title: FCD tissue, type IIa, biological rep 9

city: Campinas

first: Cristiane

middle: de Souza

last: Rocha

state: São Paulo

address: Av Tessália Vieira de Camargo, 126 Cidade Universitária "Zeferino Vaz"

department: Medical genetics

country: Brazil

institute: Unicamp

description: microRNA expression of brain tissue from type IIa FCD patient

hyb_protocol: Following FlashTag Biotin HSR Ligation, RNA were hybridized for 16 hr at 48°C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console® Software (AGCC)

data_processing: The data were analyzed with using the RMA function (background correction, summarization and normalization) in the Bioconductor package.

source_name: FFPE brain tissue from biopsy

label_protocol: Biotinylated RNA were prepared according to the FlashTag™ Biotin HSR  RNA Labeling Affymetrix protocol from 300ng total RNA.

extract_protocol: Extraction of total RNA was performed using the Recover All kit (Ambion Inc. Austin, USA), following the manufacturer’s recommendations

tag: disease state

value: focal cortical dyplasia, type II

tag: Sex

value: male

value: 12 years old

value: brain

tag: brain region

value: frontal lobe


status: Public on Apr 03 2018

type: RNA

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 1 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA). Microarray data were extracted, the background subtracted and LOWESS normalisation performed using the standard procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

molecule: total RNA

organism: Equus caballus

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling, according to manufacturer protocol.

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation equine satellite cells were pre-incubated with HMB for 24h (50 µM) and exposed to hydrogen peroxide (3mM, last 1h during 24h pre-incubation with HMB).

tag: Stage

value: 3rd day of differentiation

tag: tissue

value: m. semitendinosus


title: FCD tissue, type IIa, biological rep 8

label: biotin

organism: Homo sapiens

value: female

tag: age

value: 15 years old


title: Preadipocyte  - 3T3-L1 cell line (VFCO1)

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: Labeled DNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

organism: Mus musculus

source_name: Preadipocyte  - 3T3-L1 cell line

label_protocol: Fragmentation and labelling were performed using Encode Biotin Module (Nugen; 4200-60)

growth_protocol: Preadipocytes were maintained in Proliferation medium.Two day post-confluent (T=0) cell were induced to diferentiate with Differentiation medium until T=7.

extract_protocol: RNA was isolated using Trizol / RNeasy method (Qiagen RNeasy mini kit (#74104)). Library preparation and amplification were performed using Ovation RNA Amp System V (Nugen;3100-60)

treatment_protocol: Preadipocytes were transduced with lentiviruses encoding scrambled or TP53INP2 siRNA sequences.

value: Adipose tissue

tag: cell line

tag: genotype/variation

value: Control

tag: time

value: day 0 of differentiation

tag: cell type

value: preadipocyte

tag: replicate


title: FCD tissue, type IIa, biological rep 7

value: 10 years old

value: fronto-parieto site


title: Preadipocyte  - 3T3-L1 cell line (VFCO2)


title: QSBS miRNA-Seq

type: SRA

city: Guangzhou

first: Ruixue

last: Chen

state: Guangdong

address: Huangpu Avenue West 601

department: School of Chinese Medicine

country: China

institute: Jinan University

library_source: transcriptomic

data_processing:
Original images were transformed into raw reads by Base Calling.
Quality control of the reads was conducted.
The sequences of the same reads were combined to obtain the unique sequence.
The annotation of measured small RNAs was mapped to Rfam database.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: TMM (trimmed means of M-values method) to standardize read count data obtained in the analysis of miRNA expression level, then applied DEGseq to do the difference analysis using a Benjamini q-value of 0.001 as the cut-off (corrected p-value < 0.001), combined with fold change (FC) > 2 (value indicated the normalized count of samples)

source_name: human umbilical vein endothelial cells

growth_protocol: CRL-1730 HUVECs (ATCC, USA) were cultured in culture flasks (1 × 105/ml, 25 ml) in Dulbecco's modified Eagle's medium (DMEM) (Gibco, USA) containing 10% fetal bovine serum (FBS) (Gibco, USA) for 24 hours at 37 °C plus 5% CO2.

extract_protocol:
The cells were digested in the culture flasks for 3 minutes with 1 ml TRIzol and the cells observed under an inverted microscope.
The small RNA library (140~160 bp) was constructed by Illumina Truseq Small RNA. The human small RNA sequence analysis was performed by the Hiseq2000 platform with 1 * 51 bp.

treatment_protocol: Then a 10% serum of QDBS, QSBS, CCBS, HABS, NBS and NC was added to 6 culture flasks for 24 hours. Finally, the cell models of QDBS, QSBS, CCBS, HABS, NBS and NC were established.

value: CRL-1730 human umbilical vein endothelial cells


title: Control [ATAC-Seq]

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

library_source: genomic

data_processing:
Paired-end reads were mapped to the mm10 reference genome using Bowtie2. Only concordantly mapped pairs were kept for further analysis.
Peak calling was performed using MACS2 to identify areas of sequence tag enrichment.
BedTools was used to find common intersection between identified peaks (1bp minimum overlap) and to create a merged peak list.
ATAC-seq tag enrichment and DNA motif analysis across the merged peak list  were computed using HOMER (homer.salk.edu)
Genome_build: mm10
Supplementary_files_format_and_content: peak files with quantitative data for each Sample

molecule: genomic DNA

source_name: TIL

growth_protocol: 1 million E.G7 were inoculated subcutaneously into 6-8 wk female mice on Day 0

extract_protocol:
On Day 21, OVA-specific CD8+ TILs were sorted using BD FACSAria Cell Sorter.
ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina.

treatment_protocol: control antibodies, 100μg anti-B7S1, 75μg anti-PD-1 (J43, Bioxcell) or 100μg anti-B7S1+ 75μg anti-PD-1 were injected i.p. every 3 days starting from Day 9.

tag: strain

value: tumor

tag: genotype

value: wild type


title: QDBS miRNA-Seq


title: NC RNA-Seq

data_processing:
The total mRNA was purified and cleaved into fragments.
the cDNA fragments were purified, resolved and ligated with the sequencing adapters.
An Illumina TruSeqTM RNA Sample Prep kit was used to sequence the cDNA library (300 bp).
the chromatogram data from the sequencing were transformed into millions of nucleotide sequences with Base Calling.
The sequences were stored in a FASTQ format file to call the reads.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: The expression levels of the transcripts were calculated according to the RPKM/FPKM values.

extract_protocol:
The cells were digested in the culture flasks for 3 minutes with 1 ml TRIzol and the cells observed under an inverted microscope.
The samples for the transcriptome analysis were prepared using an Illumina kit (San Diego, CA, USA) according to the manufacturer’s instructions.


title: NBS RNA-Seq


title: FCD tissue, type IIb, biological rep 6

description: microRNA expression of brain tissue from type IIb FCD patient

value: focal cortical dyplasia, type II

value: male


title: HABS RNA-Seq


title: CCBS RNA-Seq


title: QDBS RNA-Seq


title: QSBS RNA-Seq


title: Ets1 at 100 nM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots, applying a natural logarithm transformation, and then normalized the signal to the [0,1] range.

label: Alexa 488

molecule: protein

source_name: Human Ets1

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

growth_protocol: Gateway-compatible clones containing the full-length genes for Ets1, Elk1, and Gabpa were purchased from GeneCopoeia and the genes were transferred into pDEST15 using the LR Clonase reaction (Life Technologies). This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions.

tag: transcription factor

tag: protein concentration

value: Protein concentration:100nM


title: Gabpa at 100 nM concentration

source_name: Human Gabpa

value: Gabpa


title: Elk1 at 100 nM concentration

source_name: Human Elk1


title: Elk1 at 50 nM concentration

value: Protein concentration:50nM


title: FCD tissue, type IIb, biological rep 5

value: 52 years old

value: brain

value: frontal lobe


title: FCD tissue, type IIb, biological rep 3

value: 6 years old

value: temporo-occipital lobe


title: FCD tissue, type IIb, biological rep 4

value: female

value: 33 years old

value: occipital lobe


title: Mad1 at 1 uM concentration and Max at 100 nM concentration

description: same as raw data file from GSE59845, sample GSM1447394

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

source_name: Human Mad1 and Max

label_protocol: Proteins were tagged with N-terminal His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen).

growth_protocol: Plasmids were transformed into BL21 (DE3) expression strain of E. coli (New England BioLabs).  Overnight bacterial culture (5 mL) was diluted into 1 L LB (10 g BACTO Tryptone (BD); 5 g BACTO Yeast Extract (BD); 10 g NaCl; pH 7.5) and grown to OD 0.6 (600 nm visible light). Protein expression was then induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 3 hours at 37ºC. Cells were pelleted by centrifugation @ 12,000 rpm for 10 min and stored at -20ºC. Each pellet (from 1 L culture) was thawed in 15 ml lysis buffer (150 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM dithiothreitol (DTT); 1 tablet complete Mini, EDTA-free protease inhibitor cocktail (Roche, #11 836 170 001); 50 uM C4H10O6Zn (zinc acetate); 1 mg/ml chicken egg white lysozyme (Sigma, # L6876)) and subjected to two freeze-thaw cycles in dry ice/ethanol. To digest DNA, to each 15 ml lysis solution was added 10 uL recombinant, RNase-free DNAse I (Roche, #04 716 728 001, 10 U/ul), 30 uL 1 M MgCl2, and 2 mL 10% Triton X-100,  and digested at room temperature until solution was runny (~1 hr).  Solutions were centrifuged at 12,000 rpm for 25 min at 4ºC, and supernatant was used for protein purification.

extract_protocol: Full-length open reading frames were cloned into the Gateway pDEST17 (N-terminal His-tag) expression vector by recombinational cloning from previously created pENTR clones. All proteins were produced by over-expression in E. coli BL21 (DE3) cells (New England BioLabs), and purified by FPLC (AKTAprime plus) using HisTrap FF affinity columns (GE Healthcare). Anti-His Western blots were performed to assess protein quality and concentration.

