title: Sputum_Healthy_10

value: HC

value: RLT

value: m

value: alveolar macrophages (%):57.875

value: neutrophils (%):33.125

value: eosinophils (%):1.125

value: lymphocytes (%):1.625

value: ciliated cells (%):2.625

value: monocytes (%):0.875

value: squamous cells (%):2.75


title: MG-Hal+Prog-D8

status: Public on Oct 25 2020

type: RNA

city: Davis

first: Russell

last: Hovey

state: CA

address: 1 Shields Ave

department: Animal Science

country: USA

institute: University of California Davis

description: Mammary gland gene expression from pigs given bromocriptine treatment for 8 days then haloperidol+progesterone treatment for 5 days

hyb_protocol: Amplified biotinylated-cRNA was hybridized to Affymetrix GeneChip Porcine Genome Arrays for 16 h at 45oC. Genechips were washed and stained in the GeneChip® Fluidics Station 450 with Streptavidin-conjugated to phycoerythrin, then biotin-coupled polyclonal anti-streptavidin antibody and streptavidin-phycoerythrin again.

scan_protocol: GeneChips were scanned using Affymetrix Genechip scanner

data_processing: The data were RMA-normalized and transformed using log to the base 2. Data were filtered to remove probesets that were not expressed in at least 2 samples in at least one treatment group

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: Pig mammary gland, ovariectomized, haloperidol+progesterone treated

label_protocol: 1ug total RNA was reverse transcribed to double stranded cDNA using reverse transcriptase (Superscript II) and oligo-dT priming.  Following double-stranded cDNA preparation, biotinylated-cRNA was synthesized by in vitro transcription (Enzo Life Sciences BioArray).

growth_protocol: Female peripurbertal yucatan miniature swine (5 months old) were housed in groups with free access to water and maintained on a diet of Pig and Sow pellets provided twice daily.

extract_protocol: TrReagent extraction of total RNA was performed according to the manufacturer's instructions. Dnase treatment of the total RNA was performed using the Zymo Research DNA-free RNA kit. An agilent was used to verify RNA quantity and quality.

treatment_protocol: On Day 1, 32 females were ovariectomized and 4 females underwent an operation that left the ovaries intact. The next day bromocriptine treatment was started on the 32 ovariectomized animals, while the sham animals received saline.  After 8 days of bromocriptine, animals (n=4) were assigned either bromocriptine, haloperidol, bromocriptine+estrogen, bromocriptine+progesterone, bromocriptine+estrogen+progesterone, haloperidol+estrogen, haloperidol+progesterone or haloperidol+estrogen+progesterone for 5 days (day 9 - day 14).  Pigs were injected with BrDU 24 hours before euthanasia to label proliferating cells.

tag: status

value: ovariectomized

tag: treatment

value: haloperidol+progesterone

tag: tissue

value: Mammary gland


title: Sputum_Healthy_7

city: Großhansdorf

first: Espen

middle: E

last: Groth

address: Wöhrendamm 80

department: Department of Pulmonology

country: Germany

institute: LungenClinic Grosshansdorf

hyb_protocol: A total of 1650 ng of labeled cRNA per sample was hybridized to Agilent Human GE 4x44k v2 arrays according to the manufacturer's instructions.

scan_protocol: Hybridized arrays were scanned using an Agilent SureScan scanner system (resolution 5 µm, default protocol).

data_processing: Scan images were analyzed with the Agilent Feature Extraction Software (version 11.5.1, default parameters, protocol GE1_1105_Oct12). Output txt files were imported into the R/Bioconductor programming environment applying functions from the limma package (version 3.42.2). Background correction was performed on median foreground signals (substracting the median background and setting post-subtraction negative intensities equal to half the minimum of the positive corrected intensities of each array). Subsequently, quantile normalization and log2-transformation were performed. Control probes as well as probes flagged as IsNotUniform, IsSaturated or IsPopOutlier by the default Agilent Feature Extraction software algorithm were removed from the dataset. Following further exclusion of probes that were not flagged as IsFound and IsPosSig in at least 50% of biological replicates in any one disease condition, probe summarization was performed for downstream probe-level analysis.

organism: Homo sapiens

source_name: Healthy sputum sample

label_protocol: RNA was processed using the Low Input Quick Amp labelling Kit (Agilent, Cy3, following manufacturer's standard protocols), followed by purification via Qiagen RNeasy columns. Dye incorporation and RNA yield were measured on an NanoDrop 6000 spectrophotometer (Thermo Fisher).

extract_protocol: Depending on the method of fixation/preservation, sputum samples were: 1) thawed and directly supplied to nucleic acid extraction, or: 2) sputum cells were extracted from paraffin bocks (by cutting thick slices with a microtome using alcohol- and heat-sterilized blades) and deparaffinized by incubation with xylene and ethanol, followed by a drying step using a vacuum centrifuge. Extraction of nucleic acids was performed using the AllPrep Micro Kit (Qiagen) following the manufacturer's standard instructions. Nucleic acid yield was measured using a NanoDrop spectrophotometer (Thermo Fisher). Total RNA integrity was assessed with an Agilent BioAnalyzer and RNA 6000 Nano Kit. Samples with RIN < 3 were excluded from further processing.

