title: 73895: mga2delta SDC+All Replicate3


title: 73884: ino4delta SDC+All Replicate1

status: Public on Aug 17 2021

type: SRA

city: Vienna

first: Alwin

last: Köhler

state: Vienna

address: Dr. Bohr-Gasse 9/3

department: Medical Biochemistry

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

library_source: transcriptomic

data_processing:
The reads were mapped to the Saccharomyces cerevisiae Ensembl R64-1-1 reference genome with STAR (version 2.5.1b).
The read counts for each gene were detected using HTSeq (version 0.5.4p3).
The counts were normalised using the TMM normalization from edgeR package in R.
Prior to statistical testing the data was voom transformed and then the differential expression between the sample groups was calculated with limma package in R.
Genome_build: Saccharomyces cerevisiae Ensembl R64-1-1 reference genome
Supplementary_files_format_and_content: xlsx files containing raw and normalized count values for each sample

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Exponentially growing yeast cells

growth_protocol: Yeast cells were grown in synthetic media and expenentially growing cells were harvested.

extract_protocol:
Total RNA was extracted from 12 mL of an exponentially growing yeast cell cultures using the hot phenol method.
For RNA sequencing, total RNA was depleted from ribosomal RNA and then reverse transcribed using random oligomer primers (RiboZero, NEB). Sequencing was performed on an Illumina platform

tag: strain

tag: plasmid

tag: growth media

value: SDC+All


title: 73880: WT pRS316-GPDprom-Ole1-mCh Replicate1

value: wild-type (BY4741)

value: SDC-URA


title: 73882: mga2delta pRS316-GPDprom-Mga2-mCh Replicate1


title: 73881: mga2delta SDC+All Replicate1


title: NGT_HGI_48h_i04

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz

data_processing:
1) Reads were trimmed using Trim_Galore! (v0.4.3) on default settings
2) Trimmed reads were aligned using STAR (v2.5.3a) aligner with Ensembl human annotation (GRCh38, release 92)
3) Gene read coverages were counted using featureCounts from subread (v1.5.2) package
4) The lowly expressed genes were discarded from downstream analysis using filterByExpr function from edgeR package (v3.32.1) resulting 18,482 genes for downstream analysis
5) Batch effect caused by "individuals" are removed from CPM values by using removeBatchEffect function from limma (v3.46.0)
6) Batch effect removed logCPM values are used for rhythmicity and differential rhythmicity analysis by RAIN (v1.20.0) and DODR (v0.99.3), respectively
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts and logCPM (log counts per million) values (batch effect caused by individuals are removed)

organism: Homo sapiens

source_name: Primary myotubes from vastus lateralis

growth_protocol: Primary myoblasts from skeletal muscle biopsies from men with NGT and T2D were grown in DMEM/F12+Glutamax with 16% FBS and 1% Antibiotic-Antimycotic (100X). Differentiation was induced at 80% confluence, by incubating the cells for 4-5 days in fusion medium consisting of 76% DMEM Glutamax with 25 mmol/l glucose, 20% M199 (5.5 mmol/l), 2% HEPES and 1% Antibiotic-Antimycotic (100X), with 0.03 μg/ml zinc sulfate and 1.4 mg/ml Vitamin B12, with a further addition of 100 μg/ml apo-transferrin and 0.286 IU/ml insulin prior to use. Experiments were performed on differentiated myotubes after an additional 3-5 days incubation in the same media containing 2% FBS (post fusion media).

extract_protocol:
Cells were lysed and RNA extracted using E.Z.N.A.® Total RNA Kit I (SKU: R6834-01, Omega Bio-tek, GA, USA). RNA was checked for quality using the Agilent RNA 600 nano kit and Bioanalyser instrument (Agilent Technologies, Santa Clara, CA). Aliquots of RNA (1 µg) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina).
Ribosomal RNA was removed from the sample using 35 µl rRNA removal beads (Illumina) on a magnetic plate followed by clean-up of the ribosomal-depleted RNA with 193 µl Agencourt RNAClean XP beads (Beckman Coulter), 70% ethanol wash and elution into 10 µl Elution buffer (Illumina). The RNA sample was fragmented for 4 min at 94°C in Elute, Prime, Fragment High Mix (Illumina) and then subjected to first strand cDNA synthesis with 1 µl Superscript III reverse transcriptase (Life Technologies) per sample using a thermocycler programmed to 25°C for 10 min, 50°C for 15 min and 70°C for 15 min. Second strand cDNA was synthesized by addition of Second Strand Marking Master Mix and samples were incubated at 16°C for 60 min. Samples were subject to another bead clean up prior to A-tailing and ligation of adapters as per kit instructions (Illumina). Following a third bead clean-up, samples were enriched for DNA fragments by amplification using the Illumina PCR Primer Cocktail and PCR Master Mix, subjected to 98°C for 30 min, followed by a pre-defined cycle (98°C for 10 s, 60°C for 30 s and 72°C for 30 s) that was repeated 3-15 times, based on each individual sample, and finally incubated for 5 min at 72°C. Samples were cleaned, and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyser instrument.
Libraries were subjected to 100-bp single-end sequencing on the X Ten platform (Illumina) at the Beijing Genomics Institute (BGI), Hong Kong, China. Approximately 20 million reads/sample were assigned to genes with 18,482 genes surviving the expression threshold.

treatment_protocol: After post fusion, DMEM with 5.5 mmol/l glucose was used in the post fusion medium to create a low glucose condition. After 22 hrs, cells were synchronized by serum shock (media containing 50% FBS, 2 hrs) and then switched back to low glucose media. Skeletal muscle myotubes from men with either T2D or NGT were lysed at 6-hr intervals from 12 hrs to 54 hrs. Zeit-time (ZT) was determined as time after synchronization.  All transfections were performed using 250ng of plasmid DNA total. Treatment conditions: all cells received 5uM Rosiglitazone 48hrs post-transfection.

tag: disease

value: NGT

tag: treatment

value: HGI

tag: group

tag: time

tag: individual


title: 73879: WT SDC+All Replicate1


title: NGT_HGI_36h_i04


title: T2D_HGI_18h_i05


title: T2D_HGI_42h_i05


title: T2D_HGI_30h_i05


title: 73885: ino4delta pRS316-GPDprom-Mga2deltaTM-mCh Replicate1


title: T2D_HGI_54h_i05


title: T2D_CTL_54h_i05

value: CTL


title: T2D_CTL_42h_i05


title: 73883: mga2delta pRS316-GPDprom-Mga2deltaTM-mCh Replicate1


title: NGT_HGI_24h_i04


title: NGT_HGI_12h_i04


title: T2D_CTL_30h_i05


title: T2D_CTL_18h_i05


title: T2D_HGI_36h_i05


title: T2D_HGI_48h_i05


title: Subject_78_timepoint_1_baseline_NO_phytochemicals [IP78-1]

type: RNA

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

description: Gene expression in colonic tissue of  subject 78 at baseline

hyb_protocol: Microarray hybridization was performed on Agilent 8x44K whole human genome microarrays according to Agilent instructions.

scan_protocol: Slides were scanned using the Agilent Technologies G2565CA DNA Microarray Scanner according to the Agilent protocol. Cy3 was excited at a wavelengths of 532 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots.

data_processing: Quality control check was done in R (www.r-project.org) using Bioconductor, including local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transformation and normalization. Data were normalized per batch (date of microarray hybridization) using quantile normalization. Genes with less than 30% flagged bad spots were used as a pre-processed input file. Replicates were merged using the median and missing values were imputed by k-nearest neighbours (KNN) imputation (N=15).

label_protocol: dye-labeled cRNA (Cy3) was synthesised following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands).

growth_protocol: 6 small colonic biopsies were collected, transferred to an Eppendorf container and immediately stored in liquid nitrogen.

extract_protocol: Colon biopsies were dissolved in QIAzol® (Qiagen, Venlo, The Netherlands) using a tissue disruptor. RNA was isolated according to the manufacturer’s protocol l and followed by DNase I (Qiagen) treatment. Upon purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies) (average RNA integrity number: 7.1 ± 1.0).

treatment_protocol: There are 2 study groups (1 and 2), and in each study group there are 2 meat intervention periods (A and B), separated by a wash-out period (O). During intervention period “A”, participants were asked to consume the provided red processed meat products (red processed meat group), while in period “B” red processed meat products enriched with natural compounds were provided. For study group 1, the meat products of both period ”A” and “B” had standard nitrite levels (standard nitrite PHYTOME meat), while in study group 2 the nitrite levels in period “B” were reduced (reduced nitrite PHYTOME meat). At the beginning of the study and after each intervention period of 2 weeks, colonic biopsies were collected during an endoscopic examination and analysed for gene expression changes.

tag: subject id

tag: gender

value: Male

tag: age

tag: sample group

tag: time point

tag: tissue

value: Colonic tissue


title: Subject_77_timepoint_2_red meat_NO_phytochemicals [IP77-2]

description: Gene expression in colonic tissue of  subject 77 after consumption of two weeks of red meat without phytochemicals

source_name: timepoint_2_red meat_NO_phytochemicals

value: Female

value: red meat_NO_phytochemicals


title: T2D_HGI_24h_i05


title: Subject_78_timepoint_2_red meat_NO_phytochemicals [IP78-2]

description: Gene expression in colonic tissue of  subject 78 after consumption of two weeks of red meat without phytochemicals


title: Subject_76_timepoint_4_red meat_YES_phytochemicals [IP76-4]

description: Gene expression in colonic tissue of  subject 76 after consumption of two weeks of red meat with phytochemicals

source_name: timepoint_4_red meat_YES_phytochemicals

value: red meat_YES_phytochemicals


title: Subject_77_timepoint_3_white meat_NO_phytochemicals [IP77-3]

description: Gene expression in colonic tissue of  subject 77 after consumption of two weeks of white meat

value: white meat_NO_phytochemicals


title: Subject_77_timepoint_4_red meat_YES_phytochemicals [IP77-4]

description: Gene expression in colonic tissue of  subject 77 after consumption of two weeks of red meat with phytochemicals


title: Subject_78_timepoint_4_red meat_YES_phytochemicals [IP78-4]

description: Gene expression in colonic tissue of  subject 78 after consumption of two weeks of red meat with phytochemicals


title: Subject_77_timepoint_1_baseline_NO_phytochemicals [IP77-1]

description: Gene expression in colonic tissue of  subject 77 at baseline


title: Subject_78_timepoint_3_white meat_NO_phytochemicals [IP78-3]

description: Gene expression in colonic tissue of  subject 78 after consumption of two weeks of white meat


title: Subject_75_timepoint_3_white meat_NO_phytochemicals [IP75-3]