value: Mad1, Max

value: Protein concentration:100nM Max, 1uM Mad1


title: Mad1 at 1 uM concentration and Max at 100 nM concentration (replicate)


title: Max at 100 nM concentration

description: same as raw data file from GSE59845, sample GSM1447392

source_name: Human Max

value: Max


title: Normal tissue, biological rep 2

description: microRNA expression of brain tissue from control individual

source_name: FFPE brain tissue from autopsy

value: normal control

value: 30 years old


title: FCD tissue, type IIa, biological rep 2

description: microRNA expression of brain tissue from typw IIa FCD patient

value: focal cortical dyplasia, type II

value: male

value: 26 years old

value: temporal lobe


title: Normal tissue, biological rep 3

value: 29 years old


title: Normal tissue, biological rep 5

value: 45 years old

value: brain


title: Normal tissue, biological rep 4

value: 20 years old

value: frontal lobe


title: sample_1162

city: Kansas City

first: Shui

middle: Q

last: Ye

state: MO

address: 2411 Holmes Street

department: Departmetn of Biomedical and Health Informatics

institute: University of Missouri Kansas City School of Medicine

data_processing:
The raw base calling (.bcl) files were converted to demultiplexed compressed FASTQ files using Illumina’s bcl2fastq v2.17.1.14 software.
TopHat 2.0.9 was used to map RNA-seq reads against the mouse reference genome using default parameters.
Transcript assembly and abundance estimation and comparing expression were conducted with Cufflinks v2.2.1 and reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Cuffdiff was used to calculate statistical significance changes of gene expression.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text file of a matrix table generated using Cufflinks v2.2.1 and reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

source_name: Nampt +/+_Saline (IG)_liver

growth_protocol: Mice were aged 11-12 weeks.

extract_protocol:
Samples were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina cat. RS-122-2201, San Diego, CA)
Clusters were generated using the   TruSeq Paired-End Cluster Kit v3-cBot-HS (Illumina cat. PE-401-3001, San Diego, CA).
Paired-end sequencing (2x101 cycles) was completed using the TruSeq SBS kit v3-HS (Illumina cat. FC-401-3001, San Diego, CA).

treatment_protocol: Mice were sacrificed 24h after IP or IG injection with 200-300mg/kg APAP or saline.

tag: strain background

tag: age (weeks)

value: Nampt +/+

tag: treated with

value: Saline (IG)

tag: liver perfusion

value: no

value: liver


title: sample_968

source_name: Nampt OE_200 mg/kg APAP_liver

tag: Sex

value: Nampt OE

value: 200 mg/kg APAP

value: yes


title: sample_611

source_name: Nampt +/+_Saline_liver

value: Saline


title: sample_589

source_name: Nampt +/-_Saline_liver

value: Nampt +/-


title: FCD tissue, type IIb, biological rep 1

tag: disease state

value: focal cortical dyplasia, type II

value: male

value: 40 years old

tag: brain region

value: temporo-parieto-occipital site


title: sample_569

tag: tissue


title: c-Myc at 1 uM concentration and Max at 100 nM concentration

description: same as raw data file from GSE59845, sample GSM1447393

source_name: Human c-Myc and Max

value: c-Myc, Max

value: Protein concentration:100nM Max, 1uM c-Myc


title: sample_563

source_name: Nampt OE _Saline_liver


title: AWA-specific pull-down mRNA Replicate 4

city: Hong Kong

first: king

middle: L.

last: Chow

state: Hong Kong

address: clear water bay

department: Life Science

country: Hong Kong

institute: HKUST

hyb_protocol: Oligonucleotide microarrays were conducted with Agilent C. elegans Oligo 4 × 44 K Microarray (Agilent, USA) in Agilent microarray hybridization chamber, following the protocol of Agilent Two-color Microarray-Based Gene Expression Analysis (Capra et al., 2008).cRNA amound for hybridization: 0.825ug.

scan_protocol: Scanned on Agilent microarray scanner

data_processing: Agilent Feature Extraction Software 10.5.1.1 was used for background subtraction, background method: Spatial Detrend Surface Value, Siganal Measurement Method: density-mean background and the total amount of cy3 and cy5 signal was normalized to each other with the method of rank consistency linear LOWESS normalization.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: AWA-specifc pull-down mRNA

label_protocol: Sample label using Cy3-CTP and CY5-CTP following Agilent Quick Amp labeling Kit manufacturer's instructions

growth_protocol: All C. elegans strains were incubated and grown on the Nematode Growth Medium (NGM) agar plates contained 20g agar, 4g Tryptone, 2g NaCl, 0.55g Tris-Cl, 0.24g Tris-Base and 1mL of 8mg/mL Cholesterol (dissolved in ethanol) per liter, final pH of the agar adjusted to 7. The growth culture plates pre-seeded with Escherichia coli strain OP50. C. elegans are grown at 20℃.

extract_protocol: The integration line packed worms were fixed in 1% paraformaldehyde in M9. Paraformaldehyde is inactive by 0.133 V of Glycine (125 M, pH 3.5). Animals were lysed by cell disrupter at 25 kpsi. Debris was sedimented by centrifugation. RNA bound to FLAG::PAB-1 was enriched with ANTI-FLAG® M2 Affinity Gel. The RNA extraction steps were done as described in TRIZOL manufacturer’s manual. The Agilent 2100 bioanalyzer in combination with the RNA 6000 LabChip® kit was used to provide detailed information about the condition of mRNA samples in the form of highly sensitive electropherograms

treatment_protocol: Masculinization plasmid Prab-3::fem3 and AWA-specific PABP expression plasmid Podr-7::flag-tag::pab-1::unc-54 3'UTR are injected with the unc-119 transformation marker, M142ΔXbaI (Maduro, 2015), with unc-119 mutant as the transformation background. After injection, the stabilized transgenic line has been integrated by UV treatment. Integration was performed by irradiating with UV.

value: AWA neurons

tag: age

value: Mixed stage

source_name: whole C. elegans lysate

value: whole animals


title: sample_537

source_name: Nampt +/+_200 mg/kg APAP_liver

tag: genotype/variation

value: Nampt +/+


title: sample_647


title: AWA-specific pull-down mRNA Replicate 2


title: AWA-specific pull-down mRNA Replicate 1


title: NDC1.2.iPMP.3

city: St Louis

first: Sabine

last: Dietmann

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were quality-trimmed using Trim Galore!, and mapped to the human reference genome (hg38) using TopHat2 with the parameters “--max-multihits 1 --read-mismatch 2 --b2-sensitive”. ENSEMBL (release 86) gene models were used to guide alignments with the “–GTF” option. Read counts for genes  were obtained using featureCounts with the parameters “–O --minOverlap 10 ”. Read counts were normalized, and the statistical significance of differential expression was assessed using the R Bioconductor DESeq2 package. Gene counts - normalized by DESeq2 size factors - were subsequently normalized by their effective transcript length/1000, and log2-transformed. Effective transcript lengths were obtained with featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Files with read counts per ENSEMBL (82) transcript obtained by 'featureCounts'

source_name: Human stem cell-derived primitive macrophage precursors

growth_protocol: For full cell culture details please see manuscript.

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen) as per manufacturer's instructions.
Libraries were prepared using 250ng of input RNA with a TruSeq Stranded Total RNA kit (Illumina), and subjected to 50bp single end sequencing.

tag: origin

value: Human stem cell-derived

tag: parent ipsc line


title: NDC1.2.iMG.3

source_name: Human stem cell-derived microglia

tag: cell type

value: Human stem cell-derived microglia


title: NDC1.2.iPMP.2

value: Human stem cell-derived primitive macrophage precursors


title: NDC1.2.iPMP.1


title: NDC1.2.iMG.2


title: Wild-type_Skin_Dermis

city: Singapore

first: Ming Keat

last: Sng

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: Pparb/d^fl/fl Dermis

hyb_protocol: 2 ug of cDNA were hybridized for 18hrs at 45C on GeneChip Mouse Gene 1.0ST Array inside genechip hybridization oven 640. Genechip fluidics station 450 was used for the washing and staining of the chips.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Partek genomic suite 6.6 with RMA was used to analyze samples

source_name: Wild-type mouse, male, 4 weeks, dermis, telogen phase of hair cycle

label_protocol: Further sample processing of the RNA was carried out using Applause® WT-Amp ST System (NuGEN), followed by the NuGEN Encore biotin label kit

growth_protocol: Pparb/d^fl/fl mice, having the exon 4 of their Pparb/d gene flanked by loxP sites, were mated with mice harbouring the Cre transgene under the control of the FSP promoter. FSPCre-Pparb/d^fl/+ progenies were then bred with Pparb/d^fl/fl mice to obtain FSPCre-Pparb/d^fl/fl mice and the wild-type control mice. To sustain this genotype, we bred FSPCre-Pparb/d^fl/fl progenies with Pparb/d^fl/fl mice. Mice were housed in a specific-pathogen free facility with a 12 h/12 h light/dark cycle. Food and water were provided ad libitum. Animal experiments were carried out in accordance to the guidelines of the University Institutional Animal Care and Use Committee (IACUC, ARF-SBS/NIE-A0216AZ), Singapore.

extract_protocol: RNA was extracted from the respective treatments with Trizol according to the manufacturer’s protocol.

treatment_protocol: Mice in the telogen phase of their hair cycle were anaesthetized and depilated on their dorsal back before being subjected to a biopsy punch (~4 mm). The skin biopsy was then treated with 3.8% ammonium thiocyanate (Sigma, USA) in 1X PBS for 30 min at 37 oC. Subsequently, the epidermis was mechanically separated from the dermis with a pair of forceps. The dermis was then curetted with a 30-gauge needle.

