injected compound

value: Kainic acid

tag: days after injection

value: 1 day


title: Kit KA 2w rep3

description: small RNAs

value: 14 days


title: Kit KA 24h rep3

description: small RNAs


title: Kit control 2w rep2

description: small RNAs

value: PBS


title: PIN 120 Tumour

source_name: Human pancretic tumour material

value: Human Pancreas Tumour


title: PIN 120 F1 Generation

source_name: 1st generation of PDX tumour material from SCID mice

value: Tumour generated in SCID mice


title: PIN 161 Tumour


title: PIN 89 F1 Generation


title: PIN 140 Normal


title: PIN 112 F1 Generation


title: Kit control 2w rep3

description: small RNAs


title: Kit KA 2w rep2

description: small RNAs


title: PIN 80 Normal


title: PIN 161 F1 Generation


title: PIN 140 Tumour


title: Kit control 24h rep3

description: small RNAs


title: PIN 80 F1 Generation


title: PIN 89 Tumour


title: Kit control 24h rep2

description: small RNAs


title: PIN 112 Normal


title: PIN 160 F1 Generation


title: PIN 160 Tumour


title: PIN 140 F1 Generation


title: Kit KA 2w rep1

description: small RNAs


title: PIN 80 Tumour


title: PIN 160 Normal


title: PIN 120 Normal


title: PIN 112 Tumour


title: PIN 65 F1 Generation


title: Kit control 2w rep1

description: small RNAs


title: Kit KA 24h rep1

description: small RNAs


title: UC KA 2w rep3

description: small RNAs

value: ultracentrifugation


title: Kit control 24h rep1

description: small RNAs


title: UC control 2w rep3

description: small RNAs


title: UC KA 24h rep3

description: small RNAs


title: UC KA 24h rep2

description: small RNAs


title: UC control 24h rep2

description: small RNAs


title: UC control 2w rep2

description: small RNAs


title: UC control 2w rep1

description: small RNAs


title: UC control 24h rep3

description: small RNAs


title: UC KA 2w rep1

description: small RNAs


title: UC KA 2w rep2

description: small RNAs


title: UC control 24h rep1

description: small RNAs


title: hela-siH2A.Z-repli-seq_S5

first: Liwei

last: Zhang

address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

department: National Laboratory of Biomacromoluclues

institute: Institute of Biophysics

description:
BrdU
SI.S50.bw

data_processing:
ChIP-seq: clean reads were mapped to hg38 and mm10 reference genomes using bowtie2 with default parameters. Unique aligments were then retained for further analysis.ChIP-seq and NS-seq peaks were called using MACS (version 1.4.2, p-value ≤ 1e-5) and PeakSeq (version 1.3.1, false discovery rate ≤ 0.005) against their corresponding native genomic input data with a shift size of 75 bp. Peaks of ORC1, with distances between which were less than 500 bp, were further merged using bed-tools.
RNA-seq: clean reads were mapped to hg38 and mm10 reference genomes using TopHat (version 2.2.0) with default parameters. Differential expression analysis were performed using cufflinks (version 2.2.0). Genes with |log2(ratio)|≥ 1 and FDR less than 0.05 were selected as differentially expressed genes.
NS-seq: clean reads were mapped to hg38 and mm10 reference genomes using bowtie2 with default parameters. Unique alignments were then retained. RNase-untreated sample was initially used to call peak as described for ChIP-seq. Then RNase treated sample was used to remove non-NS derived noise using Fisher's exact test, peaks with low signals after RNase digestion were remained as true NS peaks (FDR≤0.05, log2(untreated/treated)≥log2(1.5)).
Genome_build: hg38, mm10
Supplementary_files_format_and_content: bigWig

source_name: Hela cell

growth_protocol: Hela cells were cultured in medium with 90% DMEM, 10%FBS, 1% Pen/Strep in standard incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ORC1 ChIP, the chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280). For native ChIP-seq, cells were collected and digested by MNase to get the mono-nucleosome. For BrdU-IP-seq, genomic DNA were extracted from cells and then sonicated to 200-500bp. The ChIP-seq antibodies are as following: Anti-H2A.Z, Abcam, ab4174; Anti-BrdU, BD, BD44; Anti-H4K20me1, Abcam, ab9051; Anti-H4K20me2, Abcam, ab9052; Anti-H4K20me3, Abcam, ab9053.
H2A.Z, H4K20me, ORC1,BrdU Libraries(sample 1-22, 35-44, 49-52) were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