description: Gene expression in colonic tissue of  subject 75 after consumption of two weeks of white meat


title: T2D_CTL_48h_i05


title: Subject_76_timepoint_3_white meat_NO_phytochemicals [IP76-3]

description: Gene expression in colonic tissue of  subject 76 after consumption of two weeks of white meat


title: T2D_HGI_12h_i05


title: Subject_76_timepoint_2_red meat_NO_phytochemicals [IP76-2]

description: Gene expression in colonic tissue of  subject 76 after consumption of two weeks of red meat without phytochemicals


title: Subject_75_timepoint_4_red meat_YES_phytochemicals [IP75-4]

description: Gene expression in colonic tissue of  subject 75 after consumption of two weeks of red meat with phytochemicals


title: Subject_75_timepoint_2_red meat_NO_phytochemicals [IP75-2]

description: Gene expression in colonic tissue of  subject 75 after consumption of two weeks of red meat without phytochemicals


title: T2D_CTL_24h_i05


title: Subject_76_timepoint_1_baseline_NO_phytochemicals [IP76-1]

description: Gene expression in colonic tissue of  subject 76 at baseline


title: T2D_CTL_36h_i05


title: NGT_HGI_48h_i10


title: T2D_CTL_12h_i05


title: NGT_HGI_36h_i10


title: Subject_75_timepoint_1_baseline_NO_phytochemicals [IP75-1]

description: Gene expression in colonic tissue of  subject 75 at baseline


title: Subject_71_timepoint_4_red meat_YES_phytochemicals [IP71-4]

description: Gene expression in colonic tissue of  subject 71 after consumption of two weeks of red meat with phytochemicals


title: Subject_71_timepoint_3_white meat_NO_phytochemicals [IP71-3]

description: Gene expression in colonic tissue of  subject 71 after consumption of two weeks of white meat


title: NGT_HGI_12h_i10

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz


title: Subject_70_timepoint_4_red meat_YES_phytochemicals [IP70-4]

description: Gene expression in colonic tissue of  subject 70 after consumption of two weeks of red meat with phytochemicals


title: Subject_71_timepoint_1_baseline_NO_phytochemicals [IP71-1]

description: Gene expression in colonic tissue of  subject 71 at baseline


title: Subject_70_timepoint_3_white meat_NO_phytochemicals [IP70-3]

description: Gene expression in colonic tissue of  subject 70 after consumption of two weeks of white meat


title: Subject_69_timepoint_2_red meat_NO_phytochemicals [IP69-2]

description: Gene expression in colonic tissue of  subject 69 after consumption of two weeks of red meat without phytochemicals


title: Subject_68_timepoint_4_red meat_YES_phytochemicals [IP68-4]

description: Gene expression in colonic tissue of  subject 68 after consumption of two weeks of red meat with phytochemicals


title: Subject_71_timepoint_2_red meat_NO_phytochemicals [IP71-2]

description: Gene expression in colonic tissue of  subject 71 after consumption of two weeks of red meat without phytochemicals


title: Subject_70_timepoint_1_baseline_NO_phytochemicals [IP70-1]

description: Gene expression in colonic tissue of  subject 70 at baseline


title: Subject_69_timepoint_4_red meat_YES_phytochemicals [IP69-4]

description: Gene expression in colonic tissue of  subject 69 after consumption of two weeks of red meat with phytochemicals


title: Subject_69_timepoint_3_white meat_NO_phytochemicals [IP69-3]

description: Gene expression in colonic tissue of  subject 69 after consumption of two weeks of white meat


title: Subject_69_timepoint_1_baseline_NO_phytochemicals [IP69-1]

description: Gene expression in colonic tissue of  subject 69 at baseline


title: NGT_HGI_24h_i10


title: Subject_68_timepoint_2_red meat_NO_phytochemicals [IP68-2]

description: Gene expression in colonic tissue of  subject 68 after consumption of two weeks of red meat without phytochemicals


title: T2D_CTL_36h_i03


title: T2D_CTL_48h_i03


title: Subject_68_timepoint_1_baseline_NO_phytochemicals [IP68-1]

description: Gene expression in colonic tissue of  subject 68 at baseline


title: T2D_HGI_24h_i03


title: T2D_HGI_36h_i03


title: T2D_HGI_12h_i03


title: Subject_67_timepoint_4_red meat_YES_phytochemicals [IP67-4]

description: Gene expression in colonic tissue of  subject 67 after consumption of two weeks of red meat with phytochemicals


title: Subject_68_timepoint_3_white meat_NO_phytochemicals [IP68-3]

description: Gene expression in colonic tissue of  subject 68 after consumption of two weeks of white meat


title: Subject_70_timepoint_2_red meat_NO_phytochemicals [IP70-2]

description: Gene expression in colonic tissue of  subject 70 after consumption of two weeks of red meat without phytochemicals


title: Subject_67_timepoint_3_white meat_NO_phytochemicals [IP67-3]

description: Gene expression in colonic tissue of  subject 67 after consumption of two weeks of white meat


title: T2D_CTL_24h_i03

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz


title: T2D_CTL_12h_i03


title: Subject_66_timepoint_4_red meat_YES_phytochemicals [IP66-4]

description: Gene expression in colonic tissue of  subject 66 after consumption of two weeks of red meat with phytochemicals


title: Subject_66_timepoint_3_white meat_NO_phytochemicals [IP66-3]

description: Gene expression in colonic tissue of  subject 66 after consumption of two weeks of white meat


title: T2D_HGI_48h_i03


title: Subject_67_timepoint_1_baseline_NO_phytochemicals [IP67-1]

description: Gene expression in colonic tissue of  subject 67 at baseline


title: Subject_67_timepoint_2_red meat_NO_phytochemicals [IP67-2]

description: Gene expression in colonic tissue of  subject 67 after consumption of two weeks of red meat without phytochemicals


title: Subject_66_timepoint_2_red meat_NO_phytochemicals [IP66-2]

description: Gene expression in colonic tissue of  subject 66 after consumption of two weeks of red meat without phytochemicals


title: Subject_65_timepoint_3_white meat_NO_phytochemicals [IP65-3]

description: Gene expression in colonic tissue of  subject 65 after consumption of two weeks of white meat


title: NGT_HGI_54h_i01


title: Subject_64_timepoint_3_white meat_NO_phytochemicals [IP64-3]

description: Gene expression in colonic tissue of  subject 64 after consumption of two weeks of white meat


title: NGT_HGI_48h_i01


title: Subject_63_timepoint_2_red meat_NO_phytochemicals [IP63-2]

description: Gene expression in colonic tissue of  subject 63 after consumption of two weeks of red meat without phytochemicals


title: Subject_64_timepoint_2_red meat_NO_phytochemicals [IP64-2]

description: Gene expression in colonic tissue of  subject 64 after consumption of two weeks of red meat without phytochemicals


title: Subject_64_timepoint_1_baseline_NO_phytochemicals [IP64-1]

description: Gene expression in colonic tissue of  subject 64 at baseline


title: NGT_HGI_30h_i01


title: NGT_HGI_42h_i01


title: T2D_HGI_42h_i07


title: Subject_65_timepoint_2_red meat_NO_phytochemicals [IP65-2]

description: Gene expression in colonic tissue of  subject 65 after consumption of two weeks of red meat without phytochemicals


title: Subject_64_timepoint_4_red meat_YES_phytochemicals [IP64-4]

description: Gene expression in colonic tissue of  subject 64 after consumption of two weeks of red meat with phytochemicals


title: NGT_HGI_36h_i01


title: NGT_HGI_12h_i01


title: T2D_HGI_54h_i07


title: NGT_HGI_18h_i01


title: Subject_63_timepoint_3_white meat_NO_phytochemicals [IP63-3]

description: Gene expression in colonic tissue of  subject 63 after consumption of two weeks of white meat


title: Subject_65_timepoint_1_baseline_NO_phytochemicals [IP65-1]

description: Gene expression in colonic tissue of  subject 65 at baseline


title: Subject_63_timepoint_1_baseline_NO_phytochemicals [IP63-1]

description: Gene expression in colonic tissue of  subject 63 at baseline


title: Subject_66_timepoint_1_baseline_NO_phytochemicals [IP66-1]

description: Gene expression in colonic tissue of  subject 66 at baseline


title: Subject_63_timepoint_4_red meat_YES_phytochemicals [IP63-4]

description: Gene expression in colonic tissue of  subject 63 after consumption of two weeks of red meat with phytochemicals


title: Subject_61_timepoint_4_red meat_YES_phytochemicals [IP61-4]

description: Gene expression in colonic tissue of  subject 61 after consumption of two weeks of red meat with phytochemicals


title: Subject_62_timepoint_1_baseline_NO_phytochemicals [IP62-1]

description: Gene expression in colonic tissue of  subject 62 at baseline


title: T2D_HGI_30h_i07

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz


title: T2D_HGI_24h_i07


title: T2D_CTL_54h_i07


title: Subject_60_timepoint_4_red meat_YES_phytochemicals [IP60-4]

description: Gene expression in colonic tissue of  subject 60 after consumption of two weeks of red meat with phytochemicals


title: Subject_60_timepoint_2_red meat_NO_phytochemicals [IP60-2]

description: Gene expression in colonic tissue of  subject 60 after consumption of two weeks of red meat without phytochemicals


title: T2D_HGI_18h_i07


title: Subject_62_timepoint_3_white meat_NO_phytochemicals [IP62-3]

description: Gene expression in colonic tissue of  subject 62 after consumption of two weeks of white meat


title: T2D_CTL_48h_i07


title: T2D_HGI_12h_i07


title: T2D_CTL_42h_i07


title: T2D_CTL_30h_i07


title: T2D_CTL_36h_i07


title: Subject_60_timepoint_3_white meat_NO_phytochemicals [IP60-3]

description: Gene expression in colonic tissue of  subject 60 after consumption of two weeks of white meat


title: Subject_65_timepoint_4_red meat_YES_phytochemicals [IP65-4]

description: Gene expression in colonic tissue of  subject 65 after consumption of two weeks of red meat with phytochemicals


title: T2D_HGI_48h_i07


title: Subject_62_timepoint_4_red meat_YES_phytochemicals [IP62-4]

description: Gene expression in colonic tissue of  subject 62 after consumption of two weeks of red meat with phytochemicals


title: NGT_HGI_54h_i11


title: Subject_59_timepoint_4_red meat_YES_phytochemicals [IP59-4]

description: Gene expression in colonic tissue of  subject 59 after consumption of two weeks of red meat with phytochemicals


title: T2D_CTL_18h_i07


title: Subject_62_timepoint_2_red meat_NO_phytochemicals [IP62-2]

description: Gene expression in colonic tissue of  subject 62 after consumption of two weeks of red meat without phytochemicals