tag: strain

value: Wild-type

tag: gender

value: Male

value: 4 weeks

value: Skin Dermis

tag: skin stage

value: Telogen phase of hair cycle


title: AWA-specific pull-down mRNA Replicate 3


title: NDC1.2.iMG.1


title: sample_463

value: male

value: 200 mg/kg APAP

value: no

value: liver


title: Wild-type_Skin_Epidermis

description: Pparb/d^fl/fl Epidermis

source_name: Wild-type mouse, male, 4 weeks, epidermis, telogen phase of hair cycle

value: Skin Epidermis


title: sample_465

source_name: Nampt +/-_200 mg/kg APAP_liver

value: Nampt +/-


title: Normal tissue, biological rep 1

value: normal control

value: 22 years old

value: brain

value: frontal lobe


title: sample_450


title: sample_333

source_name: Nampt OE_300 mg/kg APAP_liver

value: Nampt OE

value: 300 mg/kg APAP


title: sample_534

value: Nampt +/+


title: sample_348

source_name: Nampt OE_Saline_liver

value: Saline

value: yes


title: Fibroblast-specific Pparb/d knockout_Skin_Epidermis

description: FSPCre-Pparb/d^fl/fl Epidermis

source_name: Fibroblast-specific Pparb/d knockout mouse, male, 4 weeks, epidermis, telogen phase of hair cycle

value: Fibroblast-specific Pparb/d knockout

value: Male

value: 4 weeks


title: AD3.4.iMG.3

value: Human stem cell-derived microglia

value: Human stem cell-derived


title: AD3.4.iPMP.2

value: Human stem cell-derived primitive macrophage precursors


title: sample_11

value: male

value: liver


title: c-Myc at 1 uM concentration and Max at 100 nM concentration [Universal PBM 4x44k]

description: MycMax

data_processing:
To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. Next, the Seed-and-wobble algorithm (Berger et al., Nature Biotechnology 2006) was applied to compute enrichment scores (E-scores) and median intensities for all possible 8-mers.
Enrichment scores (E-scores), median intensities, and z-scores for 8-mers
*8mers_11111111.txt files contain 5 columns; 8-bp sequence, 8-bp sequence (the reverse complement),  E-score,  Median and  Z-score.

tag: transcription factor

value: c-Myc, Max

tag: protein concentration

value: 100nM Max, 1uM c-Myc


title: Mad1 at 1 uM concentration and Max at 100 nM concentration [Universal PBM 4x44k]

description: MadMax

source_name: Human Mad1 and Max

value: Mad1, Max

value: 100nM Max, 1uM Mad1


title: Max at 100 nM concentration [Universal PBM 4x44k]

description: Max

source_name: Human Max

value: Max


title: AD3.4.iMG.2


title: sample_6

tag: strain background

tag: age (weeks)

value: Nampt +/-

value: 200 mg/kg APAP


title: Fibroblast-specific Pparb/d knockout_Skin_Dermis

description: FSPCre-Pparb/d^fl/fl Dermis

source_name: Fibroblast-specific Pparb/d knockout mouse, male, 4 weeks, dermis, telogen phase of hair cycle

value: Skin Dermis

value: Telogen phase of hair cycle


title: AD3.4.iMG.1


title: Nectary line 467 replicate 2

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description:
Nec467 S2 UQN
sun_nectary_467_2_S20

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Contigs mapped to closest Arabidopsis thaliana and Uniref50 references
genome_build: Uniref50 data downloaded from Uniprot:
ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/
A. thaliana reference Araport 11, release 201606:
https://www.araport.org/downloads/Araport11_Release_201606
Supplementary_files_format_and_content: Excel file of normalized counts mapped to assembled contigs, with averages and standard deviations; contigs annotated with Arabidopsis thaliana and Uniref50 closest matches

organism: Helianthus annuus

source_name: Nectary line 467

extract_protocol:
RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-four TruSeq RNA v2 libraries were created (triplicate samples for nectaries from seven lines and triplicate leaf samples from one line) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two lanes to achieve the equivalent of approximately one lane of output. This generated 330 M reads and the average quality scores were above Q30.
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

tag: line

value: line 467

tag: nectar production

value: high

value: Nectary tissue


title: Nectary line ER replicate 1

description:
NecER S1 UQN
sun_nectary_ER_1_S1

source_name: Nectary line ER

value: maintainer line (ER)


title: Nectary line ER replicate 3

description:
NecER S3
sun_nectary_ER_3_S3


title: Nectary line 467 replicate 1

description:
Nec467 S1 UQN
sun_nectary_467_1_S19


title: JG11 Genotype Stress 3 Vegetative stage

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

data_processing:
quadtrim command line was used to remove low quality reads.
High quality filtered reads were aligned to the CDC frontier kabuli v2.6.3 (Edwards, D; 2016) using tophat2 (tophat-gcc/2.0.13)
To analyse gene expression, the accepted.hit.bam file obtained from tophat analyses was subjedted to the HTSeq to obtain the genes counts.
The gene counts from three biological replicates were subjected to DESeq2 analyses to obtain the differentially expressed genes. A gene was considered to be differentially expressed if the FDR values were less than 0.05.

organism: Cicer arietinum

source_name: Chickpea Root tissue

growth_protocol: In this study, two parental lines which segregate for salt tolerance (JG 11) and salt sensitivity (ICCV 2) were subjected to the 40 mM NaCl treatment at two developmental stages. The experiment was set-up in Random Complete Block (RCBD) design including three biological replicates at control and stress conditions. The salt treatment was maintained at electrical conductivity of ~1 dS/m and plants were maintained at the field capacity of the sandy soil in glasshouse.

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kit
The sequencing for root samples was performed by Ion-Proton PGM sequencer. Four samples were pooled together in equimolars on a sequencing chip to to generate single end reads.
The raw Fasta files generated by sequencing were obtained and were cropped and trimmed using q-trim command line tool to remove low-quality reads and adapter sequences. Followed by Alignment and differential expression studies.

treatment_protocol: Total RNA was extracted from root tissues using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. The quality and quantity of isolated RNA were confirmed by using Nanodrop spectrophotometer (NanoDrop Technologies) and Agilent Bioanalyzer. mRNA was isolated from the tolatal RNA using Dynabead PolyA RNA isolation kit (Ambion).

tag: cultivar

tag: Stage

value: Vegetative Stage

tag: treatment

value: Salt Stress

value: Root


title: Nectary line 456 replicate 3

description:
Nec456 S3 UQN
sun_nectary_456_3_S18

source_name: Nectary line 456

value: line 456

value: medium

tag: tissue


title: Nectary line 456 replicate 2

description:
Nec456 S2 UQN
sun_nectary_456_2_S17


title: JG11 Genotype Stress 1 Vegetative stage


title: Nectary line 456 replicate 1

description:
Nec456 S1 UQN
sun_nectary_456_1_S16


title: Nectary line 452 replicate 3

description:
Nec452 S3 UQN
sun_nectary_452_3_S15

source_name: Nectary line 452

value: line 452


title: JG11 Genotype Stress 2 Reproductive stage

value: Reproductive Stage


title: Nectary line ER replicate 2

description:
NecER S2 UQN
sun_nectary_ER_2_S2


title: JG11 Genotype Stress 3 Reproductive stage


title: JG11 Genotype Stress 1 Reproductive stage


title: sample_10

source_name: Nampt +/+_Saline_liver

tag: Sex

value: male

tag: genotype/variation

value: Nampt +/+

tag: treated with

value: Saline

tag: liver perfusion

value: yes

value: liver


title: Patient_3_-D-LP, biological replicate 3

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

country: Germany

institute: University of Rostock

description: Gene expression data of patient

hyb_protocol: Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).

scan_protocol: Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.

data_processing: Data were processed by SST-RMA (signal space transformation with robust multichip averaging) using TAC 4.0 (transcriptome analysis console 4.0, Applied Biosystems)

source_name: PBMCs by density-gradient centrifugation

label_protocol: 200 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).

growth_protocol: After thawing, the cells were cultured in RPMI-1640 medium supplemented with 10 % FCS  and 1 % penicillin/streptomycin (all reagents from Biochrom/Merck, Berlin, Germany).

extract_protocol: Total RNA was extracted using  the RNeasy Plus kit (Qiagen, Hilden, Germany) according to the manufacturer`s instruction.

treatment_protocol: 1α,25-dihydroxyvitamin D3 (Santa Cruz Biotechnology, Dallas, Texas,  USA) at 40 nM was used for an incubation period of 20 h at 37 °C in a 5 % CO2  humidified atmosphere.  Lipopolysaccharide (LPS; 1 μg/ml; Sigma-Aldrich, Deisenhofen,  Germany) and peptidoglycan (PGN; 10 μg/ml; Sigma-Aldrich) were added to the cells  and incubated for another 6 h.

value: PBMC

tag: disease state

value: Crohn’s disease


title: Patient_2_-D-LP, biological replicate 2

description: Gene expression data of patient


title: Nectary line 452 replicate 2

description:
Nec452 S2 UQN
sun_nectary_452_2_S14


title: Patient_3_-D+LP, biological replicate 3

description: Gene expression data of patient treated with lipopolysaccharide and peptidoglycan

value: lipopolysaccharide and peptidoglycan


title: Patient_2_-D+LP, biological replicate 2


title: AD3.4.iPMP.3

source_name: Human stem cell-derived primitive macrophage precursors

tag: cell type

tag: origin

value: Human stem cell-derived

tag: parent ipsc line


title: Patient_1_-D-LP, biological replicate 1

description: Gene expression data of patient


title: Nectary line 441 replicate 3

description:
Nec441 S3 UQN
sun_nectary_441_3_S12

source_name: Nectary line 441

value: line 441

value: low

value: Nectary tissue


title: JG11 Genotype Control 1 Reproductive stage

value: No Treatment

value: Root


title: JG11 Genotype Control 3 Vegetative stage

value: Vegetative Stage


title: JG11 Genotype Control 2 Reproductive stage


title: Nectary line 441 replicate 2

description:
Nec441 S2 UQN
sun_nectary_441_2_S11


title: Patient_1_+D-LP, biological replicate 1

description: Gene expression data of patient treated with Vitamin D

value: Vitamin D


title: Patient_1_-D+LP, biological replicate 1


title: Patient_3_+D+LP, biological replicate 3

description: Gene expression data of patient treated with Vitamin D/lipopolysaccharide/peptidoglycan


title: Patient_3_+D-LP, biological replicate 3


title: Nectary line 434 replicate 3

description:
Nec434 S3 UQN
sun_nectary_434_3_S9

source_name: Nectary line 434

value: line 434

value: high


title: Patient_2_+D-LP, biological replicate 2


title: Patient_1_+D+LP, biological replicate 1


title: JG11 Genotype Control 3 Reproductive stage

value: Reproductive Stage


title: Nectary line 452 replicate 1

description:
Nec452 S1 UQN
sun_nectary_452_1_S13

value: line 452

value: medium


title: JG11 Genotype Control 1 Vegetative stage


title: Control_3_-D-LP, biological replicate 3

description: Gene expression data of healthy donor

value: healthy donor


title: Nectary line 434 replicate 2

description:
Nec434 S2 UQN
sun_nectary_434_2_S8


title: Control_2_-D-LP, biological replicate 2

description: Gene expression data of healthy donor

value: PBMC


title: Nectary line 434 replicate 1

description:
Nec434 S1 UQN
sun_nectary_434_1_S7


title: Control_1_-D-LP, biological replicate 1

description: Gene expression data of healthy donor


title: ICCV2 Genotype Stress 3 Vegetative stage

value: ICCV2 (salt-sensitive)

