title: wt cisplatin, INPUT, biological rep 2

type: genomic

city: A Coruña

first: Angel

last: Vizoso-Vázquez

address: Púa da Fraga, 10

institute: University of A Coruña

description:
glass beads + 5 min sonication
Cisplatin_vs_Input_signal.chp
Whole cell DNA from Z1580 cells grown in complete synthetic medium and treated with 600 µM cisplatin in DMSO

hyb_protocol: Samples were prepared and hybridized to GeneChip  S.cerevisiae  Tiling  1.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 250 bp bandwidth and perfect match only.
The resulting CHP files are generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: a minimum run of 150 bp and a maximum gap of 250 bp, and p-value threshold (-10log10 scale) of 40

source_name: wild-type S. cerevisiae treated with cisplatin in DMSO

growth_protocol: Cell were inoculated at initial OD600 = 0.1 in 200 mL SD and grown in 1 L Erlenmeyer flasks at 30 ºC and with agitation of 250 rpm

extract_protocol: 200 mL of yeast culture were collected at OD600 of ≈ 0.9-1. Cross-linking was performed by adding 1% formaldehyde to the culture and incubating at room temperature for 20 min. 125 mM of glycine was then added and culture was incubated 5 min. Cells were then harvested and washed four times with 50 mL Tris-HCl buffer saline (20 mM Tris-HCl, pH 7,5, 150 mM NaCl) at 4 ºC. The cell breakage was performed in 800 μL of lysis buffer (50 mM HEPES-KOH, pH 7,5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0,1% sodium deoxycholate, 2X complete protease inhibitor cocktail, Roche, and 2X complete phosphatase inhibitor cocktail, Roche) with glass beads, and the cell extracts were sonicated for 5 min in 10 sec on/59 sec off cycles (chromatin was sheared into an average size of 400 bp). The immunoprecipitations were performed with magnetic Dynabeads (Invitrogen) following manufacturer’s instructions and using anti-(c-Myc) antibodes (sc47694; Santa Cruz Biotechnology) for specific Ixr1p–(c-Myc) immunoprecipitation. Negative controls, with rabbit IgG immunoprecipitation, were also performed. Samples were washed three times with 1 mL of Lysis buffer, three times with 1 mL of Lysis buffer high salt (50 mM HEPES-KOH, pH 7,5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0,1% sodium deoxycholate), three times with 1 mL of Wash buffer (10 mM Tris-HCl, pH 8, 250 mM LiCl, 0,5% NP-40, 0,5% sodium deoxycholate, 1 mM EDTA), and once with 1 mL of TE Buffer (10 mM TrisCHCl, pH 8, 1 mM EDTA). Immunoprecipitations were then eluted in 250 μL of elution buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS) and treated overnight with 30 μL of proteinase K (20 mg/mL, NewEngland Biolabs). Next day, immunoprecipitated DNA were cleaned with the kit USB PrepEase DNA Clean-Up (USB). Next steps were rigorously followed in the manufacturer’s instructions (Affymetrix) (http://cmgm.stanford.edu /pan/section_html/GE/protocols/Chromatin%20Immunoprecipitation%20Assay%2 0Protocol.pdf).

treatment_protocol: When cells reached OD600 = 0.6, a stock solution of cisplatin 20 mM in DMSO was prepared and the drug was added to the treated cultures at a final concentration of 600 µM. An  equivalent  volume of DMSO was added to the control cultures.

value: 600 µM cisplatin

tag: additional treatment


title: WAT3

status: Public on Feb 21 2018

type: RNA

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

description:
raw data file: WAT34_US83300186_252644110852_S01_GE2_1105_Oct12_1_3.txt
Gene expression in 11d chicken embryo liver injected with distilled water

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas, Biological Theory, 11(3):123-137, 2016.
We used the multiple yellow hybridization design in which differently labeled biological replicates are cohybridized with the microarray, expression levels of similarly labled samples from the two conditions are compared and results averaged over the two fluorescent labels. Therefore, this is like a one-color experiment.
Data table contains normalized ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because it is a control feature, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal.

molecule: total RNA

organism: Gallus gallus

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Fertilized specific pathogen free premium white leghorn chicken (Gallus gallus) eggs of undetermined sex were purchased from Charles River (North Franklin, CT). Upon arrival, eggs were numbered, weighed and randomly divided into control and dosed groups (at least 10 eggs per group). The first day of incubation was designated as Day 0. Eggs were incubated in GQF Manufacturing Company Hova Bator Model 2362N styrofoam incubators (Murray McMurray Hatchery, Webster City, IA) with automatic egg turners at 37 ± 0.5 °C and 60 ± 5 % humidity. Viability was assessed on day 8 by transillumination, eggs that did not developed were eliminated. Control and dosed eggs were separated to avoid cross contamination.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Four eggs (labelled as WAT1-4) were injected with 0.15 ml/egg deionized water in days 9, 10 an 11 post incubation while four eggs (labeled CTR1-4) were kept as environmental controls. We found that water injections had a very small effect, regulating less than 1% of the genes. Both WAT and CTR data sets were used as refernces in further experiments for eggs expossed to various water-soluble carcinogenic compounds.

tag: tissue

value: embryo liver

tag: developmental stage

value: 11th day of incubation

tag: treatment

value: injected with distilled water


title: CTR1

description:
raw data file: CTR12_US83300186_252644110852_S01_GE2_1105_Oct12_1_2.txt
Gene expression in Control 11d chicken embryo liver

source_name: Control 11d chicken embryo liver

value: control


title: KWT2

city: Barcelona

first: Eva

middle: C

last: Vaquero

address: Carrer Villarroel 170

country: Spain

institute: Hospital Clínic

description: Neoplastic cells treated with Pancreatic Stellate Cells Wild Type medium, replicate 2

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized toAgilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray for 40h at 65ºC in a rotating Agilent hybridization oven

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Mus musculus

source_name: Neoplastic cells

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of double stranded cDNA using the SureTag Complete DNA Labeling kit (Agilent 5190-4240) according to manufacturer’s instructions

extract_protocol: total RNA extraction

value: Neoplastic cells


title: KWT3

description: Neoplastic cells treated with Pancreatic Stellate Cells Wild Type medium, replicate 3


title: Mouse pdH pc-/- rep1

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Mouse pdH pc-/- 1088.AVG_Signal

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)
The data were normalized using quantile method

label: biotin

source_name: mouse with KO of PDHA1 gene

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vivo

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufacturer’s recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyzer).

treatment_protocol: knockdown of Pten Gene or PDHA1 gene or both

tag: genotype

value: KO of PDHA1


title: Pten pc-/- pdh pc-/- rep1

description: Pten pc-/- pdh pc-/- 1056.AVG_Signal

source_name: mouse with KO of Pten and Pdha1 gene, double KO

value: KO of Pten and Pdha1 gene


title: KWT1

description: Neoplastic cells treated with Pancreatic Stellate Cells Wild Type medium, replicate 1


title: Pten pc-/- ctrl rep3

description: Pten pc-/- ctrl3.AVG_Signal

source_name: mouse with KO of Pten

value: KO of Pten


title: Pten pc-/- pdh pc-/- rep2

description: Pten pc-/- pdh pc-/- 1074.AVG_Signal


title: Pten pc-/- pdh pc-/- rep3

description: Pten pc-/- pdh pc-/- 1049.AVG_Signal


title: SPA (A-3 2015.11.10)

city: Gifu

first: Kazuo

last: Kajita

address: Yanagido 1-1

department: General Internal Medicine

country: Japan

institute: Gifu University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX.

source_name: small proliferative adipocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Epididymal fat from 20-weeks-old male C57/BL mice were digested with collagenase, and then centrifuged at 9 xg for 1 sec. The floating cells were separated from the lower phase (SVC). The floating cell fraction was centrifugazed at 226 xg for 3 min. The resultant floating cells and sediment cells were regarded as mature adipocytes (MA) and SPA, respectively. SVC and SPA were cultured in DMEM. When the cultured cells reached 90% confluency, they were harvested, and total RNA was extracted.

extract_protocol: Total RNA was extracted using TRIzol(Thermo Fisher Scientific), followed by DNase I (TaKaRa) digestion and repurified with phenol/chloroform.

value: Epididymal fat

tag: gender

value: male

tag: age

tag: strain


title: KHT1

description: Neoplastic cells treated with Pancreatic Stellate Cells heterozygous, replicate 1


title: wt cisplatin, INPUT, biological rep 1

department: Cellular and Molecular Biology Department

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Samples were prepared and hybridized to GeneChip  S.cerevisiae  Tiling  1.0R Array according to Affymetrix specifications.


title: Pten pc-/- ctrl rep2

description: Pten pc-/- ctrl2.AVG_Signal


title: Mouse pdH pc-/- rep2

description: Mouse pdH pc-/- 1090.AVG_Signal


title: CTR3

description:
raw data file: CTR34_US83300186_252644110852_S01_GE2_1105_Oct12_1_1.txt
Gene expression in Control 11d chicken embryo liver


title: Pten pc-/- ctrl rep1

description: Pten pc-/- ctrl1.AVG_Signal


title: KC3

description: Neoplastic cells control, replicate 3


title: KC2

description: Neoplastic cells control, replicate 2


title: wt cisplatin, biological rep 1

description:
glass beads + 5 min sonication + anti-Myc
Cisplatin_vs_Input_signal.chp
Ixr1 DNA binding data from Z1580 cells grown in complete synthetic medium and treated with 600 µM cisplatin in DMSO

value: anti-Myc


title: BAL_normal control_rep16

city: London

first: Chih-hsi

middle: Scott

last: Kuo

address: South Kensington Campus

department: Department of Computing

country: United Kingdom

institute: Imperial College London

description: BAL_normal control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: The data were quality controlled and pre-processed using R code of Affymetric Analysis QC workflow from ArrayAnalysis.org with Robust Multichip Average (RMA) as normalization method.

