title: Caski_cisplatin_2

city: nakagami-gun

first: Shinichiro

last: Kina

state: Okinawa

address: 207 Uehara, Nishihara

department: Department of Clinical Neuroscience Oral and Maxillofacial Functional Rehabilitation

institute: University of Ryukyus

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (RMA) were used Affymetrix® Expression Console™ Software.

source_name: Caski cells treated with cisplatin for 12h

extract_protocol: RNA from cell lines was prepared using the RNeasy Mini Kit (Qiagen).

tag: cell

value: Caski

tag: treatment

value: cisplatin exposure for 12h


title: Caski_cisplatin + C1_3

status: Public on Dec 01 2018

type: RNA

country: Japan

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Caski cells treated with cisplatin plus C1 for 12h

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

value: cisplatin exposure with EphA4 inhibitor C1 for 12h


title: 1627C: Adjacent Mucosa of Patient 1627

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

department: DPDS

country: Belgium

institute: Janssen R&D

hyb_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

data_processing: Data were analyzed using Bioconductor 3.2 running on R 3.2.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

source_name: Patient 1627

extract_protocol: Qiagen RNAeasy FFPE

tag: patient id

tag: age

tag: gender

value: Female

tag: tissue

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign

tag: tnm

tag: uicc


title: Caski_control_1

source_name: Control Caski cells

value: no treatment


title: Monoculture, 1mM, Rep-1

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

description: US10293825_253949443385_S01_GE1_107_Sep09_2_2.txt:gProcessedSignal

hyb_protocol: Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data analysis was performed using GeneSpring version GX11.5 (Agilent Technologies) The DNAN exposure experiments were analyzed individually.  Raw microarray data were first normalized to the 75th percentile within each array followed by median scaling among all exposures. The effects of the two main experimental conditions, culture (mono- versus co-culture) and chemical exposure level (DMSO+ control, dose 1 and dose 2), were tested for effects on  expression using two-way ANOVA where p = 0.01, including Benjamini-Hochberg multiple test corrections. Pairwise comparisons among experimental treatment levels were conducted using Welch unpaired unequal variance t-tests including a 1.5 fold cutoff. Finally, principal component analysis (PCA) was performed to visualize summary-level trends in expression among treatments.

label_protocol: The Agilent Low Input QuickAmp Labelling Kit protocol (Agilent Technologies) was utilized for cRNA synthesis with microarray hybridizations following manufacturer’s recommendations. Fifteen ng of total RNA was used for starting material and 600 ng of Cy3 labelled cRNA was used for hybridizations.

growth_protocol: Five cell lines (kidney proximal tubule epithelial cells: HK-2; liver: THLE-3; lung: NuLi-1; vascular endothelium: TeloHAEC; heart: AC10; all from American Type Culture Collection, ATCC®, Manassas, VA) derived from normal tissues were chosen for the broad representation of organ systems to maximize coverage of toxicity screening.  Cells were kept in an incubator at 37°C, 90% humidity and 5% CO2.  Culture vessels (25 and 75 cm2 tissue culture flasks) for liver, lung and heart muscle cells were coated with collagen as per manufacturer instructions (ATCC®, Manassas, VA).  Manufacturer recommended media and additives were used for each cell line.

extract_protocol: RNA from the mono- and co-culture cell samples was extracted using the NucleoSpin RNA XS kit (Clontech Laboratories Inc., Mountain View, CA, USA) following manufacturer instructions.  RNA quantity was assessed using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific Inc.).  RNA integrity was assessed through microelectrophoresis analysis using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) run on an Agilent Bio-Analyzer (Agilent Technologies).  Only samples with RNA integrity numbers > 7 were used for the microarray hybridizations.

treatment_protocol: The IdMOC system is a 96-well plate divided into 16 chambers, each containing 6 wells that can be submerged with culture media in order to create a co-culture exposure.  For cells requiring a collagen coated surface (liver, lung and heart muscle cells), individual wells were coated with collagen/fibronectin as needed in advance of the addition of cells to the co-culture plate.  Each cell line was then placed in a well of an IdMOC chamber in its respective growth media as per manufacturer instructions within an initial monoculture exposure and then incubated for 24 hours.  After having confirmed that each cell line formed a confluent (80-95%) layer, cell line specific media was replaced by the pre-determined co-culture media (Universal Primary Cell Plating Media, In vitro ADMET Laboratories®), covering the entire set of wells.  Plates were then incubated on shakers at low speed for an additional 24 hours while exposed to the four exposure concentrations of DNAN (plus controls) as determined by the cell viability assays described above where each treatment included four replicates.  Each 6 member well served as a statistical replicate in our IdMOC experiments.  Parallel to the co-culture exposures, monocultures in 96 well culture tissue plates were established using identical plating techniques, incubations, munitions exposure concentrations, and replication as described for the co-culture exposures to provide direct comparative testing of effects among the mono- and co-culture assays.  Upon exposure completion, all cells were then harvested, flash- frozen using liquid nitrogen and stored at -80°C.  The samples from the kidney cells exposed to the two highest concentrations of toxicants were selected for further investigation via transcript expression analysis in addition to kidney cells from the control exposures.  Kidney cells were selected due to the renal toxicity observed in mammalian TNT exposures (Levine et al. 1984, Dilley et al. 1982b, Levine et al. 1990b, US Army 1984a), and to test if potential TNT metabolism by liver cells in co-culture affected the overall toxicological response in kidney cells.

tag: cell line

tag: cell type

value: Kidney proximal tubule epithelial cells

tag: culture type

value: monoculture

tag: exposed to

value: 1mM 2,4-dinitroanisole (DNAN)


title: 25A: Adenoma of Patient 25

scan_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

source_name: Patient 25

value: Male

value: Adenoma

value: Tubular Adenoma (Sessile)


title: Monoculture, 100µM, Rep-3

description: US10293825_253949443384_S01_GE1_107_Sep09_2_3.txt:gProcessedSignal

value: 100µM 2,4-dinitroanisole (DNAN)


title: 4507B: Tumor of Patient 4507

source_name: Patient 4507

label_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

value: Tumor

value: Adenocarcinoma of the Rectum

value: pT3, pN0, pMX

value: IIA


title: Monoculture, 100µM, Rep-1

description: US10293825_253949443384_S01_GE1_107_Sep09_1_4.txt:gProcessedSignal


title: 25B: Tumor of Patient 25

value: Infiltrating Adenocarcinoma

value: pT3, pN1, pMX

value: IIIB


title: 25C: Adjacent Mucosa of Patient 25

value: Adjacent Mucosa


title: 4507C: Adjacent Mucosa of Patient 4507

value: Female

value: Benign


title: 4507A: Adenoma of Patient 4507

value: Tubular Adenoma with High Grade Dysplasia


title: control, biological replicate B

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from Luciferase-infected monocytes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization. RMA data have been batch corrected using ComBat.

source_name: CD14+ cells isolated from buffy coat infected with luciferase-encoding lentivirus

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: Freshly-isolated human monocytes from buffy coats were infected for four hours by spin-inoculation and cultured for 18 hours in RPMI 10% FBS

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

treatment_protocol: Human monocytes were infected with Luciferase- or c-FLIP- lentiviruses

tag: sample type

value: in vitro infected monocytes from healthy donors

tag: infection

value: Luciferase-infected


title: control, biological replicate A


title: Monoculture, DMSO Control, Rep-4

description: US10293825_253949443384_S01_GE1_107_Sep09_1_1.txt:gProcessedSignal

source_name: HK-2_Monoculture_DMSO Control

value: Kidney proximal tubule epithelial cells

value: monoculture

value: DMSO Control


title: bipolar disorder lymphoblast pool, lithium treated, technical replicate 2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: lymphoblast pool from 10 bipolar disorder patients cultured in the presence of lithium, technical replicate 2

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Human Genome U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: Lymphoblasts were cultured in RPMI1640 medium supplemented with 15% fetal bovine serum (FBS) and 2 mM L-glutamine; fibroblasts were cultured in DMEM medium supplemented with 10% FBS; culture conditions for both cell types were 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Protect Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: For lithium treatment, culture medium was supplemented with 1 mM LiCl2.

tag: disorder

value: bipolar disorder

value: lithium

value: lymphoblast


title: control lymphoblast pool, lithium treated, technical replicate 2

description: lymphoblast pool from 11 control individuals cultured in the presence of lithium, technical replicate 2

value: control


title: Monoculture, 100µM, Rep-2

description: US10293825_253949443442_S01_GE1_107_Sep09_2_1.txt:gProcessedSignal

value: 100µM 2,4-dinitroanisole (DNAN)


title: 5543A: Adenoma of Patient 5543

source_name: Patient 5543

value: Male

value: Adenoma

value: Tubulovillous Adenoma


title: bipolar disorder fibroblast pool, lithium treated

description: fibroblast pool from 10 bipolar disorder patients cultured in the presence of lithium

value: fibroblast


title: bipolar disorder lymphoblast pool, lithium treated, technical replicate 1

description: lymphoblast pool from 10 bipolar disorder patients cultured in the presence of lithium, technical replicate 1


title: control fibroblast pool, lithium treated

description: fibroblast pool from 11 control individuals cultured in the presence of lithium


title: 5543B: Tumor of Patient 5543

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: bipolar disorder lymphoblast pool, vehicle treated, technical replicate 1

description: lymphoblast pool from 10 bipolar disorder patients cultured in the presence of vehicle substance, technical replicate 1

value: vehicle


title: bipolar disorder lymphoblast pool, vehicle treated, technical replicate 2

description: lymphoblast pool from 10 bipolar disorder patients cultured in the presence of vehicle substance, technical replicate 2


title: Monoculture, DMSO Control, Rep-2

description: US10293825_253949444910_S01_GE1_107_Sep09_2_4.txt:gProcessedSignal

value: Kidney proximal tubule epithelial cells


title: Monoculture, DMSO Control, Rep-3

description: US10293825_253949443384_S01_GE1_107_Sep09_2_1.txt:gProcessedSignal

value: monoculture


title: Monoculture, DMSO Control, Rep-1

description: US10293825_253949443443_S01_GE1_107_Sep09_2_1.txt:gProcessedSignal

value: DMSO Control


title: 5543C: Adjacent Mucosa of Patient 5543

value: Adjacent Mucosa

value: Benign


title: 5570A: Adenoma of Patient 5570

source_name: Patient 5570

value: Female


title: PDGF 48h n=2

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

source_name: HT29 cells with PDGF treatment at 48h

growth_protocol: 1.5 mio cells were seeded, recovering time 24h

extract_protocol: RNA was extracted according to manufactures' guidelines for QiaCube device (Qiagen).

treatment_protocol: cells were treated with PDGF (100ng/ml) and VEGF (100ng/ml) for 24, 48, and 72 hours

value: human colorectal adenocarcinoma cell line

tag: treated with

value: PDGF (100ng/ml) for 48hrs

tag: sample group

value: PDGF

tag: replicate

tag: rin

tag: hyb date


title: control lymphoblast pool, vehicle treated, technical replicate 1

description: lymphoblast pool from 11 control individuals cultured in the presence of vehicle substance, technical replicate 1

value: control

tag: treatment

value: lymphoblast


title: control fibroblast pool, vehicle treated

description: fibroblast pool from 11 control individuals cultured in the presence of vehicle substance

value: fibroblast


title: control lymphoblast pool, lithium treated, technical replicate 1

description: lymphoblast pool from 11 control individuals cultured in the presence of lithium, technical replicate 1

value: lithium


title: PDGF 72h n=2

source_name: HT29 cells with PDGF treatment at 72h

value: PDGF (100ng/ml) for 72hrs


title: control lymphoblast pool, vehicle treated, technical replicate 2

description: lymphoblast pool from 11 control individuals cultured in the presence of vehicle substance, technical replicate 2


title: control_PDGF 72h n=2

source_name: HT29 controls for PDGF treatment at 72h

value: PDGF vehicle for 72hrs


title: 2967A: SSA of Patient 2967

source_name: Patient 2967

tag: patient id

tag: age

tag: gender

value: Male

tag: tissue

value: SSA

value: Sessile Serrated Adenoma


title: VEGF 72h n=2

source_name: HT29 cells with VEGF treatment at 72h

tag: cell line

value: VEGF (100ng/ml) for 72hrs

value: VEGF


title: 5570B: Tumor of Patient 5570

value: Tumor

tag: adenomadiagnosis

value: Infiltrating Adenocarcinoma

tag: tnm

value: pT1, pN0, pMX

tag: uicc

value: I


title: 4155A: Adenoma of Patient 4155

source_name: Patient 4155

value: Adenoma

value: Tubulovillous Adenoma


title: VEGF 48h n=2

source_name: HT29 cells with VEGF treatment at 48h

tag: cell type

value: human colorectal adenocarcinoma cell line

value: VEGF (100ng/ml) for 48hrs


title: bipolar disorder fibroblast pool, vehicle treated

description: fibroblast pool from 10 bipolar disorder patients cultured in the presence of vehicle substance

value: bipolar disorder

value: vehicle

value: fibroblast


title: 4155C: Adjacent Mucosa of Patient 4155

value: Adjacent Mucosa

value: Benign


title: 4155B: Tumor of Patient 4155

value: Male

value: Adenocarcinoma


title: cFLIP, biological replica C

description: Gene expression data from c-FLIP-infected monocytes.

