title: HBDJKDAT02_N726_S517

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N724_S521

status: Public on May 31 2018

type: SRA

city: Berkeley

first: Daniel

middle: J

last: Kramer

state: Ca

address: 291 Life Sciences Addition #3200

country: USA

institute: UC Berkeley

library_source: transcriptomic

data_processing:
Illumina CASAVA bcl2fastq_v2.17 software used for basecalling.
Reads were aligned to the GRCm38.3 (mm10, patch release 3) mouse genome assembly with Tophat2 (Version 2.1.1), and low quality reads were removed with Trimmomatic (Version 0.3.2).
Gene level counts were calculated using Tophat (Version 2.1.1) alignments and featureCounts (Version 1.5.0-p3).
Genome_build: GRCm38.3 (mm10, patch release 3)
Supplementary_files_format_and_content: tab-delimited text files include gene level count values for each sample derived from Cufflinks and featureCounts
Supplementary_files_format_and_content: ExpressionSet and matrix that include all metadata and the appropriate count data
Supplementary_files_format_and_content: Files:
Supplementary_files_format_and_content: KramerDAT_eSet_phenoData.txt: metadata on samples including experimental condition and batch
Supplementary_files_format_and_content: KramerDAT_eSet_counts_table.txt: abundance measurements (featureCounts) prior to filtering, text file
Supplementary_files_format_and_content: KramerDAT_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: KramerDAT_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: KramerDAT_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data, prior to filtering
Supplementary_files_format_and_content: KramerDAT_imageAfterFiltering.RData: R data object containing expressionSet of filtered count data and vector for gene filtering

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
single cell isolation, lysis, RT, amplification: Cells were brought to a concentration of 200,000/ml. The Fluidigm C1 system was used for single cell capture, cell lysis, and reverse transcription to make cDNA, and amplification (C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq; SMARTer Ultra Low RNA Kit for the Fluidigm C1 System). Cell capture was performed at room temperature.
sequencing library synthesis: The Nextera XT DNA Sample Preparation Kit (Illumina cat# FC-131-1096) and Index Kit A-D (cat# FC-131-2001-4) were used to synthesize sequencing libraries.
sequencing library synthesis: RNA libraries were prepared for sequencing using standard Illumina protocols.
sequencing strategy: Single-cell RNA-sequencing.  scRNA-Seq was performed on an Illumina HISEQ 2500 sequencer; up to 192 samples were sequenced per lane, often in Rapid Run mode.

treatment_protocol:
dissociation protocol: Postnatal day 26 (P26) to P34 male and female DATIRESCre;Ai9 mice were briefly anesthetized with isoflurane and decapitated, and brains were removed and placed in ice-cold, oxygenated artificial CSF. The brain was cut coronally into 275-m sections on a vibratome (Leica VT1000 S) in oxygenated ice-cold choline cutting solution.
dissociation protocol: Midbrain sections were incubated for 15 min in ACSF at 34˚C. Midbrain (including the hypothalamus) was dissected in ACSF using forceps under a dissection microscope.
dissociation protocol: Midbrain sections were incubated in 10 ml oxygenated papain solution in ACSF for 25 min at 34˚C. Following papain digestion, tissue was placed into 9 ml oxygenated STOPovomucoid inhibitor solution and bubbled gently at 34˚C. 8 ml of the supernatant solution was removed, and the tissue was triturated serially in the remaining 2 ml of solution with polished 3-, 2-, and 1-mm glass pipettes to create a single-cell suspension. The 2-mL single-cell suspension was spun down in a 20% Percoll solution at 430 g for 6 min at room temperature (RT). The supernatant was aspirated, leaving 50 l of solution and the cell pellet. The pellet was resuspended in 1 ml HEPES-ACSF with 1 mM kynurenic acid and 5% FBS. This single-cell suspension was sorted on a BD Influx cell sorter in the Flow Cytometry Facility at UC Berkeley.
dissociation protocol: Cells were gated for PI-/tdTomato and sorted into a PCR tube. Based on the number of neurons sorted and cell viability count, neurons were brought to 200,000 neurons/ml.

tag: strain

tag: tissue

value: midbrain

tag: cell type

value: dopamine neuron

tag: age

value: M

value: TdTomato+ (PI -)

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

value: SMEAGOL


title: HBDJKDAT02_N726_S518

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: HBDJKDAT02_N726_S515

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id


title: HBDJKDAT02_N726_S516

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N724_S522

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N724_S517

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N724_S518

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N727_S520

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N724_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N724_S516

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N723_S520

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N723_S518

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N723_S516

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N723_S515

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N724_S515

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N723_S513

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N723_S517

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N726_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N724_S520

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N722_S522

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N722_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N722_S516

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N722_S521

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N722_S517

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N722_S513

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N722_S518

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N722_S515

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N721_S522

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N721_S521

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N723_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N723_S521

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N721_S518

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N721_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N721_S517

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N721_S515

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N721_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N720_S518

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N721_S516

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N720_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N720_S521

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N720_S520

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N720_S516

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N720_S517

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N720_S515

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N720_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N719_S521

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N719_S522

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N719_S520

tag: strain

tag: tissue

tag: cell type

tag: age

value: F

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N719_S518

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N719_S517

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N718_S521

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N719_S516

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N718_S522

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N719_S515

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N718_S518

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N718_S520

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N719_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N718_S516

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N718_S513

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N716_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N716_S521

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N716_S517

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N716_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N716_S518

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N716_S516

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N716_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: dilution plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N716_S515

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N718_S517

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: GMP treated Bacteria Rep 1

type: RNA

city: Fermoy

first: Rita

last: Hickey

state: County Cork

address: Moorepark

department: Food Bioscience

country: Ireland

institute: Teagasc Food Research Centre

description: SAMPLE 4

hyb_protocol: 600ng of each Cyanine-labelled cRNA sample was fragmented and prepared for one-color hybridisation cRNA samples were hybridised at 65C for 17 hrs on separate Agilent 15K Gene expression arrays (8x15k format). After hybridisation the microarrays were washed with increasing stringency using Gene-expression wash buffers followed by drying with acetonitrile.