treatment_protocol: Cells were transfected with siRNA oligos by lipo2000. Active CD4+ T cells were induced by by anti-CD3 and anti-CD28 for 72h from naïve CD4+ T cells of H2A.Zf/f and CD4creH2A.Zf/f mice

tag: cell line

value: Hela cell

tag: chip antibody

value: BD, BD44, S5

tag: library strategy

value: ChIP-seq


title: hela-siH2A.Z-repli-seq_S4

description:
BrdU
SI.S50.bw

value: BD, BD44, S4


title: hela-siSuv420H1/2-H4K20me2_rep2


title: D4-act-7g, replicate 1

city: Hong Kong

first: William Shu Biu

last: Yeung

address: Laboratory Block, 21 Sassoon Road

department: Obstetrics and Gynaecology

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: The cDNA was hybridized to GenChipTM Mouse Gene 2.0 ST array in duplicates

scan_protocol: Affymetrix protocol

data_processing: Microarray data was analyzed by the Partek Genomics Suite 6.6 following manufacturer's protocol. Quantile normalization was used with RMA background correction.

label: Biotin

source_name: Day 4-activated let-7g blastocysts

label_protocol: Biotin labeling

growth_protocol: The embryos were collected at blastocyst stage from let7g-transgenic mice in either D4-activated (D4-act-7g), in-vivo dormant (Dor-7g) or in-vitro let-7-induced dormant (DOX-7g) groups

extract_protocol: RNA was collected from 10 blastocysts from each group. Total RNA was extracted by heating the embryos in 10 ul of water for 5 minutes

value: Blastocysts

tag: strain/genotype

value: let7g-transgenic mice


title: D4-act-7g, replicate 2


title: hela-siNC-repli-seq_S5

description:
BrdU
NC.S50.bw

value: siNC


title: hela-siNC-repli-seq_S3

description:
BrdU
NC.S50.bw

value: BD, BD44, S3


title: hela-siH2A.Z-repli-seq_S2

description:
BrdU
SI.S50.bw

value: BD, BD44, S2


title: Dor-7g, replicate 2

source_name: in-vivo dormant blastocysts on Day 7


title: hela-siNC-repli-seq_S4

description:
BrdU
NC.S50.bw


title: hela-siH2A.Z-repli-seq_S3

description:
BrdU
SI.S50.bw


title: hela-siNC-repli-seq_S2

description:
BrdU
NC.S50.bw


title: UC KA 24h rep1

description: small RNAs

value: hippocampus

value: exosomes


title: DOX-7g, replicate 2

source_name: in-vitro DOX-induced dormant blastocysts on Day 7


title: DOX-7g, replicate 1


title: Dor-7g, replicate 1


title: IgG

city: Durham

first: Benjamin

last: Alman

state: NC

address: 200 Trent Drive, Orange Zone 5th floor

institute: Duke University

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly by using Bowtie program.
GLI Binding regions were identified by using the Picard package from MIT Broad Institute.
The transcriptome data in raw format were downloaded and quantile normalized by using the R Bioconductor Limma package to detect Differentially Expressed Genes.
Gene Ontology Pathway analysis of GLI targets and differentially expressed genes were performed by using GREAT and David tools.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated by using BEDTools. The Signal Intensity Score identified in GLI Binding Regions indicate the level of enrichment of ChIP-DNA in the region.

source_name: chondrosarcoma

growth_protocol: Cells were isolated from primary chondrosarcoma and cultured to 70% confluency.

extract_protocol:
Samples were subjected to chromatin immunoprecipitation and prepared for sequencing using the Active Motif ChIP-IT kit, according to the manufacturer's instructions.
Libraries were prepared according to the Illumina protocol at The Centre for Applied Genomics at The Hospital for Sick Children.

treatment_protocol: Shh ligand was applied at 0.5ug/mL for 48 hours.