source_name: CD14+ cells isolated from buffy coat infected with FLIP-encoding lentivirus

tag: sample type

value: in vitro infected monocytes from healthy donors

tag: infection

value: c-FLIP-infected


title: control_VEGF 72h n=2

source_name: HT29 controls for VEGF treatment at 72h

tag: treated with

value: VEGF vehicle for 72hrs


title: wild-type mammary epithelial cells, biological replicate 2

city: Ann Arbor

first: Stephen

middle: J.

last: Weiss

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

hyb_protocol: Following labeling procedure, 3 ug of cDNA were hybridized at 48C on Mouse ST 2.1 Arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical language version 3.1.1. RMA was used to fit log2 transformed expression values.

organism: Mus musculus

source_name: wild-type mammary epithelial cells

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico kit protocol (GeneChip® WT Pico Reagent Kit Manual P/N 703262 Rev. 1) from 50 ng total RNA

growth_protocol: Mammary epithelial cells were isolated from inguinal mammary gland tissue from 4 week-old mice.

extract_protocol: Inguinal (lymph node-free) mammary gland tissue was minced, collagenase-digested and subjected to differential centrifugations to remove the stromal cell fraction. Isolated mammary epithelial cell aggregates were then lysed in 1 mL TRIzol (Ambion, Life Technologies). Total RNA was extracted with chloroform according to standard protocols and purified with QIAGEN RNeasy  Mini-kit columns.

tag: strain background

value: congenic FVB/NJ

tag: genotype/variation

value: wild-type

value: 4 weeks

value: mammary epithelial cells


title: 2967B: Tumor of Patient 2967

value: Tumor

value: Infiltrating Adenocarcinoma

value: pT3, pN1, pM1

value: IV


title: wild-type mammary epithelial cells, biological replicate 1


title: control_VEGF 48h n=2

source_name: HT29 controls for VEGF treatment at 48h

value: human colorectal adenocarcinoma cell line

value: VEGF vehicle for 48hrs

tag: sample group

tag: replicate

tag: rin


title: 2967C: Adjacent Mucosa of Patient 2967

tag: patient id

value: Adjacent Mucosa


title: PDGF 24h n=2

source_name: HT29 cells with PDGF treatment at 24h

value: PDGF (100ng/ml) for 24hrs

value: PDGF

tag: hyb date


title: MMTV-PyMT+/MMTV-Cre+/Mmp14(f/f) intact tumor, biological replicate 3

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse ST 2.1 Arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.0.0. RMA was used to fit log2 transformed expression values.

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Intact MMTV-PyMT mammary tumors were harvested from the inguinal and thoracic mammary glands of 3-4 month-old mice.

extract_protocol: MMTV-PyMT mammary tumors were flash frozen in liquid nitrogen and homogenized in 1mL TRIzol (Ambion, Life Technologies). Total RNA was extracted with chloroform according to standard protocols and purified with QIAGEN Rneasy Mini-kit columns.

value: conditional knockout [MMTV-Cre+/Mmp14(f/f)] MMTV-PyMT

tag: age

value: 3-4 months

value: MMTV-PyMT mammary tumors


title: 435B: Tumor of Patient 435

source_name: Patient 435

tag: gender

value: Female

tag: tissue

value: Invasive Adenocarcinoma

value: pT3, pNX, pMX

value: IIA


title: MMTV-Cre+ mammary epithelial cells, biological replicate 2

source_name: MMTV-Cre+ mammary epithelial cells

value: congenic FVB/NJ

value: Cre-expressing [MMTV-Cre+]

value: 4 weeks

value: mammary epithelial cells


title: 435A: Adenoma of Patient 435

value: Adenoma

tag: adenomadiagnosis

value: Tubulovillous Adenoma


title: control_PDGF 24h n=2

source_name: HT29 controls for PDGF treatment at 24h

tag: cell line

value: human colorectal adenocarcinoma cell line

value: PDGF vehicle for 24hrs


title: 435C: Adjacent Mucosa of Patient 435

value: Adjacent Mucosa

value: Benign

tag: tnm

tag: uicc


title: VEGF 24h n=2

source_name: HT29 cells with VEGF treatment at 24h

tag: cell type

value: VEGF (100ng/ml) for 24hrs

value: VEGF


title: control_PDGF 48h n=2

source_name: HT29 controls for PDGF treatment at 48h

value: PDGF vehicle for 48hrs


title: MMTV-Cre+ mammary epithelial cells, biological replicate 1


title: MMTV-PyMT+/MMTV-Cre+/Mmp14(f/f) intact tumor, biological replicate 4

value: conditional knockout [MMTV-Cre+/Mmp14(f/f)] MMTV-PyMT

value: 3-4 months

value: MMTV-PyMT mammary tumors


title: control_VEGF 24h n=2

source_name: HT29 controls for VEGF treatment at 24h

value: VEGF vehicle for 24hrs


title: MMTV-PyMT+/Mmp14(f/f) intact tumor, biological replicate 3

source_name: MMTV-PyMT+/Mmp14(f/f) intact tumor

value: congenic FVB/NJ

value: wild-type [Mmp14(f/f)] MMTV-PyMT


title: 1246A: Adenoma of Patient 1246

source_name: Patient 1246

value: Female

value: Tubular Adenoma


title: MMTV-PyMT+/Mmp14(f/f) intact tumor, biological replicate 4


title: PDGF 72h n=1

source_name: HT29 cells with PDGF treatment at 72h

value: PDGF (100ng/ml) for 72hrs

value: PDGF


title: MMTV-PyMT+/Mmp14(f/f) intact tumor, biological replicate 2


title: MMTV-PyMT+/MMTV-Cre+/Mmp14(f/f) intact tumor, biological replicate 2


title: MMTV-PyMT+/MMTV-Cre+/Mmp14(f/f) intact tumor, biological replicate 1


title: 1246C: Adjacent Mucosa of Patient 1246


title: 4390A: SSA of Patient 4390

source_name: Patient 4390

value: SSA

value: Sessile Serrated Adenoma


title: MMTV-PyMT+/Mmp14(f/f) intact tumor, biological replicate 1


title: 4390B: Tumor of Patient 4390

value: Tumor

value: Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: control_PDGF 72h n=1

source_name: HT29 controls for PDGF treatment at 72h

value: human colorectal adenocarcinoma cell line

value: PDGF vehicle for 72hrs


title: control_VEGF 72h n=1

value: VEGF vehicle for 72hrs


title: MMTV-Cre+/Mmp14(f/f) mammary epithelial cells, biological replicate 2

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.1.1. RMA was used to fit log2 transformed expression values.

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico kit protocol (GeneChip® WT Pico Reagent Kit Manual P/N 703262 Rev. 1) from 10 ng total RNA

value: 4 weeks

value: mammary epithelial cells


title: 4733A: Adenoma of Patient 4733

source_name: Patient 4733

value: Male

value: Adenoma

value: Adenomatous Polyp with Moderate Dysplasia


title: Mmp14(f/f) mammary epithelial cells, biological replicate 3

source_name: Mmp14(f/f) mammary epithelial cells

value: congenic FVB/NJ

value: wild-type [Mmp14(f/f)]


title: VEGF 72h n=1

source_name: HT29 cells with VEGF treatment at 72h

value: VEGF (100ng/ml) for 72hrs

value: VEGF


title: PDGF 48h n=1

source_name: HT29 cells with PDGF treatment at 48h

value: PDGF (100ng/ml) for 48hrs

value: PDGF


title: 4733B: Tumor of Patient 4733

value: Tumor

value: Adenocarcinoma

value: pT2, pN1, pMX

value: IIIA


title: 6513A: Adenoma of Patient 6513

source_name: Patient 6513

value: Tubular Adenoma


title: Mmp14(f/f) mammary epithelial cells, biological replicate 2


title: MMTV-Cre+/Mmp14(f/f) mammary epithelial cells, biological replicate 1


title: Mmp14(f/f) mammary epithelial cells, biological replicate 1


title: control_PDGF 48h n=1

value: human colorectal adenocarcinoma cell line

value: PDGF vehicle for 48hrs


title: 4390C: Adjacent Mucosa of Patient 4390

value: Female

value: Adjacent Mucosa

value: Benign


title: VEGF 24h n=1

value: VEGF (100ng/ml) for 24hrs


title: 6513B: Tumor of Patient 6513

value: Male

value: Mucin-producing Adenocarcinoma

value: pT3, pN0, pM1

value: IV


title: PDGF 24h n=1

source_name: HT29 cells with PDGF treatment at 24h

value: PDGF (100ng/ml) for 24hrs


title: control_PDGF 24h n=1

value: PDGF vehicle for 24hrs


title: 6513C: Adjacent Mucosa of Patient 6513


title: control_VEGF 48h n=1

source_name: HT29 controls for VEGF treatment at 48h

value: VEGF vehicle for 48hrs


title: 6758B: Tumor of Patient 6758

source_name: Patient 6758

value: Tumor

value: Invasive Adenocarcinoma

value: pT2, pN0, pMX

value: I


title: MiR-137 knockdown in SH-SY5Y cells, replicate 3

description: SH-SY5Y cells transfected with anti-miR-137, replicate 3

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy; background correction, quantiles normalization and RMA probeset summary were performed with the rma command using default parameter settings.

growth_protocol: SH-SY5Y cells have been seeded in 24-well plates at a density of 1x10^5 cells per well and cultured at 37°C with DMEM/F12 medium containing 10% FBS.

extract_protocol: 72 hours post transfection total RNA was isolated using the Direct-zol RNA Mini Prep Kit (Zymo Research) following the manufacturers instructions.

treatment_protocol: 24 hours after seeding cells have been transfected with 15pM hsa-miR-137 anti-miR miRNA (Ambion) or Anti-miR Negative Control #1 (Ambion) using Lipofectamine RNAiMAX according to manufacturers instructions.