organism: Homo sapiens

source_name: BAL_normal control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, Copyright 2005-2009, Affymetrix)

extract_protocol: column-based extraction of total RNA was performed according to the manufacturer's instructions

tag: smoking history

value: non-smoker

tag: technical batches

value: C


title: wt cisplatin, biological rep 2


title: wt cisplatin, biological rep 3


title: wt non treated, INPUT, biological rep 1

description:
glass beads + 5 min sonication
DMSO_vs_Input_signal.chp
Whole cell DNA from Z1580 cells grown in complete synthetic medium suplemented with DMSO

source_name: control, wild-type S. cerevisiae treated with DMSO

value: DMSO


title: wt non treated, biological rep 2

description:
glass beads + 5 min sonication + anti-Myc
DMSO_vs_Input_signal.chp
Ixr1 DNA binding data from Z1580 cells grown in complete synthetic medium suplemented with DMSO


title: wt non treated, biological rep 3


title: wt non treated, INPUT, biological rep 2


title: wt non treated, biological rep 1


title: PSC_HT_2

description: Pancreatic Stellate Cells heterozygous, replicate 2

source_name: Pancreatic Stellate Cells

value: Pancreatic Stellate Cells


title: PSC_HT_3

description: Pancreatic Stellate Cells heterozygous, replicate 3


title: rRNA_propagylated

type: SRA

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

library_source: transcriptomic

data_processing:
The adapter was clipped from fastq files and reads trimmer by 3nt at the start and 4nt at the end with the FASTX-Toolkit version 0.0.14 (clipped and trimmed files are uploaded here as raw data files).
Reads derived from synthetic oligos were mapped against the sequence of the oligo using bowtie 2 version 2.3.2 in end-to-end alignment mode
RNAseq data from total RNA was mapped against human rRNA (NR_003287.2, NR_023379.1, NR_003285.2, NR_003286.2) using bowtie[8] version 1.1.2
Coverage was assesed using IGV version 2.4
Genome_build: human rRNA: NR_003287.2, NR_023379.1, NR_003285.2, NR_003286.2
Supplementary_files_format_and_content: bed files of reads mapped to human rRNA (see above) or RNA oligos

source_name: propagylated HeLa rRNA

growth_protocol: HeLa cells (Sigma Aldrich) were cultured in MEM Earl´s with 10 % (v/v) fetal bovine serum (FCS, Biochrom), 1 % (v/v) non-essential amino acids (NEAS, Biochrom) and 1 % (v/v) glutamine solution (200 mM in PBS, Biochrom) and maintained in a humidified incubator at 37 °C and 5 % CO2.

extract_protocol:
The cells were washed with PBS, trypsinized and suspended in 20 mL of supplemented MEM Earl´s. The suspension was centrifuged (800 rpm, 10 min), the medium was removed and the pellet was stored at -80 °C. Cell pellets from HeLa cells (~2.5 – 3.0•105 cells) were lysed mechanically by pipetting up and down in 5 mL lysis buffer (10 mM TrisHCl (pH = 8.0), 150 mM NaCl, 0.5 mM NP40, adjusted to pH 7.5 with HCl). Total RNA was purified by two consecutive phenol-chloroform extractions (4:1 and 2:1) followed by back-extraction with NaCl (0.9 %) and EtOH precipitation. The resulting total RNA was treated with 1 U DNase I (Thermo Fisher) in 1× DNase buffer (Thermo Fisher) for 30 min at 37°C, followed by phenol-chloroform (5:1) extraction and EtOH precipitation.
For sequencing of total RNA/rRNA, total RNA was digested with 44 mM NaHCO3, 6 mM Na2HCO3 and 1 mM EDTA for 20 min at 95°C. The samples were precipitated with ethanol, followed by separation via denaturing PAGE and SYBRGold staining. The region from 50–80 nt was excised, RNA was eluted and precipitated. For total RNA and synthetic oligos RNA was dephosphorylated at the 5′-end using T4 PNK  (Thermo Scientific), followed by either magnetic separation and washing with ddH2O (biotinylated RNA) or phenol/chloroform extraction and precipitation (unmodified RNA). Ligation of a short, 5'-adenylated linker (40 ng/µL, NGS 4N linker) was performed with T4 RNA Ligase 2(truncated K227Q) (NEB) . Again, RNA was purified by magnetic separation and washing with ddH2O (biotinylated RNA) or phenol/chloroform extraction and precipitation (unmodified RNA). For the RT, biotinylated RNA remained on the magnetic streptavidin beads. To this end, 1 µM NGS RT-primer was hybridized and incubated with Maxima H Minus. After RT, template RNA was degraded by alkaline hydrolysis (125 mM NaOH at 80 °C, 10 min) before neutralizing with HCl. The obtained cDNA was separated via denaturing PAGE (10 % PAA gel, 8 M urea, 1× TBE) and visualized with SYBRGold staining. The region from 130–200 nt was excised, cDNA was eluted and precipitated. The purified cDNA was circularized using CircLigase II (Epicentre).  Circularized cDNA was then amplified with primers introducing an index to label samples for sequencing, and purified by native PAGE.

treatment_protocol: Propargyl-L-selenohomocysteine (0.25 mM) was then added to the medium and the cells were cultivated for another 16 h.

value: HeLa cells


title: PSC_HT_1

description: Pancreatic Stellate Cells heterozygous, replicate 1


title: rRNA_control

source_name: unpropagylated HeLa rRNA


title: KC1

description: Neoplastic cells control, replicate 1


title: PSC_WT_1

description: Pancreatic Stellate Cells Wild Type, replicate 1


title: PSC_WT_3

description: Pancreatic Stellate Cells Wild Type, replicate 3


title: pcDNA3.1(+) empty vector (CP-A1)

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

description:
Gene expression after transfected with pcDNA3.1(+) empty vector for 48h
CP-A1

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4851B) was used for the analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4851B/G4851B

scan_protocol: A total of 2 µg RNA from each sample was then labeled with the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). After hybridization, the slides were scanned with the Agilent Microarray Scanner (Agilent p/n G2505C),

data_processing: Quantified signals were extracted and analyzed by using the Agilent Feature Extraction Software, in accordance with MIAME guidelines

source_name: pcDNA3.1(+) empty vector

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: The FHs 74 Int human small intestine epithelial cells were obtained from ATCC and cultured in Hybri-Care Medium ATCC 46-X supplemented with 30 ng/ml epidermal growth factor (EGF), 10% fetal bovine serum and antibiotics (100 IU/ml of penicillin and 100 µg/ml of streptomycin). Atmosphere: air, 95%; carbon dioxide (CO2), 5% ; Temperature: 37°C

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The FHs 74 Int  were grown to 80% confluence for three groups:  pcDNA3.1(+) empty vector (Group CP-A, cells transfected with pcDNA3.1(+) empty vector), pcDNA3.1(+)_cdg2_FLc_0220 full-length (Group CP-B, cells transfected with pcDNA3.1(+)_cdg2_FLc_0220 full-length ) and pcDNA3.1(+)_cdg7_FLc_1000 full-length (Group CP-C, cells transfected with pcDNA3.1(+)_cdg7_FLc_1000 full-length ). 48h later, total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

tag: cell type

value: Small intestine epithelial cell

tag: cell line

value: FHs 74 Int

tag: transfection

value: pcDNA3.1(+) empty vector


title: pcDNA3.1(+)_cdg7_FLc_1000 full-length (CP-C3)

description:
Gene expression after transfected with pcDNA3.1(+)_cdg7_FLc_1000 full-length for 48h
CP-C3

source_name: pcDNA3.1(+)_cdg7_FLc_1000 full-length

value: pcDNA3.1(+)_cdg7_FLc_1000 full-length


title: genomic DNA from osteoarthritic distal femur trabecular bone [B06A]

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

description: medial condyle osteoarthritic distal femur trabecular bone from baboon

hyb_protocol: Infinium Human Methylation450 BeadChip

scan_protocol: standard illumina scanner

data_processing:
Minfi Bioconductor Package

matrix_raw_signal.csv:
Raw fluorescent data were processed using theÂ preprocessRaw() function in the R package minfi to produce the raw unmethylated and methylated signals, as well as the detection p-values.

matrix_norm_alignmentfilter_beta.csv AND matrix_norm_genesymbolfilter_beta.csv:
Raw fluorescent data were normalized using the Noob background correction method with dye-bias normalization followed with a between-array normalization method (functional normalization) as implemented in the R package minfi. After normalization, methylation values (beta values) for each site were calculated as the ratio of methylated probe signal intensity to the sum of both methylated and unmethylated probe signal intensities.
Those probes with failed detection levels (p-value > 0.05) in greater than 10% of samples were removed. Cross-reactive probes, probes containing SNPs at the CpG site, probes detecting SNP information, probes detecting methylation at non-CpG sites, and probes targeting sites within the sex chromosomes were also removed using the minfi package in R.
Lastly, probes that were determined to be non-specific to the baboon genome were also removed. This was accomplished using one of two methods (see citations and descriptions in [2-1]). This filtering retained a final set of 120,305 probes for the alignment filter criteria and 112,760 probes for the gene symbol criteria.

Filtering for matrix_norm_alignmentfilter_beta.csv was based on:
Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and great ape evolution. PLOS Genet 2013;9:e1003763.
Mapped all 485,512 probes onto the Papio anubis genome and retained probes that successfully mapped to the baboon genome, had only 1 unique hit, and targeted CpG sites. Then, we only retained probes that had 0 mismatches in 5bp closest to and including the CpG site, and had 0-2 mismatches in 45bp not including the CpG site.