scan_protocol: Flourescent signal intensities were detected with Scan Control A8.4.1 Software (Agilent Technologies) on the Agilent DNA microarray Scanner and the images processed using Feature Extraction 10.7.3.1 Software (Agilent technologies)

data_processing: The microarray data were processed using the LIMMA package of the R statistics software suite, background correction was done using the normexp method with offset = 16. Data was normalised by Quantile normalisation.

molecule: total RNA

organism: Bifidobacterium longum subsp. infantis

source_name: GMP treated Bacteria

label_protocol: 500ng of total RNA per sample was used in a RT-IVT reaction. Prior to RT-IVT the total RNA samples were spiked with in-vitro synthesised polyadenylated transcripts (One-Color RNA Spike-in Mix, Agilent) to serve as an internal labelling control. The spiked total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in-vitro transcription incorporating Cyanine-3-CTP.

growth_protocol: Bacterial culture stocks were maintained at -80C and subcultured twice before being used in any experiment.

extract_protocol: Bacterial cells were pelleted by centrifugation and the pellets treated with 200 microlitres of lysis buffer containing 10mg lysozyme and 200U mutanolysin for 30 minutes at 37C. The lysates were mixed with 750 microlitres of buffer RLT (Qiagen) and homogenised in 2ml screw cap tubes with FastPrep Lysing Matrix D (MP Biomedicals) and homogenised using the Tissue lyser (Qiagen) for 3 cycles of 30 seconds. The supernatanmt was mixed with 500 microlitres of ethanolloaded onto RNeasy Mini Columns (Qiagen) and processed according to the manufacturers instructions, including an on-column DNase step and the RNA eluted to a final volume of 40 microlitres. The integrity of the isolated RNA wasdetermined using a BioAnalyser.

treatment_protocol: Untreated bacteria were grown on de Mann Rogosa and Sharpe (MRS) broth either unsupplemented (Untreated) or containing either 2mg/ml GMP (GMP treated) or 2mg/ml GMPP (GMPP treated)

tag: cell type

value: Bacterial cells

tag: treated with

value: 2mg/ml Glycomacropeptide (GMP)


title: HBDJKDAT02_N715_S522

tag: strain

tag: tissue

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: Untreated bacteria Rep 3

description: SAMPLE 3

source_name: Untreated bacteria

value: none (untreated control)


title: GMP-P Treated bacteria Rep 2

description: SAMPLE 8

source_name: GMP-P Treated bacteria

value: 2mg/ml periodate denatured GMP-P


title: GMP treated Bacteria Rep 2

description: SAMPLE 5


title: Untreated bacteria Rep 2

description: SAMPLE 2


title: GMP treated Bacteria Rep 3

description: SAMPLE 6


title: GMP-P Treated bacteria Rep 1

description: SAMPLE 7


title: HBDJKDAT02_N715_S520

tag: expt condition

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N715_S518

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N715_S521

tag: strain

tag: tissue

tag: age

tag: dilution plate coordinate

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT02_N718_S515

tag: expt condition

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: ercc spike-in dilution


title: HBDJKDAT02_N715_S517

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: GMP-P Treated bacteria Rep 3

description: SAMPLE 9

tag: treated with


title: Untreated bacteria Rep 1

description: SAMPLE 1


title: HBDJKDAT02_N715_S515

tag: strain

tag: tissue

tag: age

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N715_S513

tag: expt condition

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N714_S522

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N714_S521

tag: strain

tag: tissue

tag: age

tag: dilution plate coordinate

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date


title: HBDJKDAT02_N714_S518

tag: expt condition

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 chip size

value: LARGE


title: HBDJKDAT02_N714_S520

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N714_S513

tag: strain

tag: tissue

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT02_N714_S517

tag: expt condition

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: dob

tag: facs & c1 date


title: HBDJKDAT02_N714_S516

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: index set

tag: c1 chip size


title: HBDJKDAT02_N714_S515

tag: strain

tag: tissue

tag: age

tag: dilution plate coordinate

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N715_S516

tag: expt condition

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)


title: P3/PE3 r2

city: Warsaw

first: Anna

middle: Justyna

last: Kornakiewicz

address: Ksiecia Trojdena 2a

country: Poland

institute: School of Molecular Medicine

description: Parental/ Parental treated with everolimus, 3 biological replicate, 2 technical

hyb_protocol: according to the manufacturer's protocol (Protocol for use with Agilent Gene Expression oligo microarrays Version 6.9.1, August 2015)

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Microarray data normalization, quality control, principal component analysis, and filtered on flags were performed using GeneSpring GX 13.0 (Agilent, Santa Clara, CA, USA). Statistical analysis of the gene expression microarray data was performed using moderate T-test and multiple testing corrected with Bonferonni FWER algorithm. The statistical significance was assessed at p<0.05 and fold change cut off >2.0 (up-/down-regulated).

organism: Homo sapiens

source_name: Parental treated with everolimus

growth_protocol: Human kidney cancer stem cells (HKCSC) and human parental kidney cancer stem cells (HPKCSC)  of two histological types – clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (ppRCC) were purchased from Cellprogen (Torrance, CA, USA).HKCSC were cultured in Human Kidney Cancer Stem Cell Complete Medium with Serum, and HKPCSC in Human Kidney (Parental) Stem Cell Complete Media with Serum (as  per manufactures protocol).All cell lines were cultured in standard incubation culture conditions.Cells were in the logarithmic growth phase at the beginning of all experiments.

extract_protocol: Total cellular RNA isolated using High Pure Isolation Kit (Roche Life Science), according to the manufacturer’s protocol.

treatment_protocol: HKCSC and HPKCSC cell lines were treated with everolimus for 3 days. HPKCSC cells were treated  with dose near half of IC50 calculated for HPKCSC cell line (4µM). More resistant HKCSC cells were treated with 1 µM higher dose than HPKCSC (5µM).

