title: RDEB_1.cDNA.001.C10

value: RDEB

tag: cell type

tag: passage number


title: px0494-CCGTCCA_deep

status: Public on Apr 01 2018

type: SRA

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
Basecalls performed using Illumina's CASAVA software, version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The first 6 bases were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.1 using the parameters --clip_R1 6 --clip_R2 6 –paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), –a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ? 20), and –u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17. Duplicates were marked with Picard V1.31 (http://picard.sourceforge.net).
Methylation of each cytosine was called using SAMtools mpileup (-B -C 0 -q 30 -d 500) followed by Novomethyl V1.01 (-o Consensus -%) (www.novocraft.com). Cytosine calls with Phred quality score ?15 were discarded. Methylation percentage of each CpG di-nucleotide (found by searching the genome with a custom java script) was calculated by taking a weighted average of each cytosine using the map command from the bedtools suite (Quinlan and Hall, 2010). In most cases, only one base within a CpG dinucleotide had coverage; in these cases, the methylation information of the covered base was extrapolated to the other base.
Genome_build: hg19
Supplementary_files_format_and_content: bed file for CpG methylation. Columns are as follows: chr, start, end, fractional methylation, methylated C's, total C's, # of CpGs covered in the dinucleotide (1=just one, 2=both C and G covered)

molecule: genomic DNA

organism: Homo sapiens

source_name: CD49f Hematopoetic stem cell

extract_protocol:
Sorted cells were lysed in 96 well plates in 4 uL of lysis buffer (20 mM Tris-HCl, pH 8.0, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL Qiagen Protease) for 30 minutes at 50 degrees.
The lysed cells were then spiked-in with 1 uL of 60 fg/uL purified T7 phage DNA (GeneON). The DNA mixture was then bisulfite converted with the MethylEdge Bisulfite Conversion kit (Promega) using a modified bead-based protocol which enables automation (Domanico et al., 2013): 5 uL of the lysis/spike-in mixture was combined with 32.5 uL of MethylEdge Conversion reagent and incubated at 98°C for 8 minutes and 54°C for 60 minutes in a PCR machine. After incubation, the plate was briefly spun down and placed on an Agilent Bravo robot for subsequent steps. The 37.5 uL of bisulfite converted DNA was mixed with 180 uL of MethylEdge Binding Buffer and 1.8 uL of 20 mg/mL MagSi-DNA allround magnetic silica beads (MagnaMedics) and incubated at room temperature for 15 minutes. The beads were then collected on a magnet for 3 minutes and washed twice with 220 uL of 80% ethanol for 30 seconds while on the magnet. 60 uL of MethylEdge desulfonation buffer was added and incubated for 15 minutes. The desulfonation buffer was then removed and the beads were washed twice with 100 uL of 80% ethanol. The beads were then air-dried for 1 minute, resuspended in 20 uL of Qiagen elution buffer, and incubated at 56°C in a shaking incubator at 2,000 rpm for 15 minutes. The beads were then collected on a magnet for 30 seconds and the supernatant containing the DNA was removed. The bisulfite-converted ssDNA from above was added directly into a mixture containing 1.25 uL of 10 mM dNTPs and 1 uL of 500 uM random hexamers (3’ phosphothioate). The reactions were incubated at 98°C for 1 minute and snap frozen on ice for 2 minutes. A mastermix of 0.5 uL of 50 U/uL Klenow fragment [3’?5’ exo-] (NEB M0212M), and 2.5 uL of 10X NEB Buffer 2 was added on ice and mixed well. The reactions incubated in a PCR machine as follows: 4?C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes. The entire reaction was denatured again at 98?C for 1 minute and snap frozen on ice for 2 minutes. The reaction was transferred on a pre-chilled CoolRack by robot into a new plate containing 5 uL mixture of 20 uM random hexamers (3’ phosphothioate), 0.5 mM dNTPs, 1X NEB buffer and 25 U of Klenow fragment [3’?5’ exo-]. The wells were mixed well and the reaction was cycled once again: 4?C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes, and heat-inactivated at 70°C for 10 minutes. 20 uL of Qiagen Elution Buffer was added to each reaction to make it up to 50 uL, and each reaction was purified using 50 uL of Sera-Mag beads before proceeding to the standard illumina adapter ligation library construction protocol. The 25 uL of cleaned-up adapter-ligated fragments were PCR amplified in 50 uL containing 1 U of Phusion U Hot Start DNA Polymerase (Life Technologies F-555S), 1X HF buffer, 3% DMSO, 200 uM dNTPs, 0.5 uM PCR primer 1.0 (need sequence) (IDT), and corresponding 0.5 uM indexing PCR primer 2.0. The reactions were incubated in a PCR machine as follows: initial 98?C for 1 minute; 10 cycles of 98?C for 30 seconds, 65?C for 15 seconds, 72?C for 15 seconds; and a final extension of 72?C for 5 minutes. The 50 uL reaction was cleaned up with 40 uL of Sera-Mag beads and eluted in 15 uL.

tag: type

value: single-cell

tag: donor

tag: markers


title: pair14 primary tumor

type: genomic

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

country: USA

institute: NCI

description:
P14a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

scan_protocol: Scanned on an Agilent microarray scanner G2565BA.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1). Rank segmentation algorithm (significance threshold: 5E-6) of Nexus Copy Number 9 was applied to analyze aCGH data. Significance threshold: 5E6

source_name: colorectal adenoma

label_protocol: Protocol Version 3.2, Oct 2010, Agilent. Sex-matched human genomic DNA (Promega) was used as reference DNA.

extract_protocol: Genomic DNA was isolated from formalin-fixed paraffin-embedded colorectal adenoma samples using Gentra Puregene Kit (handbook, June 2011) according to the manufacturer's instructions (Qiagen, Hilden, Germany). DNA quality and quantity were assessed using a Nanodrop ND1000 spectrophotometer.

tag: tissue

value: primary colorectal adenoma

tag: Sex

value: male

tag: age

tag: recurrence

value: yes

tag: ploidy

value: near 2N

tag: sample type

source_name: Control DNA

value: reference


title: px0494-CACGATA_deep


title: Colon biopsy from UC [1F06_14072200037]

type: RNA

city: Cambridge

first: William

last: Gordon

address: 1 Portland Street

institute: Pfizer Inc

description:
SAMPLE 8
RNA from Ulcerative Colitis biopsies

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Primeview 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings

label: biotin

molecule: total RNA

source_name: Human Colon Tissue Biopsy_Lesional

label_protocol: Biotinylated cRNA were prepared according to the standard Nugen protcol from 1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiazol extraction of total RNA was performed according to the manufacturer's instructions with on column DNASE digestion

treatment_protocol: Colon biopsies were placed in RNAlater and stored at -80 until processed

tag: patient id

value: Female

tag: disease

value: Ulcerative Colitis

tag: tissue state

value: Lesional

tag: hospital site

value: Brigham and Womens

tag: hybe kit

value: Nugen Ovation V2

tag: tissue location

value: Intestine;Colon;Descending

tag: secondary id


title: RDEB_1.cDNA.001.C08

city: Minneapolis

first: Jakub

last: Tolar

state: MN

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota, Twin Cities

library_source: transcriptomic

data_processing:
Reads were mapped to hg19 using Bowtie2 (version 2.2.4) and Tophat (version 2.0.9)
Two single-cell samples sequenced as population controls with high read counts were sub-sampled (random sub-sampling, 10% of total reads)
Gene expression levels were calculated using Cuffquant (Cufflinks version 2.2.1 with parameters -u -max-bundle-frags 10000000) and Cuffnorm (Cufflinks version 2.2.1)
FPKM values as estimated by Cufflinks were added a value of 1 (to avoid zeros) and log2 transformed
Lowly expressed genes (average log2 (FPKM) < 1.5) were excluded from further analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimted text file includes FPKM values

source_name: Human dermal fibroblasts

growth_protocol: Dermal fibroblasts from patients with recessive dystrophic epidermolysis bullosa and their human leukocyte antigen (HLA) matched healthy siblings were obtained from skin biopsies and cultured in DMEM high glucose (Thermo Fisher Scientific) containing 10% fetal bovine serum (MilliporeSigma), 1% Pen/Strep (Thermo Fisher Scientific), 1% L-glutamine (Thermo Fisher Scientific), and 1% MEM NEAA (Thermo Fisher Scientific). For sub-culture, the medium was removed and cells were washed with 1X PBS (Thermo Fisher Scientific) and detached using Trypsin/EDTA (Thermo Fisher Scientific).

extract_protocol:
Fibroblasts were collected by trypsinization and resuspended in 5 ul of fibroblast medium for loading into the C1 capture chip.
cDNA was created from selected cells using the SMARTer Ultra Low RNA kit designed for the C1 system (Clontech). mRNA libraries were constructed using the the Nextera XT kit (Illumina) according to the manufacturer’s protocol.

tag: cell type

value: Fibroblast

tag: passage number

tag: c1 chip size

value: Medium


title: pair12 primary tumor

description:
P12a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

hyb_protocol: Protocol Version 3.2, Oct 2010, Agilent.