treatment_protocol: Induced sputum samples were obtained following inhalation of nebulized saline. Following manual separation from saliva and contaminants, sputum plugs were incubated with Sputolysin (DTT, Calbiochem), followed by suspension in PBS, filtration through nylon meshes and centrifugation (with removal of supernatant). Purified sputum cell pellets were resuspended in BSA/PBS and aliquots were taken for preparation of cytospin slides. The latter were subsequently stained (Giemsa) und subjected to differential cell counting. Remaining sputum cell suspensions were again pelleted by centrifugation and, depending on the method of fixation/preservation applied, 1) resuspended in RLT lysis buffer and subsequently stored at -80°C, or, 2) preserved with HOPE medium and later casted into a paraffin block (as commonly performed in routine pathology protocols) with subsequent storage at 4°C.

tag: disease group

tag: fixation/preservation technique

tag: age (years)

tag: gender

value: f

tag: inhalative corticosteroid dose (daily fluticasone equivalent µg)

tag: cumulative packyears

tag: diff cell count

value: alveolar macrophages (%):27.625

value: neutrophils (%):68.125

value: eosinophils (%):0.625

value: lymphocytes (%):2.125

value: ciliated cells (%):0.375

value: monocytes (%):0.25

value: squamous cells (%):0.875

tag: rna integrity number (rin)


title: MG-Hal+Est+Prog-D9

description: Mammary gland gene expression from pigs given bromocriptine treatment for 8 days then haloperidol+estrogen+progesterone treatment for 5 days

source_name: Pig mammary gland, ovariectomized, haloperidol+estrogen+progesterone treated

value: haloperidol+estrogen+progesterone


title: MG-Progesterone-D4

description: Mammary gland gene expression from pigs given bromocriptine for 8 days, then bromocriptine+progesterone for 5 days

source_name: Pig mammary gland, ovariectomized, bromocriptine+progesterone treated

value: bromocriptine+progesterone


title: mAST-CTX

type: SRA

city: Seoul

first: Jae-Jin

last: Song

address: 222, Wangsimni-ro

department: Hanyang Biomedical Research Institute

country: South Korea

institute: Hanyang university

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were mapped to mouse genome (mm9) using STAR program.
Read counts were calculated using HTSeq program.
The differential expression analysis was performed using DESeq and FPKM(Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reat counts and FPKM for each sample

organism: Mus musculus

source_name: cortex

growth_protocol: Astrocytes were isolated from mouse or rat VMs or cortices (Ctx) on postnatal day 5–7 and cultured in astro-medium

extract_protocol:
Total RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) through the RNA isolation protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Astrocyte progenitor cells

value: cortex

tag: developmental stage

value: postnatal day 5

tag: passages

tag: strain

value: ICR


title: Sputum_Healthy_6

value: HC

value: RLT

value: alveolar macrophages (%):80

value: neutrophils (%):14.25

value: eosinophils (%):0

value: lymphocytes (%):1.875

value: ciliated cells (%):2.375

value: monocytes (%):0

value: squamous cells (%):1.5


title: MG-sham-D1

description: Mammary gland gene expression from pigs given saline treatment for 13 days

source_name: Pig mammary gland, sham-operated, saline treated

value: sham-operated

value: saline

value: Mammary gland


title: Sputum_Healthy_5

value: HOPE

value: m

value: alveolar macrophages (%):81.25

value: neutrophils (%):6.5

value: eosinophils (%):0.25

value: lymphocytes (%):7.625

value: ciliated cells (%):1.625

value: monocytes (%):0.375

value: squamous cells (%):2.375


title: MG-Bromo-D2

description: Mammary gland gene expression from pigs given bromocriptine treatment for 13 days

source_name: Pig mammary gland, ovariectomized, bromocriptine treated

value: ovariectomized

value: bromocriptine


title: mNPC-CTX

value: Neural progenitor cells

value: cortex

value: E12 embryos

value: ICR


title: Sputum_Healthy_2

value: HC

value: RLT

value: alveolar macrophages (%):44

value: neutrophils (%):46.75

value: eosinophils (%):0

value: lymphocytes (%):0.875

value: ciliated cells (%):2.625

value: monocytes (%):0.125

value: squamous cells (%):5.625


title: MG-Hal+Prog-C8

value: haloperidol+progesterone

value: Mammary gland


title: Sputum_Healthy_1

value: HOPE

value: m

value: alveolar macrophages (%):16.25

value: neutrophils (%):71.375

value: eosinophils (%):0.125

value: lymphocytes (%):0

value: ciliated cells (%):1.875

value: monocytes (%):0

value: squamous cells (%):10.375


title: DKO MEF, p63, etoposide treatment x 6 hours

city: New York

first: Emily

last: Cheng

state: NY

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: SV40 transformed Bax/Bak DKO MEF_p63_etoposide

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen Ovation PicoSL WTA System V2 system from 500pg-50 ng total RNA

growth_protocol:
Embryo at E13.5 was used for preparation of mouse embryonic fibroblast
Mouse embryonic fibroblasts were cultured under standard tissue culture conditions, at 37 degrees C in DMEM supplemented with 10% FBS