tag: cell line

value: parental clear cell renal cell carcinoma ccRCC-PCSC (HKPCSC -human parental kidney cancer stem cells)

tag: treatment

value: 3 day treatment with everolimus

source_name: Parental untreated

value: 3 days  of growth after passage


title: P3/PE3 r3

description: Parental/ Parental treated with everolimus, 3 biological replicate, 3 technical

label_protocol: according to the manufacturer's protocol (Protocol for use with Agilent Gene Expression oligo microarrays Version 6.9.1, August 2015)


title: HBDJKDAT02_N712_S522

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: M3/ME3 r2

description: Stem cells/ Stem cells treated with everolimus, 3 biological replicate, 2 technical

source_name: Human Kidney Cancer Stem Cells treated with everolimus

value: ccRCC-CSC - clear cell renal cell carcinoma -cancer stem cells (HKCSC - human kidney cancer stem cells)

source_name: Human Kidney Cancer Stem Cells untreated


title: M3/ME3 r1

description: Stem cells/ Stem cells treated with everolimus, 3 biological replicate, 1 technical


title: HBDJKDAT02_N712_S521

tag: strain

tag: tissue

value: midbrain

tag: age

tag: expt condition

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: P3/PE3 r4

description: Parental/ Parental treated with everolimus, 3 biological replicate, 4 technical

tag: cell line

tag: treatment


title: M3/ME3 r4

description: Stem cells/ Stem cells treated with everolimus, 3 biological replicate, 4 technical


title: M3/ME3 r3

description: Stem cells/ Stem cells treated with everolimus, 3 biological replicate, 3 technical


title: M1/ME1 r3

description: Stem cells/ Stem cells treated with everolimus, 1 biological replicate, 3 technical


title: HBDJKDAT02_N712_S520

tag: cell type

value: dopamine neuron

tag: Sex

tag: number of animals

tag: facs selection

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)


title: M2/ME2 r2

description: Stem cells/ Stem cells with everolimus, 2 biological replicate, 2 technical


title: M2/ME2 r3

description: Stem cells/ Stem cells with everolimus, 2 biological replicate, 3 technical


title: M2/ME2 r4

description: Stem cells/ Stem cells with everolimus, 2 biological replicate, 4 technical


title: P3/PE3 r1

description: Parental/ Parental treated with everolimus, 3 biological replicate, 1 technical


title: P2/PE2 r4

description: Parental/ Parental treated with everolimus, 2 biological replicate, 4 technical


title: P2/PE2 r2

description: Parental/ Parental treated with everolimus, 2 biological replicate, 2 technical


title: M2/ME2 r1

description: Stem cells/ Stem cells with everolimus, 2 biological replicate, 1 technical


title: HBDJKDAT02_N712_S513

tag: strain

tag: tissue

tag: age

tag: expt condition

value: M

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N712_S518

tag: cell type

tag: Sex

value: TdTomato+ (PI -)

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N712_S516

tag: number of animals

tag: facs selection

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)


title: P2/PE2 r3

description: Parental/ Parental treated with everolimus, 2 biological replicate, 3 technical

tag: cell line

tag: treatment


title: M1/ME1 r4

description: Stem cells/ Stem cells treated with everolimus, 1 biological replicate, 4 technical


title: HBDJKDAT02_N712_S515

tag: strain

tag: tissue

tag: age

tag: expt condition

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: M1/ME1 r2

description: Stem cells/ Stem cells treated with everolimus, 1 biological replicate, 2 technical


title: HBDJKDAT02_N711_S520

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N711_S517

tag: strain

tag: tissue

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT02_N711_S518

tag: age

tag: expt condition

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N711_S521

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id


title: M1/ME1 r1

description: Stem cells/ Stem cells treated with everolimus, 1 biological replicate, 1 technical

tag: cell line

tag: treatment


title: HBDJKDAT02_N711_S515

tag: strain

tag: tissue

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N711_S513

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N711_S516

tag: strain

tag: tissue

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id


title: HBDJKDAT02_N710_S522

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 machine id

tag: ercc spike-in dilution


title: P1/PE1 r2

description: Parental/ Parental treated with everolimus, 1 biological replicate, 2 technical

tag: cell line

tag: treatment


title: HBDJKDAT02_N712_S517

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: P1/PE1 r4

description: Parental/ Parental treated with everolimus, 1 biological replicate, 4 technical


title: P1/PE1 r1

description: Parental/ Parental treated with everolimus, 1 biological replicate, 1 technical


title: HBDJKDAT02_N710_S517

tag: strain

tag: tissue

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: sequencing run id


title: HBDJKDAT02_N710_S518

tag: cell type

tag: age

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 machine id

tag: ercc spike-in dilution


title: P1/PE1 r3

description: Parental/ Parental treated with everolimus, 1 biological replicate, 3 technical

tag: cell line

tag: treatment


title: HBDJKDAT02_N710_S520

tag: strain

tag: tissue

tag: expt condition

tag: Sex

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N710_S521

tag: cell type

tag: age

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: sequencing run id


title: HBDJKDAT02_N711_S522

tag: strain

tag: tissue

tag: barcode

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N710_S516

tag: expt condition

tag: Sex

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N710_S515

tag: cell type

tag: age

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id


title: HBDJKDAT02_N710_S513

tag: strain

tag: tissue

tag: library plate coordinate

tag: barcode

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)


title: P2/PE2 r1

description: Parental/ Parental treated with everolimus, 2 biological replicate, 1 technical

tag: cell line

tag: treatment


title: HBDJKDAT02_N707_S518

tag: expt condition

tag: Sex

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N707_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id


title: HBDJKDAT02_N707_S520

tag: expt condition

tag: Sex

tag: library plate coordinate

tag: barcode

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT02_N707_S517

tag: c1 batch id

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N707_S516

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs selection

tag: dilution plate coordinate


title: HBDJKDAT02_N707_S513

tag: expt condition

tag: Sex

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: sequencing run id


title: HBDJKDAT02_N707_S515

tag: c1 batch id

tag: index set

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N706_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N706_S521