value: Salt Stress


title: Control_3_-D+LP, biological replicate 3

description: Gene expression data of healthy donor treated with lipopolysaccharide and peptidoglycan

value: lipopolysaccharide and peptidoglycan


title: ICCV2 Genotype Stress 2 Vegetative stage


title: Nectary line 412 replicate 3

description:
Nec412 S3 UQN
sun_nectary_412_3_S6

source_name: Nectary line 412

value: line 412


title: Control_2_-D+LP, biological replicate 2


title: ICCV2 Genotype Stress 1 Vegetative stage


title: JG11 Genotype Control 2 Vegetative stage


title: Control_1_-D+LP, biological replicate 1


title: Ly6clow/CX3CR1high_day30_R3

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US) at 55ºC, 20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed 5 minutes at room temperature with GE Wash Buffer 1 (Cat#5188-5327, Agilent technologies, Santa Clara, CA, U) and 5 minutes at 37ºC with GE Wash Buffer 2 (Cat#5188-5327, Agilent technologies, Santa Clara, CA, U).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analysed with Feature Extraction Software (Agilent technologies, Santa Clara, CA, US) to obtain background substracted and spatially detrended Processed Signal intensities.

source_name: Cardiac macrophages

label_protocol: miRNA from 100ng total RNA was Cyanine-3 (Cy3) labeled by miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA,including small RNAs, was isolated from two-three independent biological replicates using miRNeasy Micro Kit with RNeasy MinElute Spin Columns (Qiagen) with DNaseI treatment.

treatment_protocol: Cryoinjury was used as myocardial infarction model. Animals were randomly sacrificed by CO2 inhalation 3, 7 and 30 days post-MI. Samples from healthy animals were not subjected to any surgery and were included as control.

tag: strain

value: Heart

tag: age

value: 2-3 month

tag: condition

value: 30 days post cryoinjury


title: ICCV2 Genotype Stress 3 Reproductive stage

value: Root


title: Nectary line 412 replicate 1

description:
Nec412 S1 UQN
sun_nectary_412_1_S4

tag: line

value: low

value: Nectary tissue


title: Nectary line 412 replicate 2

description:
Nec412 S2 UQN
sun_nectary_412_2_S5

tag: nectar production


title: ICCV2 Genotype Stress 2 Reproductive stage

tag: cultivar


title: Nectary line 467 replicate 3

description:
Nec467 S3 UQN
sun_nectary_467_3_S21

value: line 467


title: Leaf replicate 3

description:
Leaf S3 UQN
sun_leaf_434_3_S24

source_name: Leaf

value: line 434

value: high

value: Leaf tissue


title: ICCV2 Genotype Stress 1 Reproductive stage

tag: Stage

value: Reproductive Stage


title: Leaf replicate 2

description:
Leaf S2 UQN
sun_leaf_434_2_S23


title: ICCV2 Genotype Control 3 Reproductive stage

tag: treatment

value: No Treatment


title: ICCV2 Genotype Control 2 Reproductive stage

tag: tissue


title: Leaf replicate 1

description:
Leaf S1 UQN
sun_leaf_434_1_S22


title: Ly6clow/CX3CR1high_day30_R2


title: Ly6clow/CX3CR1high_day7_R3

value: 7 days post cryoinjury


title: Ly6clow/CX3CR1high_day7_R2


title: Ly6clow/CX3CR1high_day30_R1


title: Ly6clow/CX3CR1high_day7_R1


title: Ly6chigh/CX3CR1low_day3_R2

value: 3 days post cryoinjury


title: WT-IL-25 stimulation  rep2

data_processing:
Basecalls performed using Zebracall process version 0.5.0.13875
Adaptors were trimmed  and low quality reads were filtered to get clean reads, then mapped to mm10 genome using hisat2.
featureCounts program  was used for reads summarization and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: keratinocyte

growth_protocol: Skin tissues from newborn C57BL/6 mice were obtained for primary keratinocyte culture with medium M154CF

extract_protocol:
Total RNAs were isolated with RNAprep pure Tissue Kit (DP431)
The RNA-seq library was prepared by the Beijing Genomics Institute.

treatment_protocol: Cells were then stimulated with or without IL-25 (Biolegend) for 8hrs.

value: skin

value: post natal day 1

tag: genotype

value: wild type

value: keratinocyte


title: WT-IL-25 stimulation  rep1


title: Ly6chigh/CX3CR1low_day3_R3

value: Heart

value: 2-3 month


title: WT-MOCK  rep2


title: Ly6chigh/CX3CR1low_day3_R1


title: Control_3_+D-LP, biological replicate 3

description: Gene expression data of healthy donor treated with Vitamin D

value: PBMC

value: healthy donor

value: Vitamin D


title: Control_1_+D-LP, biological replicate 1


title: Control_2_+D-LP, biological replicate 2


title: Control_3_+D+LP, biological replicate 3

description: Gene expression data of healthy donor treated with Vitamin D/lipopolysaccharide/peptidoglycan


title: Runx2 at 50 nM concentration

source_name: Human Runx2

growth_protocol: Gateway-compatible clones containing the full-length genes for Ets1, Elk1, Gabpa, Runx1, and Runx2 were purchased from GeneCopoeia and the genes were transferred into pDEST15 using the LR Clonase reaction (Life Technologies). This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

tag: transcription factor

tag: protein concentration

value: Protein concentration:50nM


title: Control_2_+D+LP, biological replicate 2


title: Runx2 at 10 nM concentration

value: Protein concentration:10nM


title: Control_1_+D+LP, biological replicate 1


title: ICCV2 Genotype Control 3 Vegetative stage

value: ICCV2 (salt-sensitive)

value: Vegetative Stage

value: Root


title: ICCV2 Genotype Control 2 Vegetative stage

value: No Treatment


title: Runx1 at 50 nM concentration

source_name: Human Runx1


title: WT-MOCK  rep1


title: ICCV2 Genotype Control 1 Reproductive stage

value: Reproductive Stage


title: Ly6clow/CX3CR1high_day0_R2

value: uninfarcted heart


title: Runx1 at 10 nM concentration


title: ICCV2 Genotype Control 1 Vegetative stage


title: JG11 Genotype Stress 2 Vegetative stage

value: Salt Stress


title: Nectary line 441 replicate 1

description:
Nec441 S1 UQN
sun_nectary_441_1_S10

value: line 441

value: low

value: Nectary tissue


title: Ly6clow/CX3CR1high_day0_R1

value: Heart


title: without diuron (CT02 exp)_biological rep2

status: Public on Apr 02 2018

city: Lisboa

first: Cristina

middle: Anjinho

last: Viegas

address: Av Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Técnico

description: Gene expression data from cells incubated without diuron

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org, Wong Lab, Harvard) applying a probeset mask file excluding all probes on the array representing Schizosaccharomyces pombe transcripts. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the 36 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001). Replicate data for the same sample type were weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2 .

organism: Saccharomyces cerevisiae

source_name: Cell population incubated without diuron

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Exponential cell populations (OD640nm = 0.25 ± 0.05) of S. cerevisiae BY4741 were incubated in minimal growth medium (pH 6.5), at 30ºC, with orgital agitation (250 RPM) in each of the exposure conditions indicated above.

extract_protocol: Total RNA isolation was performed using the hot-phenol method (Koher & Domdey, 1991, Methods in Enzimology 194:398-405).

treatment_protocol: Cells were harvested by centrifugation (10000 rpm, 3 min, 0ºC) and immediately frozen in liquid nitrogen and stored at -80ºC until RNA extraction.

value: without diuron (CT02 exp)

tag: cell population

value: Exponential cells (O.D.640nm = 0.25 ± 0.05)


title: with 80 mg/L diuron (IC20)_biological rep3

description: Gene expression data from cells incubated with the IC20 of diuron

source_name: Cell population incubated with 80 mg/L diuron (IC20DIU)

value: with 80 mg/L diuron (IC20)


title: with 220 mg/L S-metolachlor (IC20)_biological rep2

description: Gene expression data from cells incubated with the IC20 of S-metolachlor

source_name: Cell population incubated with 220 mg/L S-metolachlor (IC20S-MET)

value: with 220 mg/L S-metolachlor (IC20)


title: with 220 mg/L S-metolachlor (IC20)_biological rep3


title: without MCPA-ME (CT02 exp)_biological rep2

description: Gene expression data from cells incubated without MCPA-ME

source_name: Cell population incubated without MCPA-ME

value: without MCPA-ME (CT02 exp)


title: without MCPA-ME (CT02 exp)_biological rep1


title: Ventricular resection zebrafish_21dpi

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

description: Gene expression after 21dpi in ventricular resection-injured zebrafish

hyb_protocol: The fragmented labeled cRNA was then hybridized to oligo microarray at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA),  image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Danio rerio

source_name: Ventricular resection-injured zebrafish, 21dpi

label_protocol: 1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Not applicable

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's recommendations. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

treatment_protocol: Not applicable.