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

treatment_protocol: DKO MEFs were mock treated or treated with etoposide (10 ug/mL) for 6 hours prior to RNA extraction

tag: strain background

value: mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: SV40 transformed BAX/BAK double knockout (DKO)

tag: transduced with

value: retrovirus expressing p63

tag: treated with

value: etoposide (10 micrograms/ul) for 6 hrs


title: DNA from sputum sample Healthy_4

type: genomic

hyb_protocol: Standard Illumina Infinium HumanMethylation 450K BeadChip protocol.

scan_protocol: Illumina iScan system on standard settings.

data_processing: In silico analysis was performed within the R/Bioconductor programming environment. IDAT read-in, data processing and normalization were performed using functions from the minfi package (version 1.32.0). No further filtering steps have been performed to the data submitted to GEO.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Genomic DNA was bisulfite converted usind the EZ DNA Methylation kit (ZymoResearch, standard protocol). Further processing followed the standard Illumina Infinium HumanMethylation 450K BeadChip protocol.

extract_protocol: Depending on the method of fixation/preservation, sputum samples were: 1) thawed and directly supplied to nucleic acid extraction, or: 2) sputum cells were extracted from paraffin bocks (by cutting thick slices with a microtome using alcohol- and heat-sterilized blades) and deparaffinized by incubation with xylene and ethanol, followed by a drying step using a vacuum centrifuge. Extraction of nucleic acids was performed using the AllPrep Micro Kit (Qiagen) following the manufacturer's standard instructions. Nucleic acid yield was measured using a NanoDrop spectrophotometer (Thermo Fisher).

treatment_protocol: Induced sputum samples were obtained following inhalation of nebulized saline. Following manual separation from saliva and contaminants, sputum plugs were incubated with Sputolysin (DTT, Calbiochem), followed by suspension in PBS and filtration through nylon meshes and centrifugation (with removal of supernatant). Purified sputum cell pellets were resuspended in BSA/PBS and aliquots were taken for preparation of cytospin slides. The latter were subsequently stained (Giemsa) und subjected to differential cell counting. Remaining sputum cell suspensions were again pelleted by centrifugation and, depending on the method of fixation/preservation applied, 1) resuspended in RLT lysis buffer and subsequently stored at -80°C, or, 2) preserved with HOPE medium and later casted into a paraffin block (as commonly performed in routine pathology protocols) with subsequent storage at 4°C.

value: Healthy

value: RLT

tag: inhalative corticosteroid dose (daily fluticasone equivalent ug)

value: alveolar macrophages (%):47.875

value: neutrophils (%):41.875

value: eosinophils (%):0

value: lymphocytes (%):0.875

value: ciliated cells (%):2.125

value: monocytes (%):0.125

value: squamous cells (%):7.125


title: Sputum_Healthy_3

tag: disease group

value: HC

value: HOPE

value: f

value: alveolar macrophages (%):21.375

value: neutrophils (%):76.125

value: lymphocytes (%):1

value: ciliated cells (%):0.875

value: monocytes (%):0.25

value: squamous cells (%):0.375


title: MG-Hal+Est+Prog-C9

tag: status

value: ovariectomized

tag: treatment

value: haloperidol+estrogen+progesterone

tag: tissue

value: Mammary gland


title: DNA from sputum sample Healthy_5

value: Healthy

tag: fixation/preservation technique

tag: age (years)

tag: gender

value: m

value: alveolar macrophages (%):81.25

value: neutrophils (%):6.5

value: eosinophils (%):0.25

value: lymphocytes (%):7.625

value: ciliated cells (%):1.625

value: monocytes (%):0.375

value: squamous cells (%):2.375


title: Sputum_COPD_10

source_name: COPD sputum sample

value: CN

value: HOPE

tag: inhalative corticosteroid dose (daily fluticasone equivalent µg)

tag: cumulative packyears

tag: diff cell count

value: alveolar macrophages (%):6.875

value: neutrophils (%):90.875

value: eosinophils (%):0

value: lymphocytes (%):0.375

value: ciliated cells (%):0.125

value: monocytes (%):0

value: squamous cells (%):1.75

tag: rna integrity number (rin)


title: DNA from sputum sample Healthy_3

value: Healthy

value: f

value: alveolar macrophages (%):21.375

value: neutrophils (%):76.125

value: lymphocytes (%):1

value: ciliated cells (%):0.875

value: monocytes (%):0.25

value: squamous cells (%):0.375


title: DNA from sputum sample Healthy_10

value: RLT

value: m

value: alveolar macrophages (%):57.875

value: neutrophils (%):33.125

value: eosinophils (%):1.125

value: lymphocytes (%):1.625

value: ciliated cells (%):2.625

value: monocytes (%):0.875

value: squamous cells (%):2.75


title: DNA from sputum sample Healthy_9

value: Healthy

value: alveolar macrophages (%):66.25

value: neutrophils (%):28

value: eosinophils (%):0.25

value: lymphocytes (%):2.5

value: ciliated cells (%):1

value: monocytes (%):0

value: squamous cells (%):2


title: DNA from sputum sample Healthy_2

value: RLT

value: alveolar macrophages (%):44

value: neutrophils (%):46.75

value: eosinophils (%):0

value: lymphocytes (%):0.875

value: monocytes (%):0.125

value: squamous cells (%):5.625


title: MG-Hal+Estrogen-C7

description: Mammary gland gene expression from pigs given bromocriptine treatment for 8 days then haloperidol+estrogen treatment for 5 days