title: pair13 primary tumor

description:
P13a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: female


title: px0494-CAGGCGA_deep

tag: type

tag: donor

tag: markers


title: RDEB_1.cDNA.001.C07


title: px0494-CACCGGA_deep


title: RDEB_1.cDNA.001.C02


title: px0494-CAAAAGA_deep


title: px0494-ATTCCTA_deep


title: Colon biopsy from UC [1D06_14072200023]

description:
SAMPLE 5
RNA from Ulcerative Colitis biopsies

tag: Sex

tag: age

value: Intestine;Colon;Transverse


title: Colon biopsy from UC [1F02_14072200033]

description:
SAMPLE 7
RNA from Ulcerative Colitis biopsies


title: px0494-CAACTAA_deep


title: Colon biopsy from UC [1D08_14072200025]

description:
SAMPLE 6
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Sigmoid


title: pair11 primary tumor

description:
P11a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

tag: tissue

tag: recurrence

tag: ploidy


title: px0494-ATGAGCA_deep

value: single-cell


title: pair11 recurrent tumor

description:
P11b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: recurrent colorectal adenoma

tag: sample type


title: Colon biopsy from UC [1C07_14072200017]

description:
SAMPLE 4
RNA from Ulcerative Colitis biopsies

tag: patient id

value: Male

tag: disease

tag: tissue state


title: Colon biopsy from UC [1C06_14072200016]

description:
SAMPLE 3
RNA from Ulcerative Colitis biopsies

tag: hospital site

tag: hybe kit

tag: tissue location


title: pair10 primary tumor

description:
P10a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma

value: male

value: yes


title: px0494-ATGTCAA_deep


title: liver2rep1

city: Fukuoka

first: Junko

middle: K

last: Fujiyoshi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pediatrics

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

description: This sample is of primary human hepatocyte. It is the second of two donors used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed for 19h at 42C to the human Nimblegen Gene Expression arrays　(100718_HG18_opt_expr_HX12, Roche NimbleGen, Madison, WI, USA) .

scan_protocol: GeneChips were scanned using the Gene Pix 4000B (Molecular Devices Corporation) .

data_processing: The raw data (tif) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5. (Roche NimbleGen, Inc.).

source_name: primary human hepatocyte

label_protocol: Nimblegen one-color cy3 labeling

growth_protocol:
SHEDs were incubated with 15% fetal bovine serum (Equitech-Bio), 100 µM L-ascorbic acid 2-phosphate (Wako Pure Chemicals), 2 mM L-glutamine (Nacalai Tesque), and premixed antibiotics containing 100 U/ml penicillin and 100  µg/ml streptomycin (Nacalai Tesque) in alpha Modification of Eagle's Medium (Invitrogen) in a CO2 (5%) incubator at 37°C. The passaged 3 (P3) cells were used for this experiment.
SHEDs were induced to hepatocyte like cells, SHED-Hep cells  by a modified previous method. (Lee KD, et al. Hepatology. 2004. 40:1275-1284)

extract_protocol: Total RNA was extracted using the RNeasy Fibrous Tissue (Qiagen Inc., Valencia, CA, USA) and amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA). RNA quality and concentration was determined by analysis with NanoDrop at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA

tag: cell type

value: primary hepatocyte

tag: deveiopmental stage

value: differentiated


title: px0494-ATCTATA_deep

tag: type


title: pair10 recurrent tumor

description:
P10b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: near 2N

value: reference


title: S-S4-3rep2

description: This sample is of SHED-Hep. It is the third of three donors used in this experiment, each from separate cultures.

source_name: SHED-Hep

value: hepatocyte-like cell derived mesenchymal stem cell

value: hepatic transdifferentiated


title: liver1rep1

description: This sample is of primary human hepatocyte. It is the first of two donors used in this experiment, each from separate cultures.


title: S-S4-3rep1


title: liver1rep2


title: Colon biopsy from UC [1B04_14072200007]

description:
SAMPLE 1
RNA from Ulcerative Colitis biopsies

value: Female

value: Ulcerative Colitis

value: Lesional

value: Brigham and Womens

value: Nugen Ovation V2

tag: secondary id


title: Colon biopsy from UC [1B06_14072200009]

description:
SAMPLE 2
RNA from Ulcerative Colitis biopsies

value: Intestine;Colon;Sigmoid


title: pair09 recurrent tumor

description:
P9b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: recurrent colorectal adenoma

value: female


title: pair09 primary tumor

description:
P9a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma


title: px0494-ATCACGA_deep

value: single-cell

tag: donor

tag: markers


title: px0494-ATCCTAA_deep


title: px0494-ATACGGA_deep


title: L3.6pl_JQ1_1

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Affymetrix console, PrimeView Human Gene Expression Array, RMA normalization

source_name: pancreatic cancer

label_protocol: not provided

growth_protocol: DMEM 10% fetal bovine serum

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: 500nM JQ1 for 24 hours or DMSO

tag: cell line

tag: treatment

value: pancreatic cancer


title: pair08 primary tumor

description:
P8a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

tag: tissue

tag: Sex

tag: age

tag: recurrence

value: yes


title: L3.6pl_JQ1_2


title: px0494-ATAATTA_deep


title: pair08 recurrent tumor

description:
P8b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

tag: ploidy

tag: sample type


title: S-S4-2rep2

description: This sample is of SHED-Hep. It is the second of three donors used in this experiment, each from separate cultures.


title: px0494-AGTTCCA_deep


title: L3.6pl_DMSO_2

value: DMSO


title: L3.6pl_DMSO_1


title: px0494-AGGCCGA_deep


title: S-S4-1rep2

description: This sample is of SHED-Hep. It is the first of three donors used in this experiment, each from separate cultures.


title: pair06 recurrent tumor

description:
P6b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: male

value: near 2N


title: pair07 primary tumor

description:
P7a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: reference


title: pair07 recurrent tumor

description:
P7b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: near 4N


title: MiaPaCa_JQ1_2

value: MiaPaCa


title: S-S4-1rep1

value: hepatocyte-like cell derived mesenchymal stem cell

value: hepatic transdifferentiated


title: S-S4-2rep1


title: MiaPaCa_DMSO_2


title: pair06 primary tumor

description:
P6a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: px0494-AGCGCTA_deep


title: S-S1-3rep2

description: This sample is of SHED. It is the third of three donors used in this experiment, each from separate cultures.

source_name: SHED

value: mesenchymal stem cell

value: undifferentiated


title: px0494-AGGTTTA_deep


title: pair05 recurrent tumor

description:
P5b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: MiaPaCa_JQ1_1


title: pair05 primary tumor

description:
P5a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: RNA_Census_rep3

city: Los Angeles

first: Guillaume

last: Urtecho

state: CA

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Total RNA
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the third biological replicate.
barcode_counts_normalized.txt

data_processing:
Counts for each unique barcode in the census files were complete in Unix as follows: Raw sequences were extracted from each fastq file and the first 20 bp (corresponding to the barcode) was extracted. This sequence was reverse complemented and the entire file was sorted before counting the number of counts of each barcode. Counts were normalized as a proportion of totals reads per sample and all samples aggregated together in R.
Barcode mapping was completed as follows: Demultiplexed reads were paired using Paired-End reAd mergeR (PEAR v0.9.1, default settings). Custom python code was used to identify reads corresponding to perfectly synthesized promoters and their respective barcodes. Briefly, this code searched the first 150 bp of each read for perfect matches to library variants. For reads with perfect matches, the last 20 bp of each read (the barcode) was extracted and a list was compiled mapping each barcode to the most frequently associated library variant. A single barcode appears many times in the sequencing data, and we took steps to ensure a barcode consistently mapped to the same variant. We required that all variants mapped to a single barcode be within an edit distance (Levenshtein distance) of 5 from one another (five single bp changes between the two sequences). We determined this number by bootstrapping a distribution of the edit distance between any two random sequences in our variant library, and setting the threshold to the first percentile (1%) of this bootstrapped distribution. Additionally, each barcode had to appear at least three times in order to be considered for downstream analysis. This step hopefully eliminates barcodes which contained sequencing errors. Promoter-barcode associations can be found in barcode_mapping.txt
Promoter variant expression was calculated in R by assigning barcodes to their mapped promoter and, for each promoter, dividing the sum of all RNA counts for all of its barcodes by the sum of all DNA counts for all of its barcodes. The result of this is in sigma70_variant_data.txt.
Genome_build: U00096.2
barcode_mapping.txt: columns: Barcode, Mapped Variant Sequence, Mapped Variant Name
barcode_counts_normalized.txt: columns: barcode, rLP5_min_DNA_rep1.1, rLP5_min_DNA_rep1.2, rLP5_min_RNA_rep1.1, rLP5_min_RNA_rep1.2, rLP5_min_DNA_rep2, rLP5_min_RNA_rep2, rLP5_min_DNA_rep3, rLP5_min_RNA_rep3
sigma70_variant_data.txt: columns: name, UP_element, Minus35, Spacer, Minus10, Background, RNA_exp_average

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: MOPS EZ-Rich + .2% Glucose

extract_protocol: Qiagen RNeasy Midi Kit

tag: strain


title: MiaPaCa_DMSO_1


title: pair03 recurrent tumor

description:
P3b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: RNA-Census_rep2

description:
Total RNA
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the seconds biological replicate.
barcode_counts_normalized.txt


title: S-S1-3rep1


title: px0494-AGATAGA_deep


title: px0494-AGAAGAA_deep


title: DNA-Census_rep3

description:
Genomic DNA
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 3rd biological replicate.
barcode_counts_normalized.txt

extract_protocol: Qiagen Puregene Yeast/Bact. Kit 2


title: px0494-AGCATCA_deep


title: DNA-Census_rep2

description:
Genomic DNA
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd biological replicate.
barcode_counts_normalized.txt


title: px0494-ACTGATA_deep


title: px0494-ACTCTCA_deep


title: SQUU-BC

first: Naoki

last: Kaneko

department: Division of Maxillofacial Diagnostic and Surgical Sciences

institute: Kyushu University Faculty of Dental Science

description: control

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: OSCC, control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: All cell lines were maintained in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: All cell lines cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Sigma-Aldrich, MO, USA) supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin/streptomycin.