tag: treatment

value: miR-137 knockdown


title: 6758C: Adjacent Mucosa of Patient 6758


title: control_VEGF 24h n=1

value: human colorectal adenocarcinoma cell line

tag: treated with

value: VEGF vehicle for 24hrs


title: 1716B: Tumor of Patient 1716

source_name: Patient 1716

value: Female

value: Infiltrating Adenocarcinoma

value: pT3, pN1, pMX

value: IIIB


title: Anti-miR negative control-treated SH-SY5Y cells, replicate 3

description: SH-SY5Y cells transfected with anti-miR negative control, replicate 3

value: control


title: 1716C: Adjacent Mucosa of Patient 1716

value: Adjacent Mucosa

value: Benign


title: MiR-137 knockdown in SH-SY5Y cells, replicate 2

description: SH-SY5Y cells transfected with anti-miR-137, replicate 2


title: Division 2 T cells

type: SRA

city: Stanford

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

library_source: transcriptomic

data_processing:
Cell Ranger pipeline v2.1.0, including batch effect removal that includes combining individual samples into 1 file with read-depth normalization (10X Genomics).
The Cell Ranger cell-gene matrix was processed using Cell Ranger R Kit (10X Genomics) as described by Zheng, G.X. et al. (Nature Communications, 2017). Briefly, we first selected genes with ≥1 UMI counts in any given cell (19,222 genes). UMI counts were then normalized to UMI sums for each cell and multiplied by a median UMI count across cells. Next, the data were transformed by taking a natural logarithm of the resulting data matrix. We selected 1,000 most variably expressed genes based on normalized dispersion to calculate cell diversity, DPT, and create a force-directed layout graph.
Genome_build: GRCh38
Supplementary_files_format_and_content: An h5 file containing Cell Ranger pipeline output for filtered cell-gene data: columns contain cells batch-normalized across divisions and sorted by division ID (552 division 0 cells, 1,777 division 1 cells, and 1,731 division 2 cells).
Supplementary_files_format_and_content: A CSV file containing processed data for every cell (in rows, sorted by division ID) that includes gene expression and calculated parameters (in columns): Region (ID #1-4 based on cell coordicates in a force-directed layout graph); Region_50 (50 cells selected from each region based on DPT: #1 and #4 are DPT1/2-low, #2 is DPT2-high, #3 is DPT1-high); X, Y (cell coordicates in a force-directed layout graph); DC1-DC1 (diffusion components calculated using angular distance based on 1,000 most variably expressed genes); DPT1, DPT2; Division; all genes detected in at least 1 cell sorted according to normalized dispersion.

molecule: polyA RNA

source_name: Blood CD8+ T lymphocytes

growth_protocol: ~40 million peripheral blood mononuclear cells (PBMCs) from healthy donors were plated into a well of a 24-well plate with 2 mL cell culture medium (CCM; RPMI 1640 containing 10% FBS, 1x L-glutamine, and 1x penicillin/streptomycin) and 600 ng anti-CD3ε antibody (clone OKT3, Biolegend #317304). Starting at 48 hours post-activation, cells were maintained at ~2 million cells/mL in CCM containing 300 ng/mL anti-CD3ε antibody and 50 U/mL (5 ng/mL) recombinant human IL-2 (PeproTech #200-02).

extract_protocol:
Droplet-based single-cell RNA-sequencing on 10X Genomics Chromium platform.
10X Genomics Single Cell 3' v2 Kit

treatment_protocol: On day 0, naïve T cells were labeled with CFSE dye that enables cell tracking and cell division quantification and mixed with CFSE-negative PBMCs depleted of naive T cells to restore original cell proportions. On day 3, 10,000 CFSE+ single live CD8+ T cells were sorted based on CFSE division peaks into division 0, 1, or 2.

tag: division


title: MiR-137 knockdown in SH-SY5Y cells, replicate 1

description: SH-SY5Y cells transfected with anti-miR-137, replicate 1


title: 2866A: Adenoma of Patient 2866

source_name: Patient 2866

value: Male

value: Adenoma

value: Tubulovillous Adenoma


title: Anti-miR negative control-treated SH-SY5Y cells, replicate 1

description: SH-SY5Y cells transfected with anti-miR negative control, replicate 1


title: 2866C: Adjacent Mucosa of Patient 2866


title: 6758A: Adenoma of Patient 6758


title: 2866B: Tumor of Patient 2866

value: Tumor

value: Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: Nasal Polyp ALI at day 28, biological rep 7 (mRNA)

city: BARCELONA

first: Borja

last: Callejas-Díaz

state: CATALUÑA

address: Carrer de Casanova, 143, CELLEX Sector 2B

department: Clinical and Experimental Respiratory Immunoallergy

country: Spain

institute: IDIBAPS, HOSPITAL CLÍNIC

description: Gene expression data from NP ALI Cultures at day 28

hyb_protocol: Global transcriptional analysis using the GeneChip® 3’ IVT Express kit and the Human Genome U219 24-Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.

scan_protocol: GeneTitan Affymetrix genetic analysis system

data_processing: Microarray data (Affymetrix .cel files) were processed for raw data quality control analysis by using Robust Multichip Analysis (RMA) algorithm, which perform background correction, probe-level normalization, and probe-set summary.

source_name: NP ALI at day 28

label_protocol: Total RNA (100 ng, RIN ≥ 9) was processed for global transcriptional analysis using the GeneChip® 3’ IVT Express kit and the Human Genome U219 24-Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.

growth_protocol: Human primary basal cells were obtained from CRSwNP patients (n=7) and healthy subjects (NM, n=7) by the explant technique in BEGM™ (LONZA) media suplemented with SingleQuots™ (LONZA) containing: BPE, hydrocortisone, hEGF, epinephrine, insulin, triiodothyronine, transferrin, GA-1000, and retinoic acid. Cells were cultured and differentiated at the air-liquid interface (ALI) system for 28 days in differentiation media composed of B-ALI™ (Lonza) supplemented with suplemented with SingleQuots™ (LONZA) containing: BPE, hydrocortisone, hEGF, epinephrine, insulin, triiodothyronine, transferrin, GA-1000, and retinoic acid.

extract_protocol: Total RNA, including small RNAs, was isolated from cells using the miRNeasy Mini Kit from Qiagen (Valencia, CA, USA). Briefly, cells were lysed with Qiazol lysis buffer (Qiagen), with cells from three inserts pooled for each time point, followed by passage through a Qiashredder column (Qiagen). Total RNA was extracted via RNeasy mini spin columns. All incubation and washing steps were performed following the manufacturer’s instructions.

treatment_protocol: Human primary basal stem/progenitor cells were not treated during ALI culture. Mucociliary differentiation was only induced by differentiation media (B-ALI (Lonza) supplemented with SingleQuots™ kit containing: BPE, hydrocortisone, hEGF, epinephrine, insulin, triiodothyronine, transferrin, GA-1000, inducer, and retinoic acid) and exposure to air.

tag: individual

value: CRSwNP patient

tag: age (years)

value: M

tag: previous treatment

value: No

tag: atopy

value: Yes

value: BSC

tag: cells isolated from

value: NP

tag: protocol

value: ALI culture

tag: time

value: day 28


title: 1716A: SSA of Patient 1716

tag: patient id

tag: age

tag: gender

value: Female

value: SSA

value: Sessile Serrated Adenoma


title: Division 1 T cells


title: Nasal Polyp ALI at day 28, biological rep 6 (mRNA)


title: Nasal Polyp ALI at day 28, biological rep 5 (mRNA)


title: Anti-miR negative control-treated SH-SY5Y cells, replicate 2

description: SH-SY5Y cells transfected with anti-miR negative control, replicate 2

tag: cell line

value: control

tag: rin


title: 5647A: SSA of Patient 5647

source_name: Patient 5647

tag: tissue

tag: adenomadiagnosis

tag: tnm

tag: uicc


title: Division 0 T cells

tag: division


title: 5647B: Tumor of Patient 5647

value: Adenocarcinoma with focal signet ring formation

value: pT1, pN0, pMX

value: I


title: Nasal Polyp ALI at day 28, biological rep 3 (mRNA)

tag: individual

value: F

tag: cell type


title: Nasal Polyp ALI at day 28, biological rep 4 (mRNA)

tag: age (years)

tag: previous treatment


title: 5647C: Adjacent Mucosa of Patient 5647

value: Adjacent Mucosa

value: Benign


title: Nasal Polyp ALI at day 28, biological rep 2 (mRNA)

value: CRSwNP patient

value: M

tag: atopy

tag: cells isolated from


title: 4T

city: Shanghai

first: MENG

last: DUAN

state: Shanghai

address: 180 Fenglin Road

country: China

institute: Zhongshan Hospital

description: processed data file: read_count_matrix.csv

data_processing:
Basecalls performed using CASAVA version 1.4.
A raw sequencing read was discarded if it had: (1) an Illumina adaptor, (2) more than 10% N bases, or  (3) more than 50% bases with Q< 20.
Filtered reads were mapped to human genome (GRCh37) using HISAT2 with default parameters and sorted by samtools.
Gene abundance was then estimated using Stringtie and a matrix containing read counts for each gene and each sample was generated by preDE.py (provided on Stringtie website).
Differential expression analysis was performed using GLM model in edgeR. Genes with logFC > 1 and P-value < 0.01 were considered as differentially expressed genes.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: read_count_matrix.csv: Comma-separated text file containing read counts for each gene.
Supplementary_files_format_and_content: *.gene.abundance.txt: Tab-delimited text files containing FPKM and TPM values for each gene.

source_name: HCC tumoral tissues

extract_protocol:
RNA was extracted from 5000 cells using a miRNeasy Micro Kits (Qiagen, German). RNA quality was assessed with an Agilent RNA 6000 Pico Kit (Agilent Technologies, cat#5067-1513, USA) on an Agilent 2100 Bioanalyzer. Each library was prepared from 2ng of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease status

value: HCC

tag: tissue source

value: Tumor

value: Immune cells

tag: cell subset

value: CD4- MAIT cells

tag: subset definition


title: 3T


title: 5T


title: 2T


title: 1865B: Tumor of Patient 1865

source_name: Patient 1865

tag: patient id

tag: age

tag: gender

value: Male

value: Colonic Adenocarcinoma

value: pT3, pN1, pMX

value: IIIB


title: 4733C: Adjacent Mucosa of Patient 4733

tag: tissue

tag: adenomadiagnosis


title: Nasal Polyp ALI at day 28, biological rep 1 (mRNA)

value: No

value: BSC

value: NP

tag: protocol

value: ALI culture

tag: time

value: day 28


title: HDL4

source_name: Normal liver tissues

value: Healthy

value: Liver


title: HDL3


title: Nasal Mucosa ALI at day 28, biological rep 7 (mRNA)

description: Gene expression data from CONTROL NM ALI Cultures at day 28

source_name: Control NM ALI at day 28

tag: individual

value: healthy subject

value: NM


title: 3392C: Adjacent Mucosa of Patient 3392

source_name: Patient 3392

value: Female

value: Adjacent Mucosa

value: Benign

tag: tnm

tag: uicc


title: 1865C: Adjacent Mucosa of Patient 1865


title: HDL1

tag: cell type

value: Immune cells

value: CD4- MAIT cells


title: 3679A: Adenoma of Patient 3679

source_name: Patient 3679

value: Male

value: Adenoma

value: Adenomatous Polyp


title: 3392A: Adenoma of Patient 3392

value: Tubular Adenoma


title: 3679B: Tumor of Patient 3679

value: Tumor

value: Infiltrating Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: Nasal Mucosa ALI at day 28, biological rep 6 (mRNA)

tag: age (years)

value: M

tag: previous treatment

value: No

tag: atopy

value: BSC

value: ALI culture

value: day 28


title: Nasal Mucosa ALI at day 28, biological rep 3 (mRNA)

value: healthy subject

tag: cells isolated from

value: NM


title: Nasal Mucosa ALI at day 28, biological rep 2 (mRNA)

value: F


title: 1865A: SSA of Patient 1865

value: SSA

value: Sessile Serrated Adenoma


title: 392A: Adenoma of Patient 392

source_name: Patient 392

value: Female

value: Adenoma

value: Tubulovillous Adenoma


title: Nasal Mucosa ALI at day 28, biological rep 5 (mRNA)


title: 3392B: Tumor of Patient 3392

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN1, pMX

value: IIIB


title: 5P

source_name: HCC peritumoral tissues

tag: disease status

value: HCC

tag: tissue source

value: Peritumor

value: Immune cells

tag: cell subset

value: CD4- MAIT cells


title: Nasal Mucosa ALI at day 28, biological rep 4 (mRNA)

value: M

value: No

value: BSC

value: ALI culture

value: day 28


title: Nasal Polyp ALI at day 14, biological rep 7 (mRNA)