source_name: Pig mammary gland, ovariectomized, haloperidol+estrogen treated

value: ovariectomized

value: haloperidol+estrogen

value: Mammary gland


title: DKO MEF, p63, mock treatment x 6 hours

source_name: SV40 transformed Bax/Bak DKO MEF_p63_mock

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

value: SV40 transformed BAX/BAK double knockout (DKO)

value: retrovirus expressing p63

value: mock-treated


title: Sputum_COPD_9

value: CN

value: HOPE

value: m

value: alveolar macrophages (%):21.125

value: neutrophils (%):76.625

value: eosinophils (%):0.625

value: lymphocytes (%):0.75

value: ciliated cells (%):0.125

value: squamous cells (%):0.75


title: MG-Haloperidol-C6

description: Mammary gland gene expression from pigs given bromocriptine treatment for 8 days then haloperidol treatment for 5 days

source_name: Pig mammary gland, ovariectomized, haloperidol treated

value: haloperidol


title: DNA from sputum sample COPD_10

value: COPD

value: alveolar macrophages (%):6.875

value: neutrophils (%):90.875

value: eosinophils (%):0

value: lymphocytes (%):0.375

value: monocytes (%):0

value: squamous cells (%):1.75


title: DNA from sputum sample COPD_7

value: alveolar macrophages (%):15

value: neutrophils (%):83.375

value: eosinophils (%):0.25

value: lymphocytes (%):0

value: ciliated cells (%):0.5

value: squamous cells (%):0.875


title: DKO MEF, GFP, mock treatment x 6 hours

source_name: SV40 transformed Bax/Bak DKO MEF_GFP_mock

tag: strain background

value: mouse embryonic fibroblasts (MEFs)

value: SV40 transformed BAX/BAK double knockout (DKO)

value: retrovirus expressing GFP

value: mock-treated


title: DKO MEF, GFP, etoposide treatment x 6 hours

source_name: SV40 transformed Bax/Bak DKO MEF_GFP_etoposide

tag: genotype/variation

value: etoposide (10 micrograms/ul) for 6 hrs


title: PDAC_poor prognosis_rep9

city: Shenyang

first: CE

last: Li

address: Nanjing Street

country: China

institute: China Medical University

description: Each probe is printed in triplicate on an array for computing averages. Positive control  probes are used for normalization and assay quality control

hyb_protocol: Prepare the labeled RNA sample for hybridization by combining with 2x Hyb buffer and water. The volumes of each component to be added will depend on the volume of the hybridization chamber. Incubate the sample at 90-95º C for 5 min to denature.Cool sample by spinning down briefly.Inject the sample into the hybridization chamber. Run hybridization at 42º C with agitation for 16 hours (or longer).Run three wash cycles at 25 ºC using diluted Wash Buffer I. Wash time: 20 sec.,soak time: 10 sec.Inject the 1:250 diluted SA-S dye stain solution into the hybridization chamber.Incubate at 25ºC for 30 min. Shield the chamber from light to minimize effects of photobleaching of the dye.After the incubation, unload chip from the hybstation and transfer into an appropriately sized container filled with Wash Buffer I, use no less than 20ml Wash Buffer I per chip per wash. Wash chip at room temperature for 5 minutes with periodic, gentle agitation.Transfer chip to a second container with fresh Wash Buffer I. Wash chip again at room temperature for 5 minutes with periodic, gentle agitation. Transfer chip to a third container filled with Wash Buffer II. Wash at room temperature for 30 sec with continuous, gentle agitation. Dry chip by air blower or centrifugation at 600 x g for 3 min.

scan_protocol: Consult the scanner manufacturer instructions for laser and PMT settings. The SA-S dye stain signal can be detected using the scanner’s 635 nm wavelength (Cy5) channel. When scanning, start from the end of the chip opposite the label.

data_processing:
The .gal web file download provides an array list in .txt file and .gal file formats. Visit http://www.genosensorcorp.com/microRNA_full_kit.html for downloads. Multiple subarrays were printed on each chip. The name and location of each chemical probe is listed and labeled in the software. Each chemical was printed in triplicate. Arrays include known microRNA probes as well as both positive and negative controls. Load the .gal files or convert the text file to the correct format that your scanner requires. Since the first chemicals on each sub-array are positive controls, you should see them on the upper-left corner of each sub-array, and they are in triplicate. Proceed with data computation after gridding
Normalization is represented by the ratio of the average of gene signal intensity of a specific gene vs. global signal intensity.  The file Copy of Data Summary CMU-2.xls includes all raw data, statistics normalized signal and fold-changes. The sample tables include data for all samples except the negative control 'buffer' (Two values of 'buffer' signal are available in the file Copy of Data Summary CMU-2.xls).