title: T2D_CTL_24h_i07


title: T2D_CTL_12h_i07


title: Subject_59_timepoint_2_red meat_NO_phytochemicals [IP59-2]

description: Gene expression in colonic tissue of  subject 59 after consumption of two weeks of red meat without phytochemicals


title: Subject_61_timepoint_2_red meat_NO_phytochemicals [IP61-2]

description: Gene expression in colonic tissue of  subject 61 after consumption of two weeks of red meat without phytochemicals


title: Subject_61_timepoint_3_white meat_NO_phytochemicals [IP61-3]

description: Gene expression in colonic tissue of  subject 61 after consumption of two weeks of white meat


title: Subject_60_timepoint_1_baseline_NO_phytochemicals [IP60-1]

description: Gene expression in colonic tissue of  subject 60 at baseline


title: Subject_59_timepoint_3_white meat_NO_phytochemicals [IP59-3]

description: Gene expression in colonic tissue of  subject 59 after consumption of two weeks of white meat


title: NGT_HGI_18h_i11


title: Subject_61_timepoint_1_baseline_NO_phytochemicals [IP61-1]

description: Gene expression in colonic tissue of  subject 61 at baseline


title: Subject_59_timepoint_1_baseline_NO_phytochemicals [IP59-1]

description: Gene expression in colonic tissue of  subject 59 at baseline


title: NGT_HGI_42h_i11


title: Subject_53_timepoint_2_red meat_NO_phytochemicals [IP53-2]

description: Gene expression in colonic tissue of  subject 53 after consumption of two weeks of red meat without phytochemicals


title: Subject_53_timepoint_1_baseline_NO_phytochemicals [IP53-1]

description: Gene expression in colonic tissue of  subject 53 at baseline


title: NGT_HGI_30h_i11

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz


title: Subject_52_timepoint_4_red meat_YES_phytochemicals [IP52-4]

description: Gene expression in colonic tissue of  subject 52 after consumption of two weeks of red meat with phytochemicals


title: Subject_55_timepoint_2_red meat_NO_phytochemicals [IP55-2]

description: Gene expression in colonic tissue of  subject 55 after consumption of two weeks of red meat without phytochemicals


title: NGT_HGI_48h_i11


title: NGT_HGI_24h_i11


title: NGT_HGI_36h_i11


title: Subject_55_timepoint_3_white meat_NO_phytochemicals [IP55-3]

description: Gene expression in colonic tissue of  subject 55 after consumption of two weeks of white meat


title: Subject_53_timepoint_3_white meat_NO_phytochemicals [IP53-3]

description: Gene expression in colonic tissue of  subject 53 after consumption of two weeks of white meat


title: NGT_HGI_12h_i11


title: Subject_53_timepoint_4_red meat_YES_phytochemicals [IP53-4]

description: Gene expression in colonic tissue of  subject 53 after consumption of two weeks of red meat with phytochemicals


title: Subject_55_timepoint_4_red meat_YES_phytochemicals [IP55-4]

description: Gene expression in colonic tissue of  subject 55 after consumption of two weeks of red meat with phytochemicals


title: mac_spiB_Ile_003

city: New York

first: Tomasz

last: Ahrends

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefellere University

data_processing:
Raw fastq files were processed by using the mouse transcriptome (gencode M23) with the kallisto (v0.46) software
Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R
To spot statistically significantly expressed genes between group pairs, we used the wald-test function. Genes with false discovery rate less than 0.01 and 2 or 4 log2 fold-change were used in downstream analysis.
Genome_build: gencode M23
Supplementary_files_format_and_content: fold_change data

organism: Mus musculus

source_name: Ileum muscularis

extract_protocol:
(1000 cells) were lysed in guanidine thiocyanate buffer (TCL buffer, Qiagen) supplemented with 1% b-mercaptoethanol. RNA was isolated by solid-phase reversible immobilization bead cleanup using RNAClean XP beads (Agentcourt), reverse-transcribed and amplified
Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions

treatment_protocol: S. venezuelensis, Y. pseudotuberculosis or Salmonella spiB infection

tag: agent

value: Salmonella spiB


title: Subject_49_timepoint_4_red meat_YES_phytochemicals [IP49-4]

description: Gene expression in colonic tissue of  subject 49 after consumption of two weeks of red meat with phytochemicals


title: Subject_52_timepoint_2_red meat_NO_phytochemicals [IP52-2]

description: Gene expression in colonic tissue of  subject 52 after consumption of two weeks of red meat without phytochemicals


title: Subject_52_timepoint_1_baseline_NO_phytochemicals [IP52-1]

description: Gene expression in colonic tissue of  subject 52 at baseline


title: Subject_55_timepoint_1_baseline_NO_phytochemicals [IP55-1]

description: Gene expression in colonic tissue of  subject 55 at baseline


title: Subject_52_timepoint_3_white meat_NO_phytochemicals [IP52-3]

description: Gene expression in colonic tissue of  subject 52 after consumption of two weeks of white meat


title: Subject_48_timepoint_4_red meat_YES_phytochemicals [IP48-4]

description: Gene expression in colonic tissue of  subject 48 after consumption of two weeks of red meat with phytochemicals


title: Subject_49_timepoint_1_baseline_NO_phytochemicals [IP49-1]

description: Gene expression in colonic tissue of  subject 49 at baseline


title: mac_spiB_Ile_002


title: mac_Yp_Ile_001

value: Y. pseudotuberculosis


title: Subject_49_timepoint_2_red meat_NO_phytochemicals [IP49-2]

description: Gene expression in colonic tissue of  subject 49 after consumption of two weeks of red meat without phytochemicals


title: mac_Yp_Ile_003


title: Subject_49_timepoint_3_white meat_NO_phytochemicals [IP49-3]

description: Gene expression in colonic tissue of  subject 49 after consumption of two weeks of white meat


title: Subject_48_timepoint_3_white meat_NO_phytochemicals [IP48-3]

description: Gene expression in colonic tissue of  subject 48 after consumption of two weeks of white meat


title: mac_Sv_Ile_002

value: S. venezuelensis


title: mac_Sv_Ile_001


title: mac_Yp_Ile_002


title: mac_Sv_Ile_003


title: mac_NI_Ile_001


title: mac_NI_Ile_002


title: mac_NI_Ile_003


title: Subject_47_timepoint_2_red meat_NO_phytochemicals [IP47-2]

description: Gene expression in colonic tissue of  subject 47 after consumption of two weeks of red meat without phytochemicals


title: Subject_47_timepoint_3_white meat_NO_phytochemicals [IP47-3]

description: Gene expression in colonic tissue of  subject 47 after consumption of two weeks of white meat


title: Subject_46_timepoint_3_white meat_NO_phytochemicals [IP46-3]

description: Gene expression in colonic tissue of  subject 46 after consumption of two weeks of white meat


title: Subject_48_timepoint_1_baseline_NO_phytochemicals [IP48-1]

description: Gene expression in colonic tissue of  subject 48 at baseline


title: H2107_KRAS_Dox_Day7_rep3

city: Vancouver

first: William

last: Lockwood

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: BC Cancer

hyb_protocol: cDNA was hybridized according to manufacturer's instructions at The Centre for Applied Genomics

scan_protocol: GeneChips were scanned according to manufacturer's instructions at The Centre for Applied Genomics

data_processing:
Experssion data was RMA normalized by The Centre for Applied Genomics
HuGene-2_1-st.pgf
HuGene-2_1-st.mps

label: biotin

source_name: H2107, KRAS, Dox, Day7

label_protocol: 150ng of RNA was converted to cDNA according to manufacturer's instructions and labelled at The Centre for Applied Genomics

growth_protocol: All cells were cultured at 37℃ with 5% CO2 in humidified atmosphere. H82 cells were grown in RPMI-1650 with 10% FBS. H2107 cells were grown in DMEM with with 5% fetal bovine serum and 1% Glutamax.

extract_protocol: Total RNA was extracted from biological triplicates using a Quick-RNA Miniprep Kit. Sample quality was assessed using an Agilent Bioanalyzer and subsequent sample preparation, array hybridization, and data acquisition was performed by the Centre for Applied Genomics Microarray Facility (Toronto, Ontario).

treatment_protocol: Cells were treated with (100 ng/mL) or without doxycycline for the indicated time frames.

tag: cell line

tag: construct

value: Dox


title: Subject_48_timepoint_2_red meat_NO_phytochemicals [IP48-2]

description: Gene expression in colonic tissue of  subject 48 after consumption of two weeks of red meat without phytochemicals


title: Subject_45_timepoint_3_white meat_NO_phytochemicals [IP45-3]

description: Gene expression in colonic tissue of  subject 45 after consumption of two weeks of white meat


title: Subject_46_timepoint_2_red meat_NO_phytochemicals [IP46-2]

description: Gene expression in colonic tissue of  subject 46 after consumption of two weeks of red meat without phytochemicals


title: Subject_45_timepoint_4_red meat_YES_phytochemicals [IP45-4]

description: Gene expression in colonic tissue of  subject 45 after consumption of two weeks of red meat with phytochemicals


title: Subject_45_timepoint_2_red meat_NO_phytochemicals [IP45-2]

description: Gene expression in colonic tissue of  subject 45 after consumption of two weeks of red meat without phytochemicals


title: H2107_KRAS_Dox_Day7_rep1


title: Subject_44_timepoint_2_red meat_NO_phytochemicals [IP44-2]

description: Gene expression in colonic tissue of  subject 44 after consumption of two weeks of red meat without phytochemicals


title: Subject_47_timepoint_4_red meat_YES_phytochemicals [IP47-4]

description: Gene expression in colonic tissue of  subject 47 after consumption of two weeks of red meat with phytochemicals


title: Subject_47_timepoint_1_baseline_NO_phytochemicals [IP47-1]

description: Gene expression in colonic tissue of  subject 47 at baseline


title: Subject_44_timepoint_1_baseline_NO_phytochemicals [IP44-1]

description: Gene expression in colonic tissue of  subject 44 at baseline


title: Subject_43_timepoint_4_red meat_YES_phytochemicals [IP43-4]

description: Gene expression in colonic tissue of  subject 43 after consumption of two weeks of red meat with phytochemicals


title: Subject_45_timepoint_1_baseline_NO_phytochemicals [IP45-1]

description: Gene expression in colonic tissue of  subject 45 at baseline


title: Subject_46_timepoint_4_red meat_YES_phytochemicals [IP46-4]

description: Gene expression in colonic tissue of  subject 46 after consumption of two weeks of red meat with phytochemicals


title: Subject_46_timepoint_1_baseline_NO_phytochemicals [IP46-1]