Filtering for matrix_norm_genesymbolfilter_beta.csv was based on:
Ong M-L, Tan PY, MacIsaac JL, Mah SM, Buschdorf JP, Cheong CY, et al. Infinium monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis). G3amp58 GenesGenomesGenetics 2014;4:1227-34. Mapped all 485,512 probes onto the Papio anubis genome and retained probes that successfully mapped to the baboon genome, had only 1 unique hit, and targeted CpG sites. Then, we identified the closest baboon gene to each probe site, checked for corresponding gene name matches between humans and baboons, and only retained those probes with partial or complete gene matches.

label: Cy5 and Cy3

organism: Papio sp.

label_protocol: approximately 500ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)

extract_protocol: genomic DNA was extracted from pulverized trabecular bone or homogenized cartilage using a phenol-cholorform protocol

tag: baboon id

value: baboon 11729

tag: Sex

value: female

tag: age (years)

tag: disease state

value: osteoarthritic

tag: tissue type

value: bone


title: genomic DNA from osteoarthritic distal femur articular cartilage [C06A]

description: medial condyle osteoarthritic distal femur articular cartilage from baboon

value: cartilage


title: pcDNA3.1(+) empty vector (CP-A3)

description:
Gene expression after transfected with pcDNA3.1(+) empty vector for 48h
CP-A3


title: pcDNA3.1(+)_cdg2_FLc_0220 full-length (CP-B2)

description:
Gene expression after transfected with pcDNA3.1(+)_cdg2_FLc_0220 full-length for 48h
CP-B2

source_name: pcDNA3.1(+)_cdg2_FLc_0220 full-length

value: pcDNA3.1(+)_cdg2_FLc_0220 full-length


title: pcDNA3.1(+)_cdg7_FLc_1000 full-length (CP-C2)

description:
Gene expression after transfected with pcDNA3.1(+)_cdg7_FLc_1000 full-length for 48h
CP-C2


title: pcDNA3.1(+)_cdg2_FLc_0220 full-length (CP-B1)

description:
Gene expression after transfected with pcDNA3.1(+)_cdg2_FLc_0220 full-length for 48h
CP-B1


title: PSC_WT_2

description: Pancreatic Stellate Cells Wild Type, replicate 2

tag: tissue


title: genomic DNA from osteoarthritic distal femur articular cartilage [C05A1]

source_name: osteoarthritic distal femur articular cartilage from baboon

value: baboon 11926


title: genomic DNA from osteoarthritic distal femur trabecular bone [B04A]

description: lateral condyle osteoarthritic distal femur trabecular bone from baboon

value: baboon 10988


title: genomic DNA from healthy distal femur articular cartilage [C05U1]

description: medial condyle healthy distal femur articular cartilage from baboon

value: baboon 11755

value: healthy


title: genomic DNA from osteoarthritic distal femur trabecular bone [B02A]

source_name: osteoarthritic distal femur trabecular bone from baboon

value: baboon 10038


title: pcDNA3.1(+)_cdg2_FLc_0220 full-length (CP-B3)

description:
Gene expression after transfected with pcDNA3.1(+)_cdg2_FLc_0220 full-length for 48h
CP-B3


title: genomic DNA from healthy distal femur trabecular bone [B03U1]

description: medial condyle healthy distal femur trabecular bone from baboon

value: baboon 8786


title: genomic DNA from osteoarthritic distal femur trabecular bone [B05A]


title: pcDNA3.1(+) empty vector (CP-A2)

description:
Gene expression after transfected with pcDNA3.1(+) empty vector for 48h
CP-A2


title: genomic DNA from healthy distal femur articular cartilage [C02U]

source_name: healthy distal femur articular cartilage from baboon

value: baboon 7855


title: genomic DNA from healthy distal femur trabecular bone [B06U]

source_name: healthy distal femur trabecular bone from baboon

value: baboon 10241


title: pcDNA3.1(+)_cdg7_FLc_1000 full-length (CP-C1)

description:
Gene expression after transfected with pcDNA3.1(+)_cdg7_FLc_1000 full-length for 48h
CP-C1

value: Small intestine epithelial cell

value: FHs 74 Int


title: genomic DNA from osteoarthritic distal femur articular cartilage [C02A]


title: genomic DNA from osteoarthritic distal femur articular cartilage [C04A]


title: genomic DNA from healthy distal femur articular cartilage [C03U]


title: genomic DNA from healthy distal femur trabecular bone [B05U1]


title: genomic DNA from healthy distal femur articular cartilage [C06U]


title: genomic DNA from healthy distal femur trabecular bone [B02U1]


title: SVC (S-3 2015.11.10)

source_name: stromal vascular cells

value: Epididymal fat

value: male


title: SKNBE2C_6d_PCI-34051_R2

city: Heidelberg

first: Emily

last: Koeneke

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The standard Illumina scanning protocol was used

data_processing: The data were quantile normalized using Illumina BeadStudio Data Analysis Software version v4_r2

label_protocol: 1mcg total RNA per sample was amplified and biotin labeled using Invitrogen Illumina total Prep reagents, following the standard protocol

extract_protocol: Total RNA was isolated using the RNeasy MiniKit (Qiagen)

value: neuroblastoma cells (SK-N-BE(2)-C)

tag: treated with

value: HDAC8 inhibitor PCI-34051 (4µM) for 6 days


title: genomic DNA from osteoarthritic distal femur articular cartilage [C01A]

value: baboon 9197

value: female

value: osteoarthritic


title: SKNBE2C_6d_DMSO_R1

value: solvent control (DMSO) for 6 days


title: genomic DNA from healthy distal femur articular cartilage [C01U]

value: baboon 7196

value: cartilage


title: SKNBE2C_6d_PCI-34051_R3


title: E50 Meta, 50 days after larviposition

city: Braunschweig

first: Eugenia

last: Sanchez

address: Mendelssonhstrasse 4

department: Zoological Institute

institute: Technische Universität Braunschweig

hyb_protocol: Agilent Low Input Quick Amp Labelling kit for “One-Color Microarray-Based Gene Expression Analysis”.

scan_protocol: Agilent DNA Microarray Scanner type C

data_processing: We used a customized R code (Czypionka et al., 2015) to normalize between arrays and to filter genes expressed below the detection limit.

molecule: polyA RNA

organism: Salamandra salamandra

source_name: Tail-clip

extract_protocol: RNA was extracted from tail-clip samples using a Trizol protocol.

tag: development stage

value: metamorphic climax


title: SSC-A(high) MHC-II(pos) macrophages (BMN_SH27)

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: SSC-A(high) MHC-II(pos) macrophages

label_protocol: 3 to 20 ng of total RNA from each sample was used to synthesize biotinylated probes, using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit, according to NuGEN recommendations, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from sorted cell subsets with the Qiagen RNeasy PLUS Micro Kit, according to the manufacturer protocol.

treatment_protocol: None. Mice were untreated.

tag: phenotype

value: SSC-A(low) CD11b(pos) CD24(neg) CD64(pos), CCR2(neg) Ly6c(neg) MHC-II(pos)

value: MHC-II(pos) macrophages

value: Skin

value: B6 wild-type SPF

tag: treatment

value: Untreated


title: SKNBE2C_6d_DMSO_R3


title: SSC-A(high) MHC-II(pos) macrophages (BMN_SH32)


title: E29 Meta, 56 days after larviposition


title: SSC-A(high) MHC-II(neg) melanophages (BMN_SH24)

source_name: SSC-A(high) MHC-II(neg) melanophages

value: SSC-A(high) CD11b(pos) CD24(neg) CD64(pos) CCR2(neg) Ly6c(neg) MHC-II(neg)

value: MHC-II(neg) melanophages


title: L3-Brain_atoIP_1

city: Leuven

first: Mark

last: Fiers

address: Herestraat 49

department: Center for Brain and Disease

country: Belgium

institute: VIB

library_source: genomic

data_processing:
Basecalls performed with BaseSpace FastQ Version: 1.0.0
Raw reads adapter and low quality trimmed using fastq-mcf version 1.04.807
Read mapped using Bowtie version 2.2.1 to the Drosophila Melanogaster genome DM3 build
Peaks called with Macs 2.1.0
Genome_build: DM3
Supplementary_files_format_and_content: BED files containing the “narrowPeak” peaks called with Mac2 (default parameters) using the IP samples as treatment and input samples as control

organism: Drosophila melanogaster

source_name: L3 Brains

growth_protocol: The Drosophila knock in IMAGO line ato:GFP was keept at 25 degrees at standard conditions

extract_protocol:
400 L3 larvae of the ato:GFP genotype were dissect to isolate 400 brains that were later fixed and sonicated. A 10% of the sonicated volume was used as the input. The rest was used to isolate the DNA bound to the transcription factor Atonal using anti GFP antibodies.
TruSeqLT

treatment_protocol: The sample was keept under normal growing contions and was not treated before dissection

tag: developmental stage

value: brains

tag: chip antibody

value: anti-GFP

tag: replicates


title: genomic DNA from osteoarthritic distal femur trabecular bone [B01A]

value: bone


title: L3-Brain_input_2


title: E26 Meta, 60 days after larviposition


title: SSC-A(high) MHC-II(neg) macrophages (BMN_SH21)

source_name: SSC-A(high) MHC-II(neg) macrophages

value: SSC-A(low) CD11b(pos) CD24(neg) CD64(pos), CCR2(neg) Ly6c(neg) MHC-II(neg)

value: MHC-II(neg) macrophages

tag: strain


title: SSC-A(high) MHC-II(neg) macrophages (BMN_SH31)

tag: cell type


title: L3-Brain_atoIP_2


title: genomic DNA from healthy distal femur trabecular bone [B01U]

value: female

value: healthy


title: L3-Brain_input_1


title: SSC-A(high) MHC-II(pos) melanophages (BMN_SH25)

source_name: SSC-A(high) MHC-II(pos) melanophages

value: SSC-A(high) CD11b(pos) CD24(neg) CD64(pos) CCR2(neg) Ly6c(neg) MHC-II(pos)

value: MHC-II(pos) melanophages


title: SSC-A(high) MHC-II(neg) melanophages (BMN_SH29)


title: SSC-A(high) MHC-II(pos) melanophages (BMN_SH30)


title: SSC-A(high) MHC-II(neg) macrophages (BMN_SH26)


title: SSC-A(high) MHC-II(pos) macrophages (BMN_SH22)


title: SKNBE2C_6d_PCI-34051_R1

value: neuroblastoma cells (SK-N-BE(2)-C)