description: Gene expression data from NP ALI Cultures at day 14

source_name: NP ALI at day 14

value: CRSwNP patient

value: Yes

value: NP

value: day 14


title: 4P

tag: subset definition


title: HDL2

value: Healthy

value: Liver


title: 3P


title: 2P


title: 1P


title: Nasal Polyp ALI at day 14, biological rep 6 (mRNA)

tag: gender


title: Nasal Polyp ALI at day 14, biological rep 5 (mRNA)


title: Nasal Polyp ALI at day 14, biological rep 4 (mRNA)


title: 392B: Tumor of Patient 392

tag: patient id

tag: age

value: Female

tag: tissue

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN1, pMX


title: Week_4_Intermittent_DrugOff_rep_3

city: Boulder

first: Natalie

middle: G

last: Ahn

state: CO

address: 596 UCB

department: Department of Biochemistry

institute: University of Colorado Boulder

data_processing:
Adapter sequences and low quality base reads were removed using Trimmomatic (v.0.32, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Reads were then mapped to the Homo sapiens genome (GRCh38) using the alignment software, HISAT2 (v.2.0.3-beta, –dta –rna-strandness F)
The resulting SAM file was converted to a sorted BAM file using SAMtools (v.0.1.18)
Reads that mapped to genes in the GRCh38.84.gtf annotation file were counted using the htseq-count script in HTSeq (v.0.6.1, -f bam -r pos -s yes -t exon -m union -i gene_id)
Genome_build: GRCh38
Supplementary_files_format_and_content: complete_unnormalized_counts.txt:  Tab delimited text fil with unnormalized gene counts for each sample

source_name: Metastatic Melanoma Cell Line

extract_protocol:
Cells were rinsed with PBS, trypsinized, and centrifuged for 5 min at 300xg, then washed with 1 mL PBS and centrifuged again. After aspirating away PBS, cells were immediately frozen in liquid nitrogen and stored at -80ºC. At the end of the timecourse, all samples were thawed on ice and total RNA was purified using the Quick-RNA microprep kit (Zymo Research) according to the manufacturer’s protocol.
100 ng RNA was used to prepare mRNA libraries using the Universal Plus mRNA-seq kit (NuGEN).

tag: cell line

value: WM239A overexpressing BRAF-V600E

tag: drug treatment

value: 500nM LGX818 for 7d, DMSO for 7d,  500nM LGX818 for 7d, then DMSO for 7d


title: Week_4_Intermittent_DrugOff_rep_2


title: 392C: Adjacent Mucosa of Patient 392

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign

tag: tnm


title: Nasal Polyp ALI at day 14, biological rep 2 (mRNA)

tag: individual

value: M

value: No

tag: cell type

value: BSC

tag: protocol

tag: time


title: Week_4_Intermittent_DrugOff_rep_1


title: 1093A: Adenoma of Patient 1093

source_name: Patient 1093

value: Male

value: Adenoma

value: Adenovillous Polyp

tag: uicc


title: 4298A: Adenoma of Patient 4298

source_name: Patient 4298

value: Tubulovillous Adenoma


title: 1093C: Adjacent Mucosa of Patient 1093


title: Nasal Polyp ALI at day 14, biological rep 3 (mRNA)

value: CRSwNP patient

tag: age (years)

value: F

tag: previous treatment

tag: atopy

tag: cells isolated from

value: NP

value: ALI culture

value: day 14


title: Nasal Polyp ALI at day 14, biological rep 1 (mRNA)

tag: gender


title: 4298C: Adjacent Mucosa of Patient 4298

tag: patient id


title: 1246B: Tumor of Patient 1246

source_name: Patient 1246

tag: age

value: Female

value: Tumor

value: Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: Nasal Mucosa ALI at day 14, biological rep 7 (mRNA)

description: Gene expression data from CONTROL NM ALI Cultures at day 14

source_name: Control NM ALI at day 14

value: healthy subject

value: M

value: NM


title: A8776924-5

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 9.

source_name: tissue biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: Mucosal biopsies were collected 15 to 20 cm from the anal verge at screening during endoscopies from a subset of patients who participated in the PURSUIT (n=87) study.  Independent of the PURSUIT study , biopsies were also collected from 21 healthy normal subjects to serve as control.  Biopsies were immediately placed in RNAlater and subsequently stored at –80oC until RNA preparation.

tag: subject

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

tag: tissue

value: Colon


title: Nasal Mucosa ALI at day 14, biological rep 5 (mRNA)

value: No

value: BSC


title: VEGF 48h n=1

source_name: HT29 cells with VEGF treatment at 48h

tag: cell line

value: human colorectal adenocarcinoma cell line

tag: treated with

value: VEGF (100ng/ml) for 48hrs

tag: sample group

value: VEGF

tag: replicate

tag: rin

tag: hyb date


title: Nasal Mucosa ALI at day 14, biological rep 6 (mRNA)

tag: individual

tag: age (years)

tag: cell type

tag: protocol

value: ALI culture

tag: time

value: day 14


title: A8278373-5

value: Extensive


title: Week_4_continuous_rep_2

value: WM239A overexpressing BRAF-V600E

tag: drug treatment

value: 500nM LGX818 for 28d


title: 1093B: Tumor of Patient 1093

tag: patient id

tag: age

tag: gender

value: Male

value: Tumor

tag: adenomadiagnosis

value: Mucinous Adenocarcinoma

tag: tnm

value: pT2, pN0, pMX

tag: uicc

value: I


title: Week_4_continuous_rep_1

tag: cell line


title: Week_3_Intermittent_DrugOn_rep_3

value: 500nM LGX818 for 7d, DMSO for 7d, then 500nM LGX818 for 7d


title: Week_3_Intermittent_DrugOn_rep_2


title: E6089807-5

tag: subject

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

tag: tissue

value: Colon


title: Week_3_Intermittent_DrugOn_rep_1


title: Nasal Mucosa ALI at day 14, biological rep 4 (mRNA)

tag: individual

value: healthy subject

value: M

tag: previous treatment

value: No

tag: atopy

value: BSC

tag: cells isolated from

value: NM


title: 4298B: Tumor of Patient 4298

value: Colonic Adenocarcinoma

value: pT3, pN0, pMX

value: IIA


title: 7030A: Adenoma of Patient 7030

source_name: Patient 7030

value: Male

value: Adenoma

value: Tubulovillous Adenoma


title: Week_3_continuous_rep_3

value: WM239A overexpressing BRAF-V600E

value: 500nM LGX818 for 21d


title: 7030C: Adjacent Mucosa of Patient 7030

value: Adjacent Mucosa

value: Benign


title: 9060A: Adenoma of Patient 9060

source_name: Patient 9060

value: Female

value: Tubulovillos Adenoma with moderate cytologic atypia


title: 9060B: Tumor of Patient 9060

value: Tumor


title: Nasal Mucosa ALI at day 28, biological rep 1 (mRNA)

value: healthy subject

tag: age (years)

value: M

tag: cell type

tag: protocol

value: ALI culture

tag: time

value: day 28


title: Nasal Mucosa ALI at day 14, biological rep 3 (mRNA)

tag: gender

value: No

value: BSC

value: NM

value: day 14


title: A8357931-1

value: Extensive

value: Ulcerative Colitis (UC)

tag: age

value: Colon


title: Week_3_continuous_rep_2

value: WM239A overexpressing BRAF-V600E

tag: drug treatment

value: 500nM LGX818 for 21d


title: 9060C: Adjacent Mucosa of Patient 9060

tag: patient id

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign

tag: tnm

tag: uicc


title: Nasal Mucosa ALI at day 14, biological rep 2 (mRNA)

value: F


title: A8226350-1

tag: subject

tag: diseaseextent

value: Limited

tag: disease


title: Nasal Mucosa ALI at day 14, biological rep 1 (mRNA)

tag: individual

value: healthy subject

tag: previous treatment


title: E5625763-5

tag: tissue


title: 7030B: Tumor of Patient 7030

value: Male

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN1, pMX

value: IIIB


title: Nasal Polyp ALI at day 0, biological rep 7 (mRNA)

description: Gene expression data from NP ALI Cultures at day 0

source_name: NP ALI at day 0

value: CRSwNP patient

tag: age (years)

value: M

value: No

tag: atopy

value: Yes

value: BSC

tag: cells isolated from

value: NP

value: ALI culture

value: day 0


title: Week_3_continuous_rep_1

tag: cell line

value: WM239A overexpressing BRAF-V600E

value: 500nM LGX818 for 21d


title: A8347469-13

value: Limited

value: Ulcerative Colitis (UC)

value: Colon


title: 9684B: Tumor of Patient 9684

source_name: Patient 9684

tag: gender

value: Male

value: Tumor

value: pT2, pN1, pMX

value: IIIA


title: A8621077-5

tag: age


title: Nasal Polyp ALI at day 0, biological rep 5 (mRNA)

value: CRSwNP patient

tag: cell type

tag: protocol

tag: time


title: A8595462-9

value: Extensive


title: Week_2_Intermittent_DrugOff_rep_3

tag: drug treatment

value: 500nM LGX818 for 7d, DMSO for 7d


title: Week_2_Intermittent_DrugOff_rep_2


title: Week_2_Intermittent_DrugOff_rep_1

value: 500nM LGX818 for 7d, then DMSO for 7d


title: 9684A: Adenoma of Patient 9684

tag: patient id

value: Adenoma

tag: adenomadiagnosis

value: Tubulovillous Adenoma

tag: tnm

tag: uicc


title: A8347774-1

tag: subject

tag: diseaseextent

tag: disease


title: Week_2_continuous_rep_2

value: 500nM LGX818 for 14d


title: Nasal Polyp ALI at day 0, biological rep 6 (mRNA)

tag: individual

tag: age (years)

value: M

tag: previous treatment

value: No

value: Yes

value: BSC

value: NP

value: ALI culture

value: day 0


title: 1T

source_name: HCC tumoral tissues

tag: disease status

value: HCC

tag: tissue source

value: Tumor

value: Immune cells

tag: cell subset

value: CD4- MAIT cells

tag: subset definition


title: 290A: Adenoma of Patient 290

source_name: Patient 290

tag: age

tag: gender

value: Male

tag: tissue

value: Tubulovillous Adenoma with Moderate Dysplasia


title: A8532027-5

value: Limited

value: Ulcerative Colitis (UC)

value: Colon


title: Week_2_continuous_rep_1

tag: cell line

value: WM239A overexpressing BRAF-V600E

tag: drug treatment

value: 500nM LGX818 for 14d


title: Nasal Polyp ALI at day 0, biological rep 3 (mRNA)

value: CRSwNP patient

value: F

value: No

tag: atopy

tag: cell type

tag: cells isolated from

tag: protocol

tag: time


title: Nasal Polyp ALI at day 0, biological rep 4 (mRNA)

tag: individual

value: M

value: BSC

value: NP


title: 9684C: Adjacent Mucosa of Patient 9684

tag: patient id

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign

tag: tnm

tag: uicc


title: Week_2_continuous_rep_3


title: 10743A: Adenoma of Patient 10743

source_name: Patient 10743

value: Adenoma

value: Tubulovillous Adenoma with High Grade Dysplasia


title: Nasal Polyp ALI at day 0, biological rep 1 (mRNA)

tag: age (years)

tag: previous treatment

value: ALI culture

value: day 0


title: E5524610-5

tag: subject

tag: diseaseextent

value: Limited

tag: disease

tag: age


title: E5921403-5

value: Ulcerative Colitis (UC)

tag: tissue


title: 10743B: Tumor of Patient 10743

tag: gender

value: Male

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN2, pMX

value: IIIB


title: Nasal Mucosa ALI at day 0, biological rep 7 (mRNA)

description: Gene expression data from CONTROL NM ALI Cultures at day 0

source_name: Control NM ALI at day 0

value: healthy subject

value: No

tag: atopy

tag: cell type

value: NM


title: Nasal Mucosa ALI at day 0, biological rep 6 (mRNA)