description: Gene expression in colonic tissue of  subject 46 at baseline


title: H2107_EGFR_Dox_Day7_rep3

source_name: H2107, EGFR, Dox, Day7


title: H2107_KRAS_NoDox_rep2

source_name: H2107, KRAS, No Dox

value: No Dox

value: day 0


title: H2107_KRAS_NoDox_rep3


title: H2107_KRAS_Dox_Day1_rep2

source_name: H2107, KRAS, Dox, Day1


title: H2107_EGFR_Dox_Day7_rep2


title: Subject_44_timepoint_4_red meat_YES_phytochemicals [IP44-4]

description: Gene expression in colonic tissue of  subject 44 after consumption of two weeks of red meat with phytochemicals


title: H2107_KRAS_NoDox_rep1


title: H2107_KRAS_Dox_Day1_rep3


title: H2107_KRAS_Dox_Day1_rep1


title: Subject_43_timepoint_3_white meat_NO_phytochemicals [IP43-3]

description: Gene expression in colonic tissue of  subject 43 after consumption of two weeks of white meat


title: Subject_43_timepoint_1_baseline_NO_phytochemicals [IP43-1]

description: Gene expression in colonic tissue of  subject 43 at baseline


title: Subject_44_timepoint_3_white meat_NO_phytochemicals [IP44-3]

description: Gene expression in colonic tissue of  subject 44 after consumption of two weeks of white meat


title: H2107_KRAS_Dox_Day7_rep2


title: H2107_EGFR_Dox_Day1_rep1

source_name: H2107, EGFR, Dox, Day1


title: Subject_41_timepoint_4_red meat_YES_phytochemicals [IP41-4]

description: Gene expression in colonic tissue of  subject 41 after consumption of two weeks of red meat with phytochemicals


title: mac_spiB_Ile_001


title: H2107_EGFR_Dox_Day1_rep2


title: Subject_43_timepoint_2_red meat_NO_phytochemicals [IP43-2]

description: Gene expression in colonic tissue of  subject 43 after consumption of two weeks of red meat without phytochemicals


title: Subject_41_timepoint_3_white meat_NO_phytochemicals [IP41-3]

description: Gene expression in colonic tissue of  subject 41 after consumption of two weeks of white meat


title: RFP_positive_rep2

city: NEW YORK

first: RUI

last: FU

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

data_processing:
Reads were aligned by STAR v2.7.3a, and then quantified by FeatureCounts from Subread using paired setting
Genome_build: R64-1-1
Supplementary_files_format_and_content: comma delimited file, table of raw counts for every gene and every sample

source_name: MATalpha spores from SK1-background diploid strain with CUP1-promoter-driven Ime1 and mCherry and hygromycin resistance integrated at the MATa allele.

growth_protocol: Diploid cells were induced to sporulate by the addition of copper to sporulation medium and incbuated at 30˚C with shaking.

extract_protocol:
Total RNA was extracted using a hot acid phenol method following spore lysis with freezing and vortexing with garnet and zirconium beads.
100 ng total RNA was used as input for library preparation with a Tecan Universal Plus mRNA-seq Library Preparation Kit with NuQuant (Cat # 0520)

treatment_protocol: After 7 days of sporulation, haploid spores were isolated by enzymatic digestion, sorted according to mCherry fluorescence, and frozen.

tag: strain


title: RFP_negative_rep2

value: MATalpha spores from SK1-background diploid strain with CUP1-promoter-driven Ime1 and mCherry and hygromycin resistance integrated at the MATa allele.


title: RFP_negative_rep1

source_name: MATa spores from SK1-background diploid strain with CUP1-promoter-driven Ime1 and mCherry and hygromycin resistance integrated at the MATa allele.


title: Subject_41_timepoint_2_red meat_NO_phytochemicals [IP41-2]

description: Gene expression in colonic tissue of  subject 41 after consumption of two weeks of red meat without phytochemicals


title: Subject_40_timepoint_3_white meat_NO_phytochemicals [IP40-3]

description: Gene expression in colonic tissue of  subject 40 after consumption of two weeks of white meat


title: H2107_EGFR_Dox_Day7_rep1


title: H2107_EGFR_NoDox_rep3

source_name: H2107, EGFR, No Dox


title: Subject_40_timepoint_1_baseline_NO_phytochemicals [IP40-1]

description: Gene expression in colonic tissue of  subject 40 at baseline


title: Subject_41_timepoint_1_baseline_NO_phytochemicals [IP41-1]

description: Gene expression in colonic tissue of  subject 41 at baseline


title: H2107_EGFR_Dox_Day1_rep3


title: Subject_40_timepoint_4_red meat_YES_phytochemicals [IP40-4]

description: Gene expression in colonic tissue of  subject 40 after consumption of two weeks of red meat with phytochemicals


title: Subject_40_timepoint_2_red meat_NO_phytochemicals [IP40-2]

description: Gene expression in colonic tissue of  subject 40 after consumption of two weeks of red meat without phytochemicals


title: H2107_EGFR_NoDox_rep1


title: Subject_38_timepoint_2_red meat_NO_phytochemicals [IP38-2]

description: Gene expression in colonic tissue of  subject 38 after consumption of two weeks of red meat without phytochemicals


title: Subject_38_timepoint_1_baseline_NO_phytochemicals [IP38-1]

description: Gene expression in colonic tissue of  subject 38 at baseline


title: LNCaP-R-MDV FARE-seq rep3

city: Tampere

first: Sinja

last: Taavitsainen

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

library_source: genomic

data_processing:
library strategy: FAIRE-seq
Sequencing reads were aligned using bwa v0.7.8-r455 (Li and Durbin, 2010) against hg19. Duplicates were marked and realigned using Picard 1.118.
Peak calling was performed on the aligned files using MACS2 v2.1.0 (Zhang et al., 2008) using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: LNCaP-R-MDV

growth_protocol: Parental and RES-A cells were cultured for three days in RPMI medium supplemented with 5% DCC FBS and 10 µM enzalutamide was added only to the resistant cell line.

extract_protocol:
FAIRE was performed on parental and LNCaP-ResA cells according to the standard protocol (Simon et al., 2012).
The DNA fragments isolated by FAIRE were used for library preparation with the Roche KAPA library prep kit according to the manual and sequenced on the Illumina HiSeq 2500 to produce 50 bp single-end reads at the Genomics core (KU Leuven).

treatment_protocol: After culturing, both sublines were treated with DMSO (control), DHT (10nM; Sigma Aldrich), enzalutamide (10µM, Selleckchem), or a combination of DHT and enzalutamide for 18 hours.

value: LNCaP

tag: cell type

value: prostate cancer cell line

tag: enzalutamide sensitivity

value: resistant

value: enzalutamide (10µM) for 18 hours


title: H2107_GFP_Dox_Day7_rep2

source_name: H2107, GFP, Dox, Day7

value: TetO-GFP


title: Subject_38_timepoint_4_red meat_YES_phytochemicals [IP38-4]

description: Gene expression in colonic tissue of  subject 38 after consumption of two weeks of red meat with phytochemicals

value: Male

value: Colonic tissue


title: H2107_GFP_Dox_Day7_rep3


title: Subject_37_timepoint_2_red meat_NO_phytochemicals [IP37-2]

description: Gene expression in colonic tissue of  subject 37 after consumption of two weeks of red meat without phytochemicals

value: Female

value: red meat_NO_phytochemicals


title: Subject_37_timepoint_4_red meat_YES_phytochemicals [IP37-4]

description: Gene expression in colonic tissue of  subject 37 after consumption of two weeks of red meat with phytochemicals

value: red meat_YES_phytochemicals


title: LNCaP-R-MDV FARE-seq rep1


title: Subject_38_timepoint_3_white meat_NO_phytochemicals [IP38-3]

description: Gene expression in colonic tissue of  subject 38 after consumption of two weeks of white meat

value: white meat_NO_phytochemicals


title: H2107_GFP_Dox_Day1_rep3

source_name: H2107, GFP, Dox, Day1


title: Subject_37_timepoint_3_white meat_NO_phytochemicals [IP37-3]

description: Gene expression in colonic tissue of  subject 37 after consumption of two weeks of white meat


title: T2D_HGI_36h_i07

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz

tag: disease

value: HGI


title: LNCaP-R-DMSO FARE-seq rep3

source_name: LNCaP-R-DMSO

tag: treatment

value: DMSO for 18 hours


title: RFP_positive_rep1


title: LNCaP-R-DMSO FARE-seq rep2


title: Subject_36_timepoint_2_red meat_NO_phytochemicals [IP36-2]

description: Gene expression in colonic tissue of  subject 36 after consumption of two weeks of red meat without phytochemicals


title: LNCaP-R-MDV FARE-seq rep2


title: Subject_35_timepoint_4_red meat_YES_phytochemicals [IP35-4]

description: Gene expression in colonic tissue of  subject 35 after consumption of two weeks of red meat with phytochemicals


title: H2107_GFP_Dox_Day7_rep1

value: Dox


title: H2107_GFP_Dox_Day1_rep2


title: Subject_32_timepoint_4_red meat_YES_phytochemicals [IP32-4]

description: Gene expression in colonic tissue of  subject 32 after consumption of two weeks of red meat with phytochemicals


title: Subject_37_timepoint_1_baseline_NO_phytochemicals [IP37-1]

description: Gene expression in colonic tissue of  subject 37 at baseline


title: H2107_GFP_NoDox_rep2

source_name: H2107, GFP, No Dox

value: No Dox


title: Subject_36_timepoint_3_white meat_NO_phytochemicals [IP36-3]

description: Gene expression in colonic tissue of  subject 36 after consumption of two weeks of white meat


title: LNCaP-R-DMSO FARE-seq rep1


title: H2107_GFP_Dox_Day1_rep1


title: LNCaP-R-DHT-MDV FARE-seq rep3

source_name: LNCaP-R-DHT-MDV

value: DHT (10nM) and enzalutamide (10µM) for 18 hours


title: Subject_35_timepoint_1_baseline_NO_phytochemicals [IP35-1]

description: Gene expression in colonic tissue of  subject 35 at baseline


title: Subject_35_timepoint_2_red meat_NO_phytochemicals [IP35-2]

description: Gene expression in colonic tissue of  subject 35 after consumption of two weeks of red meat without phytochemicals

source_name: timepoint_2_red meat_NO_phytochemicals


title: LNCaP-R-DHT-MDV FARE-seq rep2


title: Subject_32_timepoint_2_red meat_NO_phytochemicals [IP32-2]

description: Gene expression in colonic tissue of  subject 32 after consumption of two weeks of red meat without phytochemicals


title: Subject_35_timepoint_3_white meat_NO_phytochemicals [IP35-3]

description: Gene expression in colonic tissue of  subject 35 after consumption of two weeks of white meat