value: tongue

value: oral squamous cell carcinoma

value: SQUU-BC

tag: gender


title: S-S1-2rep2

description: This sample is of SHED. It is the second of three donors used in this experiment, each from separate cultures.


title: RNA_Census_rep1.2

description:
Total RNA
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
barcode_counts_normalized.txt


title: RNA-Census_rep1.1

description:
Total RNA
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
barcode_counts_normalized.txt


title: px0494-ACGATAA_deep


title: SQUU-BO

description: with constitutive expression of DNp63b

source_name: OSCC,  ΔNp63-overexpressed

value: SQUU-BO

value: female


title: pair02 recurrent tumor

description:
P2b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: recurrent colorectal adenoma


title: S-S1-1rep2

description: This sample is of SHED. It is the first of three donors used in this experiment, each from separate cultures.


title: S-S1-2rep1


title: S-S1-1rep1


title: pair03 primary tumor

description:
P3a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma

value: yes


title: DNA-Census_rep1.2

description:
Genomic DNA
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
barcode_counts_normalized.txt


title: px0494-ACCGGCA_deep

value: single-cell


title: DNA-Census_rep1.1

description:
Genomic DNA
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
barcode_counts_normalized.txt


title: px0494-ACCCAGA_deep


title: pair02 primary tumor

description:
P2a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: near 2N


title: pair01 recurrent tumor

description:
P1b
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: reference


title: pair01 primary tumor

description:
P1a
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: MUG-Chor1 TNF 1 year 1

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

description: Gene expression data from monolayer MUG-Chor1 cell line  grown under TNF-α for 1 year

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strpis were washed and stained in the GeneAtlas Fluidics station (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner

data_processing:
The resulting data were analyzed with Transcriptome Analysis Console 3 software
RMA

source_name: MUG-Chor1 cells grown under 10 ng/mL TNF-α 1 year

label_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

growth_protocol: Cells were cultured in culture flasks or well plates coated with 0.1% gelatin (SIGMA-ALDRICH cat. no. G1890-100G), (IMDM/RPMI (4:1) containing 10% fetal bovine serum and 1% antibiotics)

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

treatment_protocol: 10 ng/mL human recombinant TNF-α in medium has been administered to cell lines except control groups for 1 year.


title: MUG-Chor1 TNF 1 year 2


title: case30 primary tumor

description:
A30
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: male

value: near 4N


title: case29 primary tumor

description:
A29
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: U-CH1 TNF 1 year 2

description: Gene expression data from monolayer U-CH1 cell line grown under TNF-α   for 1 year

source_name: U-CH1 cells grown under 10 ng/mL TNF-α for 1 year


title: MUG-Chor1 TNF 1 week

description: Gene expression data from monolayer MUG-Chor1 cell line  grown under TNF-α for 1 week

source_name: MUG-Chor1 cells grown under 10 ng/mL TNF-α 1 week

treatment_protocol: 10 ng/mL human recombinant TNF-α in medium has been administered to cell lines except control groups for 1 week.


title: U-CH1 TNF 1 week

description: Gene expression data from monolayer U-CH1 cell line grown under TNF-α   for 1 week

source_name: U-CH1 cells grown under 10 ng/mL TNF-α for 1 week


title: px0494-ACAGTGA_deep


title: px0494-AATAGGA_deep


title: case28 primary tumor

description:
A28
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: px0494-AAGGACA_deep


title: px0494-AAGCGAA_deep


title: px0494-ACATCTA_deep


title: U-CH1 TNF 1 year 1


title: case26 primary tumor

description:
A26
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: case27 primary tumor

description:
A27
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: case23 primary tumor

description:
A23
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: HvA99, Sexual, replicate 2

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

description: Intact Hydra viridissima A99, sexual, replicate 2

hyb_protocol: A set of fluorescently labeled cRNA targets (1.65ug for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.

scan_protocol: Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.

data_processing: The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.7 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default condition of the software. Some probes which were judged beyond analysis by Feature Extraction 10.7 software were eliminated from the following analysis.

organism: Hydra viridissima

source_name: intact H.viridissima in sexual phase

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were synthesized from 400 ng total RNA using Quick Amp Labeling Kit for one color detection (Agilent Technology) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hydra viridissima strain A99 (Australian) was obtained from Dr. Richard Campbell, Irvine.

extract_protocol: Total RNA was extracted from polyps of H. viridissima A99 and purified using PureLink RNA Mini (Thermo Fisher Scientific) following the manufacturer's protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Intact H.viridissima A99 in asexual phase, that in sexual phase, aposymbiotic H.viridissima A99 which removed symbiotic algae and H.viridissima A99 which removed symbiotic algae and artificially infected Chlorella variabilis NC64A (symbiont in paramecium) were prepared. Polyps of each group were fixed after 6 hours in a light phase.

value: whole body

tag: reproduction

value: sexual

tag: symbiotic algae

value: Chlorella sp. A99


title: case25 primary tumor

description:
A25
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: px0494-AAGACTA_deep

source_name: CD49f Hematopoetic stem cell


title: HvA99, Sexual, replicate 3

description: Intact Hydra viridissima A99, sexual, replicate 3


title: HvA99, Sexual, replicate 1

description: Intact Hydra viridissima A99, sexual, replicate 1


title: case24 primary tumor

description:
A24
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

source_name: colorectal adenoma


title: MUG-Chor1 ctrl 3

description: Gene expression data from monolayer MUG-Chor1 cell line grown under normal conditions

source_name: MUG-Chor1 cells grown under normal conditions


title: MUG-Chor1 ctrl 1


title: MUG-Chor1 ctrl 2


title: px0494-AACTTGA_deep


title: Lab LD ZT16 rep3

city: Seattle

first: Takato

last: Imaizumi

state: WA

address: 24 Kincaid Hall, Box 351800

department: Department of Biology

institute: University of Washington

data_processing:
Basecalling and demultiplexing performed using Illumina bcl2fastq v2.17.1.14.
FASTQ sequence files were preprocessed in two steps. A Python library (clipper.py, https://github.com/mfcovington/clipper) was used to trim off the first 8 nucleotides of each read to remove potential mismatches to the reference sequence caused by annealing of a random hexamer required for library synthesis. Trimmomatic v0.36 (http://www.usadellab.org/cms/?page=trimmomatic) was used to remove adapter sequences and trim or filter reads based on quality The parameters used for Trimmomatic were "ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50".
Preprocessed reads were mapped to the Arabidopsis thaliana TAIR10 cDNA reference sequence (ftp://ftp.ensemblgenomes.org/pub/plants/release-34/fasta/arabidopsis_thaliana/cdna/Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz) using bowtie2 with the "--norc" parameter to enforce strand-specific alignment.
Read counts for each transcript in the cDNA reference were calculated using a Perl script (simple_counts.pl, https://github.com/mfcovington/read_counter).
The R package edgeR was used to identify differentially expressed transcripts between lab LD conditions and each of LD+FR+temp conditions, outdoor samples from the solstice of 2013, and 2014 July at ZT4. Transcripts were retained for analysis if they had more than two counts per million in at least three samples. After normalization factors were calculated and dispersion estimated, the counts per million values for expressed transcripts were saved to the file 'cpm.txt'.
Genome_build: Arabidopsis_thaliana TAIR10 cDNA
Supplementary_files_format_and_content: Counts files: tab-delimited text files including raw counts values for each transcript for each sample; CPM file: tab-delimited text file including counts per million for each expressed transcript for each sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: whole seedlings, 14 days old

growth_protocol: All plants were grown on soil (Sunshine Mix #4; Sun Gro Horticulture).

extract_protocol:
Whole seedlings were flash-frozen. Total RNA was isolated from seedlings using Illustra RNAspin Mini kit (GE Healthcare). mRNA was purified by using NEBNext Poly(A) mRNA magnetic isolation kit (New England Biolabs).
RNA-Seq libraries were prepared by using the YourSeq 3'-Digital Gene Expression RNAseq Library Kit (Amaryllis Nucleics).

treatment_protocol: For outdoor experiments, seeds were stratified on soil at 4°C for at least three days and then transferred to an open cage under natural long-day conditions indicated. To prevent excess direct sunlight exposure, the cage was covered by double layers of Reemay Garden Blanket (Reemay) to reduce sunlight intensity without changing the red/far-red ratio (R/FR). The R/FR ratio was measured by LightScout Red/Far Red meter (Spectrum Technologies), as well as UV-VIS Spectrometer (StellarNet Inc). The light intensity changes around the summer solstices were measured using LI-250A light meter (LI-COR). Information for temperature was directly monitored by HOBO Pendant Temperature/Light 64K Data Loggers (Onset) for Edinburgh as well as Seattle. The air temperature was obtained from nearby weather station data,  http://www.meteoswiss.admin.ch/home/research-and-cooperation/nccs.html for Zurich and http://www-k12.atmos.washington.edu/k12/grayskies/nw_weather.html for Seattle.  Normal lab long-day conditions were described previously (Song et al., 2012). For FR light supplement in LD+FR+temp conditions, weak 730 nm far-red LED light (BML Horticulture) was provided together with full-spectrum white fluorescent light (F017/950/24”, Octron Osram Sylvania) in order to set the R/FR=1. The R/FR ratio was adjusted using LightScout Red/Far Red meter (Spectrum Technologies), and confirmed using UV-VIS spectrometer.   For temperature fluctuation settings in LD+FR+temp conditions, temperature data for 7 days around the summer solstice of 2013, from June 21 to 27, in Seattle was obtained from the website (http://www-k12.atmos.washington.edu/k12/grayskies/nw_weather.html) and averaged. Based the averaged temperature data, a multi-steps program shown in fig. S8G was set in ramping mode as follows: ZT0, 15.9°C; ZT2, 16.2°C; ZT4, 17.9°C; ZT5.46, 19.4°C; ZT9, 22.2°C; ZT10.23, 22.6°C; ZT11, 22.8°C; ZT12, 22.1°C; ZT15, 19.8°C; ZT17, 18.3°C; ZT20, 16.6°C; ZT23, 15.8°C. The temperature changes were confirmed using HOBO Pendant Temperature/Light 64K Data Loggers (Onset).