source_name: PDAC

label_protocol: The GenoExplorer™ miRNA Labeling Kit (patent pending) was used. 1-2.5 micrograms of RNA used to prepare labeled RNA.

growth_protocol: Among the 120 cases, 20 cases with similar clinicopathologic features and treatment but considerable different outcomes, composed the initial screening cohort for the miRNA microarray. What’s more, half of the patients had an extremely poor prognosis dying within the first year of diagnosis and were classified as “poor prognosis”, and the other 10 cases survived more than 21 months, which were classified as “good prognosis”.

extract_protocol: RNA was extracted by FFPE PDAC tissues with a miRNeasy FFPE kit(Qiagen, USA),following the manufacturer's instructions.

treatment_protocol: A total of 20 consecutive patients underwent surgery for potentially resectable primary pancreatic carcinoma at the Shengjing Hospital of China Medical University. And we got FFPE tissue sample after surgery

tag: prognosis

value: poor

value: male

value: PDAC-FFPE

tag: Stage

value: IIB


title: PDAC_poor prognosis_rep10

value: IIA


title: DNA from sputum sample COPD_9

value: COPD

value: HOPE

value: m

tag: inhalative corticosteroid dose (daily fluticasone equivalent ug)

value: alveolar macrophages (%):21.125

value: neutrophils (%):76.625

value: eosinophils (%):0.625

value: lymphocytes (%):0.75

value: ciliated cells (%):0.125

value: monocytes (%):0

value: squamous cells (%):0.75


title: MG-Estrogen+Prog-C5

description: Mammary gland gene expression from pigs given bromocriptine for 8 days, then bromocriptine+estrogen+progesterone for 5 days

source_name: Pig mammary gland, ovariectomized, bromocriptine+estrogen+progesterone treated

value: ovariectomized

value: bromocriptine+estrogen+progesterone

value: Mammary gland


title: DNA from sputum sample COPD_8

tag: disease group

value: alveolar macrophages (%):10.75

value: neutrophils (%):87.25

value: eosinophils (%):1.75

value: lymphocytes (%):0

value: ciliated cells (%):0.25

value: squamous cells (%):0


title: Sputum_COPD_8

value: CN

value: HOPE

value: m


title: MG-Estrogen-C3

description: Mammary gland gene expression from pigs given bromocriptine for 8 days, then bromocriptine+estrogen for 5 days

source_name: Pig mammary gland, ovariectomized, bromocriptine+estrogen treated

tag: status

value: bromocriptine+estrogen


title: Sputum_COPD_7

value: alveolar macrophages (%):15

value: neutrophils (%):83.375

value: eosinophils (%):0.25

value: ciliated cells (%):0.5

value: squamous cells (%):0.875


title: MG-Progesterone-C4

value: ovariectomized

tag: treatment

value: bromocriptine+progesterone


title: PDAC_poor prognosis_rep8

value: poor

value: female

tag: tissue

value: PDAC-FFPE

value: IIB


title: DNA from sputum sample Healthy_1

value: Healthy

tag: fixation/preservation technique

value: alveolar macrophages (%):16.25

value: neutrophils (%):71.375

value: eosinophils (%):0.125

value: lymphocytes (%):0

value: ciliated cells (%):1.875

value: monocytes (%):0

value: squamous cells (%):10.375


title: Sputum_COPD_5

value: CN

value: RLT

tag: age (years)

value: m

value: alveolar macrophages (%):2.75

value: neutrophils (%):96.125

value: eosinophils (%):0.875

value: ciliated cells (%):0

value: squamous cells (%):0.25


title: MG-Bromo-C2

value: ovariectomized

value: bromocriptine

value: Mammary gland


title: PDAC_poor prognosis_rep7

value: poor

tag: gender

value: male

value: PDAC-FFPE

value: IIA


title: DNA from sputum sample COPD_6

value: COPD

value: HOPE

value: alveolar macrophages (%):1.125

value: neutrophils (%):98.125

value: eosinophils (%):0.375

value: lymphocytes (%):0

value: monocytes (%):0

value: squamous cells (%):0.375


title: Sputum_COPD_3

value: CN

value: m

tag: inhalative corticosteroid dose (daily fluticasone equivalent µg)