value: M

value: BSC

tag: cells isolated from

tag: protocol


title: A8168418-1

value: Colon


title: 290B: Tumor of Patient 290

value: Invasive Adenocarcinoma

value: pT2, pN0, MX

value: I


title: Nasal Polyp ALI at day 0, biological rep 2 (mRNA)

tag: individual

value: CRSwNP patient

value: NP

value: ALI culture

tag: time

value: day 0


title: 290C: Adjacent Mucosa of Patient 290

tag: patient id

value: Male

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign


title: S1692529-5

value: Limited

value: Ulcerative Colitis (UC)


title: 10743C: Adjacent Mucosa of Patient 10743

tag: tnm

tag: uicc


title: Nasal Mucosa ALI at day 0, biological rep 5 (mRNA)

value: healthy subject

tag: age (years)

value: F

tag: previous treatment

value: No


title: Week_1_rep_3

tag: cell line

value: WM239A overexpressing BRAF-V600E

tag: drug treatment

value: 500nM LGX818 for 7d


title: 11218A: Adenoma of Patient 11218

source_name: Patient 11218

tag: age

value: Female

value: Adenoma

value: Tubulovillous Adenoma with High Grade Dysplasia


title: E5687711-5

tag: subject

tag: diseaseextent

value: Extensive

tag: disease

tag: tissue

value: Colon


title: Week_1_rep_2


title: Week_1_rep_1


title: V600E_LGX_rep_3

value: 500nM LGX818 for 20hr


title: Nasal Mucosa ALI at day 0, biological rep 4 (mRNA)

tag: gender

value: M

tag: atopy

tag: cell type

value: BSC

tag: cells isolated from

value: NM

value: ALI culture

value: day 0


title: V600E_LGX_rep_2


title: V600E_LGX_rep_1


title: V600E_rep_3


title: V600E_rep_2


title: V600E_rep_1


title: E5667255-5

value: Ulcerative Colitis (UC)


title: E5616213-1

value: Limited


title: E5528464-5


title: Nasal Mucosa ALI at day 0, biological rep 2 (mRNA)

tag: individual

value: healthy subject

value: F

tag: protocol

tag: time


title: E5688736-5


title: Nasal Mucosa ALI at day 0, biological rep 1 (mRNA)

value: No


title: E5589384-5


title: 11218B: Tumor of Patient 11218

tag: patient id

value: Tumor

tag: adenomadiagnosis

value: Colonic Adenocarcinoma

tag: tnm

value: pT3a/b, pN0, pMX

tag: uicc

value: IIA


title: 921B: Tumor of Patient 921

source_name: Patient 921

value: Male

value: Invasive Adenocarcinoma

value: pT1, pN0, pMX

value: I


title: 921C: Adjacent Mucosa of Patient 921

value: Adjacent Mucosa

value: Benign


title: Nasal Mucosa ALI at day 0, biological rep 3 (mRNA)

tag: age (years)

value: M

tag: previous treatment

value: BSC

value: NM

value: ALI culture


title: Vector_rep_2

source_name: Metastatic Melanoma Cell Line

tag: cell line

tag: drug treatment


title: 1506A: Adenoma of Patient 1506

source_name: Patient 1506

tag: age

value: Adenoma

value: Tubulovillous Adenoma with Moderate Mucosal Dysplasia


title: 921A: Adenoma of Patient 921

tag: tissue

value: Villous Adenoma with High Grade Dysplasia


title: 974A: Adenoma of Patient 974

source_name: Patient 974

tag: gender

value: Tubulovillous Adenoma


title: 1506C: Adjacent Mucosa of Patient 1506


title: 1506B: Tumor of Patient 1506

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN2, pMX

value: IIIB


title: E5669879-5

tag: subject

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

value: Colon


title: 974B: Tumor of Patient 974

value: Male

value: pT3, pN0, pMX

value: IIA


title: Vector_rep_1


title: P0443221-5


title: 974C: Adjacent Mucosa of Patient 974

value: Adjacent Mucosa

value: Benign


title: E5668791-6


title: E5666732-1

value: Extensive


title: E5674360-1


title: Vector_rep_3


title: P0436600-5


title: 449C: Adjacent Mucosa of Patient 449

source_name: Patient 449

value: Female


title: 984A: SSA of Patient 984

source_name: Patient 984

value: SSA

value: Sessile Serrated Adenoma


title: 449B: Tumor of Patient 449


title: 12071B: Tumor of Patient 12071

source_name: Patient 12071

value: pT3a/b, pN0, pMX


title: E6139867-1

source_name: tissue biopsy


title: 12071C: Adjacent Mucosa of Patient 12071


title: E6126340-5


title: 9872A: Adenoma of Patient 9872

source_name: Patient 9872

value: Adenoma

value: Flat Tubulovillous Adenoma


title: A8357932-5


title: A8355535-5


title: E6126341-5


title: 12071A: SSA of Patient 12071


title: E5625808-1


title: Nasal Polyp ALI at day 28, biological rep 6 (miRNA)

description: microRNA expression data from NP ALI Cultures at day 28

hyb_protocol: Global microRNA transcriptional analysis using the microRNA 4.1 Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.

data_processing:
Microarray data (Affymetrix .cel files) were processed for raw data quality control analysis by using Robust Multichip Analysis (RMA) algorithm, which perform background correction, probe-level normalization, and probe-set summary.
Only the normalized data for human mature microRNA is available.

source_name: NP ALI at day 28

label_protocol: Total RNA (300 ng, RIN ≥ 9) was processed for global transcriptional analysis using the microRNA 4.1 Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.

tag: individual

value: CRSwNP patient

value: M

value: No

tag: atopy

value: Yes

tag: cell type

value: BSC

tag: cells isolated from

value: NP

value: ALI culture

value: day 28


title: S1692415-5

value: Ulcerative Colitis (UC)

value: Colon


title: 9872B: Tumor of Patient 9872

tag: patient id

value: Tumor

tag: adenomadiagnosis

value: Colonic Adenocarcinoma

value: pT3, pN2, pMX

value: IIIB


title: A8226349-1

value: Limited


title: Nasal Polyp ALI at day 28, biological rep 4 (miRNA)

tag: protocol

tag: time


title: 9872C: Adjacent Mucosa of Patient 9872

value: Female

value: Adjacent Mucosa

value: Benign

tag: tnm

tag: uicc


title: Nasal Polyp ALI at day 28, biological rep 7 (miRNA)

value: CRSwNP patient

tag: age (years)

value: M

tag: previous treatment


title: HDL5

source_name: Normal liver tissues

tag: disease status

value: Healthy

tag: tissue source

value: Liver

value: Immune cells

tag: cell subset

value: CD4- MAIT cells

tag: subset definition


title: 984B: Tumor of Patient 984

tag: age

tag: gender

tag: tissue

value: pT1, pN0, pMX

value: I


title: 3763A: Adenoma of Patient 3763

source_name: Patient 3763

value: Male

value: Adenoma

value: Adenovillous Polyp


title: Nasal Polyp ALI at day 28, biological rep 5 (miRNA)

tag: individual

value: No

tag: atopy

value: Yes

tag: cell type

value: BSC

value: NP

value: ALI culture

value: day 28


title: E5902681-1

tag: subject

tag: diseaseextent

value: Extensive

tag: disease

value: Ulcerative Colitis (UC)

value: Colon


title: E5528512-5


title: P0443222-5

value: Limited


title: E5613746-1


title: E5674359-5


title: Nasal Polyp ALI at day 28, biological rep 3 (miRNA)

value: CRSwNP patient

value: F

tag: cells isolated from

tag: protocol

tag: time


title: 3763B: Tumor of Patient 3763

tag: patient id

value: Tumor

tag: adenomadiagnosis

value: Adenocarcinoma

tag: tnm

value: pT3a/b, pN2, pMX

tag: uicc

value: IIIB


title: E5666159-1


title: IFNB-Input

city: New York

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 with the following settings --sensitive-local -p $(( SLURM_CPUS_PER_TASK - 2 )) --no-unal
Genome_build: mm9

molecule: genomic DNA

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were grown in Dulbucco’s minimal essential medium (DMEM) containing 10% donor bovine serum at 37°C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and nuclei were pelleted after sequential wash and resuspended in sonication buffer (0.1% SDS, 1mM EDTA, 10mM Tris (pH8.1)) and sonicated in a Covaris to shear the chromatin into 200-300 bp  fragments and 10% Chromatin was decrosslinked and used as Input DNA.
ChIP-seq libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). DNA sequence was performed by NextSeq system (Illumina).

treatment_protocol: WT MEFs were treated with mouse recombinant IFNβ (100 units/ml, PBL Interferon Source) for 6h.

tag: strain background

value: Murine embryonic fibroblasts (MEFs)

tag: passages

tag: genotype

value: wild type

tag: treatment

value: IFN-Beta

tag: chip antibody

value: none (input)


title: Nasal Polyp ALI at day 28, biological rep 2 (miRNA)

tag: individual

tag: age (years)

tag: gender

value: M

tag: previous treatment

value: No

tag: atopy

value: BSC

value: NP


title: Nasal Polyp ALI at day 28, biological rep 1 (miRNA)

tag: cell type

tag: cells isolated from

value: ALI culture

value: day 28


title: Nasal Mucosa ALI at day 28, biological rep 7 (miRNA)

description: microRNA expression data from CONTROL NM ALI Cultures at day 28

source_name: Control NM ALI at day 28

value: healthy subject

value: NM

tag: protocol

tag: time


title: NT-Input

tag: age

value: none (untreated)


title: Nasal Mucosa ALI at day 28, biological rep 6 (miRNA)


title: 3763C: Adjacent Mucosa of Patient 3763

tag: patient id

value: Male

tag: tissue

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign

tag: tnm


title: Nasal Mucosa ALI at day 28, biological rep 5 (miRNA)

value: F


title: Nasal Mucosa ALI at day 28, biological rep 4 (miRNA)


title: 5960A: Adenoma of Patient 5960

source_name: Patient 5960

value: Adenoma

value: Adenomatous Polyp

tag: uicc


title: E5613726-1

tag: subject

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

value: Colon


title: MEF-H3f3b-HA-IFNB

data_processing:
deepTools(2.4.3-1)
Bamcoverage
bamCoverage --bam ${j}.bam -of bigwig -o ${j}.SeqDepthNorm.bw --binSize 10 --normalizeTo1x 2150570000 --ignoreForNormalization chrX --extendReads 150 --centerReads --smoothLength 30
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Murine embryonic fibroblasts (MEFs)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and nuclei were pelleted after sequential wash and resuspended in sonication buffer (0.1% SDS, 1mM EDTA, 10mM Tris (pH8.1)) and sonicated in a Covaris to shear the chromatin into 200-300 bp fragments. 50ug of chromatin was immunoprecipitated using aanti-HA antibody (Abcam). Immunoprecipitated chromatin was de-crosslinked and DNA purified.
ChIP-seq libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). DNA sequence was performed by NextSeq system (Illumina).