value: HDAC8 inhibitor PCI-34051 (4µM) for 6 days


title: E39 PreM, 20 days after larviposition

value: premetamorphosis


title: 0.1d_50T_methylated

molecule: other

organism: synthetic construct

source_name: methylated oligo 0.1mM dNTPs, 50°C

value: synthetic oligo


title: E42 Meta, 44 days after larviposition

value: metamorphic climax


title: SSC-A(high) MHC-II(neg) melanophages (BMN_SH19)

value: Skin

value: B6 wild-type SPF

value: Untreated


title: SSC-A(high) MHC-II(pos) melanophages (BMN_SH20)


title: E48 Meta, 48 days after larviposition


title: 0.01d_37T_methylated

source_name: methylated oligo 0.01mM dNTPs, 37°C


title: 0.01d_50T_biotinylated

source_name: biotinylated oligo 0.01mM dNTPs, 50°C


title: 0.1d_50T_biotinylated

source_name: biotinylated oligo 0.1mM dNTPs, 50°C


title: 0.1d_37T_methylated

source_name: methylated oligo 0.1mM dNTPs, 37°C


title: TRAMP-Jα18-/-, 16 weeks, rep 3

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 16 weeks old
J_140_16

hyb_protocol: Hybridization was performed using the Affymetrix GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips. Targets were diluted in hybridization buffer at a concentration of 23 ng/ul, denatured at 99 °C for 5 minutes, incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the Array Strip PEG. A single Mouse ST 2.1 Arry Strip was then hybridized with each biotin-labeled target. Hybridizations were performed for 20 hours at 48°C in the GeneAtlas™ Hybridization Station. The Array Strips were washed and stained in the GeneAtlas™ Personal Fluidics Station .

scan_protocol: Array strips were imaged using the GeneAtlas Imaging Station. Affymetrix GeneAtlas Command Console software was used to acquire the Array Strip images and generate .CEL files.

data_processing: The raw intensity signals were normalized using the justRMA function of the affy package (v. 1.52) from Bioconductor and custom Brain Array CDF file (v. 20), thus leading to the definition of 23,748 unique genes.

source_name: Prostate infiltrating CD45+ leukocytes of TRAMP iNKT-deficient mice

label_protocol: Total RNA was isolated by the RNeasy mini kit (Qiagen), reverse transcribed with Ovation Pico WTA System V2 and labeled with the Encore Biotin Module. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: TRAMP mice (Greenberg et al., 1995) were crossed with Jα18-/- . Mice were housed and bred in a specific pathogen free (SPF) animal facility; tumor bearing animals were monitored 2-3 times a week and euthanized in case of distress.

extract_protocol: A single cell suspension was obtained from prostates of TRAMP and TRAMP- Jα18-/- animals via digestion with collagenase A, B and D (Roche). Cells were stained with CD45 and DAPI, and viable CD45+ leukocytes were sorted on MoFlo XDP (Beckman Coulter). Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: not applicable

tag: genotype/variation

value: Prostate

tag: age

value: 16 weeks old

tag: cell type (sorted)

value: CD45+ leukocyte


title: 1d_37T_methylated

source_name: methylated oligo 1mM dNTPs, 37°C


title: 1d_50T_biotinylated

source_name: biotinylated oligo 1mM dNTPs, 50°C


title: TRAMP-Jα18-/-, 16 weeks, rep 2

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 16 weeks old
J_56_16


title: 1d_50T_methylated

source_name: methylated oligo 1mM dNTPs, 50°C


title: 0.01d_37T_biotinylated

source_name: biotinylated oligo 0.01mM dNTPs, 37°C


title: E35 late ProM, 56 days after larviposition

value: late prometamorphosis


title: E08 Meta, 52 days after larviposition


title: TRAMP-Jα18-/-, 16 weeks, rep 1

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 16 weeks old
J_52_16


title: TRAMP-Jα18-/-, 12 weeks, rep 3

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 12 weeks old
J_44_12

value: 12 weeks old


title: E38 Meta, 62 days after larviposition


title: TRAMP-Jα18-/-, 12 weeks, rep 1

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 12 weeks old
J_88_12


title: E09 late ProM, 56 days after larviposition


title: E16 late ProM, 64 days after larviposition


title: TRAMP-Jα18-/-, 8 weeks, rep 2

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 8 weeks old
J_132_8

value: 8 weeks old


title: 0.1d_37T_biotinylated

source_name: biotinylated oligo 0.1mM dNTPs, 37°C


title: TRAMP-Jα18-/-, 12 weeks, rep 2

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 12 weeks old
J_92_12


title: TRAMP-Jα18-/-, 8 weeks, rep 3

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 8 weeks old
J_136_8


title: E18 late ProM, 64 days after larviposition

source_name: Tail-clip


title: frozen_preserved_cells_nuclei_200_UBCs

city: Seattle, WA 98195

first: Alexander

middle: B

last: Rosenberg

state: WA

address: 4000 15th Ave NE

department: Electrical Engineering

institute: University of Washington

description: frozen at -80°C for ~2 weeks

data_processing:
Fastq files were aligned to either a combined mm10-hg19 genome or a mm10 genome using STAR/2.4.1d
Single cell/nuclei transcriptomes were assembled by combining aligned reads with the same combination of barcodes using a custom script (see Supplementary Materials for more details).
Genome_build: mm10 or mm10-hg19 combined genome
Supplementary_files_format_and_content: .mat with digital gene expression, genes, barcodes, sample type, cluster assignment (if applicable), and spinal cord cluster assignment (if applicable)

organism:
Homo sapiens
Mus musculus

source_name: HEK293, HelaS3, and NIH/3T3

growth_protocol: HEK293 and Hela-S3 cells were cultured in DMEM + 10% FBS, while NIH/3T3 cells were cultured in DMEM + 10% FCS. Cells were rinsed twice with 1x PBS, then detached by incubating 2-5 min at room temperature with 1ml of TrypLE. Once cells were detached, they were added to 2mL of media with 10% FBS. In mouse-human species mixing experiments, cells were combined at the desired concentrations at this step

extract_protocol:
Nuclei were extracted using a modified version of the protocol described in Krishnaswami et al (PMID: 26890679).
scRNA-seq libraries were prepared using the SPLiT-seq protocol

tag: cell line

value: HEK293, HelaS3, and NIH/3T3


title: TRAMP-Jα18-/-, 8 weeks, rep 1

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP iNKT-deficient mice 8 weeks old
J_60_8


title: E36 late ProM, 60 days after larviposition


title: 1d_37T_biotinylated

source_name: biotinylated oligo 1mM dNTPs, 37°C


title: E46 late ProM, 44 days after larviposition


title: 0.01d_50T_propagylated

source_name: propagylated oligo 0.01mM dNTPs, 50°C


title: frozen_preserved_cells_nuclei_1000_UBCs

description: frozen at -80°C for ~2 weeks


title: 0.1d_50T_propagylated

source_name: propagylated oligo 0.1mM dNTPs, 50°C


title: same_day_cells_nuclei_300_UBCs


title: E07 early ProM, 40 days after larviposition

value: early prometamorphosis


title: TRAMP 16 weeks, rep 1

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 16 weeks old
T_72_16

source_name: Prostate infiltrating CD45+ leukocytes of TRAMP mice

value: TRAMP


title: E24 early ProM, 36 days after larviposition


title: same_day_cells_nuclei_3000_UBCs


title: 1d_50T_propagylated

source_name: propagylated oligo 1mM dNTPs, 50°C


title: TRAMP 12 weeks, rep 3

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 12 weeks old
T_96_12


title: E34 early ProM, 52 days after larviposition


title: 0.1d_37T_propagylated

source_name: propagylated oligo 0.1mM dNTPs, 37°C


title: Tx Low macrophage

city: Tokushima

first: Aya

last: Ushio

state: Tokushima

address: Kuramoto

department: Oral Molecular Pathology

institute: Tokushima University

data_processing:
Target gene signals normalized to housekeeping genes; 2^-deltaCt.
Matrix normalized worksheet reports normalized signal (against housekeeping genes). Fold change worksheet reports test/control ratios.

label: SYBR Green

source_name: control

label_protocol: Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences).

extract_protocol: Total RNA was extracted with Rneasy Mini Kit.

value: macrophage


title: Tx high macrophage

source_name: Test


title: 1d_37T_propagylated

source_name: propagylated oligo 1mM dNTPs, 37°C


title: E25 early ProM, 48 days after larviposition


title: 0.01d_37T_propagylated

source_name: propagylated oligo 0.01mM dNTPs, 37°C


title: TRAMP 16 weeks, rep 3

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 16 weeks old
T_112_16


title: E23 PreM, 32 days after larviposition


title: E28 early ProM, 36 days after larviposition


title: E20 PreM, 24 days after larviposition


title: E19 PreM, 12 days after larviposition


title: TRAMP 12 weeks, rep 2

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 12 weeks old
T_104_12


title: TRAMP 8 weeks, rep 3

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 8 weeks old
T_84_8


title: TRAMP 8 weeks, rep 2

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 8 weeks old
T_80_8


title: SKNBE2C_6d_DMSO_R2

value: neuroblastoma cells (SK-N-BE(2)-C)

value: solvent control (DMSO) for 6 days


title: TRAMP 12 weeks, rep 1

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 12 weeks old
T_100_12


title: TRAMP 8 weeks, rep 1

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 8 weeks old
T_68_8


title: WT pDC, biological rep2

status: Public on Feb 20 2018

city: Saint Louis

first: Vivek

last: Durai

state: MO

address: 4940 Parkview Place, Dock at CSRB, Murphy Lab 7766

department: Pathology and Immunology

institute: Washington University in St. Louis School of Medicine

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Not provided

data_processing: Data was analyzed using DNASTAR Arraystar software

label: Biotin

source_name: WT mouse spleen

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

growth_protocol: Single cells supsensions were made from mouse spleens by digestion with Collagenase B and DNAse 1

extract_protocol: Digestion of spleens with Collagenase B and DNAse 1

treatment_protocol: Mice were analyzed at steady-state

value: spleen

value: pDC

tag: genotype

value: WT


title: Flt3L KO cDC1, biological rep2

source_name: Flt3L KO mouse spleen

value: Flt3L KO


title: Flt3L KO cDC2, biological rep1


title: Flt3 KO pDC, biological rep2

source_name: Flt3 KO mouse spleen

value: Flt3 KO


title: Flt3 KO pDC, biological rep1


title: WT pDC, biological rep1


title: WT cDC2, biological rep2


title: Flt3L KO cDC1, biological rep1


title: WT cDC1, biological rep2


title: Flt3L KO cDC2, biological rep2


title: Flt3 KO cDC2, biological rep1


title: Flt3 KO cDC2, biological rep2


title: Flt3 KO cDC1, biological rep2


title: WT cDC2, biological rep1


title: Flt3 KO cDC1, biological rep1


title: TRAMP 16 weeks, rep 2

description:
Gene expression data from CD45+ leukocytes cells infiltrating the prostate of TRAMP mice 16 weeks old
T_76_16

value: Prostate


title: mouse bone marrow-derived dendritic cells_2

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing:
CHP files were generated using Affymetrix Expression Control.
Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: BMDC

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: C57BL/6J mice-derived bone marrow cells were plated in 6-well cell culture plate (2000000 cells/well).