tag: zeitgeber time

tag: light and temperature

value: LD


title: case22 primary tumor

description:
A22
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

source_name: Control DNA


title: Lab LD ZT16 rep2


title: HvA99, NC64, replicate 2

description: Hydra viridissima A99 artificially infected other algae, replicate 2

source_name: H.viridissima with foreign symbiont

value: asexual

value: Chlorella variabilis NC64A


title: HvA99, NC64, replicate 3

description: Hydra viridissima A99 artificially infected other algae, replicate 3


title: px0494-AACCCCA_deep

tag: type


title: U-CH1 ctrl 2

description: Gene expression data from monolayer U-CH1 cell line grown under normal conditions

source_name: U-CH1 cells grown under normal conditions


title: Lab LD ZT16 rep1


title: U-CH1 ctrl 3


title: 4522_21_PDX_D4 SHP099

city: Amsterdam

first: Sara

last: Mainardi

state: -- Please Select --

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
polyA+ stranded RNA Library prep from sample
PDX2 SHP099
PDX2 KRAS mutant NSCLC tumor subcutaneously implanted in Crl:NU-Foxn1nu mice. Mice were randomized to be treated (Vehicle n=6; SHP099 n=6) daily by oral gavage during 19   days. SHP099 (82.5 mg/kg) was dissolved in 0.5% (W/V)   hydroxypropil methylcellulose (Sigma).

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome.  Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
To filter out mouse reads, sequenced reads are both mapped to the host (mouse) and graft (human) refence genomes. If a read maps to both genomes, the sum of mismatches, including clipped nucleotides, of the read are considered. The read is considered human if the sum of mismatches is least in the human alignment, or if the read only did align to the human reference.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F  -k 5 --minins 0 --maxins 500 --fr --new-summary
Steps performed: link, count, QCstrandness, eset
Samples are filtered for mouse reads using XenofilteR version 0.99.0 (Roel Kluin, Oscar Krijgsman, submitted, not published yet), which determines which alignment is  best, according to the edit distance to the genome. Only the human reads  are kept.
Read counts are determined.Count parameters    Count library type stranded: true  Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf    mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: PDX2 KRAS mut lung adenocarcinoma

extract_protocol:
RNA was isolated using Rneasy Mini Kit from Qiagen
Stranded RNA libraries were prepared for sequencing according to Illumina instructions

value: lung adenocarcinoma

value: human PDX in mouse


title: LD+FR+TEMP ZT16 rep3

value: LD+FR+TEMP


title: HvA99, NC64, replicate 1

description: Hydra viridissima A99 artificially infected other algae, replicate 1


title: px0494-AAACATA_deep

tag: donor


title: 4522_20_PDX_D3 SHP099


title: LD+FR+TEMP ZT16 rep2


title: U-CH1 ctrl 1


title: case20 primary tumor

description:
A20
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: case21 primary tumor

description:
A21
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: female


title: 4522_19_PDX_D2 SHP099


title: LD+FR+TEMP ZT16 rep1


title: HvA99, Apo, replicate 3

description: Hydra viridissima A99 removed symbiotic algae, replicate 1

source_name: aposymbiotic H.viridissima

value: No


title: natural LD (2014) ZT16 rep3

value: outside (July 2014)


title: case17 primary tumor

description:
A17
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma

value: yes


title: case18 primary tumor

description:
A18
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: near 2N

value: reference


title: HvA99, Apo, replicate 1

description: Hydra viridissima A99 removed symbiotic algae, replicate 2


title: HvA99, replicate 3

description: Intact Hydra viridissima A99, asexual, replicate 3

source_name: intact H.viridissima in asexual phase


title: HvA99, Apo, replicate 2

description: Hydra viridissima A99 removed symbiotic algae, replicate 3


title: case15 primary tumor

description:
A15
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: male

value: no


title: natural LD (2014) ZT16 rep2


title: case13 primary tumor

description:
A13
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: near 4N


title: 4522_16_PDX_C1 SHP099


title: 4522_15_PDX_D5 SHP099


title: 4522_18_PDX_D1 SHP099


title: Chip9 14dNH

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

country: Germany

institute: Universität Hannover

description:
UMH/141
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

hyb_protocol: The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing:
Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.
The sample table includes the following data:
VALUE = normalized log2 Cy5/Cy3
F635 Median = Median feature pixel intensity at wavelength #1 (635 nm).
B635 = The actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median.
F532 Median = Median feature pixel intensity at wavelength #2 (532 nm).
B532 = The actual background value used for the feature in GenePix Pro calculations (see B635 above).
Flags = he type of flag associated with a feature. Examples: 0 = OK, -50 = empty.

organism: Mus musculus

source_name: mouse skin

label_protocol: The indirect labeling by the tyramide-signal-amplification method was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP(Cy3)/ Biotin-dCTP (Cy5).

growth_protocol: 8-mm excisional wounds were created on the back of BL6/57 mice and treated with saline (control Alveofact), hydrogel (control MMP inhibitors), fatty gauze (control clinical standard), Alveofact 0.01 or 0.5mg/ml, broadspectrum MMP inhibitor GM6001 (10mg/ml) or selective MMP-3 inhibitor UK370106 (10mg/ml or 5mg/ml) topically.

extract_protocol: RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MiniKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction.

treatment_protocol: Wound dressings were exchanged and renewed every other day. The experiment was terminated either at post-wounding day 8 or 14.

value: healthy tissue

value: untreated, sample taken after 14 days

source_name: mouse healthy skin and adjacient tissue

value: healthy tissue adjacient to wound

value: co-treated with NaCl, sample taken after 14 days


title: case16 primary tumor

description:
A16
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: HvA99, replicate 1

description: Intact Hydra viridissima A99, asexual, replicate 1

value: whole body

value: asexual

value: Chlorella sp. A99


title: natural LD (2013) ZT16 rep3

value: outside (June 2013)


title: HvA99, replicate 2

description: Intact Hydra viridissima A99, asexual, replicate 2


title: Chip8 14dNH

description:
148/UMH
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with 10mg/mL Inhibitor III in Hydrogel, sample taken after 14 days


title: 4522_14_PDX_C4 vehicle

description:
polyA+ stranded RNA Library prep from sample
PDX2 vehicle
PDX2 KRAS mutant NSCLC tumor subcutaneously implanted in Crl:NU-Foxn1nu mice. Mice were randomized to be treated (Vehicle n=6; SHP099 n=6) daily by oral gavage during 19   days. SHP099 (82.5 mg/kg) was dissolved in 0.5% (W/V)   hydroxypropil methylcellulose (Sigma).

value: lung adenocarcinoma

value: human PDX in mouse


title: natural LD (2014) ZT16 rep1

value: outside (July 2014)


title: case12 primary tumor

description:
A12
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma

value: near 2N


title: Chip7 14dNH

description:
147/148
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with 10mg/mL Inhibitor II in Hydrogel, sample taken after 14 days

source_name: mouse healthy skin tissue


title: 4522_17_PDX_C5 SHP099

description:
polyA+ stranded RNA Library prep from sample
PDX2 SHP099
PDX2 KRAS mutant NSCLC tumor subcutaneously implanted in Crl:NU-Foxn1nu mice. Mice were randomized to be treated (Vehicle n=6; SHP099 n=6) daily by oral gavage during 19   days. SHP099 (82.5 mg/kg) was dissolved in 0.5% (W/V)   hydroxypropil methylcellulose (Sigma).


title: Chip6 14dNH

description:
146/147
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with 10mg/mL Inhibitor I in Hydrogel, sample taken after 14 days


title: case14 primary tumor

description:
A14
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: male

value: no

value: reference


title: case11 primary tumor

description:
A11
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: female


title: 4522_13_PDX_C3 vehicle


title: Lab LD ZT04 rep3

value: LD


title: 4522_12_PDX_C2 vehicle


title: natural LD (2013) ZT16 rep1


title: 4522_10_PDX_A3_vehicle


title: Chip4 14dNH

description:
144/145
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: healthy tissue adjacient to wound

value: co-treated with 0.01mg Alveofact in NaCl, sample taken after 14 days

value: co-treated with 0.5mg Alveofact in NaCl, sample taken after 14 days


title: Lab LD ZT04 rep2


title: Lab LD ZT04 rep1


title: 4522_11_PDX_A4 vehcile


title: case10 primary tumor

description:
A10
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.