title: LNCaP-R-DHT FARE-seq rep3

source_name: LNCaP-R-DHT

value: DHT (10nM) for 18 hours


title: Subject_36_timepoint_4_red meat_YES_phytochemicals [IP36-4]

description: Gene expression in colonic tissue of  subject 36 after consumption of two weeks of red meat with phytochemicals

source_name: timepoint_4_red meat_YES_phytochemicals


title: Subject_36_timepoint_1_baseline_NO_phytochemicals [IP36-1]

description: Gene expression in colonic tissue of  subject 36 at baseline


title: Subject_29_timepoint_2_red meat_NO_phytochemicals [IP29-2]

description: Gene expression in colonic tissue of  subject 29 after consumption of two weeks of red meat without phytochemicals


title: Subject_29_timepoint_4_red meat_YES_phytochemicals [IP29-4]

description: Gene expression in colonic tissue of  subject 29 after consumption of two weeks of red meat with phytochemicals


title: Subject_32_timepoint_3_white meat_NO_phytochemicals [IP32-3]

description: Gene expression in colonic tissue of  subject 32 after consumption of two weeks of white meat


title: LNCaP-R-DHT-MDV FARE-seq rep1

value: LNCaP


title: H2107_GFP_NoDox_rep3

value: day 0


title: Subject_29_timepoint_3_white meat_NO_phytochemicals [IP29-3]

description: Gene expression in colonic tissue of  subject 29 after consumption of two weeks of white meat


title: LNCaP-R-DHT FARE-seq rep2

value: prostate cancer cell line

value: resistant


title: H82_KRAS_Dox_Day1_rep3

source_name: H82, KRAS, Dox, Day1


title: H2107_GFP_NoDox_rep1

value: TetO-GFP


title: Subject_27_timepoint_4_red meat_YES_phytochemicals [IP27-4]

description: Gene expression in colonic tissue of  subject 27 after consumption of two weeks of red meat with phytochemicals


title: Subject_32_timepoint_1_baseline_NO_phytochemicals [IP32-1]

description: Gene expression in colonic tissue of  subject 32 at baseline


title: H82_KRAS_Dox_Day7_rep2

source_name: H82, KRAS, Dox, Day7


title: Subject_29_timepoint_1_baseline_NO_phytochemicals [IP29-1]

description: Gene expression in colonic tissue of  subject 29 at baseline

value: Male


title: H82_KRAS_Dox_Day7_rep3


title: LNCaP-MDV FARE-seq rep3

source_name: LNCaP-MDV

value: sensitive

value: enzalutamide (10µM) for 18 hours


title: H82_KRAS_Dox_Day7_rep1


title: H82_KRAS_Dox_Day1_rep1


title: Subject_26_timepoint_3_white meat_NO_phytochemicals [IP26-3]

description: Gene expression in colonic tissue of  subject 26 after consumption of two weeks of white meat

value: Female

value: Colonic tissue


title: LNCaP-MDV FARE-seq rep2


title: Subject_26_timepoint_4_red meat_YES_phytochemicals [IP26-4]

description: Gene expression in colonic tissue of  subject 26 after consumption of two weeks of red meat with phytochemicals

value: red meat_YES_phytochemicals


title: LNCaP-MDV FARE-seq rep1


title: Subject_27_timepoint_2_red meat_NO_phytochemicals [IP27-2]

description: Gene expression in colonic tissue of  subject 27 after consumption of two weeks of red meat without phytochemicals

value: red meat_NO_phytochemicals


title: Subject_27_timepoint_1_baseline_NO_phytochemicals [IP27-1]

description: Gene expression in colonic tissue of  subject 27 at baseline


title: Subject_26_timepoint_2_red meat_NO_phytochemicals [IP26-2]

description: Gene expression in colonic tissue of  subject 26 after consumption of two weeks of red meat without phytochemicals


title: H82_KRAS_Dox_Day1_rep2


title: H82_KRAS_NoDox_rep2

source_name: H82, KRAS, No Dox


title: Subject_21_timepoint_4_red meat_YES_phytochemicals [IP21-4]

description: Gene expression in colonic tissue of  subject 21 after consumption of two weeks of red meat with phytochemicals


title: Subject_21_timepoint_2_red meat_NO_phytochemicals [IP21-2]

description: Gene expression in colonic tissue of  subject 21 after consumption of two weeks of red meat without phytochemicals


title: LNCaP-R-DHT FARE-seq rep1


title: Subject_27_timepoint_3_white meat_NO_phytochemicals [IP27-3]

description: Gene expression in colonic tissue of  subject 27 after consumption of two weeks of white meat

value: white meat_NO_phytochemicals


title: Subject_21_timepoint_1_baseline_NO_phytochemicals [IP21-1]

description: Gene expression in colonic tissue of  subject 21 at baseline


title: H82_KRAS_NoDox_rep3


title: Subject_26_timepoint_1_baseline_NO_phytochemicals [IP26-1]

description: Gene expression in colonic tissue of  subject 26 at baseline


title: Subject_20_timepoint_1_baseline_NO_phytochemicals [IP20-1]

description: Gene expression in colonic tissue of  subject 20 at baseline


title: LNCaP-DHT-MDV FARE-seq rep3

source_name: LNCaP-DHT-MDV


title: Subject_21_timepoint_3_white meat_NO_phytochemicals [IP21-3]

description: Gene expression in colonic tissue of  subject 21 after consumption of two weeks of white meat


title: LNCaP-DMSO FARE-seq rep2

source_name: LNCaP-DMSO

value: DMSO for 18 hours


title: LNCaP-DMSO FARE-seq rep3


title: H82_KRAS_NoDox_rep1

value: No Dox


title: Subject_20_timepoint_2_red meat_NO_phytochemicals [IP20-2]

description: Gene expression in colonic tissue of  subject 20 after consumption of two weeks of red meat without phytochemicals


title: H82_EGFR_Dox_Day1_rep3

source_name: H82, EGFR, Dox, Day1

value: Dox


title: Subject_20_timepoint_4_red meat_YES_phytochemicals [IP20-4]

description: Gene expression in colonic tissue of  subject 20 after consumption of two weeks of red meat with phytochemicals


title: Subject_19_timepoint_1_baseline_NO_phytochemicals [IP19-1]

description: Gene expression in colonic tissue of  subject 19 at baseline


title: Subject_18_timepoint_3_white meat_NO_phytochemicals [IP18-3]

description: Gene expression in colonic tissue of  subject 18 after consumption of two weeks of white meat


title: Subject_18_timepoint_2_red meat_NO_phytochemicals [IP18-2]

description: Gene expression in colonic tissue of  subject 18 after consumption of two weeks of red meat without phytochemicals


title: Subject_18_timepoint_1_baseline_NO_phytochemicals [IP18-1]

description: Gene expression in colonic tissue of  subject 18 at baseline


title: H82_EGFR_Dox_Day7_rep1

source_name: H82, EGFR, Dox, Day7


title: H82_EGFR_Dox_Day7_rep3


title: LNCaP-DHT-MDV FARE-seq rep2

value: DHT (10nM) and enzalutamide (10µM) for 18 hours


title: H82_EGFR_Dox_Day1_rep1


title: H2107_EGFR_NoDox_rep2

source_name: H2107, EGFR, No Dox


title: H82_EGFR_Dox_Day7_rep2


title: H82_EGFR_NoDox_rep3

source_name: H82, EGFR, No Dox


title: Subject_19_timepoint_4_red meat_YES_phytochemicals [IP19-4]

description: Gene expression in colonic tissue of  subject 19 after consumption of two weeks of red meat with phytochemicals


title: Subject_19_timepoint_3_white meat_NO_phytochemicals [IP19-3]

description: Gene expression in colonic tissue of  subject 19 after consumption of two weeks of white meat


title: Subject_19_timepoint_2_red meat_NO_phytochemicals [IP19-2]

description: Gene expression in colonic tissue of  subject 19 after consumption of two weeks of red meat without phytochemicals


title: Subject_20_timepoint_3_white meat_NO_phytochemicals [IP20-3]

description: Gene expression in colonic tissue of  subject 20 after consumption of two weeks of white meat


title: Subject_17_timepoint_3_white meat_NO_phytochemicals [IP17-3]

description: Gene expression in colonic tissue of  subject 17 after consumption of two weeks of white meat


title: LNCaP-DMSO FARE-seq rep1

value: LNCaP


title: LNCaP-DHT-MDV FARE-seq rep1


title: LNCaP-DHT FARE-seq rep3

source_name: LNCaP-DHT

value: DHT (10nM) for 18 hours


title: LNCaP-DHT FARE-seq rep1

value: prostate cancer cell line


title: LNCaP-DHT FARE-seq rep2


title: Subject_17_timepoint_4_red meat_YES_phytochemicals [IP17-4]

description: Gene expression in colonic tissue of  subject 17 after consumption of two weeks of red meat with phytochemicals


title: Staph_TCH_CodY_2

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: Staphylococcus aureus LAC strain = CP035369.1 ; Staphylococcus aureus TCH1516 strain = NC_010079
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Staphylococcus aureus

source_name: bacteria cells

growth_protocol: glycerol stocks of Staphylococcus aureus USA300 strains (LAC and TCH1516) were inoculated into RPMI 1640 with 10% LB media. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 degree with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated CodY-DNA complexes were isolated with CodY mouse monoclonal antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to CodY from formaldehyde cross-linked Staphylococcus aureus cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes CodY (CodY mAbs, GenScript), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

treatment_protocol: For regulatory condition, Staphylococcus aureus cells are grown under RPMI 1640 with 10% LB medim.