tag: strain background

tag: genotype/variation

value: epitope-tagged(HA) H3.3

value: Murine embryonic fibroblasts (MEFs)

tag: passages

tag: treatment

value: IFN-Beta

tag: chip antibody

value: Anti-HA tag antibody - ChIP Grade (ab9110)


title: 5960C: Adjacent Mucosa of Patient 5960

tag: gender


title: 73C: Adjacent Mucosa of Patient 73

source_name: Patient 73

value: Female


title: 73B: Tumor of Patient 73

value: Tumor

value: Colonic Adenocarcinoma

value: pT3, pN1, pMX

value: IIIB


title: 5960B: Tumor of Patient 5960

value: Male

value: Adenocarcinoma, Mucin Producing

value: pT3, pN0, pMX

value: IIA


title: A8278372-5


title: A8849313-1

value: Extensive


title: E5696061-1

value: Limited


title: Nasal Mucosa ALI at day 28, biological rep 3 (miRNA)

tag: individual

value: healthy subject

tag: age (years)

value: M

tag: previous treatment

value: No

tag: atopy

tag: cell type

value: BSC

tag: cells isolated from

value: NM

tag: protocol

value: ALI culture

value: day 28


title: P0436077-1

value: Ulcerative Colitis (UC)

tag: age

tag: tissue

value: Colon


title: 5073A: SSA of Patient 5073

source_name: Patient 5073

tag: patient id

value: SSA

tag: adenomadiagnosis

value: Sessile Serrated Adenoma

tag: tnm

tag: uicc


title: MEF-H3f3b-HA-NT

tag: strain background

tag: genotype/variation

value: epitope-tagged(HA) H3.3

value: Murine embryonic fibroblasts (MEFs)

tag: passages

value: none (untreated)

value: Anti-HA tag antibody - ChIP Grade (ab9110)


title: Nasal Mucosa ALI at day 28, biological rep 2 (miRNA)

tag: gender

value: F

tag: time


title: Nasal Mucosa ALI at day 28, biological rep 1 (miRNA)

tag: individual

tag: age (years)


title: Nasal Polyp ALI at day 14, biological rep 7 (miRNA)

description: microRNA expression data from NP ALI Cultures at day 14

source_name: NP ALI at day 14

value: CRSwNP patient

tag: previous treatment

tag: atopy

value: Yes

value: NP

value: day 14


title: 5073C: Adjacent Mucosa of Patient 5073

value: Male

value: Adjacent Mucosa

value: Benign


title: Double treatment D2

city: Chicago

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Lifelong Cl-13 infection with double treatment anti-PDL1+LPS

growth_protocol: splenocytes were harvested in R10

extract_protocol:
Spleen cells were MACS sorted to isolate CD8 T cells by MACS negative selection (STEMCELL kit). Then, DbGP276+ cells were FACS-sorted and resuspended in Trizol. RNA extraction was performed using the Agecourt RNA extraction kit as per the manufacter instructions, and extracted RNA was delivered to the NUSeq Core at Northwestern University in downtown Chicago.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD4 T cells were depleted and mice were infected intravenously with LCMV Cl-13

tag: cell type

value: CD8 T cells

tag: agent


title: Double treatment 12

value: Lifelong Cl-13 infection with double treatment anti-PDL1+LPS


title: E5625771-5

tag: subject

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

tag: age

value: Colon


title: Double treatment D3


title: Double treatment D1


title: A8347534-5

value: Extensive

tag: tissue


title: Single treatment S3

source_name: Lifelong Cl-13 infection with single treatment anti-PDL1


title: Nasal Polyp ALI at day 14, biological rep 5 (miRNA)

value: M

value: No

value: BSC

tag: cells isolated from

tag: protocol

value: ALI culture


title: E5625764-5


title: Nasal Polyp ALI at day 14, biological rep 6 (miRNA)

value: CRSwNP patient


title: Single treatment S2

value: Lifelong Cl-13 infection with single treatment anti-PDL1


title: 5073B: Tumor of Patient 5073

data_processing: Data were analyzed using Bioconductor 3.2 running on R 3.2.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

tag: patient id

value: Tumor

tag: adenomadiagnosis

value: Adenocarcinoma

tag: tnm

value: pT3, pN0, pMX

tag: uicc

value: IIA


title: 2818A: Adenoma of Patient 2818

source_name: Patient 2818

tag: gender

value: Male

value: Adenoma

value: Tubular Adenoma


title: P0463292-5

value: Limited


title: Single treatment S1

value: CD8 T cells


title: Nasal Polyp ALI at day 14, biological rep 4 (miRNA)

tag: individual

tag: age (years)

value: NP

tag: time

value: day 14


title: 2818C: Adjacent Mucosa of Patient 2818

value: Adjacent Mucosa

value: Benign


title: PDGF1GBM

city: Philadelphia

first: Yi

last: Fan

address: 3400 Civic Center Blvd

department: Department of Radiation Oncology

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
The sequences were aligned to the GRCm38 reference genome using RNA-Star (v2.4.2a) (https://github.com/alexdobin/STAR). The gene expression was normalized and calculated as FPKM (Fragments Per Kilobase Million) values by Cufflinks (v2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) with Gencode M5 gene annotations (http://www.gencodegenes.org/mouse_releases/5.html).
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKMs

source_name: Tumor cell (mouse#PDGF1)

extract_protocol:
Cells were lysed in Hank's Balanced Salt Solution buffer (Thermo Fisher) with 0.025% Tween (Thermo Fisher). mRNA was extracted and subjected to aRNA linear amplification by three rounds of reverse transcription, second strand synthesis and in vitro transcription, using SuperScript III First-Strand Synthesis SuperMix (Thermo Fisher), DNA Polymerase I (Thermo Fisher), T4 DNA polymerase (Thermo Fisher), 5x Second Strand buffer (Thermo Fisher) and a MegaScript kit (Thermo Fisher).
DNA library was constructed with a TruSeq mRNA stranded kit (Illumina). Library was subjected to next-generation sequencing analysis in a high-throughput sequencing center with a Illumina HiSeq 4000 at the Children’s Hospital of Philadelphia/Beijing Genomics Institute core facility (CHOP/BGI).

tag: individual id

tag: cell type

value: tumor cell


title: 2818B: Tumor of Patient 2818

extract_protocol: Qiagen RNAeasy FFPE

value: Mucinous Adenocarcinoma


title: E5921398-5

tag: subject

value: Ulcerative Colitis (UC)

value: Colon


title: Nasal Polyp ALI at day 14, biological rep 3 (miRNA)

value: CRSwNP patient

value: F

tag: previous treatment

value: No

tag: atopy

value: BSC

value: ALI culture


title: E5525553-1

tag: diseaseextent

value: Extensive

tag: disease

tag: age


title: 1818A: Tumor of Patient 1818

source_name: Patient 1818

value: Female

tag: tissue

value: Tumor

value: Carcinoma


title: Nasal Polyp ALI at day 14, biological rep 1 (miRNA)

tag: cells isolated from

value: NP

tag: protocol


title: E5671977-5

source_name: tissue biopsy

value: Limited


title: 1818C: Adjacent Mucosa of Patient 1818

tag: patient id

value: Adjacent Mucosa

tag: adenomadiagnosis

tag: tnm


title: E5528002-1


title: Nasal Mucosa ALI at day 14, biological rep 7 (miRNA)

description: microRNA expression data from CONTROL NM ALI Cultures at day 14

source_name: Control NM ALI at day 14

tag: individual

value: healthy subject

tag: gender

value: M

value: NM

value: day 14


title: 1818B: Tumor of Patient 1818

value: Adenocarcinoma with Focal Mucinous Features

value: pT2, pN1, pMX

tag: uicc

value: IIIA


title: PDGF1CTC

source_name: single-cell CTC (mouse#PDGF1)

tag: individual id

value: CTC


title: 1860A: Adenoma of Patient 1860

source_name: Patient 1860

value: Male

value: Adenoma

value: Adenomatous Polyp


title: E5672501-5

value: Ulcerative Colitis (UC)

value: Colon


title: E5613782-5


title: E5687747-5


title: 1168GBM

source_name: Tumor cell (mouse#1168)

tag: cell type

value: tumor cell


title: E5688772-1

tag: subject


title: Nasal Mucosa ALI at day 14, biological rep 6 (miRNA)

tag: age (years)

tag: previous treatment

value: No

value: BSC

value: ALI culture

tag: time


title: 1168CTC

source_name: single-cell CTC (mouse#1168)


title: 1157GBM

source_name: Tumor cell (mouse#1157)


title: 2488A: Tumor of Patient 2488

source_name: Patient 2488

value: Tumor

value: Carcinoma


title: 1860C: Adjacent Mucosa of Patient 1860

value: Adjacent Mucosa

value: Benign


title: 1157CTC

source_name: single-cell CTC (mouse#1157)


title: Nasal Mucosa ALI at day 14, biological rep 4 (miRNA)

value: healthy subject

value: M

tag: atopy

value: NM

value: day 14


title: E5921399-1

tag: diseaseextent

value: Limited

tag: disease

tag: age


title: Nasal Mucosa ALI at day 14, biological rep 2 (miRNA)

value: F

tag: cells isolated from

tag: protocol


title: Nasal Mucosa ALI at day 14, biological rep 3 (miRNA)


title: 2488B: Tumor of Patient 2488

tag: patient id

value: Male

tag: tissue

tag: adenomadiagnosis

value: Adenocarcinoma

value: pT3, pN0, pMx

value: IIA


title: Mx1Cre+/0; Cdc73fl/fl rep2

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

description: total RNA; ribo depleted

data_processing:
Sequencing performed on Illumina HiSeq4000 basecalls performed using Illumina software
.bcl files were converted to fastq files using Illumina bcl2fastq version 2.17
.fastq files were trimmed for quality using TrimmomaticSE
Trimmed .fastq files were aligned to the GRCm38 mouse genome assembly downloaded from GENCODE using STAR alignment program with paramtrs -sjdbOverhang 49
Aligned reads were counted using HTSeq with parameters -s reverse -r pos
Differential gene expression analysis performed using DESeq2
Genome_build: GENCODE M16 (GRCm38.p5)
Supplementary_files_format_and_content: Excel datasheet containing HTSeq counts for each sample and DE analysis for each gene

source_name: cKit+ Bone marrow

growth_protocol: Cells were harvested from 2 tibias and 2 femurs from Mx1Cre+/0 mice or Mx1Cre+/0;Cdc73fl/fl mice 2 days after 50ug polyinosinic:polycytidylic acid was injected intraperitoneally into the mice to induce Cre activation and deletion of Cdc73. Cells were stained with APC-conjugated cKit antibody (BioLegend) and with a PE-conjugated lineage cocktail (BioLegend) containing antibodies against Cd8a, Cd11c, Cd19, B220, Nk1.1, Gr-1,Ter119, TCR-B, TCR-D, and Cd11b and were sorted for cKit+, Lin- cell population on a MoFlo Astrios Cell Sorter. Cells were spun down and proceeded immediately to RNA extraction.

extract_protocol:
Total RNA was extracted using Rneasy Plus Micro Kit (Qiagen74034)
Libraries were made using SMART-Seq v4 Ultra Low-Input RNA kit (Takeda biosciences).

treatment_protocol: Mice were treated 2 days prior to harvesting with 50ug polyinosinic:polycytidylic acid injected intraperitoneally

tag: strain

value: Bone marrow

tag: cell population

value: Lin-/cKit+

tag: genotype

value: Mx1Cre+/0; Cdc73fl/fl

tag: treatment

value: single dose 50ug polyinosinic:polycytidylic acid


title: 692A: Adenoma of Patient 692

source_name: Patient 692

tag: gender

value: Adenoma

value: Tubulovillous Adenoma

tag: tnm

tag: uicc


title: A8347468-5

tag: subject

value: Ulcerative Colitis (UC)

value: Colon


title: 2505A: Adenoma of Patient 2505

source_name: Patient 2505

value: Female

value: Regular adenoma


title: Mx1Cre+/0; Cdc73fl/fl rep1

description: total RNA; ribo depleted


title: Nasal Polyp ALI at day 0, biological rep 7 (miRNA)

description: microRNA expression data from NP ALI Cultures at day 0

source_name: NP ALI at day 0

tag: individual

value: CRSwNP patient

tag: age (years)

value: M

tag: previous treatment

value: No

tag: atopy

value: Yes

tag: cell type

value: BSC

value: NP

value: ALI culture

tag: time

value: day 0


title: Mx1Cre+/0_control rep3

description: total RNA; ribo depleted

value: Bone marrow

value: Lin-/cKit+


title: Nasal Polyp ALI at day 0, biological rep 6 (miRNA)