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate


title: HBDJKDAT02_N706_S518

tag: c1 batch id

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N706_S517

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N706_S522

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N706_S513

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N706_S516

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N706_S515

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N705_S521

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N705_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N707_S521

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N705_S520

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N705_S518

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N705_S513

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N705_S517

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N705_S515

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N704_S522

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N705_S516

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N704_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N704_S521

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N704_S518

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N704_S516

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N704_S517

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N704_S513

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N703_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N703_S520

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N703_S521

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N703_S518

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N703_S516

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N703_S515

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N703_S517

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N702_S520

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N702_S522

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N702_S518

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N703_S513

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N702_S521

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N702_S515

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N702_S516

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N702_S513

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N702_S517

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N701_S521

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N701_S522

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N701_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N704_S515

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N701_S517

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N701_S516

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N701_S515

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N729_S507

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N729_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N729_S510

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N729_S506

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N729_S505

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N701_S518

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N729_S511

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N701_S513

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N729_S502

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N728_S511

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N728_S510

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N729_S503

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N728_S507

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N728_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N728_S502

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N728_S505

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N728_S503

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N727_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N727_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N727_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N727_S508

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N727_S506

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N727_S502

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N726_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N727_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N727_S505

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N724_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N726_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N724_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N726_S505

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N726_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N726_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N724_S506

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N724_S505

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N724_S502

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N728_S506

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N724_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N726_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N723_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N723_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N723_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N726_S508

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N723_S506

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N723_S505

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N722_S510

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N726_S502

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N724_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N722_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N723_S502

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N722_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N724_S510

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N722_S507

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N722_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N721_S507

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N722_S505

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N721_S511

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N722_S503

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N721_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N720_S511

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N721_S510

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N720_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N723_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N721_S506

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N721_S505

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N720_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N720_S505

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N723_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N720_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N720_S502

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N721_S502

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N720_S503

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N719_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N719_S507

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N721_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N722_S502

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N719_S505

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N719_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N719_S508

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N719_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N719_S503

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N719_S502

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N718_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

value: MEDIUM

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N718_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane

value: SMEAGOL


title: HBDJKDAT01_N718_S508

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N718_S511

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size

value: FRODO


title: HBDJKDAT01_N720_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N718_S502

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N716_S502

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N716_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N716_S510

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N716_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N716_S505

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N715_S508

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N715_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N715_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N715_S505

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N718_S506

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N715_S502

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N714_S510

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N714_S511

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N715_S503

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N714_S508

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N718_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N715_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N716_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N718_S505

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N716_S507

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N714_S506

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N714_S507

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N715_S511

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N716_S506

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N714_S503

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT01_N714_S502

tag: strain

tag: tissue

tag: cell type

tag: age

tag: number of animals

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N712_S511

tag: expt condition

tag: Sex

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N712_S510

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: set-26glp-1_rep2_H3ChIPseq

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

institute: Cornell University

description: processed data file: set-26glp1_k4_H3_pooled.bedgraph

library_source: genomic

data_processing:
RNA-seq:
Rawdata was filtered by fastq_quality_filter, adaptor was cut by cutadapt and rRNA was removed by bowtie2;
tophat2 was used to align reads to WS250 genome
cufflink was used to generate raw count for each gene
EdgeR was used to calculate the significant changed gene
ChIP-seq:
Two replicate ChIP-Seq raw data were pooled. Raw data were first filtered by fastx_trimmer and fastq_quality_filter
bowtie2 was used to align reads to WS250 genome
PCR duplicate was removed by samtools and the data were converted to bam files
bamCoverage was used to generate bedgraph files
Genome_build: Genome build: WS250
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedgraph containing z-score in 50bp window; excel containing raw counts

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: glp-1; set-26_whole_worm

growth_protocol: L4 worms were cultured and harvested on NGM plates

extract_protocol:
RNA-seq: RNA was extracted using Trizol reagent.
ChIP-seq: Crosslinked protein-DNA complex were isolated with antibody.
RNA libraries were prepared for sequencing using Ovation Human FFPE RNA-Seq Library Systems (NuGEN) kit
ChIP-seq libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB)

tag: strain background

tag: genotype/variation

value: glp-1; set-26

tag: developmental stage

tag: chip antibody

value: anti-H3 (abcam, United Kingdom ab1791)


title: set-26glp-1_rep1_H3ChIPseq


title: glp-1_rep1_H3ChIPseq

description: processed data file: glp1_k4_H3_pooled.bedgraph


title: HBDJKDAT01_N712_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N712_S507

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: glp-1_rep2_H3ChIPseq

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: chip antibody


title: F3set9set26_rep1_H3ChIPseq

description: processed data file: F3_K4_H3_pooled.bedgraph

value: F3set-9 set-26


title: F3set9set26_rep2_H3ChIPseq


title: pSpt3_free_MNase_15min

city: Seattle

first: Sebastian

last: Gruenberg

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
free MNase under control of Spt3 promoter ChEC-seq in synthetic medium for 15 min after CaCl2 addition.
barcode: GTTTCG

data_processing:
We used Novoalign 2.08.03 (http://www.novocraft.com) with options -a -r Random to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.
We extracted properly paired reads.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
We normalized base pair counts by dividing by the total number of fragment ends mapped, and then multiplying by the total number of mapped base pairs (processed data files .wig). Generation and normalization of tracks was performed with https://github.com/zentnerlab/chec-seq/blob/master/pairs_single_end_sizes.pl.
HOMER (http://homer.salk.edu) (Heinz et al, 2010) was used to generate reads per million (RPM)- normalized average plots.
Genome_build: sacCer3 from UCSC
Supplementary_files_format_and_content: See supplementary Grunberg_protocol.rtf

organism: Saccharomyces cerevisiae

source_name: free MNase ChEC-seq

growth_protocol: See supplementary Grunberg_protocol.rtf

extract_protocol: See supplementary Grunberg_protocol.rtf

tag: genotype

value: NWY05; ade2{delta}::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pRS413-pSpt3-3FLAG-MNase(83-231)-kanMX6


title: HBDJKDAT01_N714_S505

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: F1set9set26_rep2_H3ChIPseq

description: processed data file: F1_K4_H3_pooled.bedgraph

tag: strain background

value: F1set-9 set-26


title: wt_rep1_H3ChIPseq

description: processed data file: WT_K4_H3_pooled.bedgraph

tag: genotype/variation

value: wild type


title: T24RC miR200b-CDDP replicate 2

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: T24RC cells transfected with a miR-200b mimic molecule and treaded with CDDP.