title: Chip3 14dNH

description:
143/144
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with greased gauze, sample taken after 14 days


title: LD+FR+TEMP ZT04 rep3

value: LD+FR+TEMP


title: Chip9 14dW

description:
UMH/141
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: healthy tissue

value: untreated, sample taken after 14 days

source_name: mouse skin wound and adjacient tissue

value: wound tissue

value: co-treated with NaCl, sample taken after 14 days


title: Chip1 14dNH

description:
141/142
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with Hydrogel, sample taken after 14 days


title: LD+FR+TEMP ZT04 rep1


title: case08 primary tumor

description:
A8
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma

value: near 2N


title: case03 primary tumor

description:
A3
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: male


title: case05 primary tumor

description:
A5
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: no


title: Chip8 14dW

description:
148/UMH
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with 10mg/mL Inhibitor III in Hydrogel, sample taken after 14 days


title: RNAseq_P21_rep1

city: New York

first: Saša

last: Jereb

state: New York

address: 1230 York Ave

department: Laboratory of Molecular Neuro-Oncology

institute: The Rockefeller University

data_processing:
Analysis of cTag-PAPERCLIP datasets: The processing of raw reads was performed using the CIMS software package as previously described (Moore et al., 2014). Raw reads were filtered based on quality score. Filtered reads with the exact sequence were collapsed into one. Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin, 2011). Only reads that are at least 25-nt in length were mapped to mm10 reference genome. Mapping was performed using Novoalign (Novocraft) without trimming. Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single read as previously described (Moore et al., 2014). CIMS software package was then used to cluster overlapping collapsed reads from all biological replicates (for each condition) and to determine the number of reads in each cluster. To define a list of high confidence clusters we used the following criteria: clusters had to contain reads from all replicates in each condition, the number of reads in a cluster had to be at least 10% of gene total, clusters had to be located within 20 kb from 3′ ends annotated by RefSeq, clusters that were located upstream of a stretch of 6 or more adenines were excluded due to potential internal priming of the reverse transcription primer. To identify differences in APA between different conditions, Fisher’s exact test was performed comparing the ratio between reads in a particular cluster and the sum of reads in all other clusters in a gene in the two conditions. The output p-values were adjusted for multiple hypotheses testing using the Benjamini-Hochberg method.
Analysis of RNA-seq datasets: RNA-sequencing reads were mapped to the mouse genome (mm10) using Novoalign (Novocraft), reads overlapping genes were counted using HTSeq-count (Anders et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: Columns in tab-delimited files for CLIP datasets represent the following: name_cluster (name of a CLIP cluster), id_gene (Refseq gene ID), chr_cluster (chromosome where cluster is located), start_cluster (cluster start), end_cluster (cluster end), strand_cluster (strand), name2 (gene symbol) and number of reads from each replicate in a given cluster.
Supplementary_files_format_and_content: Tab-delimited text files for RNA-seq datasets represent Refseq gene ID and number of reads overlapping with exons.

source_name: Cerebellar granule cells

extract_protocol:
GFP-positive granule cells from P21 Math1-Cre; Pabpc1cTag were sorted using FACSAria II (BD). RNA was isolated from sorted cells using Roche High Pure RNA isolation kit as per manufacturer’s instructions.
RNA sequencing library was prepared using TruSeq kit from Illumina, following manufacturer’s instructions. Ribosomal RNA was removed using RiboZero kit.

tag: cell type

value: Cerebellar granule cells

value: post-natal day 21

tag: genotype

value: Math1-Cre; Pabpc1-cTag


title: RNAseq_P21_rep2


title: LD+FR+TEMP ZT04 rep2


title: Chip2 14dNH

description:
142/143
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: healthy tissue adjacient to wound

tag: treatment


title: RNAseq_P0_rep3

source_name: Cerebellar granule cell progenitors

extract_protocol:
GFP-positive granule cells from P0 Math1-Cre; Pabpc1cTag were sorted using FACSAria II (BD). RNA was isolated from sorted cells using Roche High Pure RNA isolation kit as per manufacturer’s instructions.
RNA sequencing library was prepared using TruSeq kit from Illumina, following manufacturer’s instructions. Ribosomal RNA was removed using RiboZero kit.

value: Cerebellar granule cell progenitors

value: post-natal day 0


title: RNAseq_P0_rep2


title: Chip7 14dW

description:
147/148
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

tag: tissue

value: co-treated with 10mg/mL Inhibitor II in Hydrogel, sample taken after 14 days

source_name: mouse skin wound tissue


title: Chip6 14dW

description:
146/147
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with 10mg/mL Inhibitor I in Hydrogel, sample taken after 14 days


title: case09 primary tumor

description:
A9
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

tag: Sex

value: female

value: reference


title: case04 primary tumor

description:
A4
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

tag: age


title: RNAseq_P0_rep1


title: natural LD (2014) ZT04 rep2

value: outside (July 2014)


title: Chip5 14dW

description:
145/146
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: wound tissue

value: co-treated with 0.5mg Alveofact in NaCl, sample taken after 14 days


title: Chip4 14dW

description:
144/145
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with 0.01mg Alveofact in NaCl, sample taken after 14 days


title: case02 primary tumor

description:
A2
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: primary colorectal adenoma

value: male

tag: recurrence

value: near 2N


title: natural LD (2013) ZT04 rep3

value: outside (June 2013)


title: case07 primary tumor

description:
A7
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

value: no

tag: ploidy


title: Chip3 14dW

description:
143/144
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with greased gauze, sample taken after 14 days


title: natural LD (2014) ZT04 rep3


title: Chip2 14dW

description:
142/143
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with Hydrogel, sample taken after 14 days


title: natural LD (2013) ZT04 rep1


title: Chip5 14dNH

description:
145/146
Loop 4: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 14 days after treatment.

value: healthy tissue adjacient to wound


title: px0494-TCTACCA

data_processing:
Basecalls performed using Illumina's CASAVA software, version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The first 6 bases were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.1 using the parameters --clip_R1 6 --clip_R2 6 –paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), –a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ≤ 20), and –u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17. Duplicates were marked with Picard V1.31 (http://picard.sourceforge.net).
Methylation of each cytosine was called using SAMtools mpileup (-B -C 0 -q 30 -d 500) followed by Novomethyl V1.01 (-o Consensus -%) (www.novocraft.com). Cytosine calls with Phred quality score ≤15 were discarded. Methylation percentage of each CpG di-nucleotide (found by searching the genome with a custom java script) was calculated by taking a weighted average of each cytosine using the map command from the bedtools suite (Quinlan and Hall, 2010). In most cases, only one base within a CpG dinucleotide had coverage; in these cases, the methylation information of the covered base was extrapolated to the other base.
Genome_build: hg19
Supplementary_files_format_and_content: bed file for CpG methylation. Columns are as follows: chr, start, end, fractional methylation, methylated C's, total C's, # of CpGs covered in the dinucleotide (1=just one, 2=both C and G covered)

source_name: CD49f Hematopoetic stem cell

extract_protocol:
Sorted cells were lysed in 96 well plates in 4 uL of lysis buffer (20 mM Tris-HCl, pH 8.0, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL Qiagen Protease) for 30 minutes at 50 degrees.
The lysed cells were then spiked-in with 1 uL of 60 fg/uL purified T7 phage DNA (GeneON). The DNA mixture was then bisulfite converted with the MethylEdge Bisulfite Conversion kit (Promega) using a modified bead-based protocol which enables automation (Domanico et al., 2013): 5 uL of the lysis/spike-in mixture was combined with 32.5 uL of MethylEdge Conversion reagent and incubated at 98°C for 8 minutes and 54°C for 60 minutes in a PCR machine. After incubation, the plate was briefly spun down and placed on an Agilent Bravo robot for subsequent steps. The 37.5 uL of bisulfite converted DNA was mixed with 180 uL of MethylEdge Binding Buffer and 1.8 uL of 20 mg/mL MagSi-DNA allround magnetic silica beads (MagnaMedics) and incubated at room temperature for 15 minutes. The beads were then collected on a magnet for 3 minutes and washed twice with 220 uL of 80% ethanol for 30 seconds while on the magnet. 60 uL of MethylEdge desulfonation buffer was added and incubated for 15 minutes. The desulfonation buffer was then removed and the beads were washed twice with 100 uL of 80% ethanol. The beads were then air-dried for 1 minute, resuspended in 20 uL of Qiagen elution buffer, and incubated at 56°C in a shaking incubator at 2,000 rpm for 15 minutes. The beads were then collected on a magnet for 30 seconds and the supernatant containing the DNA was removed. The bisulfite-converted ssDNA from above was added directly into a mixture containing 1.25 uL of 10 mM dNTPs and 1 uL of 500 uM random hexamers (3’ phosphothioate). The reactions were incubated at 98°C for 1 minute and snap frozen on ice for 2 minutes. A mastermix of 0.5 uL of 50 U/uL Klenow fragment [3’→5’ exo-] (NEB M0212M), and 2.5 uL of 10X NEB Buffer 2 was added on ice and mixed well. The reactions incubated in a PCR machine as follows: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes. The entire reaction was denatured again at 98˚C for 1 minute and snap frozen on ice for 2 minutes. The reaction was transferred on a pre-chilled CoolRack by robot into a new plate containing 5 uL mixture of 20 uM random hexamers (3’ phosphothioate), 0.5 mM dNTPs, 1X NEB buffer and 25 U of Klenow fragment [3’→5’ exo-]. The wells were mixed well and the reaction was cycled once again: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes, and heat-inactivated at 70°C for 10 minutes. 20 uL of Qiagen Elution Buffer was added to each reaction to make it up to 50 uL, and each reaction was purified using 50 uL of Sera-Mag beads before proceeding to the standard illumina adapter ligation library construction protocol. The 25 uL of cleaned-up adapter-ligated fragments were PCR amplified in 50 uL containing 1 U of Phusion U Hot Start DNA Polymerase (Life Technologies F-555S), 1X HF buffer, 3% DMSO, 200 uM dNTPs, 0.5 uM PCR primer 1.0 (need sequence) (IDT), and corresponding 0.5 uM indexing PCR primer 2.0. The reactions were incubated in a PCR machine as follows: initial 98˚C for 1 minute; 10 cycles of 98˚C for 30 seconds, 65˚C for 15 seconds, 72˚C for 15 seconds; and a final extension of 72˚C for 5 minutes. The 50 uL reaction was cleaned up with 40 uL of Sera-Mag beads and eluted in 15 uL.