tag: gender

value: male

value: 1 year


title: with 220 mg/L S-metolachlor (IC20)_biological rep1


title: Ventricular resection zebrafish_15dpi

description: Gene expression after 15dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 15dpi


title: without S-metolachlor (CT02 exp)_biological rep3

description: Gene expression data from cells incubated without S-metolachlor

source_name: Cell population incubated without S-metolachlor

value: without S-metolachlor (CT02 exp)


title: without MCPA-ME (CT02 exp)_biological rep3


title: with 160 mg/L carbofuran (IC20)_biological rep3

description: Gene expression data from cells incubated with the IC20 of carbofuran

source_name: Cell population incubated with 160 mg/L carbofuran (IC20CAB)

value: with 160 mg/L carbofuran (IC20)


title: with 80 mg/L diuron (IC20)_biological rep2


title: with 80 mg/L diuron (IC20)_biological rep1


title: with 115 mg/L MCPA-ME (IC20)_biological rep1

description: Gene expression data from cells incubated with the IC20 of MCPA-ME

source_name: Cell population incubated with 115 mg/L MCPA-ME (IC20MCPA-ME)

value: with 115 mg/L MCPA-ME (IC20)


title: Ventricular resection zebrafish_3dpi

description: Gene expression after 3dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 3dpi


title: without diuron (CT02 exp)_biological rep1


title: Ventricular resection zebrafish_0.25dpi

description: Gene expression after 0.25dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 0.25dpi


title: without diuron (CT02 exp)_biological rep3


title: Ventricular resection zebrafish_1dpi

description: Gene expression after 1dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 1dpi


title: Ventricular resection zebrafish_28dpi

description: Gene expression after 28dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 28dpi


title: with 115 mg/L MCPA-ME (IC20)_biological rep2


title: without S-metolachlor (CT02 exp)_biological rep2


title: without S-metolachlor (CT02 exp)_biological rep1


title: Ventricular resection zebrafish_10dpi

description: Gene expression after 10dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 10dpi


title: with 115 mg/L MCPA-ME (IC20)_biological rep3


title: Ventricular resection zebrafish_6dpi

description: Gene expression after 6dpi in ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 6dpi


title: Patient_2_+D+LP, biological replicate 2

description: Gene expression data of patient treated with Vitamin D/lipopolysaccharide/peptidoglycan

source_name: PBMCs by density-gradient centrifugation

value: PBMC

tag: disease state

value: Crohn’s disease


title: Ventricular resection zebrafish_control

description: Gene expression in no ventricular resection-injured zebrafish

source_name: Ventricular resection-injured zebrafish, 0dpi, control


title: with 160 mg/L carbofuran (IC20)_biological rep2


title: with 160 mg/L carbofuran (IC20)_biological rep1


title: RNAseq_Setdb1 cKO iMEF_4OHT_1

city: Wako

first: Masaki

last: Kato

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN

data_processing:
We aligned reads to the reference genome (UCSC mm9) using TopHat (version 2.0.12 and 2.1.1) with the exception of “-g 1”.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
After obtaining the aligned bam files, the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: iMEF

growth_protocol: Cells were cultured in DMEM (Nacalai: 08458-45) with MEM non-essential amino acids (Gibco: 11140-035), 2-mercaptoethanol (used at 0.1 mM, Nacalai), 10% FBS. Cells were split every three days.

extract_protocol:
Total RNA was extracted with RNeasy mini kit (QIAGEN: 74134).
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit protocols

treatment_protocol: For TSA treatment, Setdb1 cKO iMEFs were treated with 150 nM TSA for 24 hrs. For PD0325091 treatment, 1 µM MEK inhibitor PD0325901 for last 24 hr. For simultaneous KO of Setdb1, 4OHT was added at day 0.

tag: cell type

value: iMEF (Setdb1 cKO iMEF)

value: day 6 after 4OHT treatment


title: RNAseq_Setdb1 cKO iMEF_4OHT_2


title: RNAseq_Setdb1 cKO iMEFs_4OHT_PD_1

value: day 6 after 4OHT treatment with PD0325091


title: RNAseq_Setdb1 cKO iMEFs_PD_2

value: PD0325091 treatment


title: RNAseq_Setdb1 cKO iMEFs_TSA_2

value: TSA treatment


title: RNAseq_Setdb1 cKO iMEFs_4OHT_PD_2


title: with 200 mg/L alachlor (IC20)_biological rep3 (2)

description: Gene expression data from cells incubated with the IC20 of alachlor

source_name: Cell population incubated with 200 mg/L alachlor (IC20ALA)

value: with 200 mg/L alachlor (IC20)


title: without alachlor (CT02 exp)_biological rep2

description: Gene expression data from cells incubated without alachlor

source_name: Cell population incubated without alachlor

value: without alachlor (CT02 exp)

value: Exponential cells (O.D.640nm = 0.25 ± 0.05)


title: without carbofuran (CT02 exp)_biological rep2

description: Gene expression data from cells incubated without carbofuran

source_name: Cell population incubated without carbofuran

value: without carbofuran (CT02 exp)


title: RNAseq_Setdb1 cKO iMEFs_TSA_1


title: RNAseq_Setdb1 cKO iMEFs_Ctrl_2

value: no treatment


title: without alachlor (CT02 exp)_biological rep1


title: RNAseq_Setdb1 cKO iMEFs_Ctrl_1


title: RNAseq_Setdb1 cKO iMEFs_PD_1


title: without alachlor (CT02 exp)_biological rep3


title: without carbofuran (CT02 exp)_biological rep3


title: with 200 mg/L alachlor (IC20)_biological rep1 (2)


title: without carbofuran (CT02 exp)_biological rep1


title: with 200 mg/L alachlor (IC20)_biological rep2 (2)


title: BTDMAFF3

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho. Tsurumi

department: IMS

description: gene expression of colonic epithelial cells at 4 weeks B.theta colonization

hyb_protocol: 5 ug of cRNA were hybridized for 18 hr on GeneChip Mouse Genome 430.20 array

scan_protocol: GeneChips were scanned using the GeneChip Scanner 30007G.

data_processing: The data was analyzed with Affymetrix GeneChip Command Console Software and the data were obtained with Affymetrix Expression Console.

source_name: colonic epithelial cells with BTDMAFF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Colonic tissues were incubated with 1mM EDTA in PBS at 37 C for 20 min, and the single cell suspensions were prepared by mechanical dissociation with vigorous shaking in PBS.

extract_protocol: RNA was isolated using the RNeasy kit (QIAGEN).

treatment_protocol: The suspensions of epithelial cells were stained with anti-CD45 (30-F11) and anti-EpCAM (G8.8) (both from BioLegend), followed by propidium iodide (PI). PI-CD45-EpCAM+ fraction was sorted to 90-95% purity with BD Aria III.

value: colonic epithelial cells

value: male

value: colonized at 8weeks old, sampling at 12 weeks old


title: BTDMAFF4


title: BTWT4

source_name: colonic epithelial cells with BTWT


title: BTDMAFF2


title: BTWT3


title: BTWT2


title: BTDMAFF1


title: B4

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

description: [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version]

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix system.

data_processing: The data were analyzed with RMA using Gene Expression Console.

source_name: primary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed with miRNeasy Mini Kit Qiagen according to the manufacturer's instructions.

value: head and neck squamous cell carcinoma


title: B75


title: B35


title: B82


title: B88


title: B98


title: B97


title: B32


title: B63


title: B30


title: B100


title: B103


title: B99


title: B12/14


title: BTWT1


title: B27


title: B55


title: B62


title: B28


title: B81


title: WAT_cold_4

city: Neuherberg

first: Yiming

last: Cheng

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

data_processing:
Sequenced reads were trimmed for adaptor sequence with trim-galore and aligned with tophat softare
Genome_build: Ensembl release 81
Supplementary_files_format_and_content: tab-delimited text files include raw read count per sample

extract_protocol:
RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina)
End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the Low Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina).

treatment_protocol: All mice were bred, born and weaned at 30°C. At the age of 10-12 weeks, half of the mice were transferred to a temperature-controlled (+/- 0.5°C) climate chamber and kept for two weeks at 18°C followed by 3 weeks at 5°C. Afterwards, mice kept at 30°C and 5°C were euthanized after 2-3 hours food withdrawal, and serum and tissue samples were collected.

tag: genotype/variation

value: wild type

value: female

tag: kept at

value: Inguinal WAT


title: WAT_cold_3

tag: strain

tag: age


title: B52


title: WAT_cold_1


title: WAT_cold_2


title: WAT_4

source_name: WAT


title: B42


title: B96


title: B26


title: B90


title: B22


title: B44


title: WAT_3


title: Mtb 96h vs Mbovis 96h_rep4

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description: Rv1C(cy3) vs Mb1C(cy5)

hyb_protocol: II. Prehybridization  1. Prepare Prehybridization Solution (Fresh Each Time)  **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides.  106.0ml dH2O  3.0g BSA  1.2ml 10%SDS  2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides.  3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC.  4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down.  5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down.  6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry.  **Complete this step within one hour of hybridization    III. Hybridization  1. Add the following to the 5µl labeled sample.  0.5µl 10 mg/ml tRNA  1.0µl 20X SSC  2.5ul Formamide  1.0µl 1% SDS  2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level.  5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath  **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe.  IV. Post Hyb washes (next day)  1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.  2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.  3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix Pro 6.1.0.2 and the resulting text files were exported to Microsoft Excel.

data_processing: The chips were normalized by the print-tip Lowess method (Dudoit, 2000).  The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’.  Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip. The ratio of the average median intensity of Cy5 over the average median intensity of Cy3 was determined for each spot.

organism: Mycobacterium tuberculosis variant bovis

source_name: wild-type M.bovis 96h Starvation

label_protocol: I. Synthesis and Labeling of cDNA  1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix:  5.0µl 5X First-Strand buffer  2.5µl 100 mM DTT  2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock)  1.5ul Cy3 or Cy5  Then add 1.2ul Superscript, vortex to mix and spin to collect contents  4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine.  **Can freeze or leave at 4oC overnight if necessary  5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl).  6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.  7. Bring sample to 5µl with TE.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: Laboratory strain of M. tuberculosis H37Rv and M. bovis Ravenel. Frozen stocks were used to inoculate seed cultures in middlebrook 7H9 media with 10% OADC, 0.2% glycerol, 0.025% Tween. Starvation experiments were performed essentially as described by Betts et al. (2002), with one exception in that we used OADC instead of ADS. After growth without shaking to late log phase 100 ml cultures were started in roller bottles (Corning 490 cm2), using 1:100 inoculum from the late-log seed cultures. Log-phase cultures were grown for 7 days before nutrient starvation. An aliquot of the culture (10 ml) was removed on day 7 (log-phase samples) for RNA extraction and directly added to 4x volume of an RNA stabilization solution containing 5M Guanidinium isothiocyanate, 0.5% sodium-N-lauryl sarcosine, 0.5% Tween 80, and 0.1 M betamercaptoethanol as described elsewhere (Stewart et al., 2002). The rest of each culture was centrifuged (2000 x g for 10 min) and cell pellets were washed twice with PBS before re-suspension in PBS and transferred to 150 ml storage bottles (Corning) (30 ml in each bottle) and incubated at 37ºC without shaking. After 24h and 96h of incubation aliquots were removed from each starvation (PBS) culture and similarly added to RNA stabilization solution for the 24h and 96h starvation samples.