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: T24RC cells were cultured in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRI Reagent (COSMO BIO, Tokyo, Japan).

treatment_protocol: CDDP resistant T24 cells (T24RC) were transfected with a miR mimic negative control (NC) or a miR-200b mimic using Lipofectamine RNAiMAX and incubated for 72 h. Transfectants were then  treated with or without 1.6 μg/ml of CDDP for additional 72 h.

tag: miRNA

tag: drug

value: CDDP


title: T24RC NC-CDDP replicate 2

description: T24RC cells transfected with a miRNA mimic negative control and treaded with CDDP.

value: negative control


title: F1set9set26_rep1_H3ChIPseq

tag: developmental stage

tag: chip antibody


title: HBDJKDAT01_N712_S505

tag: strain

tag: tissue

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT01_N712_S503

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: wt_rep2_H3ChIPseq

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: chip antibody


title: T24RC miR200b-mock replicate 1

description: T24RC cells transfected with a miR-200b mimic molecule and treaded with mock.

tag: miRNA

tag: drug

value: mock


title: T24RC miR200b-CDDP replicate 1


title: T24RC miR200b-mock replicate 2


title: T24RC NC-mock replicate 2

description: T24RC cells transfected with a miRNA mimic negative control and treaded with mock.


title: T24RC NC-mock replicate 1


title: set-26glp-1_rep2_H3K4me3ChIPseq

value: H3K4me3 (Millipore, Billerica, MA 17-614, lot:2756917)


title: HBDJKDAT01_N712_S508

tag: strain

tag: tissue

value: midbrain

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: set-26glp-1_rep1_H3K4me3ChIPseq

tag: strain background

tag: genotype/variation

tag: developmental stage


title: glp-1_rep2_H3K4me3ChIPseq

tag: chip antibody


title: T24RC NC-CDDP replicate 1

tag: miRNA

tag: drug


title: F3set9set26_rep1_H3K4me3ChIPseq


title: F3set9set26_rep2_H3K4me3ChIPseq


title: HBDJKDAT01_N711_S511

tag: strain

tag: tissue

tag: cell type

value: dopamine neuron

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT01_N711_S510

value: M

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: F1set9set26_rep2_H3K4me3ChIPseq

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: chip antibody


title: HBDJKDAT01_N711_S508

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

value: TdTomato+ (PI -)

tag: lane

tag: cdna concentration (ng/ul)

tag: dob


title: F1set9set26_rep1_H3K4me3ChIPseq


title: glp-1set-26daf-16_rep2_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: set-26daf-16glp-1_2

source_name: glp-1; set-26; daf-16_whole_worm

tag: molecule subtype

value: total RNA after removing ribo-RNA


title: glp-1set-26daf-16_rep1_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: set-26daf-16glp-1_1


title: wt_rep1_H3K4me3ChIPseq


title: wt_rep2_H3K4me3ChIPseq


title: HBDJKDAT01_N711_S507

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

value: SMEAGOL

tag: ercc spike-in dilution


title: HBDJKDAT01_N711_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection


title: glp-1daf-16_rep2_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: daf-16glp-1_2

source_name: glp-1; daf-16_whole_worm

tag: strain background

tag: genotype/variation

value: glp-1; daf-16

tag: developmental stage

tag: molecule subtype


title: glp-1daf-16_rep1_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: daf-16glp-1_1


title: glp-1set-26_rep2_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: glp-1set-26_2

value: glp-1; set-26


title: glp-1set-26_rep1_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: glp-1set-26_1


title: HBDJKDAT01_N711_S505

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob


title: glp-1_rep2_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: glp-1_2


title: HBDJKDAT01_N711_S503

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: glp-1_rep1_ribominusRNAseq2

description:
processed data file: glp1set26daf16rnaseq.xls
processed data column: glp-1_1

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: molecule subtype


title: HBDJKDAT01_N711_S502

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT01_N712_S502

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: glp-1_rep1_H3K4me3ChIPseq

description: processed data file: glp1_k4_H3_pooled.bedgraph

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: chip antibody


title: F1set9set26_rep1_ribominusRNAseq2

description:
processed data file: n2f1set9set26rnaseq.xls
processed data column: f1set9set26_1

source_name: F1 set-9 set26_whole_worm

value: set-9 set-26

tag: molecule subtype


title: HBDJKDAT01_N710_S511

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: F1set9set26_rep2_ribominusRNAseq2

description:
processed data file: n2f1set9set26rnaseq.xls
processed data column: f1set9set26_2

tag: strain background


title: HBDJKDAT01_N710_S510

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: wt_rep2_ribominusRNAseq2

description:
processed data file: n2f1set9set26rnaseq.xls
processed data column: wt_2

tag: genotype/variation

tag: developmental stage

tag: molecule subtype


title: HBDJKDAT01_N710_S507

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT01_N710_S505

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: dob

tag: facs & c1 date

tag: ercc spike-in dilution


title: wt_rep1_ribominusRNAseq2

description:
processed data file: n2f1set9set26rnaseq.xls
processed data column: wt_1