value: ten

tag: markers


title: px0494-GATATAA


title: px0494-CGGAATA


title: Chip9 8dNH

description:
UMH/81
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.

value: healthy tissue

value: untreated, sample taken after 8 days

value: co-treated with NaCl, sample taken after 8 days


title: px0494-AGTCAAA


title: px0494-CATTTTA


title: Chip1 14dW

description:
141/142
Loop 3: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 14 days after treatment.

value: co-treated with NaCl, sample taken after 14 days


title: natural LD (2013) ZT04 rep2


title: Chip7 8dNH

description:
87/88
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.

value: co-treated with 10mg/mL Inhibitor II in Hydrogel, sample taken after 8 days

value: co-treated with 10mg/mL Inhibitor III in Hydrogel, sample taken after 8 days


title: Chip8 8dNH

description:
88/UMH
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.


title: Chip5 8dNH

description:
85/86
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.

value: co-treated with 0.5mg Alveofact in NaCl, sample taken after 8 days

value: co-treated with 10mg/mL Inhibitor I in Hydrogel, sample taken after 8 days


title: Chip6 8dNH

description:
86/87
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.


title: px0493-CATTTTA


title: px0493-CGGAATA


title: px0493-GATATAA


title: px0493-GTTTCGA


title: px0494-GTTTCGA


title: Chip3 8dNH

description:
83/84
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.

value: co-treated with greased gauze, sample taken after 8 days

value: co-treated with 0.01mg Alveofact in NaCl, sample taken after 8 days


title: Chip4 8dNH

description:
84/85
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.


title: Chip2 8dNH

description:
82/83
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.

value: co-treated with Hydrogel, sample taken after 8 days


title: Chip1 8dNH

description:
81/82
Loop 2: Gene expression of treated wound-adjacient healthy tissue against differently treated wound-adjacient healthy tissue and/or untreated healthy tissue, 8 days after treatment.


title: Chip9 8dW

description:
UMH/81
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.

value: wound tissue


title: px0493-AGTCAAA


title: px0493-TCTACCA


title: px0494-TTCGAAA

value: single-cell


title: px0494-TTAGGCA


title: Chip8 8dW

description:
88/UMH
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: Chip6 8dW

description:
86/87
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: Chip7 8dW

description:
87/88
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: px0494-TGCTGGA


title: px0494-TGCCATA


title: Chip5 8dW

description:
85/86
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: px0494-TGAATGA


title: px0494-TGACCAA


title: Chip3 8dW

description:
83/84
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: px0494-TCGGCAA


title: Chip2 8dW

description:
82/83
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: px0494-TTCTCCA


title: px0494-TCCCGAA


title: px0494-TCATTCA


title: px0494-TCGAAGA


title: Chip1 8dW

description:
81/82
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.


title: miRNA N.brasiliensis exosomes replicate 2

city: Cairns

first: Ramon

middle: Marc

last: Eichenberger

state: QLD

address: 14 McGregor Road

department: Australian Institute of Tropical Health and Medicine

country: Australia

institute: James Cook University

description: small RNA

data_processing:
Adapters were filtered using cutadapt softtware with QIAGEN 5' adaptor sequence GTTCAGAGTTCTACAGTCCGACGATC and 3' adaptor sequence AACTGTAGGCACCATCAAT as input.
Read were aligned to the Nippostrongylus brasiliensis genome (PRJEB511) using the mapper module of mirdeep2 which uses bowtie2 with default options that collapse dulicate reads and map read without any mismatches.
mirdeep2 was used to identify known and putative novel miRNA using closest species (Ascaris suum, Brugia malayi, Caenorhabditis elegans, Caenorhabditis brenneri, Caenorhabditis briggsae, Caenorhabditis remanei, Haemonchus contortus, Pristionchus pacificus, Panagrellus redivivus, and Strongyloides ratti) origine from miRBase release 21 (www.mirbase.org) to generate comparative mature miRNA sequences.
Genome_build: N_brasiliensis_RM07_v1_5_4
Supplementary_files_format_and_content: .bed file (column 5 reports miRNA abundance measurements)

organism: Nippostrongylus brasiliensis

source_name: Extracellular vesicles

growth_protocol: Adult worms were harvested from the caecum of infected mice 5 weeks after infection, washed in PBS containing 5× antibiotic/antimycotic (AA) and cultured in 6-well plates for 5 days in RPMI containing 1× AA, at 37°C and 5% CO2.

extract_protocol:
Three different biological replicates of EVs obtained from three different batches of worms were used. ODG fractions with a density between 1.07 and 1.09 (fractions containing pure EV samples after TRPS analysis) were pooled and excess Optiprep® solution was removed by buffer exchanging. miRNA were extracted using the mirVana miRNA Isolation Kit (ThermoFischer) according to the manufacturer’s instructions.
miRNA was prepared for sequencing using QIAseq miRNA library prepartion kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: The media obtained during the first 2 h after parasite culturing was discarded for further analysis. Excretory/secretory (ES) products were collected daily, subjected to sequential differential centrifugation at 500 g, 2,000 g and 4,000 g for 30 min each to remove eggs and parasite debris. For the isolation of ES products, media was concentrated using a 10 kDa spin concentrator and stored at -80°C until required. For the isolation of EVs, the media obtained after differential centrifugation was concentrated using a 10 kDa spin concentrator, followed by centrifugation for 45 min at 15,000 g to remove larger vesicles. A MLS-50 rotor (Beckman Coulter, USA) was used to ultracentrifuge the supernatant for 3 h at 120,000 g and the resultant pellet was resuspended in PBS and subjected to Optiprep® discontinous gradient (ODG) separation. One mL of 40%, 20%, 10% and 5% iodixanol solutions prepared in 0.25 M sucrose, 10 mM Tris-HCl, pH 7.2, was layered in decreasing density in an ultracentrifuge tube, and the resuspended EVs was added to the top layer and ultracentrifuged at 120,000 g for 18 h at 4°C. PBS was added to the control tube prepared as described above. A total of 12 fractions were recovered from the ODG, and the excess Optiprep® solution was removed by buffer exchanging with 8 ml of PBS using a 10 kDa spin concentrator.

tag: developmental stage

value: Adult worms

tag: sample type

value: Exosome-like vesicles


title: miRNA N.brasiliensis exosomes replicate 3

description: small RNA


title: miRNA N.brasiliensis exosomes replicate 1

description: small RNA


title: Bisulfite conversion and whole genome sequencing_veg

city: Foster City

first: Daniel

last: Hogan

state: California

address: private address

data_processing:
quality trimmed and filtered with Trim Galore 0.4.3 using default settings
genome alignment using bismark_v0.18.1, -n 1, -X 1000
extract methylation information using bismark command "bismark_methylation_extractor"
"CX_report.txt" files were imported into R
Genome_build: ptetraurelia_mac_51.fa
Supplementary_files_format_and_content: bismark output text file with following columns: chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

organism: Paramecium tetraurelia

source_name: whole cell DNA

growth_protocol: Paramecium tetraurelia strain 51 cells, mating type 7, were used for the experiments. Paramecium cells were grown in 1x wheat grass powder (WGP, Pines International) bacterized with a non-virulent strain of Klebsiella pneumonia. β-Sitosterol, essential for Paramecium growth (0.8 mg/l), was added to WGP medium just before the feeding the cells.

extract_protocol:
Cells were harvested and washed twice with 10mM Tris-HCl pH 7.4. The cell pellet was then incubated with the lysis buffer. Cells were incubated with 20μl of RNAse A (from GeneElute –Mammalian Genomic DNA Miniprep Kit Sigma-Aldrich) for five minutes at room temperature. Afterward, cells were incubated in three volumes of the lysis buffer (0.5M EDTA, 1% SDS, 1% N-lauryl sarcosine, 1 mg/ml of proteinase K) at 55°C for overnight. The cells were then incubated for 1hr with an equal volume of Phenol: Chloroform: IAA on a shaker with gentle shaking. After incubation, the cells were centrifuged at the maximum speed of the table top centrifuge for 10minutes. The supernatant was then transferred to a clean tube, and genomic DNA was precipitated using 800μl of isopropanol.
Ovation Ultralow Methyl-Seq kit (Nugen) with ~0.5% Phi-X spiked in.

value: whole cell DNA

tag: condition

value: vegetative unstarved


title: Bisulfite conversion and whole genome sequencing_starved

value: vegetative starved


title: px0494-TGGCGCA


title: px0494-TATAATA


title: px0494-TACAGCA


title: px0494-TAGCTTA


title: case06 primary tumor

description:
A6
Institute of Pathology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim (Germany).
Colorectal adenoma patient from Germany.

source_name: colorectal adenoma

extract_protocol: Genomic DNA was isolated from formalin-fixed paraffin-embedded colorectal adenoma samples using Gentra Puregene Kit (handbook, June 2011) according to the manufacturer's instructions (Qiagen, Hilden, Germany). DNA quality and quantity were assessed using a Nanodrop ND1000 spectrophotometer.