extract_protocol: RNA was extracted using the FastPrep System (FastRNA Pro Blue Kit and FastPrep Instrument) according to the manufacturer. Subsequently RNA samples were treated with DNase (Ambion) and purified using RNeasy Columns (Qiagen). An aliquot of each RNA sample was analyzed by agarose gel electrophoresis and the quantity of RNA in each sample was determined using a nanodrop spectrophotometer.

value: Ravenel

tag: state of culture

value: 96h starvation

organism: Mycobacterium tuberculosis

source_name: wild-type M.tb 96h Starvation (Expt 3)


title: WAT_2


title: Mtb 96h vs Mbovis 96h_rep2

description: Rv1C(cy3) vs Mb3C(cy5)

source_name: wild-type M.bovis 96h Starvation (Expt 3)

treatment_protocol: Laboratory strain of M. tuberculosis H37Rv and M. bovis Ravenel. Frozen stocks were used to inoculate seed cultures in middlebrook 7H9 media with 10% OADC, 0.2% glycerol, 0.025% Tween. Starvation experiments were performed essentially as described by Betts et al. (2002), with one exception in that we used OADC instead of ADS. After growth without shaking to late log phase 100 ml cultures were started in roller bottles (Corning 490 cm2), using 1:100 inoculum from the late-log seed cultures. Log-phase cultures were grown for 7 days before nutrient starvation. An aliquot of the culture (10 ml) was removed on day 7 (log-phase samples) for RNA extraction and directly added to 4x volume of an RNA stabilization solution containing 5M Guanidinium isothiocyanate, 0.5% sodium-N-lauryl sarcosine, 0.5% Tween 80, and 0.1 M betamercaptoethanol as described elsewhere (Stewart et al., 2002). The rest of each culture was centrifuged (2000 x g for 10 min) and cell pellets were washed twice with PBS before re-suspension in PBS and transferred to 150 ml storage bottles (Corning) (30 ml in each bottle) and incubated at 37ºC without shaking. After 24h and 96h of incubation aliquots were removed from each starvation (PBS) culture and similarly added to RNA stabilization solution for the 24h and 96h starvation samples.


title: B17


title: ddSeq

city: Seattle

first: Andrew

last: Butler

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

data_processing:
RNA-seq data was processed with the Drop-seq tools version 1.12 pipeline from the McCarrol Lab.
Genome_build: Reads were aligned to the human reference sequence GRCh37/hg19.
Supplementary_files_format_and_content: Processed data provided as a CSV expression matrix where the rows correspond to genes and the columns to either a particular replicate for the bulk data, or single cells for the ddSeq data

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMCs from a healthy donor were diluted to 2,500 cells/ml and run according to manufacturer’s protocol through 8 ddSeq wells (2 cartridges) with an expected yield of 2,400 cells in total.
Sequencing libraries were prepared according to manufacturer’s instructions.

treatment_protocol: No Treatment

tag: interferon stimulation

value: unstimulated

value: NA (unsorted PBMCs)


title: WAT_1


title: B15


title: B91


title: Mtb log vs Mbovis log_rep2

description: Rv1A(cy3) vs Mb1A(cy5)

source_name: wild-type M.bovis log-phase (Expt 3)

value: log phase

source_name: wild-type M.tb log-phase (Expt 3)


title: Mtb log vs Mbovis log_rep6

description: Rv2A(cy5) vs Mb2A(cy3)


title: Mtb log vs Mbovis log_rep1

description: Rv2A(cy5) vs Mb2A(cy3)


title: Mtb 96h vs Mbovis 96h_rep5

description: Rv1C(cy3) vs Mb1C(cy5)

source_name: wild-type M.bovis 96h Starvation (Expt 4)

source_name: wild-type M.tb 96h Starvation (Expt 4)


title: Mtb log vs Mbovis log_rep4

description: Rv1A(cy3) vs Mb3A(cy5)


title: B16


title: Mtb log vs Mbovis log_rep5

description: Rv1A(cy3) vs Mb1A(cy5)


title: Mtb 96h vs Mbovis 96h_rep6

description: Rv2C(cy5) vs Mb2C(cy3)


title: Mtb log vs Mbovis log_rep3

description: Rv2A(cy5) vs Mb4A(cy3)


title: Mtb 96h vs Mbovis 96h_rep3

description: Rv2C(cy5) vs Mb2C(cy3)


title: pDC_stim_rep3

extract_protocol:
We sorted pure populations of pDCs and cDCs based on the following panel of standard antibodies (from BioLegend and BD Pharmingen): CD3 (HIT3a), CD19 (HIB19), CD56 (HCD56), CD14 (HCD14), HLA-DR (LN3), CD11c (Bu15) and CD123 (7G3). pDCs were defined as: CD3- CD19- CD56- CD14- HLA-DR+ CD11c- CD123+. cDCs were defined as: CD3- CD19- CD56- CD14- HLA-DR+ CD11c+. Following sorting, we extracted RNA using TRIzol (Invitrogen)
We performed bulk RNA-seq using a modified version of the SMART-Seq2 protocol followed by library preparation using the Nextera XT DNA sample prep kit (Illumina) as in Mayer et. al., 2018.

treatment_protocol: PBMCs from a healthy human donor (ALLCELLS) were cultured with RPMI medium supplemented with 10% FBS and stimulated for 6 hours with IFNβ

value: stimulated

value: pDC


title: pDC_stim_rep2


title: pDC_stim_rep1


title: BAT_cold_3

value: Inguinal BAT


title: B2


title: Mtb 24h vs Mbovis 24h_rep6

description: Rv1B(cy3) vs Mb1B(cy5)

source_name: wild-type M.bovis 24h Starvation (Expt 4)

value: 24h starvation

source_name: wild-type M.tb 24h Starvation (Expt 4)


title: Mtb 24h vs Mbovis 24h_rep4

description: Rv1B(cy3) vs Mb1B(cy5)

source_name: wild-type M.bovis 24h Starvation (Expt 3)

source_name: wild-type M.tb 24h Starvation (Expt 3)


title: cDC_stim_rep3

value: cDC


title: Mtb 96h vs Mbovis 96h_rep1

description: Rv2C(cy5) vs Mb4C(cy3)


title: cDC_stim_rep2


title: cDC_stim_rep1


title: BAT_cold_4


title: pDC_control_rep3

treatment_protocol: PBMCs from a healthy human donor (ALLCELLS) were cultured with RPMI medium supplemented with 10% FBS


title: Mtb 24h vs Mbovis 24h_rep5

description: Rv2B(cy5) vs Mb2B(cy3)


title: Mtb 24h vs Mbovis 24h_rep2

description: Rv1B(cy3) vs Mb3B(cy5)


title: BAT_2

source_name: BAT


title: BAT_1


title: pDC_control_rep2


title: Mtb 24h vs Mbovis 24h_rep3

description: Rv2B(cy5) vs Mb2B(cy3)


title: pDC_control_rep1


title: cDC_control_rep2


title: ChIP-seq MCF10Ashy WCE 2.2

city: Malmö

first: Maria

middle: Alvarado

last: Kristensson

address: 59 Jan Waldenströms street

country: Sweden

institute: Lund University

data_processing:
Basecalls performed using the software Torrent Suite v5.0.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie version 1.0.0 with parameter -m 1
peaks were called using MACS2 version 2.1.1 with the following setting: FDR threshold (0.05)
Differential peak analysis was performed using the bggdiff tool as part of MACS2 Chip-seq analysis package
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using genomeCoverageBed version 2.17.0; Scores represent -log10 (FDR)

source_name: ChIP-seq MCF10Ashy WCE

growth_protocol: MCF10A cells were grown in DMEM/F12 medium (Hyclone) supplemented with 5% horse serum, 1% PEST, 20 ng/ml EGF, 0.5 ug/ml hydrocortisone, 100 ng/ml cholera toxin and 10 ug/ml insulin. Cells were grown in a p150 plate to 90 % confluency (typically 12-15 x106 cells).

extract_protocol:
Nuclei were lysed and sonicated. The sonicated nuclei were cleared and gamma-tubulin-DNA-complexes or PCNA-DNA-complexes were isolated with antibody.
Library Builder System (ThermoFisher)

treatment_protocol: Cells were subjected to dubble thymidine syncronization and released for 1h or 2 h prior to harvest.

tag: tissue source

value: Mammary gland; breast

tag: cell line

value: Breast epithelial cell

tag: stable transfection

value: gamma-tubulin shRNA

tag: selection

value: 100 ug/ml Zeocin

tag: time from release to harvest

tag: chip antibody


title: ChIP-seq MCF10Ashy WCE 2.1


title: cDC_control_rep1


title: ChIP-seq MCF10Ashy WCE 1.1


title: Bcwt in vitro culture RNA (32 hpi) rep3

city: Kaiserslautern

first: Matthias

last: Hahn

address: Paul-Ehrlich-Str. 22

department: Biology

institute: University of Kaiserslautern

description: BcWT-in vitro_32h-3

data_processing:
Clean reads were imported into CLC Genomics Workbench, and  15 5'-terminal nucleotides trimmed
Reads were were reference-aligned to annotated  reference genome of B. cinerea strain B05.10, using 0.95 lenth fraction and 0.96 similarity fraction.
Differential gene expression analysis was performed  with CLC, using normalized expression values for mapped reads. Statistical data analysis was performed using Baggerly's test.
Genes with RPKM values >5 were defined as being expressed, and used for analysis. Mean values were evaluated for statistical significance (p<0.05) with FDR-corrected p values.
Genome_build: For reference alignment, the latest version of the B. cinerea strain B05.10 annotated genome (http://fungi.ensembl.org/Botrytis_cinerea/Info/Index) was used.
Supplementary_files_format_and_content: Table S3 (Excel table): RNAseq-based expression of all B. cinerea genes in the wild type and in vel1*, lae1 and vel1 mutants
Supplementary_files_format_and_content: Table S4 (Excel table): B. cinerea genes differentially coexpressed in vel1*, lae1 and vel1 mutants compared to wild type

organism: Botrytis cinerea

source_name: Bcwt in vitro culture (32 hpi)

extract_protocol:
RNA was isolated from mycelium or infected tissue with the NucleoSpin® RNA plant kit (Macherey-Nagel, Düren, Germany).
Sequencing library was generated using TruSeq RNA Library Prep Kit
100 bp paired reads were generated with Illumina HiSeq 2000 V3 instrument by BGI (Shenzhen, China)

tag: genotype

value: wild type

tag: cultivar

tag: inoculation

tag: treatment

value: B. cinerea RNA was isolated from 22.5 ml liquid cultures (2x10^6 conidia) grown in apple wax-coated dishes for 32 h in MM (3 g l-1 GB5 salts, 10 mM KH2PO4, 25 mM glucose, pH 5.5; Leroch et al., 2013).