value: alveolar macrophages (%):4.875

value: neutrophils (%):94.5

value: eosinophils (%):0

value: ciliated cells (%):0.125

value: squamous cells (%):0.5


title: Sputum_Asthma_9

source_name: Asthma sputum sample

value: AE

value: RLT

value: f

tag: cumulative packyears

value: alveolar macrophages (%):17.375

value: neutrophils (%):66.375

value: eosinophils (%):4.25

value: lymphocytes (%):0.625

value: ciliated cells (%):0.625

value: squamous cells (%):10.75


title: MG-Hal+Est+Prog-B9

value: ovariectomized

value: haloperidol+estrogen+progesterone

value: Mammary gland


title: Sputum_COPD_4

value: CN

value: m

tag: diff cell count

value: alveolar macrophages (%):7.625

value: neutrophils (%):90.25

value: eosinophils (%):0.5

value: lymphocytes (%):0

value: ciliated cells (%):1.375

value: monocytes (%):0

value: squamous cells (%):0.25


title: MG-Hal+Prog-B8

source_name: Pig mammary gland, ovariectomized, haloperidol+progesterone treated

value: haloperidol+progesterone


title: MG-sham-C1

value: sham-operated

value: saline


title: PDAC_poor prognosis_rep5

value: poor

value: male

value: PDAC-FFPE

value: IIA


title: DNA from sputum sample COPD_3

value: COPD

value: HOPE

value: alveolar macrophages (%):4.875

value: neutrophils (%):94.5

value: eosinophils (%):0

value: ciliated cells (%):0.125

value: squamous cells (%):0.5


title: DNA from sputum sample COPD_5

value: RLT

value: m

value: alveolar macrophages (%):2.75

value: neutrophils (%):96.125

value: eosinophils (%):0.875

value: lymphocytes (%):0

value: ciliated cells (%):0


title: DNA from sputum sample COPD_4

value: alveolar macrophages (%):7.625

value: neutrophils (%):90.25

value: eosinophils (%):0.5

value: ciliated cells (%):1.375

value: monocytes (%):0

value: squamous cells (%):0.25


title: DNA from sputum sample COPD_1

value: COPD

value: HOPE

value: f

value: alveolar macrophages (%):11

value: neutrophils (%):83.125

value: eosinophils (%):4

value: lymphocytes (%):0.5

value: ciliated cells (%):0.875


title: PDAC_poor prognosis_rep6

value: poor

value: female

value: PDAC-FFPE

value: IIA


title: PDAC_poor prognosis_rep3

value: IIB


title: MG-Hal+Estrogen-B7

value: ovariectomized

value: haloperidol+estrogen

value: Mammary gland


title: DNA from sputum sample COPD_2

value: m

value: alveolar macrophages (%):8.625

value: neutrophils (%):88.5

value: eosinophils (%):1.5

value: lymphocytes (%):0.375

value: ciliated cells (%):0.25

value: monocytes (%):0

value: squamous cells (%):0.75


title: DNA from sputum sample Asthma_9

value: Asthma

value: RLT

value: f

value: alveolar macrophages (%):17.375

value: neutrophils (%):66.375

value: eosinophils (%):4.25

value: lymphocytes (%):0.625

value: ciliated cells (%):0.625

value: squamous cells (%):10.75


title: DNA from sputum sample Asthma_7

value: HOPE

value: m

value: alveolar macrophages (%):59.5

value: neutrophils (%):31.375

value: eosinophils (%):1.75

value: lymphocytes (%):1.625

value: ciliated cells (%):2.75

value: squamous cells (%):3


title: PDAC_poor prognosis_rep4

value: poor

value: male

value: PDAC-FFPE

value: IIB


title: Sputum_Asthma_6

value: AE

value: alveolar macrophages (%):13.125

value: neutrophils (%):78.875

value: eosinophils (%):5.75

value: lymphocytes (%):0.125

value: ciliated cells (%):1.625

value: monocytes (%):0.25

value: squamous cells (%):0.25

tag: rna integrity number (rin)


title: PDAC_poor prognosis_rep2

value: female


title: DNA from sputum sample Asthma_8

value: Asthma

value: RLT

value: m

value: alveolar macrophages (%):9.125

value: neutrophils (%):84.75

value: eosinophils (%):2.25

value: lymphocytes (%):0.875

value: ciliated cells (%):2.25

value: squamous cells (%):0.5


title: MG-Haloperidol-B6

value: ovariectomized

value: haloperidol

value: Mammary gland


title: MG-Estrogen+Prog-B5

value: bromocriptine+estrogen+progesterone


title: Sputum_Asthma_8

value: AE


title: DNA from sputum sample Asthma_4

value: alveolar macrophages (%):6.25

value: neutrophils (%):14.125

value: eosinophils (%):77

value: lymphocytes (%):0.125

value: ciliated cells (%):1.625

value: monocytes (%):0

value: squamous cells (%):0.875


title: DNA from sputum sample Asthma_5

value: Asthma

value: HOPE

value: m

value: alveolar macrophages (%):48.875

value: neutrophils (%):46.5

value: eosinophils (%):1.5

value: ciliated cells (%):1

value: squamous cells (%):1.25


title: PDAC_good prognosis_rep10

value: good

value: female

value: PDAC-FFPE

value: IIA


title: PDAC_good prognosis_rep8


title: PDAC_poor prognosis_rep1

value: poor

value: male

value: IIB


title: PDAC_good prognosis_rep9


title: Sputum_Asthma_7

value: AE

value: alveolar macrophages (%):59.5

value: neutrophils (%):31.375

value: eosinophils (%):1.75

value: lymphocytes (%):1.625

value: ciliated cells (%):2.75

value: monocytes (%):0

value: squamous cells (%):3


title: DNA from sputum sample Asthma_6

value: Asthma

value: HOPE

value: m

value: alveolar macrophages (%):13.125

value: neutrophils (%):78.875

value: eosinophils (%):5.75

value: lymphocytes (%):0.125

value: ciliated cells (%):1.625

value: monocytes (%):0.25

value: squamous cells (%):0.25


title: HHSEC Adult 200565-3

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

library_source: genomic

data_processing:
Trimmomatic was used for trimming reads with adapter, primer, low quality reads.
BSMAP was used for mapping processed reads to hg38 reference
Duplicate reads were removed using picard tool.
Mapped data were converted into methylation profile using methRatio.py available in BSMAP
Methylkit was used to calculate methylation difference between samples
Genome_build: hg38
Supplementary_files_format_and_content: Chromosome, Position, Start, End, Strand, pvalue, qvalue, methylation difference (LSECs adult - LSECs fetal), Overlapping SNPs