value: chondrosarcoma

tag: culture

value: primary cells

value: Shh ligand

tag: duration

value: 48 hours


title: Gli2

value: anti-Gli2 (R&D catalog number AF3526)


title: hela-siSuv420H1/2-H4K20me2_rep1


title: LTBI 310-310

type: protein

city: Guangzhou

first: Huihua

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

institute: Jinan University

description:
LTBI 310
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

hyb_protocol: 2-fold diluted culture supernatant was added to each well. After overnight incubation at 4°C and extensive washing, the biotin-labeled detection antibody was added for 2 hours and then washed away. AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 300 scanner (Innopsys, Carbonne, France).

data_processing: Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls. For protein quantification, standard curves were generated using purified proteins representing the proteins-of-interest.

label: AlexaFluor 555

molecule: protein

source_name: Culture supernatant from Mtb-stimulated whole blood

extract_protocol: Culture supernatant from whole blood

treatment_protocol: Whole blood (250 µl) collected from participants using an EDTA anticoagulation tube was cultured in serum-free medium (DKW34-EHK0100, DAKEWE) in absence or presence of 2.5 µg/ml phytohemagglutinin (PHA, L8754, Sigma) or 10 µg/ml Mtb-antigen peptide pool for 24 h at 37°C, 5% CO2, and then the supernatant was collected.

value: Whole blood

tag: histology

value: Latent tuberculosis infection

tag: groups

value: Establish and test


title: LTBI 308-308

description:
LTBI 308
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

label_protocol: AlexaFluor 555-conjugated streptavidin was then added and incubated for 1 hour at room temperature.


title: Gli1

tag: treatment

value: anti-Gli1 (R&D catalog number AF3324)


title: HC 296-296

description:
HC 296
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Healthy


title: LTBI 304-304

description:
LTBI 304
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 302-302

description:
LTBI 302
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 298-298

description:
HC 298
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 300-300

description:
HC 300
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 306-306

description:
LTBI 306
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 294-294

description:
HC 294
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 292-292

description:
HC 292
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: EDL_KO_3

city: La Jolla

first: Simon

last: Schenk

state: California

address: 9500 Gilman Drive #0863

department: Orthopaedic Surgery

institute: University of California San Diego

description: Gene expression after 5 days after knockout induction in WT and PCKO mice.

hyb_protocol: Hybridisation was done according to manufacturer's instructions (Agilent; One-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labeling)

scan_protocol: Slides were scanned usign an Agilent C Scanner with Feature extraction and analysis software.

data_processing: Raw signal intensities were normalized across samples using multiple loess normalization. Based on the visual inspection of the signal intensity distribution, a probe was considered detected if the mean (across samples) log2 signal intensity was greater than 2.5.

source_name: KO, Extensor digitorum longus muscle

label_protocol: Labeling was done according to manufacturer's instructions (Agilent; One-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labeling)

extract_protocol: RNA was extracted from EDL muscle by Tri reagent (Sigma Aldrich, Kent, UK) and purified on Reliaprep spin columns (Promega, Wisconsin, USA) using the manufacturer’s instructions.

treatment_protocol: Mice with skeletal muscle-specific and inducible knockout of p300 and CBP (PCKO) were treated with tamoxifen via oral gavage for 5 days, starting at 13-15 weeks of age. At the day after the last tamoxifen gavage, mice were sacrificed after a 4 hour fast.

tag: strain

tag: genotype

value: CBP (PCKO)

value: Skeletal muscle

tag: Sex

value: Male


title: EDL_WT_2

source_name: WT, Extensor digitorum longus muscle

value: wildtype

tag: tissue


title: Definite TB 288-288

description:
Definite TB 288
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Pulmonary tuberculosis


title: EDL_WT_1


title: EDL_KO_1


title: EDL_KO_2


title: Definite TB 286-286

description:
Definite TB 286
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: EDL_WT_3


title: HC 290-290

description:
HC 290
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: EDL_WT_4


title: Definite TB 282-282

description:
Definite TB 282
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 280-280

description:
Probable TB 280
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 284-284

description:
Definite TB 284
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 278-278

description:
Probable TB 278
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: EDL_KO_4


title: PN 276-276

description:
PN 276
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.