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

treatment_protocol: Mouse BMDCs were differentiated from bone marrow by 20 ng/ml murine GM-CSF (PeproTech) and 20 ng/ml murine IL-4 (PeproTech) for 9 days.

value: bone marrow-derived dendritic cells


title: mouse bone marrow-derived dendritic cells_1


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Insulin Replicate 1

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: Replicate 1

hyb_protocol: 750ng of cRNA from each sample was hybridized to Human HT-12 beadchip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the HiScan system (Illumina) as per manufacturer specifications.

data_processing:
Probe intensities were background subtracted using Beadstudio (Illumina) and normalized using the cross-correlation method (Chua et al., 2006) with MATLAB scripts. Gene probe sets with minimum 1.5- fold change (on a Log2 scale) over the average of the undifferentiated H1 hESC controls were identified.
references: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

label_protocol: 250ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed to biotin-labeled cRNA using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre).

growth_protocol: H1 Human ESCs were maintained in feeder-free conditions by use of mTeSR1 medium (StemCell Technologies, 05851/2).

extract_protocol: Total RNA was extracted from all cells using the RNeasy Micro kit (Qiagen) with DNase digestion according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8).

treatment_protocol: mTeSR1-grown H1 hESCs were seeded for differentiation as single cells using Accutase (Millipore, SCR005) onto Geltrex-coated plates (Thermo Fisher, A1413302) at a density of 40,000 cells/well of 12-well plates in the presence of thiazovivin (1 μM). The next day, the anterior primitive streak cell fate (day 1) was specified using definitive endoderm induction Medium A for 24 hours, followed by hPSC definitive endoderm induction medium B for 24 hours to induce Definitive Endoderm (DE, day 2, Thermo Fisher, A27654SA). DE was then patterned into posterior foregut (FG) cell fate by using A83-01 (1 μM) and RA (2 μM) in CDM3 medium (10% KOSR, 0.1% PVA, IMDM/F12 (1:1), 1% concentrated lipids and 1% Pen/Strep) for another 24 hrs. It was further differentiated into liver bud progenitors using Activin (10 ng/mL), 8-bromo-cAMP (1mM) and BMP4 (30ng/mL) in CDM3 medium for 3 days (days 4 to 6; +/- C59 [1μM] on days 4 to 5), followed by BMP4 (10 ng/mL), Oncostatin M (10 ng/mL), Dexamethasone (10 μM), RO4929097 (2μM) or DAPT (10 μM), Forskolin (10 μM), human recombinant insulin (10 μg/mL), ascorbic acid-2 phosphate (200 μg/mL) and amino acid concentrate in CDM4 base medium (amino acid supplements, 15μg/mL Transferrin, 1% Glutamax, IMDM/F12 (1:1), 1% Pen Strep and 1% concentrated lipids) for the next 6 days (day 7 to 12; SB505124 [1μM] was also added between days 7 to 8).

tag: day

value: 12 days

tag: differentiated cell type

value: Liver Progenitor


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Forskolin Replicate 4

description: Replicate 4


title: sahy9-1 150#5

city: Taipei

first: KaiChao

last: Huang

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

description: sahy9-1 gene expression after 1 Day 150 mM NaCl treatment in 10 Day germination

hyb_protocol: 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Arabidopsis 4×44K V4 Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing the microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.

organism: Arabidopsis thaliana

source_name: whole seedling, 150 mM NaCl 1 day, replicate 2

label_protocol: 200 ng of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3(CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Plants ware grown at 22℃ under a 16-hr light/8-hr dare regime with a light intensity of approximately 80-100 μmol m-2 s-1 for 10 Days

extract_protocol: Total RNA was prepared using the RNeasy® Plant Mini kit (Qiagen, cat. no. 74904) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After 10 Days growth, transfer seedlings to plates contain 150 mM NaCl, treatment 1 Day at 22℃ under a 16-hr light/8-hr dare regime with a light intensity of approximately 80-100 μmol m-2 s-1

tag: tissue

value: whole seedling

value: sahy9-1 mutant


title: WT cDC1, biological rep1


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Insulin Replicate 4

description: Replicate 4


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without AAP Replicate 1

description: Replicate 1


title: mouse bone marrow-derived dendritic cells_3


title: Col-0 150#5

description: Col-0 gene expression after 1 Day 150 mM NaCl treatment in 10 Day germination

value: Col-0 wild type


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Insulin Replicate 2

description: Replicate 2


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Forskolin Replicate 3

description: Replicate 3


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Insulin Replicate 3

description: Replicate 3


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without AAP Replicate 4

description: Replicate 4


title: sahy9-1 150#4

source_name: whole seedling, 150 mM NaCl 1 day, replicate 1


title: Col-0 150#4


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without AAP Replicate 3

description: Replicate 3


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without DAPT Notch Inhibitor Replicate 4

description: Replicate 4


title: Human ESC-derived Hepatic Progenitor Under Base Condition Replicate 4

description: Replicate 4


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without DAPT Notch Inhibitor Replicate 1

description: Replicate 1


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Forskolin Replicate 1

description: Replicate 1


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without AAP Replicate 2

description: Replicate 2


title: Human ESC-derived Hepatic Progenitor Under Base Condition Replicate 2

description: Replicate 2


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without DAPT Notch Inhibitor Replicate 3

description: Replicate 3


title: Human ESC-derived Hepatic Progenitor Under Base Condition Replicate 3

description: Replicate 3


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without DAPT Notch Inhibitor Replicate 2

description: Replicate 2


title: Human ESC-derived Hepatic Progenitor Under Base Condition Replicate 1

description: Replicate 1


title: Human ESC-derived Hepatic Progenitor Under Base Condition Without Forskolin Replicate 2

description: Replicate 2


title: Human ESC-derived Liver Bud Progenitor Replicate 2

description: Replicate 2

source_name: Human ESC-derived Liver Bud Progenitor

value: 6 days

value: Liver Bud


title: Human ESC-derived Liver Bud Progenitor Replicate 4

description: Replicate 4


title: Human ESC-derived Liver Bud Progenitor Replicate 1

description: Replicate 1


title: Human ESC-derived Definitive Endoderm Replicate 4

description: Replicate 4

source_name: Human ESC-derived Definitive Endoderm

value: 2 days

value: Definitive Endoderm


title: Nitrate replicate 3.2

city: San Vicente del Raspeig

first: Julia

last: Esclapez

state: Alicante

address: Crta San Vicente del Raspeig s/n

department: Biochemistry

institute: University of Alicante

data_processing:
Reads were trimmed and clipped for quality control in Trimmomatic v0.35 with the following parameters:  SE -phred33 ILLUMINACLIP:illumina_adapters.fa:2:30:10
Read quality was checked for each sample using FastQC v0.11.2
High-quality reads were were aligned using bowtie2 v2.2.6 into BAM files with the following parameters: --mm -p 4
Read counts for predicted sRNA were generated using htseq-count version 0.8.0, with the following parameters: intersection-nonempty -t gene
Read counts preprocessing, exploratory data analysis and differential expression analysis was performed using DESeq2 package from Bioconductor under R environment.
Genome_build: Haloferax_mediterranei_atcc_33500.GCA_000306765.2.30
Supplementary_files_format_and_content: sRNA_normCounts.txt: DESeq2 nomalized abundance measurement of each predicted sRNA in each sample. sRNA.gff3: Genomic positions of predicted sRNAs

organism: Haloferax mediterranei

source_name: Culture

growth_protocol: Hfx. mediterranei strain R4 (ATCC 33500T) was grown at 42°C with aeration at 225 rpm, contained a 25% (w/v) mixture of inorganic salts (25% SW) (Rodriguez-Valera et al., 1980) and the pH value was adjusted to 7.3. Hfx. mediterranei was grown in two different nitrogen sources, in a defined medium which contained 40 mM KNO3 or 40 mM NH4Cl and supplemented with 5 g/l glucose, 0.0005 g/l FeCls and 0.5 g/l KH2PO4-.

extract_protocol:
microRNAs were isolated with mirVanaTM miRNA isolation kit (Ambion) following product specifications. Afterwards, the RNA samples were treated with Turbo DNase (Ambion). Size-selected RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and size distribution visualized using Agilent 2200 Tapestation (Agilent Technologies, Palo Alto, CA, USA).
microRNAs libraries were constructed using TruSeq Small RNA Library Prep Kit and the TruSeq Small RNA Library Prep Guide, Part #15004197 Rev. G protocol.

treatment_protocol: Hfx. mediterranei cultures grown in the presence of two different nitrogen sources, nitrate and ammonium, to mid-exponential phase.