tag: myc-tagging

value: Wild type cell

tag: chip-exo antibody

value: CodY mouse monoclonal IgG1, Genscript


title: Staph_LAC_CodY_2

value: USA300 LAC


title: Staph_LAC_CodY_1


title: Staph_TCH_CodY_1


title: Subject_17_timepoint_2_red meat_NO_phytochemicals [IP17-2]

description: Gene expression in colonic tissue of  subject 17 after consumption of two weeks of red meat without phytochemicals

value: Male


title: Subject_15_timepoint_4_red meat_YES_phytochemicals [IP15-4]

description: Gene expression in colonic tissue of  subject 15 after consumption of two weeks of red meat with phytochemicals


title: Subject_18_timepoint_4_red meat_YES_phytochemicals [IP18-4]

description: Gene expression in colonic tissue of  subject 18 after consumption of two weeks of red meat with phytochemicals


title: Subject_15_timepoint_3_white meat_NO_phytochemicals [IP15-3]

description: Gene expression in colonic tissue of  subject 15 after consumption of two weeks of white meat


title: H82_EGFR_Dox_Day1_rep2

tag: time


title: H82_EGFR_NoDox_rep1

value: day 0


title: H82_GFP_Dox_Day7_rep3

source_name: H82, GFP, Dox, Day7

value: TetO-GFP


title: H82_EGFR_NoDox_rep2


title: Subject_14_timepoint_2_red meat_NO_phytochemicals [IP14-2]

description: Gene expression in colonic tissue of  subject 14 after consumption of two weeks of red meat without phytochemicals

tag: subject id

value: Colonic tissue


title: H82_GFP_Dox_Day7_rep1


title: H82_GFP_Dox_Day7_rep2


title: Subject_15_timepoint_1_baseline_NO_phytochemicals [IP15-1]

description: Gene expression in colonic tissue of  subject 15 at baseline

tag: gender

value: Female


title: Subject_15_timepoint_2_red meat_NO_phytochemicals [IP15-2]

description: Gene expression in colonic tissue of  subject 15 after consumption of two weeks of red meat without phytochemicals

tag: age

value: red meat_NO_phytochemicals


title: Subject_14_timepoint_1_baseline_NO_phytochemicals [IP14-1]

description: Gene expression in colonic tissue of  subject 14 at baseline

tag: sample group


title: Subject_14_timepoint_3_white meat_NO_phytochemicals [IP14-3]

description: Gene expression in colonic tissue of  subject 14 after consumption of two weeks of white meat

value: white meat_NO_phytochemicals

tag: time point


title: Subject_13_timepoint_3_white meat_NO_phytochemicals [IP13-3]

description: Gene expression in colonic tissue of  subject 13 after consumption of two weeks of white meat

tag: tissue


title: Subject_13_timepoint_4_red meat_YES_phytochemicals [IP13-4]

description: Gene expression in colonic tissue of  subject 13 after consumption of two weeks of red meat with phytochemicals

value: red meat_YES_phytochemicals


title: Subject_14_timepoint_4_red meat_YES_phytochemicals [IP14-4]

description: Gene expression in colonic tissue of  subject 14 after consumption of two weeks of red meat with phytochemicals


title: Subject_13_timepoint_2_red meat_NO_phytochemicals [IP13-2]

description: Gene expression in colonic tissue of  subject 13 after consumption of two weeks of red meat without phytochemicals


title: Subject_17_timepoint_1_baseline_NO_phytochemicals [IP17-1]

description: Gene expression in colonic tissue of  subject 17 at baseline


title: Subject_13_timepoint_1_baseline_NO_phytochemicals [IP13-1]

description: Gene expression in colonic tissue of  subject 13 at baseline


title: H82_GFP_Dox_Day1_rep1

source_name: H82, GFP, Dox, Day1


title: H82_GFP_Dox_Day1_rep2


title: K562-IgG Control

city: Quebec

first: Maeva

last: Devoucoux

state: Quebec

address: 9 rue MacMahon

institute: Laval University

data_processing:
For ChIP-seq, the single-end reads were mapped on the human genome build hg19 using bowtie version 2.1.6 (Langmead et al., 2009), using the pre-set sensitive parameter.
MACS version 2.0.10 (model-based analysis of ChIPseq) peak finding algorithm was used to identify regions of ChIP-seq enrichment over the background (Feng et al., 2012), using broad peaks parameters.
Unique mapped read values were normalized to library size. Peaks were annotated as per human genome EnsDb.Hspaiens.v75 - hg19
For  RNAseq, raw fast5 files were basecalled using Guppy v.4.2.2 using fast basecalling settings, and samples were demultiplexed according to barcodes with the guppy_barcoder.
The resulting FASTQ reads were aligned to the hg19 human reference with Minimap2 version 2.17-r941
Raw read counts were obtained with the featureCounts tool from the Subread package v 2.0.0, using the exon counting mode (Li, 2018; Liao et al., 2014) and normalized as Counts per Million (CPM).
Genome_build: hg19
Supplementary_files_format_and_content: MRG15_long_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MRG15 long CHD 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: MRG15_short_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MRG15 short CHD 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: MRGX_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MRGX 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: JCote_RNAseq.DE.sig_cpm.xlsx is a tab separated excel file containing read counts for genes normalized to CPM for all RNA-seq samples.
Supplementary_files_format_and_content: Jcote_RNAseq_splicing.xlsx is a tab separated excel file containing the venn analysis between indicated samples. Fold change of 2 is used as threshold (pVal 0.01).

source_name: K562 from ATCC

growth_protocol: RPMI, 10% FBS, 1% Glutamax

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: 1ug/ml Puromycin

value: lymphoblast from chronic myelogenous leukemia (CML)

tag: growth conditions

value: normal growth conditions

tag: chip antibody

value: IgG, Rabbit polyclonal, Millipore, Cat# PP64, RRID:AB_97852


title: K562-MRGX-FLAG

tag: cell line

value: FLAG M2 , Mouse monoclonal, Sigma-Aldrich ,Cat# F1804, RRID:AB_262044

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: K562-MRG15 short CHD-FLAG


title: Patient 4

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

institute: Utrecht University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STARSolo v2.7.8a
metadata seurat pipeline; raw counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Sparse Matrix  with raw gene counts, features and barcodes for every gene and every cell

source_name: Tonsillectomy

extract_protocol:
Tonsils were removed, washed in PBS, minced and digested with Collagenase D and Dnase. After a Percoll gradient the 21-35% fraction was collected and CD45-CD31- cells were sorted in 384-wells plates by FACS. 50% of the Cells were additionally selected for PDPN+ and CD35+
RNA libraries were prepared for sequencing using standard CEL-seq2 protocols

value: tonsil

value: Stromal-derived follicular dendritic cells (FDC)


title: H82_GFP_Dox_Day1_rep3

tag: construct

value: Dox


title: K562-MRG15 long CHD-FLAG

tag: cell type


title: Patient 3


title: Subject_12_timepoint_2_red meat_NO_phytochemicals [IP12-2]

description: Gene expression in colonic tissue of  subject 12 after consumption of two weeks of red meat without phytochemicals

source_name: timepoint_2_red meat_NO_phytochemicals


title: Subject_12_timepoint_3_white meat_NO_phytochemicals [IP12-3]

description: Gene expression in colonic tissue of  subject 12 after consumption of two weeks of white meat


title: Subject_12_timepoint_4_red meat_YES_phytochemicals [IP12-4]

description: Gene expression in colonic tissue of  subject 12 after consumption of two weeks of red meat with phytochemicals

source_name: timepoint_4_red meat_YES_phytochemicals


title: H82_GFP_NoDox_rep2

source_name: H82, GFP, No Dox

value: No Dox


title: H82_GFP_NoDox_rep1


title: H82_GFP_NoDox_rep3


title: pCIG-MEK1ca Replicate 2 (reanalysis)

city: Marseille

first: Marie-Claire

last: DELFINI

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description:
DGE_MEK1ca_HoxB8_vs_MEK1ca_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
DGE_MEK1ca_vs_pCIG_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
MEK1ca_GFPplus_2

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the galgal4 genome assembly using subread-align
Gene exon counts were made using featureCounts
RNA-Seq differentially expressed genes were called using DESeq2 using a false discovery rate (FDR;padj) cut-off of 0.01.
Genome_build: galGal4
Supplementary_files_format_and_content: Excel files containing gene counts and DGE :DESeq output of differentially expressed genes (Log2Fold Change, p-value, p-adjusted) of MEK1ca vs pCIG, and MEK1ca+HoxB8 vs MEK1ca.

organism: Gallus gallus

source_name: pCIG-MEK1ca GFP positive cells

extract_protocol:
RNA was extracted (RNeasy Mini Kit) and reverse transcribed, and cDNA was amplified using a linear amplification system and used for sequencing library building (GATC).
Random primed cDNA library, purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis, adapter ligation and adapter specific PCR amplification, Illumina technology, 50,000,000 reads paired end with 2×50 bp read length.

treatment_protocol: RNA-seq of MEK1ca GFP+ cells Rep2 (re-analysis of GSM5517716)  pCIG-MEK1ca plasmid  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.

tag: plasmid dna

value: pCIG-MEKca+pCIG

value: MEK1ca GFP expressing cells


title: pCIG-MEK1ca Replicate 1 (reanalysis)

description:
DGE_MEK1ca_HoxB8_vs_MEK1ca_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
DGE_MEK1ca_vs_pCIG_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
MEK1ca_GFPplus_1

treatment_protocol: RNA-seq of MEK1ca GFP+ cells Rep1 (re-analysis of GSM5517715)  pCIG-MEK1ca plasmid  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.


title: Control transfection Replicate 2 (reanalysis)

description:
DGE_MEK1ca_vs_pCIG_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
PCIG_GFPplus_2

source_name: pCIG GFP positive cells

treatment_protocol: RNA-seq of pCIG GFP+ cells Rep2 (re-analysis of GSM4956410)  pCIG plasmid  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.

value: pCIG

value: Control GFP expressing cells


title: Subject_10_timepoint_4_red meat_YES_phytochemicals [IP10-4]

description: Gene expression in colonic tissue of  subject 10 after consumption of two weeks of red meat with phytochemicals

value: Male

value: Colonic tissue


title: Subject_10_timepoint_1_baseline_NO_phytochemicals [IP10-1]

description: Gene expression in colonic tissue of  subject 10 at baseline


title: Control transfection Replicate 1 (reanalysis)

description:
DGE_MEK1ca_vs_pCIG_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
PCIG_GFPplus_1

treatment_protocol: RNA-seq of pCIG GFP+ cells Rep1 (re-analysis of GSM4956409)  pCIG plasmid  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.


title: Subject_10_timepoint_2_red meat_NO_phytochemicals [IP10-2]

description: Gene expression in colonic tissue of  subject 10 after consumption of two weeks of red meat without phytochemicals

value: red meat_NO_phytochemicals


title: Subject_12_timepoint_1_baseline_NO_phytochemicals [IP12-1]

description: Gene expression in colonic tissue of  subject 12 at baseline

value: Female


title: Subject_10_timepoint_3_white meat_NO_phytochemicals [IP10-3]

description: Gene expression in colonic tissue of  subject 10 after consumption of two weeks of white meat

value: white meat_NO_phytochemicals


title: Patient 2


title: Subject_8_timepoint_4_red meat_YES_phytochemicals [IP8-4]

description: Gene expression in colonic tissue of  subject 8 after consumption of two weeks of red meat with phytochemicals

value: red meat_YES_phytochemicals


title: Patient 1


title: WT into PEP-3 [TUMA_W-P_32_S62]

city: Manchester

first: Amir

middle: Saam

last: Youshani

address: Oxford Road

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: University of Manchester

description:
TUMA_W-P_32_S62
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv

data_processing:
Unmapped paired-end sequences from an Illumina HiSeq4000 sequencer were tested by FastQC.
Sequenced reads were mapped to mm9/NCBI37 whole genome and quantified using STAR v2.5.0a with parameters --alignSJDBoverhangMin 999 --outFilterMultimapNmax 10 --quantMode TranscriptomeSAM
Mapped reads were quantified using RSEM v1.3.0 with parameters --paired-end
Gene abundance estimates from RSEM output were corrected for library size as well as batch and nine surrogate variables inferred using R package sva v3.22.0 in a linear model. Low counts (less than 10 counts per million) were removed.
Genome_build: mm9/NCBI37
Supplementary_files_format_and_content: normalised_gene_counts.csv: File with comma-separated values for each experiment include normalised counts for all samples.