value: primary colorectal adenoma

value: male

value: no

value: near 2N

value: reference


title: px0494-GTGGCCA


title: Bisulfite conversion and whole genome sequencing_macdev

value: macronuclear development (DNA frag)


title: Chip4 8dW

description:
84/85
Loop 1: Gene expression of treated wound tissue against differently treated wound tissue and/or untreated healthy tissue, 8 days after treatment.

value: co-treated with 0.5mg Alveofact in NaCl, sample taken after 8 days


title: px0494-GTGAAAA


title: ffpe-breast-tumor (14-07334)

city: Salt Lake City

first: Nicola

middle: J

last: Camp

state: UT

address: 2000 Cir of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah

description: breast tumor

data_processing: Each gene was normalized to the expression of the same gene in a within-run reference sample and then normalized to the geometric average of the 5 housekeeper genes (ACTB, MRPL19, PSMC4, RPLP0, SF3A1)

label: SYBR Green

source_name: tumor FFPE

label_protocol: First-strand cDNA was synthesized using Superscript III reverse transcriptase (first Strand Kit; Invitrogen, Carlsbad, CA) and a mixture of random hexamers and gene-specific primers. PCR amplification and fluorescent melting curve analysis was done on the LightCycler 480 using SYBR Green I Master Mix (Roche Applied Science).

extract_protocol: Total RNA was extracted with High Pure RNA Paraffin Kit (Roche)

value: F

tag: intrinsic subtype

value: Luminal A


title: ffpe-breast-tumor (14-07335)

description: breast tumor


title: px0494-GTCCGCA

first: Martin

last: Hirst


title: ffpe-breast-tumor (14-07340)

description: breast tumor


title: ffpe-breast-tumor (14-07333)

description: breast tumor


title: px0494-GGCTACA


title: ffpe-breast-tumor (14-07332)

description: breast tumor

value: Luminal B


title: px0494-GTAGAGA


title: R2-1_Diff_rep1

city: Tsukuba

first: Kenji

last: Kubara

state: Ibaraki

address: Tokodai 5-1-3

department: Tsukuba Research Laboratories

institute: Eisai Co., Ltd.

data_processing:
Illumina bcl2fastq was used to de-multiplex and convert reads to FASTQ.
Trimmomatic (Bolger et al., Bioinfrmatics, 2014) was used to trim low quality bases and remove adapter sequences.
The reads were mapped to human transcriptome annotations and reference genome sequence (Ensemble 88, GRCh38) using STAR (Dobin et al.,  Bioinfomatics, 2013 ).
The RSEM was used for estimating gene-level expression reported as TPM (transcripts per million) with strand-specific option (Li and Dewey, BMC Bioinformatics, 2011).
Genome_build: hg38
Supplementary_files_format_and_content: Excel file including TPM values for each sample

source_name: iPS cells from RALD patient

growth_protocol: The iPSCs were harvested after cell dissociation with TrypLE Select, and seeded to 6-well ultra-low attachment plates (Corning) in bFGF-free StemFit containing 10 μM Y-27632 (Wako) to produce embryoid bodies (EBs). On the following day, the medium was changed to fresh one without Y-27632. After the eight-day suspension culture, EBs were collected and transferred to 0.1% gelatin (Sigma)-coated plates to initiate adherent culture. Cells were allowed to differentiate in bFGF-free StemFit containing 10% fetal bovine serum (Thermo Fisher Scientific) for additional 8 days. The media were exchanged basically every 2 days.

extract_protocol:
RNA was purified using RNeasy kit (Qiagen) following manufacturer’s instructions. SureSelect Strand Specific RNA Library Prep Kit (Agilent) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: differentiated


title: R2-2_Diff_rep1


title: ffpe-breast-tumor (14-07328)

description: breast tumor


title: ffpe-breast-tumor (14-07327)

description: breast tumor


title: C2-2_Diff_rep1

value: WT/WT


title: C2-1_Diff_rep1


title: Nootripathu Stress Root, biological_Rep_II

city: Coimbatore

first: Raveendran

last: Muthurajan

state: Tamil Nadu

address: Tamil Nadu Agricultural University

department: Department of Plant Biotechnology

country: India

institute: Tamil Nadu Agricultural University

description: Deep rooted

hyb_protocol: 10 ug of fragmented and labeled cRNA was hybridized for 18hrs at 45°C on 52K Affymetrix rice genome expression array in Affymetrix GeneChip Hybridization Oven 640. Arrays were washed and stained in the Affymetrix Fluidics Station 450 using GeneChip® Wash, and Stain Kit

scan_protocol: Hybridized and stained genome expression arrays were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The data were analyzed with Expression console v.3.0 of M/s. Affymetrix Inc., USA using Affymetrix default analysis settings for RMA and global scaling as normalization method.

label: Biotin

organism: Oryza sativa Indica Group

source_name: Roots

label_protocol: 2 ug of total RNA was processed according to standard Affymetrix protocol to produce biotinylated cRNA targets

growth_protocol: Two rice genotypes namely, IR 20 (shallow rooted, semi-dwarf and high yielding indica) and Nootripathu (deep rooted and low yielding indica landrace) were grown in PVC pipes (1m long and 15 cm diameter) filled with potting  mixture (3 coir pith : 1 soil) under greenhouse conditions. About 3-5 seeds per pipe were sown directly and later thinned to single plants at 3-4 leaf stage.

extract_protocol: Total RNA was extracted from roots of control and drought stressed plants using Trizol extraction according to manufacturer's protocol

treatment_protocol: Drought/water stress was imposed at 40 days after sowing by withholding watering after saturation to field capacity.  Plants were subjected to adequate intensity of stress (based on leaf rolling and drying symptoms) and roots were harvested by removing the plants from the pipes along with soil column and the soil adhering to the roots was removed carefully by washing with de-ionized water (only in control plants) and removing soil particles by gentle tapping (in case of stressed plants). Then the roots were collected and immediately frozen in liquid nitrogen for further use.

tag: cultivar

value: Nootripathu

tag: drought phenotype

value: Drought tolerant

value: Stress


title: Nootripathu Stress Root, biological_Rep_I

description: Deep rooted


title: Nootripathu Control Root, biological_Rep_II

description: Deep rooted

value: Control


title: Nootripathu Control Root, biological_Rep_I

description: Deep rooted


title: IR20 Stress Root, biological_Rep_II

description: Shallow rooted

value: Drought susceptible


title: R2-2_Undiff_rep1

value: undifferentiated


title: IR20 Control Root, biological_Rep_II

description: Shallow rooted


title: IR20 Stress Root, biological_Rep_I

description: Shallow rooted


title: ffpe-breast-tumor (14-07326)

description: breast tumor


title: px0494-GGCACAA

city: Vancouver

address: 2125 East Mall

institute: University of British Columbia

tag: type

value: single-cell


title: ffpe-breast-tumor (14-07325)

description: breast tumor


title: ffpe-breast-tumor (14-07329)

description: breast tumor


title: px0494-GCCTTAA

tag: donor


title: C2-2_Undiff_rep1


title: R2-1_Undiff_rep1


title: C2-1_Undiff_rep1


title: px0494-GATCAGA


title: px0494-GGCCTGA


title: ffpe-breast-tumor (14-07324)

description: breast tumor


title: px0494-GCCAATA


title: px0494-GCAAGGA


title: ffpe-breast-tumor (14-07321)

description: breast tumor


title: ffpe-breast-tumor (14-07322)

description: breast tumor


title: px0494-GAGTGGA


title: ffpe-breast-tumor (14-07320)

description: breast tumor


title: px0494-GACGGAA


title: ffpe-breast-tumor (14-07323)

description: breast tumor

value: Basal-like


title: ffpe-breast-tumor (14-07319)

description: breast tumor


title: ffpe-breast-tumor (14-07318)

description: breast tumor


title: px0494-GAATAAA


title: IR20 Control Root, biological_Rep_I

description: Shallow rooted


title: px0494-GAAACCA


title: ffpe-breast-tumor (14-07317)

description: breast tumor


title: px0494-CTTGTAA


title: px0494-CGATGTA


title: px0494-CTCAGAA


title: AU019823 gene-trapped

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
Total RNA from 300,000 cells were extracted.
cl.3 day4.5

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: AU019823 gene-trapped ESCs differentiated into Flk-1-positive early mesodermal cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: ESCs were cocultured with OP9 stromal cells, which support hematopoietic differentiation.

extract_protocol: RNA samples were extracted from cells using RNeasy plus micro kit (Quiagen).

treatment_protocol: After four-day coculture, cells were harvested and stained with an antibody against Flk-1. Flk-1-positive cells were sorted by FACS.

value: AU019823, biallelically disrupted

tag: cell type

value: Flk-1-positive early mesodermal cells


title: ffpe-breast-tumor (14-07316)

description: breast tumor


title: ffpe-breast-tumor (14-07313)

description: breast tumor


title: natural LD (2013) ZT16 rep2

source_name: whole seedlings, 14 days old

tag: zeitgeber time

tag: light and temperature

value: outside (June 2013)


title: px0494-CGAGAAA


title: ffpe-breast-tumor (14-07311)

description: breast tumor


title: ffpe-breast-tumor (14-07314)

description: breast tumor


title: ffpe-breast-tumor (14-07315)

description: breast tumor


title: AU019823 revertant

description:
Total RNA from 350,000 cells were extracted.
cl.4 day4.5

source_name: AU019823 revertant ESCs differentiated into Flk-1-positive early mesodermal cells

tag: genotype

value: AU019823, almost identical to wild-type


title: px0494-CTGCTGA


title: px0494-CTATACA


title: px0494-GCACTTA


title: px0494-CCTTAGA


title: SA7_12

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 4

institute: Max Planck Research Unit for Neurogenetics

description: SAMPLE 24

hyb_protocol: Total RNA 0.75µg per sample was hybridized with CodeSet Pao at 65°C for 19 hours.