value: Strain R4 (ATCC 33500T)


title: IDL leaf, 6 days of darkness - Rep 3

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

description: Gene expression data for individually darkened leaves, darkened for 6 days

hyb_protocol: Hybridization was carried out at 45 °C for 16 h, and the arrays were washed and stained according to the protocol described in the Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2, Affymetrix)

scan_protocol: The arrays were scanned using GeneAtlas Imaging Station (Affymetrix)

data_processing: Array data was read into R using the oligo package that retrieved the pd.aragene.1.1.st array information, which features (probeset) were annotated using Affymetrix online resources through the getNetAffx function. The technical quality of the arrays was assessed using the arrayQualityMetrics (Kauffmann et al., 2009) R package (data not shown). Next, the resulting microarray data was subjected to a variance stabilizing transformation (within-array normalization) and to cyclic-loess between-array normalization.

source_name: Arabidopsis leaf, leaf was individually darkened, 6 days darkening

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown at 22 0C under short day conditions (8 h light and 16 h dark) with 180 µmol m2 s-1 white light

extract_protocol: About 40 mg frozen material was used for RNA isolation using a RNAeasy kit from QIAGEN and followed by a DNase treatment.

treatment_protocol: For the whole darkened plant (DP), plants were isolated from light by dark boxes and were placed back in the same chamber to conserve the same temperature shift. For the individually darkened leaves (IDL), one fully expanded leaf was covered on each side of the plant (total of 2 covered leaves/plant) with plastic mittens coated with aluminum foil while the rest of the rosette remained under normal light/dark cycle (Keech et al., 2007)

tag: days in darkness

value: leaf

tag: ecotype


title: Nitrate replicate 3.1


title: Undifferentiated Human ESCs Replicate 2

description: Replicate 2

source_name: Undifferentiated Human ESCs

value: 0 days

value: hESC


title: IDL leaf, 6 days of darkness - Rep 1


title: IDL leaf, 6 days of darkness - Rep 2


title: IDL leaf, 3 days of darkness - Rep 2

description: Gene expression data for individually darkened leaves, darkened for 3 days

source_name: Arabidopsis leaf, leaf was individually darkened, 3 days darkening


title: IDL leaf, 3 days of darkness - Rep 3


title: DP leaf, 3 days of darkness - Rep 1

description: Gene expression data for leaves sampled from whole plants darkened for 3 days

source_name: Arabidopsis leaf from a whole darkened plant, 3 days darkening


title: Control leaf in light - Rep2

description: Gene expression data for control leaves grown in light

source_name: Arabidopsis leaf, in light (short day conditions)


title: Human ESC-derived Definitive Endoderm Replicate 3

description: Replicate 3


title: Human ESC-derived Definitive Endoderm Replicate 2

description: Replicate 2


title: DP leaf, 3 days of darkness - Rep 2


title: DP leaf, 6 days of darkness - Rep 2

description: Gene expression data for leaves sampled from whole plants darkened for 6 days

source_name: Arabidopsis leaf from a whole darkened plant, 6 days darkening


title: DP leaf, 3 days of darkness - Rep 3


title: Human ESC-derived Definitive Endoderm Replicate 1

description: Replicate 1


title: Undifferentiated Human ESCs Replicate 3

description: Replicate 3


title: DP leaf, 6 days of darkness - Rep 3


title: Undifferentiated Human ESCs Replicate 4

description: Replicate 4


title: Human ESC-derived Liver Bud Progenitor Replicate 3

description: Replicate 3


title: IDL leaf, 3 days of darkness - Rep 1


title: Undifferentiated Human ESCs Replicate 1

description: Replicate 1


title: DP leaf, 6 days of darkness - Rep 1


title: Nitrate replicate 2.3


title: Nitrate replicate 2.2


title: Nitrate replicate 2.1


title: Nitrate replicate 1.3


title: Ammonium replicate 8.2


title: Nitrate replicate 1.1


title: Nitrate replicate 1.2


title: Ammonium replicate 8.1


title: E55 PreM, 40 days after larviposition

source_name: Tail-clip

tag: development stage

value: premetamorphosis


title: Ammonium replicate 7.2


title: Igll1 PerC B-1a Rep1 (Igk)

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave, Smillow 307

institute: NYU

data_processing:
Library strategy: VDJ repertoire sequencing (VDJ-seq)
Reads were trimmed for adaptor sequence and masked for low-complexity of low quality sequence
Reads 1 and reads 2 were overlapped and unique sequences were filtered out
These unique sequences were subject to IMGT/High V-Quest (version 1.5.5) analysis for mapping and assigning gene segment usage, Alamyar, et al. Immunome Res. 2012
IMGT/High V-Quest output was used as input for IMGT/StatClonotype (version 1.0.3) statstical analysis and visualization, Aouinti et. Al., Front. Immunol, 2016. IMGT/StatClonotype is atool that evaluates and visualizes statstical significance of pairwise comparisons of IMGT clonotype diversity per V, D orJ gene segments .
Genome_build: IMGT/GENE-DB for Mus musculus (Giudicelli, V. et al. Nucleic Acids Res. 2005)
Supplementary_files_format_and_content: tab-delimited file that contains information on AA sequence, V and J gene segment assignment, percent alignment, etc. This file is used as input for using the IMGT/StatClonotype tool.

source_name: Pertionteal B-1a cells

extract_protocol:
Cells were sorted from 6-8 week old mice. Genomic DNA was extracted from lysed cells and this gDNA was used as template for PCR prior to library prep/adaptor ligation.
Primers were used to amplify sucessfully rearranged BCR heavy and light chains and size selected by gel extraction for 100-280bp from an agarose gel. PCR products were end-repaired using a combination of T4 PNK and T4 polymerase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of preannelaed Illumina compatible adapters, NEXTflex DNA barcodes (Bioo Scientific) which have a single 'T' base overhang at the 3’ end. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina MiSeq following the manufacturer's protocols.

value: Igll1 knockout

value: Peritoneal cavity

value: peritoneal cavity B-1a cells


title: WT PerC B-2 Rep1 (Igk)

source_name: Pertionteal B-2 cells

value: wild type

value: peritoneal cavity B-2 cells


title: WT PerC B-1a Rep1 (Igk)


title: Igll1 PerC B-1a Rep2 (Igk)


title: WT PerC B-1a Rep2 (Igk)


title: WT PerC B-2 Rep2 (Igk)


title: Ammonium replicate 7.1


title: Ammonium replicate 6.2


title: Ammonium replicate 6.1


title: Ammonium replicate 6.3


title: luminal cells_BT-474_RNASeq

city: Shanghai

first: Lixing

last: Zhan

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
Raw reads were subjected to quality control _QC_ to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows: 1_ Remove reads with adaptors;2_ Remove reads in which unknown bases are more than 10%;3_ Remove low quality reads _the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5_.
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
RSEM  was used to computed maximum likelihood abundance estimates. FPKM  method is used in calculating expression level.
Use NOISeq to screen differentially expressed genes between two groups.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: luminal cells_BT-474

growth_protocol: DMEM/RPMI1640 supplied with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit _Qiagen_ cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. Transcriptome reads from RNA-Seq experiments were mapped to the reference genome _hg19_ by using BWA/Bowtie tool. Genes expression level is quantified by a software package called RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

value: luminal breast cancer cells

value: mammary gland; breast/duct

tag: passages


title: Basal cells_SUM-159_RNASeq

source_name: Basal cells_SUM-159

value: basal breast cancer cells

value: mammary gland; breast


title: Basal cells_HBL-100_RNASeq

source_name: Basal cells_HBL-100


title: Basal cells_BT-549_RNASeq

source_name: Basal cells_BT-549


title: TGEN-B

city: Phoenix

first: Jessica

last: Lang

state: AZ

address: 445 N 5th St

institute: TGen (Translational Genomics Research Institute)

description: raw data available through dbGap

data_processing:
TopHat 1.2 was used to align fastq to genome assembly GRCh37.62. Parameters: th_paired_end="yes"; th_mate_inner_dist=35; th_mate_std_dev=40; convertBAM2SAM="no"
Cufflinks 1.3 was used to assemble alignments and estimate relative abundances (FPKM). Default parameters used
Genome_build: GRCh37.62
Supplementary_files_format_and_content: Gene list and FPKM

source_name: SCCOHT tumor tissue

extract_protocol:
Tumors were flash frozen, and RNA was later harvested using Qiagen Rneasy Mini Kit. Using the Nugen Ovation RNA-Seq System v2, 10ng of total RNA for each sample was used to generate double stranded cDNA, which was subsequently amplified using Nugen’s SPIA linear amplification process. Amplified products were cleaned using Qiagen’s QIAquick PCR Purification Kit and quantitated using Invitrogen’s Quant-iT Picogreen. 1µg of amplified cDNA was fragmented on the Covaris E210 to a target size of 300bp and Illumina’s TruSeq DNA Library Preparation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor type

value: Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT)

tag: sample site

value: lymph node metastasis

tag: tissue storage

value: snap frozen


title: TGEN-D

description: raw data not available

value: unknown (primary or metastasis)


title: TGEN-C

description: raw data not available


title: TGEN-A

description: raw data available through dbGap

value: recurrent metastasis


title: Control leaf in light - Rep1

value: leaf


title: luminal cells_T47D_RNASeq

source_name: luminal cells_T47D

value: mammary gland; derived from metastatic site:pleural effusion


title: BG3_GST_N4_rep2

city: Planegg-Martinsried

first: Sandro

last: Baldi

address: Großhaderner Strasse 9

department: BMC Molecular Biology

institute: LMU Munich

description:
tetranucleosomal DNA
replicate 2

data_processing:
base-calling for nanopore sequencing: Albacore software
mapping of nanopore reads: Graphmap v0.3.0
mapping of Illumina reads: bowtie 1.1.1, -X=1500
conversion from bam files to .bed.gz files: 1. BEDtoools v2.22.0: bamToBed -bedpe 2. Reduce .bed.gz file to chr/start/stop columns
Genome_build: dm3
Supplementary_files_format_and_content: .bed.gz files were generated by converting the mapped reads in .bam format to .bed.gz intervals