source_name: Tumour Undifferentiated Macrophage

growth_protocol: GL-261 cells were cultured in RPMI media with 10% FCS and 5mM L-glutamine. Cells were grown to confluency. After 3-days culturing, cells were trypsinised and suspended in fresh GL-261 media at an aliquot of 50,000 cells for intracranial implantation.

extract_protocol:
Single cell suspensions were obtained from four populations following mouse brain dissociation, antibody staining and flow-cell sorting. RNA and cDNA conversion was completed using the Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing, according to manufacturer's guidelines.
Library was constructed by the Genomic Core Facility at the University of Manchester.

treatment_protocol: No treatment given.

tag: recipient strain

tag: implantation

value: syngeneic GBM GL-261 cells

tag: source tissue

value: brain

value: Tumour Undifferentiated Macrophage


title: Subject_9_timepoint_2_red meat_NO_phytochemicals [IP9-2]

description: Gene expression in colonic tissue of  subject 9 after consumption of two weeks of red meat without phytochemicals


title: Subject_9_timepoint_1_baseline_NO_phytochemicals [IP9-1]

description: Gene expression in colonic tissue of  subject 9 at baseline


title: Subject_9_timepoint_3_white meat_NO_phytochemicals [IP9-3]

description: Gene expression in colonic tissue of  subject 9 after consumption of two weeks of white meat


title: Subject_8_timepoint_3_white meat_NO_phytochemicals [IP8-3]

description: Gene expression in colonic tissue of  subject 8 after consumption of two weeks of white meat


title: Subject_7_timepoint_4_red meat_YES_phytochemicals [IP7-4]

description: Gene expression in colonic tissue of  subject 7 after consumption of two weeks of red meat with phytochemicals


title: Subject_8_timepoint_1_baseline_NO_phytochemicals [IP8-1]

description: Gene expression in colonic tissue of  subject 8 at baseline


title: pCIG-MEK1ca+pCIG-HoxB8 Replicate 2

description:
DGE_MEK1ca_HoxB8_vs_MEK1ca_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
MEK1_HoxB8_GFPplus_2

source_name: pCIG-MEK1ca+pCIG-HoxB8 GFP positive cells

treatment_protocol: RNA-seq of MEK1ca+HoxB8 GFP+ cells Rep2  pCIG-MEK1ca and pCIG-HoxB8 plasmids  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl, for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl, for the HoxB8 mix : pCIG-HoxB8 1 µg/µl + pCIG 1µg/µl and for the MEK1ca+HoxB8 mix: pCIG-MEK1ca 1 µg/µl + pCIG-HoxB8 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.

value: MEK1ca+HoxB8 GFP expressing cells


title: PEP-3 into WT [TDMA_P-W_28_S58]

description:
TDMA_P-W_28_S58
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

source_name: Tumour Differentiated Macrophage

value: Tumour Differentiated Macrophage


title: WT into PEP-3 [TDMA_W-P_31_S61]

description:
TDMA_W-P_31_S61
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: Subject_7_timepoint_2_red meat_NO_phytochemicals [IP7-2]

description: Gene expression in colonic tissue of  subject 7 after consumption of two weeks of red meat without phytochemicals


title: WT into PEP-3 [TM_W-P_30_S60]

description:
TM_W-P_30_S60
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

source_name: Tumour Microglia

value: Tumour Microglia


title: Subject_8_timepoint_2_red meat_NO_phytochemicals [IP8-2]

description: Gene expression in colonic tissue of  subject 8 after consumption of two weeks of red meat without phytochemicals


title: Subject_9_timepoint_4_red meat_YES_phytochemicals [IP9-4]

description: Gene expression in colonic tissue of  subject 9 after consumption of two weeks of red meat with phytochemicals


title: pCIG-MEK1ca+pCIG-HoxB8 Replicate 1

description:
DGE_MEK1ca_HoxB8_vs_MEK1ca_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
MEK1_HoxB8_GFPplus_1

treatment_protocol: RNA-seq of MEK1ca+HoxB8 GFP+ cells Rep1  pCIG-MEK1ca and pCIG-HoxB8 plasmids  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl, for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl, for the HoxB8 mix : pCIG-HoxB8 1 µg/µl + pCIG 1µg/µl and for the MEK1ca+HoxB8 mix: pCIG-MEK1ca 1 µg/µl + pCIG-HoxB8 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.


title: Subject_5_timepoint_3_white meat_NO_phytochemicals [IP5-3]

description: Gene expression in colonic tissue of  subject 5 after consumption of two weeks of white meat


title: Subject_5_timepoint_1_baseline_NO_phytochemicals [IP5-1]

description: Gene expression in colonic tissue of  subject 5 at baseline


title: PEP-3 into WT  [TM_P-W_27_S57]

description:
TM_P-W_27_S57
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: PEP-3 into WT [TUMA_P-W_29_S59]

description:
TUMA_P-W_29_S59
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: Subject_7_timepoint_3_white meat_NO_phytochemicals [IP7-3]

description: Gene expression in colonic tissue of  subject 7 after consumption of two weeks of white meat


title: Subject_7_timepoint_1_baseline_NO_phytochemicals [IP7-1]

description: Gene expression in colonic tissue of  subject 7 at baseline


title: 3-microRNA mimic mimic 4

city: Goettingen

first: Md Rezaul

last: Islam

address: von siebold str. 3a

country: Germany

institute: DZNE

description: mimic 4

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to human genome (hg38) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Genome_build: hg38
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts after normalization text files contains gene counts

molecule: polyA RNA

source_name: brain organoids

growth_protocol: iPSCs derived brain organoids were cultured on matrigel as previously described ( Zafeiriou et al., in press).

extract_protocol:
Treated organoids were snap frozen in liquid nitrogen. Tissues were homogenized in Trizol  and RNA was prepared using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: At DIV64, Brain organoids were treated with mmic cocktail and negative control for 24 hours.

value: iPSC-derived engineered brain organoids

tag: div

tag: sample type

value: tissue


title: WT into PEP-3 [TUMA_W-P_24_S54]

description:
TUMA_W-P_24_S54
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: Control transfection Replicate 1 (re-analysis)

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the galgal4 genome assembly using subread-align
Gene exon counts were made using featureCounts
Genome_build: galGal4
Supplementary_files_format_and_content: Excel files containing gene counts and DGE :DESeq output of differentially expressed genes (Log2Fold Change, p-value, p-adjusted) of MEK1ca vs pCIG (Control).


title: pCIG-MEK1ca Replicate 2

treatment_protocol: RNA-seq of MEK1ca GFP+ cells Rep2  pCIG-MEK1ca plasmid  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.

value: pCIG-MEKca+pCIG

value: MEK1ca GFP expressing cells


title: Subject_5_timepoint_4_red meat_YES_phytochemicals [IP5-4]

description: Gene expression in colonic tissue of  subject 5 after consumption of two weeks of red meat with phytochemicals

tag: subject id


title: Subject_3_timepoint_4_red meat_YES_phytochemicals [IP3-4]

description: Gene expression in colonic tissue of  subject 3 after consumption of two weeks of red meat with phytochemicals

tag: gender


title: pCIG-MEK1ca Replicate 1

treatment_protocol: RNA-seq of MEK1ca GFP+ cells Rep1  pCIG-MEK1ca plasmid  Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.


title: Nil (PEP-3 – CD45.1) [M_P_26_S56]

description:
M_P_26_S56
experiment#2
RNA - cDNA
processed data file: normalised_gene_counts.csv

source_name: Microglia

value: Normal Microglia


title: Subject_3_timepoint_2_red meat_NO_phytochemicals [IP3-2]

description: Gene expression in colonic tissue of  subject 3 after consumption of two weeks of red meat without phytochemicals

treatment_protocol: There are 2 study groups (1 and 2), and in each study group there are 2 meat intervention periods (A and B), separated by a wash-out period (O). During intervention period “A”, participants were asked to consume the provided red processed meat products (red processed meat group), while in period “B” red processed meat products enriched with natural compounds were provided. For study group 1, the meat products of both period ”A” and “B” had standard nitrite levels (standard nitrite PHYTOME meat), while in study group 2 the nitrite levels in period “B” were reduced (reduced nitrite PHYTOME meat). At the beginning of the study and after each intervention period of 2 weeks, colonic biopsies were collected during an endoscopic examination and analysed for gene expression changes.

value: Male

tag: age


title: Subject_5_timepoint_2_red meat_NO_phytochemicals [IP5-2]

description: Gene expression in colonic tissue of  subject 5 after consumption of two weeks of red meat without phytochemicals

tag: sample group

value: Colonic tissue


title: Control transfection Replicate 2 (re-analysis)

value: pCIG

value: Control GFP expressing cells


title: Subject_2_timepoint_2_red meat_NO_phytochemicals [IP2-2]

description: Gene expression in colonic tissue of  subject 2 after consumption of two weeks of red meat without phytochemicals

value: Female

value: red meat_NO_phytochemicals

tag: time point


title: 3-microRNA mimic mimic 3

description: mimic 3


title: Subject_3_timepoint_3_white meat_NO_phytochemicals [IP3-3]

description: Gene expression in colonic tissue of  subject 3 after consumption of two weeks of white meat

value: white meat_NO_phytochemicals

tag: tissue


title: Nil (WT – CD45.2) [M_W_25_S55]

description:
M_W_25_S55
experiment#1
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: brain


title: Subject_2_timepoint_1_baseline_NO_phytochemicals [IP2-1]

description: Gene expression in colonic tissue of  subject 2 at baseline


title: WT into PEP-3 [TM_W-P_22_S52]

description:
TM_W-P_22_S52
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: syngeneic GBM GL-261 cells


title: WT into PEP-3 [TDMA_W-P_23_S53]

description:
TDMA_W-P_23_S53
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: PEP-3 into WT [TUMA_P-W_21_S51]

description:
TUMA_P-W_21_S51
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: Tumour Undifferentiated Macrophage


title: 3-microRNA mimic mimic 2

description: mimic 2


title: Subject_3_timepoint_1_baseline_NO_phytochemicals [IP3-1]

description: Gene expression in colonic tissue of  subject 3 at baseline


title: 3-microRNA mimic control 3

description: control 3


title: learning_36 [16m_10]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
samples were mapped to mouse genome (mm10) and microRNA counts were generated using miRDeep2
Genome_build: mm10
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts after normalization text files contains gene counts

source_name: 16.5 months_blood

extract_protocol:
Blood was collected from retro orbital sinus at every 6 weeks
Libraries were generated according to the instructions of TruSeq Small RNA Library Preparation Kit
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: Longitudinal analysis of blood small microRNAome in mice. Mice were investigated from 12 months upto 16.5 months.