tag: cells isolated from

tag: protocol


title: Mx1Cre+/0; Cdc73fl/fl rep3

description: total RNA; ribo depleted

tag: tissue

value: Mx1Cre+/0; Cdc73fl/fl

value: single dose 50ug polyinosinic:polycytidylic acid


title: 692B: Tumor of Patient 692

tag: patient id

tag: age

value: Male

value: Tumor

tag: adenomadiagnosis

value: Adenocarcinoma

value: pT4a, pN1, pM1

value: IV


title: 692C: Adjacent Mucosa of Patient 692

value: Adjacent Mucosa

value: Benign


title: 2505C: Adjacent Mucosa of Patient 2505

value: Female


title: A8358427-7

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

value: Colon


title: E5528001-5


title: E5921400-5

value: Extensive


title: Nasal Mucosa ALI at day 14, biological rep 1 (miRNA)

value: healthy subject

tag: gender

value: M

value: No

value: BSC

value: NM

value: ALI culture

value: day 14


title: E5665634-5


title: Nasal Polyp ALI at day 0, biological rep 5 (miRNA)

value: CRSwNP patient

value: Yes

value: NP

value: day 0


title: E5592645-8


title: Mx1Cre+/0_control rep2

description: total RNA; ribo depleted

tag: strain

value: Bone marrow

tag: cell population

value: Lin-/cKit+

tag: genotype

tag: treatment

value: single dose 50ug polyinosinic:polycytidylic acid


title: P0443223-5

tag: subject

value: Limited

value: Ulcerative Colitis (UC)


title: 1998B: Tumor of Patient 1998

source_name: Patient 1998

value: Male

value: Tumor

value: Adenocarcinoma

tag: tnm

value: pT3, pN0, pMx

tag: uicc

value: IIA


title: Nasal Polyp ALI at day 0, biological rep 4 (miRNA)

tag: individual

tag: age (years)

value: M

tag: previous treatment

value: No

tag: atopy

tag: cell type

value: BSC

tag: time


title: Mx1Cre+/0_control rep1

description: total RNA; ribo depleted

tag: tissue


title: Drought-stressed VaWRKY14-overexpressing plants replicate 2

city: Wuhan

first: langlang

last: zhang

state: HuBei

address: Cross road of Jiufeng 1 and Guanggu 7 road

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

description:
W14-2D
CL100012084_L02_7_1

data_processing:
The libraries were purified using the AMPure XP system (Beckman Coulter, Beverly, USA) and validated on the Agilent Technologies 2100 bioanalyzer. Then, the libraries were sequenced using BGISEQ-500 platform (BGI, Wuhan, China, http://www.seq500.com).
High quality reads were then mapped on the reference genome (TAIR10) of Arabidopsis with STAR (https://github.com/alexdobin/STAR). Based on the distribution of samples in a first PCA plot, the two most similar replicates per condition were considered for further statistical analyses.
Clean reads from each sample were mapped to the reference genome of vitis vinifera (Vitis_vinifera.IGGP_12x; http://plants.ensembl.org/Vitis_vinifera/Info/Index), using Hisat2 v.2.0.5 (https://ccb.jhu.edu/software/hisat2/index.shtml) with default parameters
Read summarization was then performed with featureCounts (http://bioinf.wehi.edu.au/featureCounts/) using only the reads with a mapping quality higher than 30. The statistical analysis was performed with R. Specifically, lowly expressed genes were removed with the package HTSFilter (http://www.bioconductor.org/packages/release/bioc/html/HTSFilter.html), selecting "TMM" as the normalization method
Then, the filtered genes were used to perform a differential analysis with EdgeR. Genes were considered statistically differentially expressed if the corrected p-value was lower than 0.05.
Genome_build: Arabidopsis thaliana Col-0 TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Arabidopsis thaliana

growth_protocol: Seeds of Arabidopsis thaliana (ecotype Columbia-0) were surface-sterilized with 6% sodium hypochlorite for 5 min followed by three washes with sterile water and then plated on 1/2 MS solid medium containing 0.7% agar. One-week-old seedlings were transferred from plates into pots filled with peat moss in a greenhouse under controlled environmental conditions, at 22 °C, under 50%–60% relative humidity, and under 130 µmol photons m−2 s−1 with a 16 h/8 h light/dark cycle.

extract_protocol:
Total RNA was extracted from collected samples using TIANDZ Column Plant RNAout 2.0 Kit (Tiandz, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA-Seq analysis was performed using 3-week-old transgenic Arabidopsis mixture and WT plants under normal and drought stress (without water for 5 days) conditions.

tag: ecotype background

tag: genotype/variation

tag: age

value: 3-week old

tag: treated with

value: Whole plants


title: Nasal Polyp ALI at day 0, biological rep 3 (miRNA)

value: CRSwNP patient

tag: gender

value: F

tag: cells isolated from

value: NP

tag: protocol

value: ALI culture


title: Drought-stressed VaWRKY14-overexpressing plants replicate 1

description:
W14-1D
CL100012084_L02_6_1

value: drought stress (without water for 5 days)


title: Non-stressed VaWRKY14-overexpressing plants replicate 1

description:
W14-1N
CL100012084_L02_2_1

value: none (normal condition)


title: Non-stressed VaWRKY14-overexpressing plants replicate 2

description:
W14-2N
CL100012084_L02_3_1


title: Nasal Polyp ALI at day 0, biological rep 1 (miRNA)

value: day 0


title: Nasal Polyp ALI at day 0, biological rep 2 (miRNA)


title: Nasal Polyp ALI at day 14, biological rep 2 (miRNA)

source_name: NP ALI at day 14

value: day 14


title: 2743A: Adenoma of Patient 2743

source_name: Patient 2743

tag: patient id

value: Male

value: Adenoma

tag: adenomadiagnosis

value: Tubulovillous Adenoma


title: Nasal Mucosa ALI at day 0, biological rep 7 (miRNA)

description: microRNA expression data from CONTROL NM ALI Cultures at day 0

source_name: Control NM ALI at day 0

value: healthy subject

value: NM


title: 2743B: Tumor of Patient 2743

value: Tumor

value: Adenocarcinoma

tag: tnm

value: pT2, pN0, pMx

tag: uicc

value: I


title: 1998A: Adenoma of Patient 1998

value: Tubular Adenoma


title: 449A: Adenoma of Patient 449

source_name: Patient 449

value: Female

value: Tubulovillous Adenoma with Low Grade Dysplasia


title: 2743C: Adjacent Mucosa of Patient 2743

value: Adjacent Mucosa

value: Benign


title: Drought-stressed WT plants replicate 2

description:
WT-2D
 CL100012084_L02_5_1

source_name: Drought-stressed WT plants

value: Wild type

value: 3-week old

value: drought stress (without water for 5 days)

value: Whole plants


title: 1889A: Tumor of Patient 1889

source_name: Patient 1889

value: Carcinoma


title: Nasal Mucosa ALI at day 0, biological rep 6 (miRNA)

tag: individual

tag: age (years)

value: M

value: No

value: BSC

value: ALI culture

value: day 0


title: Nasal Mucosa ALI at day 0, biological rep 5 (miRNA)

value: healthy subject

value: F

tag: previous treatment

tag: atopy

value: NM


title: E5815559-5

source_name: tissue biopsy

tag: subject

tag: diseaseextent

value: Limited

tag: disease

value: Ulcerative Colitis (UC)

value: Colon


title: P0436145-1

value: Extensive

tag: tissue


title: 1889B: Tumor of Patient 1889

tag: age

value: Female

value: Tumor

value: Adenocarcinoma

value: pT4, R1pN2b, pMx

value: IIIC


title: A8335678-1


title: Non-stressed WT plants replicate 2

description:
WT-2N
CL100012084_L02_96_1

source_name: Non-stressed WT plants

tag: ecotype background

tag: genotype/variation

value: Wild type

value: 3-week old

tag: treated with

value: none (normal condition)

value: Whole plants


title: 355A: Adenoma of Patient 355

source_name: Patient 355

tag: gender

value: Adenoma

value: Tubular Adenoma


title: Nasal Mucosa ALI at day 0, biological rep 4 (miRNA)

value: healthy subject

value: M

value: No

tag: cell type

value: BSC

tag: cells isolated from

tag: protocol

value: ALI culture

tag: time

value: day 0


title: 1889C: Adjacent Mucosa of Patient 1889

tag: patient id

value: Female

value: Adjacent Mucosa

tag: adenomadiagnosis

value: Benign

tag: tnm

tag: uicc


title: Non-stressed WT plants replicate 1

description:
WT-1N
CL100012084_L02_95_1


title: P0454349-1

tag: subject

value: Extensive

value: Ulcerative Colitis (UC)

value: Colon


title: E5687712-5

tag: diseaseextent

value: Limited


title: UPF1-KD-2

city: shanghai

first: Wangchao

last: Xu

state: shanghai

address: 320 Yue Yang Road

institute: Institute of Neuroscience

description:
mRNA
processed data file: hisat_TPM_result_2018-07-23.txt

data_processing:
Illumina bcl2fastq software was used for basecalling.
The FASTQ files containing raw sequence reads were aligned to fruit fly genome (BDGP6) by HISAT2 program (Version 2.1.o, default parameters). The number of reads mapped to each transcript were also calculated by HISAT2 (default parameters) based on the gene annotations from Ensembl Release 93 (www.ensembl.org).
The read numbers were Transcripts Per Kilobase Million (TPM) from HISAT2 result file. Compared with control PA36 group, genes with P-value<0.05 and |log2-transformed fold change|>1 were considered as differentially expressed.
Genome_build: BDGP6
Supplementary_files_format_and_content: hisat_TPM_result_2018-07-23.txt: Tab-delimited text file includes TPM values for all samples.

organism: Drosophila melanogaster

source_name: Fly heads

growth_protocol: All flies were maintained at 24 °C on a 12:12 hour light:dark cycle at 60% humidity on a standard medium.

extract_protocol:
Four groups of flies (control PA36, (G4C2)36, PR36, UPF1-RNAi) were used for RNA-Seq. Each genotype contains two replicates with total 40 female fly heads. RNA was extracted by Trizol reagent (Thermo Fisher Scientific). Whole transcriptome libraries preparation and sequencing were performed by Annoroad Gene Technology Corporation (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Elav>UPF1 RNAi

value: 5 days

tag: Sex

value: Head


title: A8869822-5

tag: disease

tag: tissue


title: Nasal Mucosa ALI at day 0, biological rep 3 (miRNA)

tag: individual

tag: age (years)

tag: previous treatment

tag: atopy

value: NM


title: Nasal Mucosa ALI at day 0, biological rep 1 (miRNA)

value: healthy subject

tag: gender

tag: cell type


title: Nasal Mucosa ALI at day 0, biological rep 2 (miRNA)

value: F

tag: cells isolated from

tag: protocol


title: E5524611-5

tag: age


title: E5921401-5


title: 119A: Adenoma of Patient 119

source_name: Patient 119

tag: patient id

value: Male

value: Adenoma

tag: adenomadiagnosis

value: Tubulovillous Adenoma


title: 355C: Adjacent Mucosa of Patient 355

tag: tnm

tag: uicc


title: UPF1-KD-1

tag: genotype/variation


title: STAT-upd-rep2

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: STAT92E mutant cells

data_processing:
Sequenced reads were trimmed with Trimmomatic version 0.36, mapped to Drosophila genome (dmel_r6.24) with STAR version 2.5.2b.
Gene counts were normalized by the gene length of the longest isoform annotated at dmel_r6.24 into RPKM.
Genome_build: dm6.24

source_name: S2R+ cell line with STAT492E knocked out using CRISPR

growth_protocol: Cells were treated with upd or control media for 1 hour before RNA extraction

extract_protocol:
RNA was extracted using Trizol reagent
RNA-seq library preparation was performed on total RNA by poly-A selection using the Wafergen PrepX RNA-Seq Library Kit for Illumina and the Apollo 343 NGS Library Prep System (Wafergen)