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: molecule subtype


title: HBDJKDAT01_N710_S508

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N710_S506

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N710_S503

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: ercc spike-in dilution


title: HBDJKDAT01_N707_S511

tag: strain

tag: tissue

tag: barcode

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N710_S502

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT01_N707_S510

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N707_S508

tag: strain

tag: tissue

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution


title: HBDJKDAT01_N707_S506

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N707_S505

value: F

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/ul)


title: HBDJKDAT01_N707_S503

tag: strain

tag: tissue

tag: library plate coordinate

tag: barcode

tag: index set

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N707_S502

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: sequencing run id

tag: ercc spike-in dilution


title: C-24-F24

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description: Sample name: SAMPLE 71

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was converted to log2, quantile median-normalized using Genespring v12.1

source_name: Fallopian tube epithelium

label_protocol: Labelled using Illumina TotoalPrep-96 Human HT-12 v4.0 beadchip arrays

growth_protocol: Surgical fallopian tube samples were dissociated and epithelial cells were cultured in a transwell system atop a collagen type IV layer until confluent.  At this point cultures from each patient were treated.

extract_protocol: total RNA was extracted from FTE using TRIzol reagent according to manufacturer's instructions and further purified using an Rneasy MiniELute cleanup kit

treatment_protocol: Cultures from each patient were treated with periovulatory follicular fluid for 24 hours in the upper well of the transwell, afterwhich the follicular fluid was removed for an additional 24 hours.  Parallel cultures were treated identically but with culture media changes instead of follicular fluid.  Cells were harvested and RNA extracted 24 hours after follicular fluid addition (F24) or 24 hours after follicular fluid replacement with culture medium (FC).  Treatment control (baseline) cultures treated with culture medium only (not exposed to follicular fluid) were harvested at the same time as F24 samples and are referred to as C24.

value: Fallopian tube epithelium

tag: brca1/2 mutation status

value: Control, No known mutation

tag: time point


title: C-23-C24

description: Sample name: SAMPLE 67


title: C-24-FC

description: Sample name: SAMPLE 72

value: FC


title: C-22-FC

description: Sample name: SAMPLE 66


title: C-22-C24

description: Sample name: SAMPLE 64


title: C-22-F24

description: Sample name: SAMPLE 65


title: C-20-F24

description: Sample name: SAMPLE 59


title: C-21-FC

description: Sample name: SAMPLE 63


title: C-18-C24

description: Sample name: SAMPLE 52


title: C-18-F24

description: Sample name: SAMPLE 53


title: C-23-F24

description: Sample name: SAMPLE 68


title: C-21-C24

description: Sample name: SAMPLE 61


title: C-19-FC

description: Sample name: SAMPLE 57


title: HBDJKDAT01_N706_S510

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 chip size

tag: c1 machine id


title: C-24-C24

description: Sample name: SAMPLE 70

tag: tissue


title: C-21-F24

description: Sample name: SAMPLE 62


title: C-19-F24

description: Sample name: SAMPLE 56


title: C-18-FC

description: Sample name: SAMPLE 54


title: HBDJKDAT01_N706_S511

tag: strain

tag: cell type

tag: age

tag: expt condition

tag: library plate coordinate

tag: barcode

tag: index set

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N707_S507

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: sequencing run id

tag: ercc spike-in dilution


title: HBDJKDAT01_N706_S508

tag: tissue

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 chip size

tag: c1 machine id


title: C-20-C24

description: Sample name: SAMPLE 58

tag: brca1/2 mutation status

tag: time point


title: C-19-C24

description: Sample name: SAMPLE 55


title: C-20-FC

description: Sample name: SAMPLE 60


title: C-17-C24

description: Sample name: SAMPLE 49


title: C-17-FC

description: Sample name: SAMPLE 51


title: HBDJKDAT01_N706_S507

tag: strain

tag: cell type

tag: age

tag: expt condition

tag: library plate coordinate

tag: barcode

tag: index set

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N706_S506

tag: tissue

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: ercc spike-in dilution


title: HBDJKDAT01_N706_S505

tag: strain

tag: cell type

tag: library plate id

tag: lane

tag: cdna concentration (ng/ul)