source_name: Human hepatic sinusoidal endothelial cells

growth_protocol: Commercial endothelial cells were ordered from ScienCell research laboratories via Provitro GmbH. All molecular materials were isolated at passage one as stated by manufacturing certificate.

extract_protocol:
Qiagen kit was used for extraction
Bisulfite conversion of purified gDNA with EpiTect Fast chemistry and subsequent library generation: i) Whole genome bisulfite library generation using QIAseq Methyl Library Kit, which include random primed double strand synthesis, adapter ligation and library aplification, ii) targeted methylation sequencing using QIAseq Methyl Panel Kit as well as TrueSeq DNA Methylation Kit, which include adapter ligation introducing the frist sequencing index and UMI sequence, target enrichment using specific primers (custom Panel CMHS-10010Z-102) and final library amplification introducing second library index.

treatment_protocol: No treatment

tag: developmental stage

value: Adult

value: Male


title: PDAC_good prognosis_rep6

value: good

value: female

value: PDAC-FFPE

value: IIB


title: MG-Bromo-B2

value: ovariectomized

value: bromocriptine

value: Mammary gland


title: Sputum_Asthma_2

value: AE

value: HOPE

value: f

value: alveolar macrophages (%):60.375

value: neutrophils (%):32.75

value: eosinophils (%):2.375

value: lymphocytes (%):0.75

value: ciliated cells (%):3.25

value: monocytes (%):0

value: squamous cells (%):0.5


title: Sputum_Asthma_5

value: m

value: alveolar macrophages (%):48.875

value: neutrophils (%):46.5

value: eosinophils (%):1.5

value: lymphocytes (%):0.875

value: ciliated cells (%):1

value: squamous cells (%):1.25


title: HHSEC Adult 200356-3

value: Adult

value: Male


title: PDAC_good prognosis_rep7

value: good

value: male

value: PDAC-FFPE

value: IIA


title: Sputum_Asthma_1

value: AE

value: RLT

value: f

value: alveolar macrophages (%):21.125

value: neutrophils (%):71.5

value: eosinophils (%):5

value: lymphocytes (%):0.125

value: monocytes (%):0.25

value: squamous cells (%):1


title: Sputum_Asthma_3

value: m

value: alveolar macrophages (%):15.625

value: neutrophils (%):66.25

value: eosinophils (%):16.375

value: lymphocytes (%):0.75

value: ciliated cells (%):0.5

value: monocytes (%):0

value: squamous cells (%):0.5


title: MG-sham-B1

value: sham-operated

value: saline

value: Mammary gland


title: Sputum_Asthma_4

value: AE

value: RLT

value: alveolar macrophages (%):6.25

value: neutrophils (%):14.125

value: eosinophils (%):77

value: ciliated cells (%):1.625

value: squamous cells (%):0.875


title: PDAC_good prognosis_rep5

value: good

value: female

value: PDAC-FFPE

value: IIB


title: DNA from sputum sample Asthma_3

value: Asthma

value: m

value: alveolar macrophages (%):15.625

value: neutrophils (%):66.25

value: eosinophils (%):16.375

value: lymphocytes (%):0.75

value: ciliated cells (%):0.5


title: HHSEC Adult 200565-2

value: Adult

value: Male


title: MG-Hal+Prog-A8

value: ovariectomized

value: haloperidol+progesterone

value: Mammary gland


title: MG-Progesterone-B4

source_name: Pig mammary gland, ovariectomized, bromocriptine+progesterone treated

value: bromocriptine+progesterone


title: MG-Hal+Est+Prog-A9

source_name: Pig mammary gland, ovariectomized, haloperidol+estrogen+progesterone treated

value: haloperidol+estrogen+progesterone


title: HHSEC Adult 200565-1


title: MG-Hal+Estrogen-A7

value: haloperidol+estrogen


title: MG-Estrogen-B3

value: bromocriptine+estrogen


title: HHSEC Adult 200356-2


title: HHSEC Adult 200356-1


title: PDAC_good prognosis_rep4

value: good

value: female

value: PDAC-FFPE

value: IIB


title: PDAC_good prognosis_rep3

value: male


title: HHSEC Fetal 11605

value: Fetal


title: PDAC_good prognosis_rep2


title: HHSEC Fetal 11359


title: MG-Estrogen-A3


title: MG-Estrogen+Prog-A5

value: bromocriptine+estrogen+progesterone


title: PDAC_good prognosis_rep1


title: MG-Bromo-A2

value: bromocriptine


title: HPAEC 11925

description:
11925
Sample 12

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw data was processed using minfi package in R. SWAN method was used for normalization. Average beta values were used for analysis.