source_name: BG3-c2 cells

growth_protocol: BG3-c2 and Kc cells were cultured at 26°C in Schneider’s Drosophila Medium (Gibco) including 10% fetal calf serum (FCS), Penicillin-Streptomycin (and for BG3-c2 cells also 10 µg/ml human insulin)

extract_protocol:
1-2 x 108 cells were harvested by centrifugation (500 x g, 5 min), washed in 15 ml cold PBS, and resuspended in 1 ml lysis buffer (15 mM HEPES pH 7.6, 0.1 mM EGTA, 1 mM EDTA, 0.15 mM spermine, 0.5 mM spermidine, 1x Protease Inhibitor cocktail (Roche)). After 1 min incubation on ice, 176 µl of 10% NP-40 was added, gently vortexed, and the cells again incubated on ice for 5 min. The released nuclei were spun down at 4°C and 1000 rpm (100 x g) for 10 min. They were then washed with 1 ml MNase buffer (10 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 2 mM CaCl2, 0.15 mM spermine, 0.5 mM spermidine) and centrifuged again (4°C, 100 x g, 10 min). The nuclei were resuspended in 1 ml MNase buffer, and distributed into five aliquots of 200 µl. Different amounts of MNase (Sigma-Aldrich) were added to the five tubes. The exact amounts depend on MNase batches and conditions and should be determined empirically. In a typical experiment, we prepared a stock solution of 1.2 x 10-3 U MNase/µl and added 1, 2, 4, 8 or 16 µl of this stock solution to the 200 µl aliquots. The chromatin was then digested for 20 min at 37°C. Digestion was stopped by transferring the tubes to ice and adding 5 µl 0.5 M EGTA. To digest proteins, 12 µl of 10% SDS and 100 µg of Proteinase K (Bioline) were added and the chromatin was incubated at 50°C for 1 h. After nucleic acids were extracted with 1 volume of phenol-chloroform-isoamyl alcohol mixture (PVA, 25:24:1, Invitrogen), 50 µg RNase A was added to digest RNA at 37°C for 30 min. DNA was extracted with 1 volume of PVA. DNA was precipitated in presence of 10 µg glycogen (Roth) by adding 1/10 volume of 3 M NaOAc and 2.5 volume. EtOH and incubation for 1h or overnight at -20°C. The precipitated DNA was pelleted at 4°C and 16,000 x g for 30 min and washed with 300 µl 70% EtOH. Pellets were shortly dried (5 min) and dissolved in 21 µl TE buffer.  1 µl of each sample was run on an Agilent Bioanalyzer 1000 DNA chip to determine degree of digestion.
Nanopore sequencing: Partially MNase-digested chromatin retaining contiguous oligonucleosomes was used for generation of libraries for nanopore sequencing. 1 µg of purified DNA was end-repaired and A-tailed with the NEBnext UltraII end repair module (New England Biolabs, Ipswich, USA), purified with Ampure XP beads (Beckman-Coulter, Brea; USA) and ligated to AMX adapter from the Oxford Nanopore 1D sequencing Kit (SQK-LSK108, Oxford Nanopore Technologies, Oxford, UK) using NEB Blunt/TA ligase mastermix. Excess adapters were removed by adding 0.5 volumes of Ampure XP beads and washing with ABB buffer from the 1D sequencing kit. Illumina sequencing: 10 µl of DNA from partially MNase-digested chromatin was run on an 11 cm 1.2 % agarose gel in 0.5x TAE buffer at 70 V and stained with ethidium bromide. The tetranucleosomal band was cut out and purified (Gel and PCR Clean Up Kit, Macherey-Nagel). 80 ng DNA was used for library preparation with the Diagenode iDeal library preparation kit.

treatment_protocol: For ISWI knockdown, 1.5 x 107 BG-c2 cells were resuspended in 4 ml medium (containing antibiotics and insulin but no FCS), seeded in a T-75 flask, and incubated with 50 µg of in vitro transcribed dsRNA (MEGAscript T7 Transcription Kit, Ambion). After gentle shaking for 45 min at room temperature, 16 ml of medium (+FCS/+antibiotics/+insulin) were added to the cells. Cells were harvested after 6 d. 2 x 106 cells were set aside and  frozen/boiled thrice in 100 µl urea buffer to test for ISWI knockdown efficiency. The remaining cells were processed for MNase digestion. H1 knockdown in Kc cells was done similarly, but after 3 d the cells were harvested and the dsRNA treatment repeated on 1.5 x 107 of the harvested cells. After another 3 d, the cells were harvested and processed for MNase digestion.

value: larval L3, central nervous system

tag: RNAi

value: control dsRNA (GST)


title: BG3_GST_N4_rep1

description:
tetranucleosomal DNA
replicate 1

tag: cell type


title: luminal cells_MCF-7_RNASeq

source_name: luminal cells_MCF-7

value: mammary gland, breast; derived from metastatic site:pleural effusion


title: miRNA_scr_maternal_1

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

description:
Small RNA
scr_maternal_1
Scrambled anti-miR was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt

data_processing:
The raw read data was processed to optionally remove an adapter sequence and trim according to a quality threshold (default Q>=20) by cutadapt.
Only reads of the desired size range are selected to limit the pool to likely mature miRNAs (default: 18-28 nt). Duplicate reads are collapsed to decrease the number of necessary homology searches.
Only those sequences present in a minimum number (default = 5) are kept for further analyses.
Next, read counts from isomiRs of the same miRNA are combined.
The resulting read sequences are compared versus murine mirBase 20 database of miRNAs. Sensitivity and specificity of this BLASTN homology search can be controlled using various parameters inside the mirpipe.pl script. Parameters are optimized for small query sequences (-num_alignments 15 -word_size 7 -evalue 10 -dust no -strand plus). The resulting hits are filtered to exclude those with too many mismatches ((read length - alignment length) + mismatches + gaps = final mismatches). Detected reference miRNA families per read are scored based on the minimum number of mismatches. If a read matched equally versus multiple miRNA families, the respective families are joined by single linkage clustering. By default, only those read sequences that are at least 5% as abundant as the most abundant sequence per miRNA family cluster are denoted.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.matrix.norm.txt: Tab-delimited text file includes library size normalized counts per sample.

source_name: Mus musculus liver tissue homogenate

extract_protocol:
PureLink™ miRNA Isolation Kit.
For small RNA sequencing, 300ng of small RNA fraction (<200nt) was used as input for TruSeq Small RNA Library Kit (Illumina). Library preparation followed the standard protocol with the exception of skipping the PAGE based size selection before PCR. Instead, complete cDNA pool was amplified and libraries were pooled based on the amount of fragments within the range of 145-160bp that correspond to insert sizes from 15-30 bp. The size selection of this pool was performed with PippinHT machine (Sage Science) on 3% Agarose cassettes with target size set to 154bp.

tag: strain/background

value: liver

value: postnatal day 7

tag: anti-mir

value: scrambled control

tag: anti-mir injection recipient

value: dam on gestational day 17


title: miRNA_scr_maternal_4

description:
Small RNA
scr_maternal_4
Scrambled anti-miR was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt

tag: age


title: miRNA_scr_maternal_5

description:
Small RNA
scr_maternal_5
Scrambled anti-miR was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_scr_maternal_3

description:
Small RNA
scr_maternal_3
Scrambled anti-miR was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_scr_maternal_2

description:
Small RNA
scr_maternal_2
Scrambled anti-miR was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_scr_direct_5

description:
Small RNA
scr_direct_5
Scrambled anti-miR was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt

value: newborn pup on postnatal day 1


title: miRNA_scr_direct_4

description:
Small RNA
scr_direct_4
Scrambled anti-miR was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_scr_direct_3

description:
Small RNA
scr_direct_3
Scrambled anti-miR was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_scr_direct_2

description:
Small RNA
scr_direct_2
Scrambled anti-miR was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: BG3_ISWI_N4_rep2

description:
tetranucleosomal DNA
replicate 2


title: miRNA_ant_maternal_5

description:
Small RNA
antagomir_maternal_5
Anti-miR-29a3p was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_ant_maternal_3

description:
Small RNA
antagomir_maternal_3
Anti-miR-29a3p was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: BG3_ISWI_N4_rep1

description:
tetranucleosomal DNA
replicate 1


title: miRNA_ant_maternal_4

description:
Small RNA
antagomir_maternal_4
Anti-miR-29a3p was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_ant_maternal_2

description:
Small RNA
antagomir_maternal_2
Anti-miR-29a3p was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_ant_maternal_1

description:
Small RNA
antagomir_maternal_1
Anti-miR-29a3p was injected to pregnant dams at gestational day 17 via i.v. route (100mg/kg); livers from the offspring were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_ant_direct_5

description:
Small RNA
antagomir_direct_5
Anti-miR-29a3p was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: miRNA_ant_direct_4

description:
Small RNA
antagomir_direct_4
Anti-miR-29a3p was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: ΔmarR1 ΔuzcR

city: Livermore

first: Dan

last: Park

state: CA

address: 7000 East Ave

department: BBTD

institute: Lawrence Livermore National Lab

data_processing:
Reads were mapped using Bowtie v1.1.1
HTSeq-0.6.1p1 was used to quantify the number of counts per genomic feature
HTSeq-0.6.1p1 output was converted to a .bam file, sorted, and indexed using samtools-0.1.19
The DESeq package in R was used to determine differential expresssion
Genome_build: GenBank accession number NC_011916.1
Supplementary_files_format_and_content: RSeQC-2.3.9 was used to normalize the counts data and generate wig files for visualization.  Triplicate samples were merged using the median value at each coordinate.  Each condition has a forward and reverse wig file associated with it

organism: Caulobacter vibrioides

growth_protocol: Strains were grown in M5G media with 1.32 mM inorganic phosphate at 30°C to mid-exponential phase

extract_protocol:
Cells were harvested and immediately added to ice-cold ethanol containing 5% (vol/vol) water-saturated phenol (pH 6.6). Total RNA was isolated using hot phenol and phenol/chloroform extractions.
5 ug of total RNA was treated with the ScriptSeq Complete Kit - Bacteria from Epicentre, an Illumina company (Cat# BB1224) for ribosomal RNA depletion and library generation with ScriptSeq Index Primers.