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N706_S503

tag: age

tag: expt condition

tag: library plate coordinate

tag: barcode

tag: index set

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N706_S502

tag: tissue

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate


title: HBDJKDAT01_N705_S511

tag: strain

tag: cell type

tag: library plate id

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: C-17-F24

description: Sample name: SAMPLE 50

tag: brca1/2 mutation status

tag: time point


title: C-23-FC

description: Sample name: SAMPLE 69


title: B2-15-FC

description: Sample name: SAMPLE 45

value: BRCA2 mutation carrier


title: HBDJKDAT01_N705_S508

tag: age

tag: expt condition

tag: library plate coordinate

tag: barcode

tag: index set

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: B2-14-F24

description: Sample name: SAMPLE 41

tag: tissue


title: HBDJKDAT01_N705_S510

tag: strain

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id


title: B2-16-F24

description: Sample name: SAMPLE 47

tag: brca1/2 mutation status

tag: time point


title: B2-16-FC

description: Sample name: SAMPLE 48


title: B2-15-F24

description: Sample name: SAMPLE 44


title: B2-16-C24

description: Sample name: SAMPLE 46


title: B2-14-C24

description: Sample name: SAMPLE 40


title: B2-14-FC

description: Sample name: SAMPLE 42


title: HBDJKDAT01_N705_S507

tag: age

tag: expt condition

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: B2-13-FC

description: Sample name: SAMPLE 39

tag: tissue


title: HBDJKDAT01_N705_S506

tag: strain

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: B2-13-F24

description: Sample name: SAMPLE 38

tag: brca1/2 mutation status

tag: time point


title: B2-13-C24

description: Sample name: SAMPLE 37


title: B2-12-C24

description: Sample name: SAMPLE 34


title: HBDJKDAT01_N705_S505

tag: age

tag: expt condition

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set


title: B2-12-F24

description: Sample name: SAMPLE 35

tag: tissue


title: B2-15-C24

description: Sample name: SAMPLE 43


title: HBDJKDAT01_N705_S502

tag: strain

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: B2-11-FC

description: Sample name: SAMPLE 33

tag: brca1/2 mutation status

tag: time point


title: HBDJKDAT01_N705_S503

tag: age

tag: expt condition

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: B2-11-F24

description: Sample name: SAMPLE 32

tag: tissue


title: B2-10-C24

description: Sample name: SAMPLE 28


title: B2-11-C24

description: Sample name: SAMPLE 31


title: B2-10-FC

description: Sample name: SAMPLE 30


title: B2-12-FC

description: Sample name: SAMPLE 36


title: B2-10-F24

description: Sample name: SAMPLE 29


title: HBDJKDAT01_N704_S511

tag: strain

tag: cell type

tag: Sex

tag: number of animals

tag: facs selection

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set


title: B2-9-C24

description: Sample name: SAMPLE 25

tag: brca1/2 mutation status

tag: time point


title: B2-9-FC

description: Sample name: SAMPLE 27


title: B2-9-F24

description: Sample name: SAMPLE 26


title: HBDJKDAT01_N704_S510

tag: age

tag: expt condition

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: HBDJKDAT01_N704_S508

tag: strain

tag: tissue

tag: cell type

tag: Sex

tag: number of animals

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N704_S507

tag: age

tag: expt condition

tag: facs selection

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set


title: B1-8-FC

description: Sample name: SAMPLE 24

tag: brca1/2 mutation status

value: BRCA1 mutation carrier

tag: time point


title: B1-8-C24

description: Sample name: SAMPLE 22

tag: tissue


title: B1-8-F24

description: Sample name: SAMPLE 23


title: B1-7-F24

description: Sample name: SAMPLE 20


title: B1-7-FC

description: Sample name: SAMPLE 21


title: B1-6-C24

description: Sample name: SAMPLE 16


title: B1-7-C24

description: Sample name: SAMPLE 19


title: HBDJKDAT01_N704_S506

tag: strain

tag: cell type

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: HBDJKDAT01_N704_S503

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N704_S505

tag: strain

tag: tissue

tag: cell type

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set


title: HBDJKDAT01_N704_S502

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: HBDJKDAT01_N703_S511

tag: age

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: dob

tag: facs & c1 date


title: B1-6-FC

description: Sample name: SAMPLE 18

tag: tissue

tag: brca1/2 mutation status

tag: time point


title: HBDJKDAT01_N703_S510

tag: strain

tag: cell type

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 chip size

tag: c1 machine id


title: B1-5-F24

description: Sample name: SAMPLE 14


title: HBDJKDAT01_N703_S508

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: B1-5-C24

description: Sample name: SAMPLE 13

tag: tissue

tag: brca1/2 mutation status

tag: time point


title: B1-4-F24

description: Sample name: SAMPLE 11


title: HBDJKDAT01_N703_S507

tag: strain

tag: cell type

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: library plate id

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N703_S506

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: barcode

tag: index set

tag: c1 chip size

tag: c1 machine id


title: B1-3-FC

description: Sample name: SAMPLE 9

tag: tissue

tag: brca1/2 mutation status

tag: time point


title: B1-4-FC

description: Sample name: SAMPLE 12


title: HBDJKDAT01_N703_S502

tag: strain

tag: cell type

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: B1-4-C24

description: Sample name: SAMPLE 10


title: B1-3-F24

description: Sample name: SAMPLE 8


title: B1-2-FC

description: Sample name: SAMPLE 6


title: B1-3-C24

description: Sample name: SAMPLE 7


title: B1-2-C24

description: Sample name: SAMPLE 4


title: B1-5-FC

description: Sample name: SAMPLE 15


title: HBDJKDAT01_N702_S510

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: B1-1-F24

description: Sample name: SAMPLE 2

tag: tissue

tag: brca1/2 mutation status

tag: time point


title: B1-1-FC

description: Sample name: SAMPLE 3


title: B1-1-C24

description: Sample name: SAMPLE 1


title: B1-2-F24

description: Sample name: SAMPLE 5


title: HBDJKDAT01_N703_S505

tag: strain

tag: cell type

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: barcode

tag: index set

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N703_S503

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: HBDJKDAT01_N702_S511

tag: strain

tag: tissue

tag: cell type

tag: library plate id

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N702_S508

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: barcode

tag: index set

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N702_S507

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane


title: HBDJKDAT01_N702_S505

tag: strain

tag: tissue

tag: cell type

tag: library plate id

tag: library plate coordinate

tag: cdna concentration (ng/ul)

tag: ercc spike-in dilution


title: HBDJKDAT01_N702_S503

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: barcode

tag: index set

tag: dob

tag: facs & c1 date


title: HBDJKDAT01_N702_S506

tag: age

tag: expt condition

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 chip size

tag: c1 machine id


title: HBDJKDAT01_N701_S511

tag: strain

tag: tissue

tag: cell type

tag: library plate id

tag: library plate coordinate

tag: sequencing run id

tag: lane


title: 6 hour post infection

city: Taoyuan

first: Sheng-Yu

last: Huang

address: No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan (R.O.C.)

country: Taiwan

institute: chang gung university

hyb_protocol: after which 2X hybridization buffer (Agilent Technologies) was added to the labeled mixture to a final volume of 45 µL. The mixture was heated for 5 minutes at 100°C and immediately cooled to 0°C. Each 45 µL sample was hybridized onto Agilent Human miRNA Oligo Microarray R12 (Agilent Technologies) at 55°C for 20 hours. A total of 866 human miRNAs and 89 viral miRNAs were represented on the microarray. After hybridization, slides were washed for 5 minutes in Gene Expression Wash Buffer 1 (Agilent Technologies) at room temperature, and then washed again for 5 minutes in Gene Expression Wash Buffer 2 (Agilent Technologies) at 37°C.

scan_protocol: Slides were scanned on an Agilent microarray scanner (Model G2505C; Agilent Technologies,) at 100% and 5% sensitivity settings.