value: Non-TB pulmonary inflammations


title: PN 270-270

description:
PN 270
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 272-272

description:
PN 272
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 274-274

description:
PN 274
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 268-268

description:
PN 268
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 266-266

description:
PN 266
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 260-260

description:
LTBI 260
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 256-256

description:
LTBI 256
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 250-250

description:
HC 250
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 264-264

description:
LTBI 264
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 262-262

description:
LTBI 262
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 258-258

description:
LTBI 258
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 252-252

description:
HC 252
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 246-246

description:
HC 246
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 242-242

description:
HC 242
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 238-238

description:
Probable TB 238
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 248-248

description:
HC 248
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 224-224

description:
PN 224
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 232-232

description:
Definite TB 232
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 228-228

description:
PN 228
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 244-244

description:
HC 244
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 240-240

description:
Definite TB 240
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 236-236

description:
Definite TB 236
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 226-226

description:
PN 226
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 230-230

description:
Definite TB 230
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 222-222

description:
PN 222
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 218-218

description:
PN 218
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 220-220

description:
PN 220
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 216-216

description:
LTBI 216
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 210-210

description:
LTBI 210
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 214-214

description:
LTBI 214
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 208-208

description:
LTBI 208
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 254-254

description:
LTBI 254
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 234-234

description:
Definite TB 234
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 206-206

description:
LTBI 206
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 200-200

description:
HC 200
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 190-190

description:
Probable TB 190
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 204-204

description:
HC 204
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 196-196

description:
HC 196
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 202-202

description:
HC 202
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 198-198

description:
HC 198
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 194-194

description:
HC 194
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 192-192

description:
Definite TB 192
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 186-186

description:
Definite TB 186
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 182-182

description:
Definite TB 182
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 180-180

description:
PN 180
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 212-212

description:
LTBI 212
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 188-188

description:
Definite TB 188
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 176-176

description:
PN 176
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 174-174

description:
PN 174
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 184-184

description:
Definite TB 184
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 168-168

description:
LTBI 168
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 164-164

description:
LTBI 164
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 170-170

description:
PN 170
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 178-178

description:
PN 178
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 162-162

description:
LTBI 162
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 166-166

description:
LTBI 166
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 156-156

description:
HC 156
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 160-160

description:
LTBI 160
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 154-154

description:
HC 154
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 152-152

description:
HC 152
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 150-150

description:
HC 150
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 158-158

description:
LTBI 158
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 172-172

description:
PN 172
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 148-148

description:
HC 148
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 142-142

description:
Definite TB 142
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 144-144

description:
Definite TB 144
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 140-140

description:
Definite TB 140
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 138-138

description:
Definite TB 138
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 132-132

description:
PN 132
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 134-134

description:
Definite TB 134
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 136-136

description:
Definite TB 136
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 146-146

description:
HC 146
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 130-130

description:
PN 130
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 124-124

description:
PN 124
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 126-126

description:
PN 126
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 128-128

description:
PN 128
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 118-118

description:
LTBI 118
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 116-116

description:
LTBI 116
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 114-114

description:
LTBI 114
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 108-108

description:
HC 108
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 106-106

description:
HC 106
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 112-112

description:
LTBI 112
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 110-110

description:
LTBI 110
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 96-96

description:
Definite TB 96
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 102-102

description:
HC 102
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: HC 98-98

description:
HC 98
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 122-122

description:
PN 122
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Probable TB 92-92

description:
Probable TB 92
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 94-94

description:
Definite TB 94
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 86-86

description:
Definite TB 86
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 90-90

description:
Definite TB 90
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: Definite TB 88-88

description:
Definite TB 88
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 76-76

description:
PN 76
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 80-80

description:
PN 80
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 82-82

description:
PN 82
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: LTBI 120-120

description:
LTBI 120
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.


title: PN 78-78

description:
PN 78
Secreted proteins
Raybio human custom sandwich based antibody array. A combination of one non-overlapping array to quantitatively measure 16 human cytokines. Each antibody, together with the positive controls is arrayed in quadruplicate.