tag: strain

value: 16.5 months

value: total blood

tag: molecule type

value: small RNA


title: learning_37 [16m_11]


title: learning_35 [16m_9]


title: learning_34 [16m_8]


title: learning_33 [16m_7]


title: PEP-3 into WT  [TM_P-W_19_S49]

description:
TM_P-W_19_S49
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: Tumour Microglia


title: Subject_2_timepoint_4_red meat_YES_phytochemicals [IP2-4]

description: Gene expression in colonic tissue of  subject 2 after consumption of two weeks of red meat with phytochemicals

value: red meat_YES_phytochemicals


title: Subject_1_timepoint_3_white meat_NO_phytochemicals [IP1-3]

description: Gene expression in colonic tissue of  subject 1 after consumption of two weeks of white meat


title: 3-microRNA mimic control 4

description: control 4

value: iPSC-derived engineered brain organoids

value: tissue


title: Subject_2_timepoint_3_white meat_NO_phytochemicals [IP2-3]

description: Gene expression in colonic tissue of  subject 2 after consumption of two weeks of white meat


title: Subject_1_timepoint_4_red meat_YES_phytochemicals [IP1-4]

description: Gene expression in colonic tissue of  subject 1 after consumption of two weeks of red meat with phytochemicals

value: Male


title: Subject_1_timepoint_1_baseline_NO_phytochemicals [IP1-1]

description: Gene expression in colonic tissue of  subject 1 at baseline

value: Colonic tissue


title: 3-microRNA mimic control 1

description: control 1


title: learning_26 [15m_5]

source_name: 15 months_blood

value: 15 months


title: learning_29 [16m_3]


title: learning_24 [15m_3]


title: learning_31 [16m_5]


title: 3-microRNA mimic control 2

description: control 2


title: PEP-3 into WT [TDMA_P-W_20_S50]

description:
TDMA_P-W_20_S50
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: Tumour Differentiated Macrophage


title: 3-microRNA mimic mimic 1

description: mimic 1


title: learning_23 [15m_2]


title: learning_32 [16m_6]


title: Subject_1_timepoint_2_red meat_NO_phytochemicals [IP1-2]

description: Gene expression in colonic tissue of  subject 1 after consumption of two weeks of red meat without phytochemicals


title: IRS1-579

description: Gene expression data from m. vastus lateralis biopsies obtained with Weil-  Blakesley conchotome instrument (Agnthos, Sweden)

hyb_protocol: Fragmented and biotinylated sense-strand DNA  target (5.5 μg) were hybridized to the arrays in GeneChip Hybridization Oven 645 at 45°C for  16-18 hrs.

scan_protocol: Arrays were washed and stained in GeneChip Fluidics Station 450 prior to scanning  in Affymetrix GeneChip Scanner.

data_processing:
1) CEL files were processed with RMA algorithm from oligo R package (v1.56.0). Resulting probeset values are reported in the expression matrix.
2) Probeset IDs were matched to their corresponding ENSEMBL IDs using biomaRt R package (v2.48.2). The non-unique probesets mapping to multiple ENSEMBL IDs are filtered out.
3) The probesets with signal value below 4 in at least 24 samples (minimum Disease group size) are discarded from the analysis.
4) Remaining probeset expression values are collapsed to ENSEMBL IDs using collapseRows function from WGCNA R package (v1.70-3) with MaxMean method.
5) The resulting expression matrix with ENSEMBL IDs were used for downstream analysis. (Supplementary File: expression_ensemblLevel.tsv.gz)

source_name: Biopsy from m. vastus lateralis

label_protocol: Amplified and biotinylated sense-strand DNA targets were generated from total RNA  using the WT Plus Kit (Thermo Fisher, MA).

growth_protocol: m. vastus lateralis biopsies obtained with Weil-Blakesley conchotome instrument (Agnthos, Sweden)

extract_protocol: mirVana™ miRNA Isolation Kit (#AM1560, Invitrogen, Waltham, Massachusetts, USA)

treatment_protocol: The participants were instructed to refrain from physical exercise 48  hrs before the visit. All investigations were performed in the morning after an overnight fast.

tag: disease

value: NGT

tag: bmi

tag: m-value

tag: lab


title: learning_30 [16m_4]


title: WT into PEP-3 [TUMA_W-P_16_S46]

description:
TUMA_W-P_16_S46
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv

tag: recipient strain

tag: cell type


title: learning_28 [16m_2]


title: IRS1-580


title: learning_20 [13m_11]

source_name: 13.5 months_blood

value: 13.5 months


title: learning_27 [16m_1]


title: PEP-3 into WT  [TM_P-W_11_S41]

description:
TM_P-W_11_S41
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv

tag: implantation

tag: source tissue


title: PEP-3 into WT [TDMA_P-W_12_S42]

description:
TDMA_P-W_12_S42
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_25 [15m_4]


title: Nil (WT – CD45.2) [M_W_17_S47]

description:
M_W_17_S47
experiment#1
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: Normal Microglia


title: WT into PEP-3 [TM_W-P_14_S44]

description:
TM_W-P_14_S44
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: brain


title: Nil (PEP-3 – CD45.1) [M_P_10_S40]

description:
M_P_10_S40
experiment#2
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_22 [15m_1]


title: WT into PEP-3 [TDMA_W-P_15_S45]

description:
TDMA_W-P_15_S45
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: syngeneic GBM GL-261 cells


title: learning_21 [13m_12]


title: Nil (WT – CD45.2) [M_W_9_S39]

description:
M_W_9_S39
experiment#1
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_18 [13m_9]


title: learning_19 [13m_10]


title: IRS1-578


title: IRS1-577


title: learning_16 [13m_7]


title: learning_11 [13m_2]


title: learning_17 [13m_8]


title: learning_14 [13m_5]


title: PEP-3 into WT [TUMA_P-W_13_S43]

description:
TUMA_P-W_13_S43
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: Tumour Undifferentiated Macrophage


title: learning_15 [13m_6]


title: learning_12 [13m_3]


title: learning_9 [12m_9]

source_name: 12 months_blood

value: 12 months


title: learning_13 [13m_4]

value: total blood


title: IRS1-576


title: IRS1-575


title: WT into PEP-3 [TDMA_W-P_7_S37]

description:
TDMA_W-P_7_S37
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: WT into PEP-3 [TM_W-P_6_S36]

description:
TM_W-P_6_S36
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_8 [12m_8]

value: small RNA


title: learning_7 [12m_7]


title: PEP-3 into WT [TUMA_P-W_5_S35]

description:
TUMA_P-W_5_S35
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_5 [12m_5]


title: IRS1-574


title: learning_6 [12m_6]


title: learning_4 [12m_4]


title: learning_3 [12m_3]


title: IRS1-573


title: IRS1-572


title: PEP-3 into WT [TDMA_P-W_4_S34]

description:
TDMA_P-W_4_S34
experiment#3
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_10 [13m_1]


title: IRS1-571


title: IRS1-570


title: learning_2 [12m_2]


title: IRS1-569


title: WT into PEP-3 [TUMA_W-P_8_S38]

description:
TUMA_W-P_8_S38
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: learning_1 [12m_1]


title: IRS1-568


title: PEP-3 into WT  [TM_P-W_3_S33]

description:
TM_P-W_3_S33
experiment#4
RNA - cDNA
processed data file: normalised_gene_counts.csv

value: Tumour Microglia


title: Nil (PEP-3 – CD45.1) [M_P_2_S32]

description:
M_P_2_S32
experiment#2
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: Nil (WT – CD45.2) [M_W_1_S31]

description:
M_W_1_S31
experiment#1
RNA - cDNA
processed data file: normalised_gene_counts.csv


title: miR-146a control 4

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Genome_build: mm10
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts after normalization text files contains gene counts

source_name: microglia

growth_protocol: Immortalized microglial cells were cultured accroding to instructions from manufacturer.

extract_protocol:
Treated cells were dissociated in Trizol. RNA was prepared using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: Once differentiated, cells were treated with miR-146 mimic and negative control for 48 hours.

value: Immortalized microglial cells

tag: sample type

value: cells


title: miR-146a control 3


title: miR-146a mimic 1


title: IRS1-566

description: Gene expression data from m. vastus lateralis biopsies obtained with Weil-  Blakesley conchotome instrument (Agnthos, Sweden)


title: YR_S3

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

country: China

institute: Qinghai university

data_processing:
Raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
Low-quality raw reads and clean tags were identified as tRNA, rRNA, snoRNA, snRNA and scRNA using GenBank and Rfam database were removed and enriched clean tags were compared with the reference genome USDA_OmykA_1.1 and the reads mapped to exons, introns and repeat sequences were removed.
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text files include norm values for each Sample …

organism: Oncorhynchus mykiss

source_name: dorsal skin

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: yellow mutant

value: dorsal skin

value: 12 months post hatching


title: miR-146a mimic 3


title: miR-146a mimic 4


title: small RNA 16.5 months 16.5m_9

description:
16.5 months
small RNA

source_name: blood


title: miR-146a mimic 2


title: WR_S3

value: wild-type


title: miR-146a control 2


title: small RNA 16.5 months 16.5m_5

description:
16.5 months
small RNA


title: small RNA 16.5 months 16.5m_4

description:
16.5 months
small RNA


title: YR_S2


title: miR-146a control 1


title: YR_S1


title: IRS1-560


title: IRS1-563


title: small RNA 16.5 months 16.5m_2

description:
16.5 months
small RNA


title: IRS1-565


title: small RNA 16.5 months 16.5m_7

description:
16.5 months
small RNA


title: IRS1-564


title: WR_S2


title: IRS1-562


title: small RNA 16.5 months 16.5m_8

description:
16.5 months
small RNA


title: small RNA 15 months 15m_10

description:
15 months
small RNA


title: small RNA 16.5 months 16.5m_6

description:
16.5 months
small RNA


title: small RNA 16.5 months 16.5m_10

description:
16.5 months
small RNA


title: small RNA 15 months 15m_8

description:
15 months
small RNA


title: small RNA 16.5 months 16.5m_3

description:
16.5 months
small RNA


title: WR_S1