data_processing:
data was analyzed by GeneSpring 7.3.1 (Agilent Technologies)
miRNAs with detected flag values labeled as present were used for further analysis. Changes in miRNA expression between experimental and control samples were calculated using Partek® software (Partek, St. Louis MO, USA). The threshold used to select differentially expressed miRNAs was a greater than 1.5-fold increase or decrease in expression over controls.

source_name: A549 cells

label_protocol: Altogether 100 ng of total RNA was dephosphorylated and subsequently labeled with pCp-Cy3 using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara CA, USA),

growth_protocol: Human type II alveolar epithelial A549 cells (ATCC CCL-185) were maintained in minimum essential medium (MEM, Gibco) containing 10%. Approximately 5 × 105 A549 cells/well were seeded in 6-well plates and incubated at 37°C in an incubator containing 5% CO2.

extract_protocol: Total RNAs were extract by using TRIzol  reagents (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: The A549 cells were infected with WSN at an MOI of 2 in serum-free MEM medium for 2, 6 and 10 hours.

tag: cell line

tag: passage

tag: agent

value: WSN

tag: time point

value: 6 hour post infection


title: Mock

value: Mock


title: 2 hour post infection

value: 2 hour post infection


title: 10 hour post infection

value: 10 hour post infection


title: HBDJKDAT01_N702_S502

value: midbrain

value: dopamine neuron

tag: age

tag: expt condition

tag: number of animals

tag: facs selection

value: TdTomato+ (PI -)

tag: c1 batch id

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: ercc spike-in dilution


title: Iso+Insl6

city: Boston

first: Chia-Ling

last: Wu

state: MA

address: 700Albany St

department: Whitaker Cardiovascular Institute

institute: Boston University

description: 3 pooled RNA samples from INSL6 treated, isoproterenol-insulted heart

hyb_protocol: Fragmented, biotinylated DNA samples were hybridized on 3 Affymetrix mouse Gene Expression Array 2.0 per the manufacturer’s instructions.

scan_protocol: A total of 3 array images were acquired by GeneChip Scanner 3000TG and quality assesed bty Affymetrix Expression Console (Santa Clara, CA)

data_processing: Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package (version 1.36.1) included in the Bioconductor software suite (version 2.12) and an Entrez Gene-specific probeset mapping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan [4,5]. Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0)

label: biotin

source_name: Heart pre-treated with INSL6 protein, isoproterenol injection

label_protocol: Biotyinated DNA was prepared per manufactureer's recommendation.

growth_protocol: C57BL/6N mice were purchased from Charles River Laboratories. All animal studies were performed with 8-12 week old male mice. Study protocols were approved by the Institutional Animal Care and Use Committee at Boston University.

extract_protocol: Heart left ventricle samples harvested at 14 days from the different experimental groups were snap frozen. An RNeasy Lipid Tissue Mini kit (Qiagen) was used to extract mRNA with a Qiacube machine according to the manufacturer’s protocol. 3 pooled RNA samples for sham, Iso with vehicle, and Iso with INSL6 protein were sent to the Boston University core facility for processing.

treatment_protocol: INSL6 protein (50-70nmol/kg/day) was infused into mice subcutaneously using an ALZET® osmotic pump (model 2002, Durect). The osmotic pump with vehicle (pH 8.5 ammonium bicarbonate) was implanted in the control group.

tag: strain

value: 8-12 weeks old

tag: gender

value: male

tag: treatment

value: INSL6 protein

tag: stress (cardiac injury)

value: 11 day isoproterenol (50mg/kg/d), i.p.

tag: tissue

value: heart left ventricle


title: HBDJKDAT01_N701_S510

tag: cell type

tag: Sex

value: F

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: sequencing run id

tag: lane

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

value: SMEAGOL


title: Control

description: 3 pooled RNA samples from vehicle treated normal heart

source_name: Heart pre-treated with vehicle, saline injection

tag: age

value: Vehicle


title: HBDJKDAT01_N701_S506

tag: expt condition

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: ercc spike-in dilution


title: HBDJKDAT01_N701_S508

tag: strain

tag: tissue

tag: cell type

tag: Sex

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id


title: HBDJKDAT01_N701_S507

tag: age

tag: expt condition

tag: library plate coordinate

tag: sequencing run id

tag: lane

tag: c1 chip size

tag: c1 machine id


title: 9_CS_ctrl

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

hyb_protocol: Standard Affymetrix hybridization protocol for GeneChipÂ® Exon 1.0 ST arrays

scan_protocol: Standard Affymetrix scanning protocol for GeneChipÂ® Exon 1.0 ST arrays

data_processing:
Probeset summarization was done by RMA and normalization by sketch quantile method (Affymetrix APT tools)
huex-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: control tissue sample

label_protocol: Whole transcriptome Affymetrix protocol with rRNA depletion.

growth_protocol: 5 patients affected by nonsynodromic sagittal synostosis or nonsyndromic metopic synostosis were enrolled in this study.

extract_protocol: Total RNA was extracted from snap-frozen calvarial tissue specimens using pestel and TRIzol Reagent (Invitrogen), and subsequently purified using silica membrane spin columns from RNeasy Mini kit (Qiagen). The yield, quality and integrity of RNA were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue specimens were collected, from each patients, both from patent and fused calvarial sutures and cryopreservated in liquid nitrogen

tag: gender

value: M

tag: diagnosis

value: Craniosynostosis (CS)

value: patent sagittal suture


title: Iso

description: 3 pooled RNA samples from vehicle treated, isoproterenol-insulted heart

source_name: Heart pre-treated with vehicle, Isoproterenol injection

tag: treatment

tag: stress (cardiac injury)


title: 8_CS_crs

source_name: pathologic tissue sample

tag: tissue

value: synostotic sagittal suture


title: HBDJKDAT01_N701_S505

tag: strain

tag: cell type

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: barcode

tag: index set

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: ercc spike-in dilution


title: 10_CS_crs

value: synostotic metopic suture