treatment_protocol: upd or control media was added for 1 hour

value: STAT92E mutant

tag: treatment

value: upd ligand treated

tag: cell line


title: A8328819-1

tag: subject

tag: diseaseextent

tag: disease

tag: tissue


title: 119C: Adjacent Mucosa of Patient 119

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

value: Adjacent Mucosa


title: G4C2-2

tag: Sex

value: Female


title: 2089A: Adenoma of Patient 2089

source_name: Patient 2089

tag: gender


title: E5613725-1


title: G4C2-1


title: STAT-control-rep2

description: STAT92E mutant cells

value: Control


title: STAT-control-rep1

description: STAT92E mutant cells


title: 2089B: Tumor of Patient 2089

value: Tumor

value: Colonic Adenocarcinoma

value: pT2, pN0, pMx

value: I


title: 119B: Tumor of Patient 119

value: Adenocarcinoma

value: pT3, pN1, pMx

value: IIIB


title: PR-1

value: 5 days

value: Head


title: S2R-upd-rep2

description: wild type S2R+ cells

source_name: S2R+ cells

value: wild type


title: PR-2


title: A8745461-1

value: Limited

value: Ulcerative Colitis (UC)

value: Colon


title: STAT-upd-rep1

description: STAT92E mutant cells

value: STAT92E mutant

value: upd ligand treated


title: E5672502-1


title: PA-2

value: Female


title: 2969B: Tumor of Patient 2969

source_name: Patient 2969

value: pT4, pN1, pMx, pV1


title: PA-1


title: E5953467-5

value: Extensive


title: A8347533-1


title: 2969A: Adenoma of Patient 2969

value: Adenoma

value: Tubulovillous Adenoma


title: S2R-control-rep1

description: wild type S2R+ cells

value: Control


title: 2089C: Adjacent Mucosa of Patient 2089

value: Adjacent Mucosa

value: Benign


title: 300B: Tumor of Patient 300

source_name: Patient 300

value: Tumor

value: Invasive Adenocarcinoma

value: pT1, pN0, pMx

value: I


title: E5666158-1

value: Limited


title: Nitrogen-Starvation 3

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

institute: Universita' degli Studi di Verona

description:
SampleTS3
processed data file: expression_data.txt

data_processing:
Adaptor trimming of the reads was performed using CutAdapt (ver. 1.6), followed by duplicates removal and then abundance normalization with khmer software (ver. 1.1).
Normalized RNA-seq reads have been assembled with de novo approach using Oases/Velvet multi-kmer pipeline (ver. 0.2.08) from k-mer 25 to k-mer 85 with steps of 10. The single k-mer assemblies have been merged with Oases-merge utility.
The multi k-mer assemblies have been concatenated into a global set and subjected to clustering and redundancy removal using software EvidentialGene (ver. 2013-07-27).
The RSEM software is used to perform the data analysis and the aligner provided to RSEM is Bowtie.
Differential expression analysis is performed using DESeq package.
Genome_build: N/A
Supplementary_files_format_and_content: expression_data.txt: Tab-delimited text file includes raw counts, FPKM, baseMean (mean normalised counts, averaged over all samples from both conditions), baseMeanA (mean normalised counts from control condition [Sample1, Sample3, and Sample6]), baseMeanB (mean normalised counts from nitrogen-starvation [SampleTS1, SampleTS2, and SampleTS3]), log2 Fold Change (nitrogen-starvation [numerator] / control condition [denominator]), p-value and padj.
Supplementary_files_format_and_content: expressed.fasta: FASTA file with expressed assembled transcripts.

organism: Tetraselmis suecica

source_name: Microalgal cells

growth_protocol: The microalgae was cultured in Keller medium. Experimental culturing (control and nitrogen starvation conditions) were performed in two-liter polycarbonate bottles (each experiment was performed in triplicate) constantly bubbled with air filtered through 0.2 µm membrane filters. Cultures were kept in a climate chamber at 19°C on a 12:12 h light:dark cycle at 100 µmol photons m-2 s-1.

extract_protocol:
Cells were lysed using half a spatula of glass beads (about 200 mg; Sigma-Aldrich, Milan, Italy) for each 2 mL tube, incubating and mixing tubes for 10 min at 60°C and maximum speed in the Thermo Shaker BS100 (Biosan). RNA was then extracted using the Direct-zolTM RNA MiniPrep (Zymo Research), following the manufacturer’s instructions. RNA quantity and purity were assessed by Nano-Drop (ND-1000 UV-Vis spectrophotometer; NanoDrop Technologies) monitoring the absorbance at 260 nm and the 260/280 nm and 260/230 nm ratios (both ratios were about 2.0). RNA quality was evaluated by gel electrophoresis that showed intact RNA, with sharp ribosomal bands. Total RNA quality was evaluated by measuring the RNA Integrity Number (RIN) with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.); high quality (RIN >8) RNA was used for the RNAseq.
RNA-Seq libraries were constructed from 2.5 µg of total RNA using the Illumina TruSeq® Stranded mRNA kit (Illumina Inc., San Diego, CA, USA) according to manufacturer instructions. The libraries were size selected using the Pippin Prep automated gel electrophoresis system (Sage Science, Beverly, MA, USA) for 350 to 550 bp. Paired-end sequencing (100 bp × 2) was performed with the HiSeq 1000 Illumina platform using the TruSeq SBS v3-HS kit (200 cycles) and TruSeq PE Cluster v3-cBot-HS kit (Illumina).

treatment_protocol: In the nitrogen-starvation condition, a reduced concentration of nitrogen was used in the medium preparation (30 µmol L-1 of NO3-).

tag: strain

tag: growth phase

value: Late stationary phase

tag: culturing condition

value: Nitrogen starvation medium


title: Nitrogen-Starvation 2

description:
SampleTS2
processed data file: expression_data.txt


title: S2R-upd-rep1

description: wild type S2R+ cells

value: wild type


title: Nitrogen-Starvation 1

description:
SampleTS1
processed data file: expression_data.txt


title: S2R-control-rep2

description: wild type S2R+ cells


title: MIT9312_PVC leachate rep2

city: Sydney

first: Sasha

last: Tetu

state: NSW

address: Macquarie University

department: Molecular Sciences

country: Australia

institute: Macquarie University

description:
MIT_P2
processed data file : MIT9312_transcript_counts.csv

data_processing:
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) v 1.3.1 was used to align reads to genome sequences (Magoc et al 2013)
Subread featurecounts script was used to summarise reads to genomic features (Liao et al 2013)
Genome_build: NCBI accessions NC_007577.1 (MIT9312) and NC_007335.2 (NATL2A)
Supplementary_files_format_and_content: Tab delimted text file with the number of reads mapping to each ORF for all replicates, gene annotations are included alongside ORF names

organism: Prochlorococcus marinus str. MIT 9312

source_name: Prochlorococcus in vitro culture

growth_protocol: Prochlorococcus marinus MIT9312 and NATL2A were cultured in acid washed glassware using AMP1 media at

extract_protocol:
Cells were collected by centrifugation for 7 mins, pellet resuspended immediately in Qiazol solution and further processed using the Qiagen MiRNeasy kit, according to the manufacturer's instructions
rRNA was depleted using Ribozero bacterial kit, RNA converted to cDNA and used to prepare TruSeq RNA-seq stranded libraries
TruSeq RNA-seq stranded libraries were prepared and sequenced using NextSeq500 75bp SR at the Ramaciotti Centre for Genomics

treatment_protocol: Three independent biological replicates were set up in 50mL volumes with control media (AMP1 only) or media containing a dilution of sterile leachate from plastic bags (HDPE, applied at 50% final volume) or plastic matting (PVC, applied at 2% final volume). PVC spiked cultures were harvested after 90 mins exposure, control and HDPE exposed cultures were harvested after 180 mins.

tag: exposed to

value: PVC leachate

tag: molecule subtype

value: rRNA depleted total RNA


title: MIT9312_PVC leachate rep3

description:
MIT_P3
processed data file : MIT9312_transcript_counts.csv


title: E5613747-1

institute: Janssen R&D

value: Ulcerative Colitis (UC)

tag: age

value: Colon


title: A8532026-5


title: Control condition 3

description:
Sample6
processed data file: expression_data.txt

value: Complete medium


title: E5667256-5


title: 3251A: Adenoma of Patient 3251

source_name: Patient 3251

tag: patient id

value: Male

value: Adenoma

tag: adenomadiagnosis

value: Tubular Adenoma with High Grade Dysplasia

tag: tnm


title: MIT9312_HDPE leachate rep3

description:
MIT_H6
processed data file : MIT9312_transcript_counts.csv

value: HDPE leachate


title: MIT9312_PVC leachate rep1

description:
MIT_P1
processed data file : MIT9312_transcript_counts.csv


title: 3251C: Adjacent Mucosa of Patient 3251

value: Adjacent Mucosa

value: Benign

tag: uicc


title: Control condition 2

description:
Sample3
processed data file: expression_data.txt


title: Control condition 1

description:
Sample1
processed data file: expression_data.txt


title: MIT9312_HDPE leachate rep2

description:
MIT_H5
processed data file : MIT9312_transcript_counts.csv


title: 1019

value: Normal


title: Nasal Mucosa ALI at day 14, biological rep 5 (miRNA)

source_name: Control NM ALI at day 14

tag: individual

value: healthy subject

tag: age (years)

value: F

tag: previous treatment

value: No

tag: atopy

tag: cell type

value: BSC

tag: cells isolated from

value: NM

tag: protocol

value: ALI culture

tag: time

value: day 14


title: P0436076-5

tag: subject

tag: diseaseextent

value: Extensive

tag: disease

value: Ulcerative Colitis (UC)

tag: tissue


title: 300A: Adenoma of Patient 300

tag: age

tag: gender

value: Female

value: Tubulovillous Adenoma


title: MIT9312_HDPE leachate rep1

description:
MIT_H4
processed data file : MIT9312_transcript_counts.csv

tag: exposed to

tag: molecule subtype

value: rRNA depleted total RNA

tag: strain


title: A8595463-1

value: Limited

value: Colon


title: MIT9312_Control rep3

description:
MIT_C6
processed data file : MIT9312_transcript_counts.csv

value: none (control)


title: 3251B: Tumor of Patient 3251

tag: patient id

value: Male

value: Tumor

tag: adenomadiagnosis

value: Adenocarcinoma

tag: tnm

value: pT1, pN0, pMx

tag: uicc

value: I


title: 3550B: Tumor of Patient 3550

source_name: Patient 3550

value: pT3, pN1, pMx

value: IIIB


title: 3550A: SSA of Patient 3550

value: SSA

value: Sessile Serrated Adenoma


title: CO12_550710M

value: Normal


title: IV8

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality trimming of raw reads was done with Sickle v1.33 with a threshold of 20.
Adapter trimming of raw reads was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 2.3.4 was used to map the reads to the appropriate references with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum ITAGv3.2 combined with either B. cinerea ASM83294v1, F. acuminatum (GGXD01000000), or R. stolonifer (GGWM01000000) transcriptomes for inoculated fruit samples.  Pathogen transcriptomes alone were used for in vitro samples.
Supplementary_files_format_and_content: Bcin_Raw_Read_Count_Matrix.csv, Facu_Raw_Read_Count_Matrix.csv, Rsto_Raw_Read_Count_Matrix.csv: comma-separated files determined by mapping trimmed sequencing reads

organism: Botrytis cinerea

source_name: In vitro fungal culture

extract_protocol:
Fungal RNA from the in vitro cultures was extracted using TRIzol (Invitrogen) and purified using the Quick-RNA MiniPrep Kit (Zymo Research).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

tag: ripening stage

tag: days post inoculation


title: MIT9312_Control rep2

description:
MIT_C5
processed data file : MIT9312_transcript_counts.csv


title: IV9


title: 3550C: Adjacent Mucosa of Patient 3550

value: Adjacent Mucosa

value: Benign


title: MIT9312_Control rep1

description:
MIT_C4
processed data file : MIT9312_transcript_counts.csv


title: NATL2A_PVC leachate rep2

description:
NAT_P2
processed data file : NATL2A_transcript_counts.csv

organism: Prochlorococcus marinus str. NATL2A

value: PVC leachate


title: 4210A: Adenoma of Patient 4210

source_name: Patient 4210

value: Female

value: Adenoma

value: Tubular Adenoma