tag: tissue

value: Mycelium from liquid medium


title: Mtb 24h vs Mbovis 24h_rep1

description: Rv2B(cy5) vs Mb4B(cy3)

value: Ravenel


title: ChIP-seq MCF10A WCE 2.2

source_name: ChIP-seq MCF10A WCE

tag: cell type


title: Bcwt in vitro culture RNA (32 hpi) rep2

description: BcWT-in vitro_32h-2


title: Mb log vs Mb 96h_rep6

description: Mb2c(cy3) vs Mb2a(cy5)

source_name: wild-type M.bovis log-phase (Expt 4)

value: 96h starvation


title: Mb log vs Mb 96h_rep3

description: Mb2A(cy5) vs Mb2C(cy3)


title: Mb log vs Mb 96h_rep1

description: Mb4A(cy5) vs Mb4C(cy3)


title: ChIP-seq MCF10A WCE 2.1


title: Mb log vs Mb 96h_rep5

description: Mb1c(cy3) vs Mb1a(cy5)


title: Bcwt in vitro culture RNA (32 hpi) rep1

description: BcWT-in vitro_32h-1


title: cDC_control_rep3

value: unstimulated


title: ChIP-seq MCF10A WCE 1.2


title: ChIP-seq MCF10Ashy WCE 1.2


title: Bcvel1 mutant in planta RNA (24 hpi) rep3

source_name: Bcvel1 mutant in planta (24 hpi)

value: vel1 mutant

value: 3 weeks old tomato

value: cv. Marmande

value: 10 µl drop inoculation

value: 10^6 conidia/ ml in GB5, 10 mM KH2PO4, 25 mM glucose, pH5.5

value: Tomato detached infected leaf


title: Bcvel1 mutant in planta RNA (24 hpi) rep2


title: Mb log vs Mb 24h_rep5

description: Mb1a(cy3) vs Mb1b(cy5)

value: 24h starvation

value: log phase


title: ChIP-seq MCF10A WCE 1.1

value: Mammary gland; breast

value: Breast epithelial cell


title: Mb log vs Mb 24h_rep3

description: Mb4A(cy5) vs Mb4B(cy3)


title: Mb log vs Mb 24h_rep6

description: Mb2a(cy3) vs Mb2b(cy5)


title: Mb log vs Mb 96h_rep4

description: Mb1A(cy3) vs Mb1C(cy5)

source_name: wild-type M.bovis 96h Starvation


title: Mb log vs Mb 96h_rep2

description: Mb3A(cy3) vs Mb3C(cy5)

source_name: wild-type M.tb 96h Starvation (Expt 3)


title: Mb log vs Mb 24h_rep4

description: Mb1A(cy3) vs Mb1B(cy5)


title: ChIP-seq MCF10Ashy ytub 2.2

source_name: ChIP-seq MCF10Ashy ytub

value: gamma-tubulin shRNA

value: 100 ug/ml Zeocin

value: gamma-tubulin (Sigma aldrich T3320 and T5196)


title: Bcvel1 mutant in planta RNA (24 hpi) rep1


title: Mb log vs Mb 24h_rep2

description: Mb3A(cy3) vs Mb3B(cy5)

source_name: wild-type M.bovis log-phase (Expt 3)


title: ChIP-seq MCF10Ashy ytub 2.1


title: H37Rv log vs H37Rv96h_rep6

description: Rv2c(cy3) vs Rv2a(cy5)

source_name: wild-type M.tb log-phase (Expt 4)


title: Mb log vs Mb 24h_rep1

description: Mb2A(cy5) vs Mb2B(cy3)


title: ChIP-seq MCF10Ashy ytub 1.2


title: Bclae1 mutant in planta RNA (24 hpi) rep3

source_name: Bclae1 mutant in planta (24 hpi)

value: lae1 mutant


title: Bclae1 mutant in planta RNA (24 hpi) rep2


title: ChIP-seq MCF10Ashy ytub 1.1


title: Bclae1 mutant in planta RNA (24 hpi) rep1


title: H37Rv log vs H37Rv96h_rep3

description: Wt1 (cy3) vs Wt5 (cy5)

source_name: wild-type 96 h starvation (Expt 1)

source_name: wild-type log-phase (Expt 1)


title: KLN-LN4K1, sub-clone of KLN-205, biological rep1

city: Chapel Hill

first: Alessandro

last: Porrello

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Gene expression data from KLN-LN4K1, a sub-clone of KLN-205 cells, after orthotopic injections in syngeneic mice and in vivo selection

hyb_protocol: Biotin-labeled cDNA at a concentration of 25 ng/ul or 2.25 ug total was hybridized to the Mouse Gene 2.1 ST peg plate. The Mouse Gene 2.1 ST peg plate was hybridized, washed, stained and scanned using the Affymetrix GeneTitan MC instrument. The default method for the Mouse Gene 2.1 peg plate was used on the GeneTitan. The hybridization time for the expression plates was 17 hours and the temperature was 48 C.

scan_protocol: The Mouse Gene 2.1 ST peg plate was scanned using the Affymetrix GeneTitan MC instrument.

data_processing: The data were analyzed using Affymetrix Expression Console and the algorithm used was RMA (with background adjustment, quantile normalization and summarization).

source_name: Sub-clone LN4K1 of the KLN-205 cell line

label_protocol: The biotin-labeled cDNA was prepared from 250 ng of total RNA using the Ambion WT Expression Kit and Affymetrix WT Terminal Labeling Kit.

growth_protocol: Cells were grown using standard tissue culture until 60-80% confluent at which point RNA was isolated.

extract_protocol: Total RNA was extracted from the cells using the Quick RNA MiniPrep Zymo Research Kit (Genesee scientific).

treatment_protocol: No cell lines were exposed to any type of treatment.

tag: cell line/background

tag: clone id

value: Sub-clone LN4K1

value: murine lung squamous carcinoma cell line

tag: cell progression

value: tumorigenic and strongly metastatic


title: ChIP-seq MCF10A ytub 2.2

source_name: ChIP-seq MCF10A ytub


title: KLN-LN4-2, sub-clone of KLN-205, biological rep3

description: Gene expression data from KLN-LN4-2, a sub-clone of KLN-205 cells, after orthotopic injections in syngeneic mice and in vivo selection

source_name: Sub-clone LN4-2 of the KLN-205 cell line

tag: strain

value: Sub-clone LN4-2

value: tumorigenic


title: KLN-LN4K1, sub-clone of KLN-205, biological rep3


title: H37Rv log vs H37Rv96h_rep5

description: Rv2A(cy5) vs Rv2C(cy3)

source_name: wild-type M.tb log-phase (Expt 3)

tag: state of culture

value: 96h starvation


title: KLN-LN4K1, sub-clone of KLN-205, biological rep2


title: Bcvel1* mutant in planta RNA (24 hpi) rep3

source_name: Bcvel1* mutant in planta (24 hpi)

value: vel1* mutant

tag: age

value: 3 weeks old tomato

value: cv. Marmande

value: 10 µl drop inoculation


title: ChIP-seq MCF10A ytub 2.1

tag: tissue source

tag: cell line


title: H37Rv log vs H37Rv96h_rep4

description: Rv1A(cy3) vs Rv1C(cy5)

value: log phase


title: ChIP-seq MCF10A ytub 1.2

value: Mammary gland; breast


title: KLN-LN4-2, sub-clone of KLN-205, biological rep2


title: KLN-LN4-2, sub-clone of KLN-205, biological rep1


title: ChIP-seq MCF10A ytub 1.1

value: Breast epithelial cell


title: KLN-LN2-2, sub-clone of KLN-205, biological rep3

description: Gene expression data from KLN-LN2-2, a sub-clone of KLN-205 cells, after orthotopic injections in syngeneic mice and in vivo selection

source_name: Sub-clone LN2-2 of the KLN-205 cell line

value: Sub-clone LN2-2


title: Bcvel1* mutant in planta RNA (24 hpi) rep1

value: 10^6 conidia/ ml in GB5, 10 mM KH2PO4, 25 mM glucose, pH5.5

value: Tomato detached infected leaf


title: KLN-LN2-2, sub-clone of KLN-205, biological rep2


title: H37Rv log vs H37Rv96h_rep1

description: Wt1 (cy3) vs Wt5B (cy5)


title: Bcvel1* mutant in planta RNA (24 hpi) rep4


title: Bcwt in planta RNA (24 hpi) rep3

source_name: Bcwt in planta (24 hpi)

value: wild type


title: Bcwt in planta RNA (24 hpi) rep2


title: Bcwt in planta RNA (24 hpi) rep1


title: Bcvel1* mutant in planta RNA (24 hpi) rep2


title: Ovarian cancer

city: Moscow

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficacy was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: Gene expression data from the multiple metachronous ovarian cancer sample was merged with gene expression data from adult normal ovarian control samples from GSE6008 (GSM139476 - GSM139479) and quantile normalized using R statistical programming language and 'preprocessCore' library.

source_name: Ovarian cancer

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

extract_protocol: RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion) was used for total RNA extraction. RNA was quantified using Nanodrop.