scan_protocol: Hybridized RNA transcripts were imaged at 194 fields of view per sample and processed using the nCounter SPRINT Profiler system.

data_processing: Processing of the raw count data was performed using nSolver Data Analysis Software 3.0 (NanoString Technologies). The first normalization was with respect to the geometric mean of the six positive control counts. The second normalization was with respect to the geometric mean of four reference genes (Ano2, Cnga4, Omp, and Trpc2). Then a background correction was done by subtracting the mean + 2*SD (standard deviation) of the eight negative control counts. Values <1 after background subtraction were fixed to 1. These processing steps were applied separately to the ΔC1 strain (Sample 1-12) and ΔC1-GFP strain (Sample 13-24), as those data were obtained from two independent NanoString cartridges. We define a gene as informative if the median of the normalized NanoString counts in wild-type mice is ≥100.

label: NanoString capture/reporter probes

source_name: Whole vomeronasal mucosa

extract_protocol: The vomeronasal organ was dissected out from the base of the nasal septum of a mouse and placed in RNA stabilization reagent RNAlater (Qiagen). The bony capsule of the vomeronasal organ was removed, and whole vomeronasal mucosa was dissected out. Tissue from each mouse was placed in a tube and lysed in RNA Lysis Buffer using a TissueLyser LT (Qiagen). Total RNA was extracted according to protocol of RNeasy Micro kit (Qiagen). Genomic DNA digestion was performed using on-column RNase-Free DNaseI (Qiagen).

tag: tissue

value: Whole vomeronasal mucosa

tag: strain name

value: Wild-type

tag: genetic background

value: mixed background (129 x C57BL/6J)

value: 10 weeks

tag: Sex

value: male


title: SA7_11

description: SAMPLE 23

value: Homozygous

tag: age


title: ffpe-breast-tumor (14-07310)

description: breast tumor

value: F

value: Unknown


title: SA7_10

description: SAMPLE 22


title: LAN control-2

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method on core dataset.

source_name: LAN control

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Human stellate cells, Lx-2, were maintained in Dulbecco's Modified Eagle’s Medium (DMEM; Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (Gibco), 1% L-glutamine (Gibco), and 1% penicillin/streptomycin (Gibco) in a humidified atmosphere of 5% CO2 at 37°C

extract_protocol: Total RNA were isolated from frozen liver tissue and cultured cells using a mirVana miRNA Isolation Kit (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Cultured cells in 12-well plates were grown to 70% confluence and LNA-antimiR-control and LNA-antimiR-214  (10 nM; Exiqon) were transfected to the cells using Lipofectamine RNAiMAX according to the manufacturer’s instructions. Transfected cells were serum-depleted for 9 h and then treated with 3 ng/mL recombinant human transforming growth factor (TGF)-β1 (Merck KGaA, Darmstadt, Germany) for 24 h.

tag: cell line

value: stellate


title: LAN 214-2

source_name: LAN 214


title: LAN control-1


title: natural LD (2014) ZT04 rep1

value: outside (July 2014)


title: LAN 214-1


title: LAN 214-3


title: LAN control-3


title: ffpe-breast-tumor (14-07309)

description: breast tumor

value: Luminal A


title: ffpe-breast-tumor (14-07312)

description: breast tumor


title: px0494-CCGTCCA

value: single-cell

tag: markers


title: px0494-CAGGCGA


title: SA7_09

description: SAMPLE 21


title: px0494-CATGGCA


title: px0494-CACTCAA


title: SA7_08

description: SAMPLE 20


title: ffpe-breast-tumor (14-07308)

description: breast tumor


title: ffpe-breast-tumor (14-07307)

description: breast tumor


title: SA7_07

description: SAMPLE 19


title: ffpe-breast-tumor (14-07306)

description: breast tumor

value: Luminal B


title: px0494-CACCGGA


title: ffpe-breast-tumor (14-07305)

description: breast tumor

value: Basal-like


title: SA7_06

description: SAMPLE 18


title: SA7_05

description: SAMPLE 17


title: ffpe-breast-tumor (14-07304)

description: breast tumor


title: SA7_04

description: SAMPLE 16


title: ffpe-breast-tumor (14-07303)

description: breast tumor


title: px0494-CAAAAGA


title: px0494-CAACTAA


title: px0494-ATTCCTA


title: SA7_03

description: SAMPLE 15


title: SA7_02

description: SAMPLE 14


title: SA7_01

description: SAMPLE 13


title: px0494-ATGTCAA


title: ffpe-breast-tumor (14-07302)

description: breast tumor


title: px0494-ATGAGCA


title: SA6_12

description: SAMPLE 12


title: px0494-CACGATA


title: px0494-ATCTATA


title: ffpe-breast-tumor (14-07299)

description: breast tumor


title: ffpe-breast-tumor (14-07300)

description: breast tumor


title: ffpe-breast-tumor (14-07298)

description: breast tumor


title: SA6_11

description: SAMPLE 11


title: px0494-ATCCTAA


title: px0494-ATCACGA


title: ffpe-breast-tumor (14-07297)

description: breast tumor


title: px0494-ATACGGA


title: SA6_10

description: SAMPLE 10


title: SA6_09

description: SAMPLE 9


title: px0494-ATAATTA


title: SA6_08

description: SAMPLE 8


title: ffpe-breast-tumor (14-07301)

description: breast tumor


title: ffpe-breast-tumor (14-07295)

description: breast tumor


title: ffpe-breast-tumor (14-07294)

description: breast tumor


title: ffpe-breast-tumor (14-07296)

description: breast tumor


title: SA6_07

description: SAMPLE 7


title: px0494-AGTTCCA


title: ffpe-breast-tumor (14-07293)

description: breast tumor


title: SA6_06

description: SAMPLE 6


title: px0494-AGGTTTA


title: px0494-AGGCCGA


title: px0494-AGCGCTA


title: ffpe-breast-tumor (14-07292)

description: breast tumor


title: SA6_03

description: SAMPLE 3


title: SA6_04

description: SAMPLE 4


title: ffpe-breast-tumor (14-07291)

description: breast tumor


title: SA6_05

description: SAMPLE 5


title: SA6_02

description: SAMPLE 2


title: ffpe-breast-tumor (14-07290)

description: breast tumor


title: ffpe-breast-tumor (14-07289)

description: breast tumor


title: ffpe-breast-tumor (14-07288)

description: breast tumor


title: SA6_01

description: SAMPLE 1


title: Pen Replicate 4

city: Medford

first: Benjamin

last: Wolfe

state: MA

address: Tufts University - Biology, 200 Boston Ave, Suite 4700

department: Biology

institute: Tufts University - Biology

description: GlutiPenRNAseqforGEO.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped and gene expression values were calculated using default parameters in Rockhopper version 2.0.3 (De novo assembly of bacterial transcriptomes from RNA-seq data. Brian Tjaden. Genome Biology, 16:1, 2015.)
Genome_build: ASM287867v1
Supplementary_files_format_and_content: Rockhopper output with raw and normalized expression values [GlutiPenRNAseqforGEO.txt]

organism: Glutamicibacter arilaitensis

source_name: Biofilm of Glutamicibacter arilaitensis with Penicillium sp. #12 growing on cheese curd agar

growth_protocol: For each experimental unit, approximately 80,000 CFUs of G. arilaitensis JB182 were spread across the surface of a 100mm Petri dish containing 20 mL of cheese curd agar.

extract_protocol:
Rind biofilms were harvested by scraping the cheese curd surface and stored in RNAProtect Reagent (Qiagen) and RNA was extracted using a standard phenol-chloroform protocol.
To confirm that the samples were free of DNA contaminants, a PCR of the 16S rRNA gene was performed with standard primers (27f and 1492r). Overall quantity and quality of the RNA preps were confirmed by Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. RNA-seq libraries were constructed from purified mRNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Pooled library samples were be sequenced using paired-end 100bp reads on an Illumina HiSeq Rapid Run by the Harvard Bauer Core Sequencing Core Facility. Each library yielded 6.8-8.9 million forward reads that were used for analysis.

treatment_protocol: For the + Penicillium sp. #12 treatment, approximately 100,000 CFUs of Penicillium were co-inoculated onto the plates with G. arilaitensis JB182. Plates were at > 90% relative humidity at 24 °C for 5 days.

tag: strain

tag: treatment

value: growing with Penicillium sp. #12

value: experimental biofilm


title: px0494-AGATAGA

department: Microbiology and Immunology


title: px0494-ACTGATA


title: px0494-AGAAGAA


title: Pen Replicate 3

description: GlutiPenRNAseqforGEO.txt


title: Pen Replicate 2

description: GlutiPenRNAseqforGEO.txt


title: ffpe-breast-tumor (14-07282)

description: breast tumor

tag: intrinsic subtype


title: ffpe-breast-tumor (14-07281)

description: breast tumor


title: px0494-ACCGGCA


title: px0494-ACGATAA


title: Alone Replicate 3

description: GlutiPenRNAseqforGEO.txt

source_name: Biofilm of Glutamicibacter arilaitensis growing on cheese curd agar

value: growing alone


title: Pen Replicate 1

description: GlutiPenRNAseqforGEO.txt