treatment_protocol: no additional treatment

tag: strain

tag: genotype

value: {delta}marR1 {delta}uzcR


title: ΔurtAP ΔuzcR

value: {delta}urtAP {delta}uzcR


title: miRNA_ant_direct_3

description:
Small RNA
antagomir_direct_3
Anti-miR-29a3p was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: enptd5a+ population 3

city: Durham

first: Michel

last: Bagnat

state: North Carolina

address: 333B Nanaline Duke Bldg

department: Cell Biology

institute: Duke University

data_processing:
HiSeq Control Software used for basecalling
Sequenced reads were trimmed for adapter sequences and low-quality reads using FASTQ Groomer and FASTQ Quality Trimmer, followed by alignment to the GRCz10 reference genome using HISAT2.
The number of reads counted for each gene was calculated using HTSeq.
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt files containing HT-seq counts for each gene in each sample.

organism: Danio rerio

source_name: Notochord sheath

extract_protocol:
Notochord sheath cells were isolated and populations were collected using fluorescence-activated cell sorting (FACS). Total RNA was prepared from each population using RNeasy Micro Plus Kit (Qiagen). Quality control was evaluated by Qubit and 2100 Bioanalyzer.
Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.

value: enptd5a+ population

value: EK

value: Notochord sheath

value: 13 days post fertilizaton

value: wild type


title: enptd5a+ population 2


title: ΔmarR2 ΔuzcR

value: {delta}marR2 {delta}uzcR


title: miRNA_ant_direct_2

description:
Small RNA
antagomir_direct_2
Anti-miR-29a3p was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: ΔuzcX ΔuzcR

value: {delta}uzcX {delta}uzcR


title: enptd5a+ population 1


title: miRNA_scr_direct_1

description:
Small RNA
scr_direct_1
Scrambled anti-miR was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: ΔuzcR

value: {delta}uzcR


title: miRNA_ant_direct_1

description:
Small RNA
antagomir_direct_1
Anti-miR-29a3p was injected via i.p. route (25mg/kg) to newborn mouse pups at postnatal day 1; livers were extracted at postnatal day 7.
Processed data file: counts.matrix.norm.txt


title: col9a2/entpd5a+ population 3

value: col9a2/entpd5a+ population


title: Kc_H1_nanopore_rep2

description:
total MNase-digested DNA
replicate 2

source_name: Kc cells

value: embryo

value: histone H1 dsRNA (primers:TAATACGACTCACTATAGGGgatgtctgattctgcagttgc/TAATACGACTCACTATAGGGgggcttcgactttatgattcc)


title: Kc_H1_nanopore_rep1

description:
total MNase-digested DNA
replicate 1


title: Kc_GST_nanopore_rep2

description:
total MNase-digested DNA
replicate 2

value: control dsRNA (GST)


title: col9a2+ population 3

value: col9a2+ population


title: Kc_GST_nanopore_rep1

description:
total MNase-digested DNA
replicate 1


title: wing feathers_repeat1

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: RNA-seq feather N-W-L.xls

data_processing:
Sequencing reads from RNA-seq were aligned to the Chicken reference genome (Version galGal4 from UCSC) using Tophat (2.1.0) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: wing contour feather in growth phase

growth_protocol: feathers were plucked from adult chicken in vivo

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: domesticus

value: feather


title: wing feathers_repeat2

description: gene expression 4-2-2017 analysis.xls


title: leg feathers_repeat2

description: gene expression 4-2-2017 analysis.xls

source_name: leg feather in growth phase


title: neck feathers_repeat2

description: gene expression 4-2-2017 analysis.xls

source_name: neck feather in growth phase


title: leg feathers_repeat1

description: RNA-seq feather N-W-L.xls


title: neck feathers_repeat1

description: RNA-seq feather N-W-L.xls


title: BG3_nanopore_rep1

description:
total MNase-digested DNA
replicate 1

value: larval L3, central nervous system


title: col9a2+ population 1


title: BG3_nanopore_rep2

description:
total MNase-digested DNA
replicate 2


title: col9a2+ population 2


title: col9a2/entpd5a+ population 2


title: 10Gy_2h_p53

status: Public on Feb 19 2018

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: Irradiated with 10Gy (1Gy/min) & 2h of recovery

data_processing:
Quality control of reads was performed with FastQC software
Reads were mapped to the human genome (hg19) with Bowtie2.0.4
Peak detection was carried with the MACS program (detected peaks are given in bed files)
p65 target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Peak intersections and their genomic coordinates were found using Bedtools software
The significance of differences between control untreated cells and cells subjected to TNFα and IR was estimated using MACS software; the FDR=0.05 level was selected as the significance threshold.
Genome_build: hg19
Supplementary_files_format_and_content: fastq - raw data from Illumina sequencer; bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: U2OS cells

growth_protocol: The wild-type U2-OS cells were purchased from ATCC (HTB-96) and used as a primary model. Cells were grown in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (HyClone) and gentamicin (40 mg/mL; Krka) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
2x10^6 cells were inoculated on 10 cm2 dish 2 days before experiments. A two-step cross-linking procedure was applied for an efficient fixation of NFκB dimers with DNA (Tian 2012). Cells were washed twice with PBS, a solution of DSG (disuccinimidyl glutarate) in 1x PBS was added to the final concentration of 2 mM, and then cells were incubated for 45 minutes at RT with rotation. Next, cells were washed twice with PBS and the second fixation was performed using 1% formaldehyde for 10 min. at RT. For analysis of p53 binding, cells were fixed only with formaldehyde (as described above). Formaldehyde fixation was quenched by glycine (125 mM final concentration) and then nuclei were isolated using buffers and protocol from iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Chromatin of nuclei re-suspended in 200 µl was sheared using Bioruptor® PLUS combined with the Bioruptor® Water cooler & Single Cycle Valve (at HIGH power setting) with 3 rounds of 5 cycles 30sec.ON/30sec.OFF; chromatin fragments with approximate length 100-600 bp were obtained. Chromatin immunoprecipitation was carried out using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode) with 3µl/sample of anti-RelA(p65) polyclonal antibody (C15310256, Diagenode) or anti-p53 polyclonal antibody (C15410083, Diagenode), or without antibody (mock-IP), according to the manufacturer protocol.
Immunoprecipitated DNA fragments and input DNA were sequenced using the HiSeq 1500 system with TruSeq workflow (Illumina)

treatment_protocol: Any treatment started 48 h after inoculation of cells; all steps, with the exception of irradiation, were carried out at 37 °C and 5% CO2. For ChIP-Seq analysis, wild-type cells were irradiated with 10 Gy IR dose at a 1Gy/min dose rate using 6 MeV photons (generated by linear accelerator Clinac 600, Varian), the medium was replaced with a fresh one, and cells were analyzed 2 or 4 hours after irradiation.

tag: cell line

value: U2OS cells

tag: tumor

value: osteosarcoma

tag: Sex

value: female

value: 15 years

tag: tissue/cells

value: bone

tag: chip antibody

value: p53 polyclonal Ab (Diagenode, C15410083)

tag: agent

value: Irradiated with 10Gy (1Gy/min)


title: 10Gy_4h_p53

description: Irradiated with 10Gy (1Gy/min) & 4h of recovery


title: 1_L28_C45

city: Stanford

first: Mark

last: Krasnow

state: Ca

address: Beckman Center, B400 279 W. Campus Dr.

institute: Stanford University

description: Adult distal lung mesenchymal cell 45

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Column headers include: tracking_id, class_code,  nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, q0_FPKM, q0_FPKM_lo, q0_FPKM_hi, q0_status.

source_name: adult mouse lung_single cell

extract_protocol:
To obtain mesenchymal cells from the adult lung, the pulmonary vasculature was cleared and lungs were gently inflated with digestion buffer prior to isolation and mincing of the lung. All tissue was digested at 37C for 45 min using Elastase and DNase I, triturated and subsequently filtered using 100µm and 40µm strainers to obtain a single cell suspension. Mesenchymal cells were enriched by magnetic-assisted cell sorting using CD45, Pecam, and EpCAM depletion. Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

tag: tissue

value: lung

tag: developmental stage

value: adult

value: mesenchymal cells


title: 1_L28_C95

description: Adult distal lung mesenchymal cell 47


title: col9a2/entpd5a+ population 1

value: col9a2/entpd5a+ population

value: EK

value: Notochord sheath

value: 13 days post fertilizaton

value: wild type


title: 1_L28_C16

description: Adult distal lung mesenchymal cell 46


title: 1_L28_C74

description: Adult distal lung mesenchymal cell 44


title: 1_L28_C56

description: Adult distal lung mesenchymal cell 43


title: control_p53

description: untreated control

value: untreated control


title: 1D_L28_C93

description: Adult distal lung mesenchymal cell 41


title: 1_L28_C88

description: Adult distal lung mesenchymal cell 42


title: 1_L28_C82

description: Adult distal lung mesenchymal cell 40


title: 1_L28_C64

description: Adult distal lung mesenchymal cell 38


title: PTC1_BTL28

description: Postive bulk cell control

source_name: adult mouse lung_bulk cells


title: 1pp_L28_C65

description: Adult distal lung mesenchymal cell 37


title: 1pp_L28_C79

description: Adult distal lung mesenchymal cell 36


title: 1pp_L28_C43

description: Adult distal lung mesenchymal cell 32


title: 1_L28_C14

description: Adult distal lung mesenchymal cell 39


title: 1p_L28_C03

description: Adult distal lung mesenchymal cell 34


title: 1pp_L28_C50

description: Adult distal lung mesenchymal cell 33


title: 1_L28_C62

description: Adult distal lung mesenchymal cell 30


title: 1pp_L28_C49

description: Adult distal lung mesenchymal cell 29


title: 1_L28_C17

description: Adult distal lung mesenchymal cell 31


title: 1_L28_C69

description: Adult distal lung mesenchymal cell 27


title: 1pp_L28_C25

description: Adult distal lung mesenchymal cell 35