tag: disease state

value: Ovarian cancer


title: KLN-205, murine LUSC cell line, biological rep3

description: Gene expression data from KLN-205 cells, after orthotopic injections in syngeneic mice

source_name: KLN-205, murine lung squamous carcinoma cell line


title: KLN-LN2-2, sub-clone of KLN-205, biological rep1

value: murine lung squamous carcinoma cell line


title: H37Rv log vs H37Rv24h_rep5

description: Rv1A(cy3) vs Rv1B(cy5)

source_name: wild-type 24h Starvation (Expt 3)

value: 24h starvation


title: H37Rv log vs H37Rv96h_rep2

description: Wt1 (cy5) vs Wt6 (cy3)

source_name: wild-type 96 h starvation (Expt 2)


title: H37Rv log vs H37Rv24h_rep6

description: Rv2a(cy3) vs Rv2b(cy5)

source_name: wild-type M.tb 24h Starvation (Expt 4)


title: Tsc2 cKO Rep 4C

status: Public on Apr 01 2018

city: St Louis

first: Dan

last: Carlin

address: 660 S Euclid Ave / Campus Box 8108

department: Neuroscience

institute: Washington University in St Louis

description: 100 FACS-sorted GFP-positive cells

data_processing:
Samples were QC’d using FastQC and not trimmed
Reads were aligned to mm10 using STAR-align with default settings  Reads aligned to mm10 using STAR-align with default settings
Reads aligned to genes were counted using Htseq-counts with default settings
Technical replicates were collapsed in DESeq2
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Counts files generated from HTseq-count

source_name: L4 dorsal root ganglia

extract_protocol:
3 days post-injury mice were sacrificed. L4 dorsal root ganglia contralateral to injury were isolated, dissociated with papain and collagenase and passed through 70 um filter. Cells were FACS sorted for GFP-positive cells into Clontech lysis buffer with 5% RiboLock Rnase Inhibitor (Thermo Fisher).
Library preparation was performed with ~100 cells collected by flow cytometry in 10 ul of Clontech’s reaction buffer using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) per manufacturer’s protocol. Three technical replicates of 100 cells each (A-C) were obtained for each biological replicate (1-4). cDNA was amplified for 13 cycles. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty cycle 20%, cycles/burst 50, time 120 seconds at room temperature. cDNA was blunt ended, had an A base added to the 3’ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

treatment_protocol: Sciatic nerve of mice was crushed with forceps.

value: mixed:C57BL/6 and AJ

value: Nav1.8-positive dorsal root ganglia neurons

value: 8-9 weeks

tag: Sex

value: female

value: Nav1.8-Cre; Tsc2 flox/null; Rosa26-ZsGreen

value: L4 dorsal root ganglia contralateral to sciatic nerve crush


title: Tsc2 cKO Rep 4A

description: 100 FACS-sorted GFP-positive cells


title: KLN-205, murine LUSC cell line, biological rep2

value: tumorigenic


title: Tsc2 cKO Rep 3C

description: 100 FACS-sorted GFP-positive cells


title: H37Rv log vs H37Rv24h_rep4

description: Rv2A(cy5) vs Rv2B(cy3)

value: log phase

source_name: wild-type M.tb 24h Starvation (Expt 3)


title: H37Rv log vs H37Rv24h_rep3

description: Wt1 (cy3) vs Wt3B (cy5)

source_name: wild-type 24 h starvation (Expt 1)


title: H37Rv log vs H37Rv24h_rep2

description: Wt1 (cy3) vs Wt3 (cy5)


title: Murine bronchial epithelial cells, biological rep4

description: Gene expression data from murine bronchial epithelial cells

source_name: Murine bronchial epithelial cells

value: Murine bronchial epithelial cells

value: healthy


title: H37Rv log vs H37Rv24h_rep1

description: Wt4 (cy3) vs Wt1 (cy5)

source_name: wild-type log-phase (Expt 1)

source_name: wild-type 24 h starvation (Expt 2)


title: Tsc2 cKO Rep 3B

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 2C

description: 100 FACS-sorted GFP-positive cells

value: male


title: Tsc2 cKO Rep 1A

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 2A

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 1C

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 2B

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 1B

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 4B

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 4C

description: 100 FACS-sorted GFP-positive cells

value: Nav1.8-Cre; Tsc2 flox/+; Rosa26-ZsGreen


title: Murine bronchial epithelial cells, biological rep3


title: Control Rep 4B

description: 100 FACS-sorted GFP-positive cells


title: KLN-205, murine LUSC cell line, biological rep1


title: Murine bronchial epithelial cells, biological rep1


title: Control Rep 3C

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 3A

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 4A

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 2C

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 3B

description: 100 FACS-sorted GFP-positive cells


title: Tsc2 cKO Rep 3A

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 1C

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 1B

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 1A

description: 100 FACS-sorted GFP-positive cells


title: Control Rep 2A

description: 100 FACS-sorted GFP-positive cells


title: Murine bronchial epithelial cells, biological rep2


title: Control Rep 2B

description: 100 FACS-sorted GFP-positive cells


title: CTC.81.20CTC.1.T2

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

data_processing:
Amplification curves were processed using SDS 2.4 and analyzed using RQ Manager 1.2.1 to obtain mean cycle threshold (Ct) of the triplicate measurements for each gene.
The mean Ct for ACTB and RPS18 was used to calculate for the ∆Cts

label: FAM

source_name: Circulating Tumor Cells

label_protocol:
Reverse transcription (RT) and preamplification were performed using Taqman® PreAmp Cells-to-CT™ kit (Ambion, Texas) following manufacturer’s instructions with some modification. These steps were performed in the same tube the cells were sorted into to avoid any loss of nucleic acids.  RT was performed on total RNA in the whole cell lysate (11µL) by adding 12.5µL of 2X RT buffer, 1.25µL of 20X RT enzyme and 0.25µL of nuclease free water and incubated in a thermal cycler for 60 min at 37°C and 5 min at 95°C to inactivate the RT enzyme. Specific transcript preamplification was performed by adding 50µL of Taqman® PreAmp Master and 25µL of the Custom PreAmp Pool to the RT reaction mix (25µL) and incubated in a thermal cycler for 10 min at 95°C followed by 14 cycles at 95°C for 15 sec and 60°C for 4 min. The Custom PreAmp Pool contained 63 Taqman® assays. The same set of Taqman® assays were also printed onto the TLDA card and used for subsequent RT-PCR. The primers for RPS18 were not included in the custom pool due to the already high expression level of this gene. Note that each assay contained specific primers for transcript specific preamplification.
Preamplified cDNA was diluted to 1/32 by adding 12.5µL of cDNA from the completed RT reaction to 187.5µL of nuclease free water and 200µL of Taqman® Universal PCR Master Mix (no UNG). Two samples were loaded in each TLDA card (100 µL per port; 4 ports per sample). RT-PCR was performed using the ABI PRISM 7900HT.

extract_protocol: Cells were sorted into reaction tubes containing 9.5µL of lysis buffer and 0.5 µL of DNAse. Lysis reaction was carried out for 5 min at room temperature and 1µL of Stop solution was added and incubated for 2 min and immediately placed on ice. Whole cell lysates were then stored in -80°C until further use.

treatment_protocol: Cell isolation via IE/FACS: If a patient had ≥1 CTC/mL the remaining volume of blood was subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) within 24-32 hr after blood draw. In the initial step, magnetic beads coated with EpCAM mAb are used to enrich for tumor cells. Enriched samples are then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+/CD45-) from leukocytes (CD45+/EpCAM-) during sorting. This procedure allows for the isolation of small pools cells, which can be subjected to downstream molecular analyses.

tag: sample type

value: Test

tag: diagnosis

value: Breast cancer

tag: tumor stage

value: Metastatic

tag: gender

value: Female

value: Peripheral Blood

value: Circulating Tumor Cells

tag: matched leukocyte sample


title: CTC.4024.12CTC

tag: tissue


title: CTC.4024.20CD45

source_name: Blood Leukocytes

value: Control

tag: cell type

value: Blood Leukocytes


title: CTC.52582.20CTC

description:
Sample name: 52582.20CTC
Matched array sample Accession Number: GSM998012
Matched array sample name: 52582_20CTC

value: no pair


title: CTC.4042.20CTC.1.T3


title: CTC.81.50CD45.T2


title: CTC.83.20CTC.1.T2


title: CTC.4037.50CD45.1


title: CTC.4037.20CTC.1

description:
Sample name: 4037.20CTC.1
Matched array sample Accession Number: GSM998009
Matched array sample name: 4037_20CTC


title: CTC.63.20CTC


title: CTC.83.20CTC.1


title: CTC.78.20CTC.1


title: CTC.4043.20CTC.1


title: CTC.4043.50CD45


title: CTC.4043.20CTC.1.T2

description:
Sample name: 4043.20CTC.1.T2
Matched array sample Accession Number: GSM998011
Matched array sample name: 4043_10CTC


title: CTC.4042.20CTC.1.T2.D1

description:
Sample name: 4042.20CTC.1.T2.D1
Matched array sample Accession Number: GSM998010
Matched array sample name: 4042_20CTC


title: CTC.4042.20CTC.1


title: CTC.83.50CD45


title: CTC.129195.50CD45


title: CTC.129195.20CTC.1


title: CTC.129195.20CTC.T2

description:
Sample name: 129195.20CTC.T2
Matched array sample Accession Number: GSM998043
Matched array sample name: 129195_8CTC


title: CTC.128914.50CD45


title: CTC.4042.50CD45


title: CTC.129063.20CTC.1


title: CTC.129063.6CD45


title: CTC.129087.20CTC


title: CTC.129093.20CTC


title: CTC.128914.20CTC.1

description:
Sample name: 128914.20CTC.1
Matched array sample Accession Number: GSM998042
Matched array sample name: 128914_20CTC


title: CTC.129093.50CD45


title: CTC.128991.20CTC


title: CTC.128449.50CD45


title: CTC.128311.20CTC.T2


title: CTC.128449.20CTC


title: CTC.128026.20CTC.T3


title: CTC.128596.20CTC.T2


title: CTC.128619.20CTC.1


title: CTC.128311.50CD45


title: CTC.128311.15CTC


title: CTC.127923.20CTC

description:
Sample name: 127923.20CTC
Matched array sample Accession Number: GSM998041
Matched array sample name: 127923_6CTC


title: CTC.128619.50CD45


title: CTC.128026.50CD45.T3


title: CTC.128099.20CTC.1


title: CTC.126969.13CTC.T2


title: CTC.127268.50CD45