label: Cy3 and Cy5

source_name: Human pulmonary arterial endothelial cells

label_protocol: standard Illumina protocol

growth_protocol: Commercial endothelial cells from ScienCell Research

extract_protocol: Qiagen Kit

value: fetal


title: MG-Progesterone-A4


title: MG-Haloperidol-A6

value: haloperidol


title: MG-sham-A1

source_name: Pig mammary gland, sham-operated, saline treated

value: sham-operated

value: saline


title: HUVEC 10297

description:
10297
Sample 13

source_name: Human umbilical vein endothelial cells

value: Male


title: HHSEC Fetal 10691


title: HUVEC 10320

description:
10320
Sample 14


title: Huvec DG-LRG1

type: protein

first: Yebin

last: Im

address: 504-302, 1, Gwanak-ro, Gwanak-gu,

department: Biological Sciences

institute: Seoul National University

description: phosphorylated and non-phosphorylated protein expression in HUVEC cell treated with DG-LRG1

hyb_protocol: Refer to Full Moon Biosystem antibody array protocol manual

scan_protocol: Slides were scanned by E-Biogen service using Full Moon Bio. Phospho Explorer

data_processing: Scanned signal intensity was log2-transformed. The log2-transformed data for two conditions (control, DG-LRG1 treated) were then quantile-normalized. The data processing including quantile normalization was done using MATLAB 9.7.0.1296695 (R2019b) Update 4.

molecule: protein

source_name: HUVEC cell, 30 minutes, 1μg/ml DG-LRG1

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were authenticated according to ATCC guidelines and used within 6 months of receipt. HUVECs were cultured in EBM-2, supplemented with EGM-2, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin on gelatin (0.1% in DDW) pre-coated plates. Cells were maintained at 37°C under humidified 5% CO2 conditions. Cells between passages 2 and 7 were used.

extract_protocol: Whole-cell lysates of control and DG-LRG1 treated HUVECs were prepared under Full Moon Biosystem antibody array protocol manual, and aliquots of lysates containing 50 μg of protein were used.

treatment_protocol: HUVECs were serum-starved for 8 hours  and then incubated with an anti-TGFβ1 antibody for 1 hour, after which HUVECs were stimulated with 1μg/ml DG-LRG1 for 30 minutes.

tag: cell line

value: HUVEC

value: 1μg/ml DG-LRG1 30 min


title: DNA from sputum sample Asthma_2

value: Asthma

value: HOPE

value: f

value: alveolar macrophages (%):60.375

value: neutrophils (%):32.75

value: eosinophils (%):2.375

value: lymphocytes (%):0.75

value: ciliated cells (%):3.25

value: monocytes (%):0

value: squamous cells (%):0.5


title: Huvec Control

description: phosphorylated and non-phosphorylated protein expression in HUVEC cell

source_name: HUVEC cell, 0 minutes

label_protocol: Refer to Full Moon Biosystem antibody array protocol manual


title: HCMEC 11926

description:
11926
Sample 9

source_name: Human cardiac microvascular endothelial cells

value: fetal


title: HPAEC 9134

description:
9134
Sample 10


title: p38 KO -2

status: Public on Oct 24 2020

city: Kyoto

first: Hiroko

last: Morimoto

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA implemented in the GeneSpring GX

source_name: p38 KO 1 day

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) were used according to Affymetrix protocol.

growth_protocol: GS cells infected with retrovirus(KD) or Adenovirus(KO) were cultured  using  GDNF  and  FGF2, as  described  previously  (Kanatsu-Shinohara  et  al.,  2011) and medium was changed on the next day of infection.

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: GS cells were seeded  onto a feeder cell layer of mitomycin C-treated mouse embryonic fibroblasts (MEFs) and infected with indicated retroviral  or  Adenovirus.

value: mouse germline stem cells (GS cells)

tag: genotype

value: p38 (Mapk14) KO


title: p38 WT -1

source_name: Control KO 1 day

value: p38 (Mapk14) WT


title: DNA from sputum sample Asthma_1

value: RLT

value: alveolar macrophages (%):21.125

value: neutrophils (%):71.5

value: eosinophils (%):5

value: lymphocytes (%):0.125

value: ciliated cells (%):1

value: monocytes (%):0.25

value: squamous cells (%):1


title: ERK5 KO -1

source_name: ERK5 KO 1 day

value: ERK5 (Mapk7) KO


title: p38 KO -1


title: HPAEC 10321

description:
10321
Sample 11

value: Male


title: p38 WT -2


title: ERK5 KO -2


title: ERK5 WT -1

value: ERK5 (Mapk7) WT


title: ChIPseq-Input-Rhesus-Testis

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

data_processing:
ChIP-seq data were mapped to the rhesus reference genome rheMac8 using Bowtie2 (version 1.1.0) with the parameter --very-sensitive. We then calculated read density normalized by sequencing depth (bigWig) across the rhesus genome.
Gene annotations and rRNA sequences are fetched from Ensembl (Release 82). All RIP-seq data were first mapped to ribosomal RNAs (rRNAs) using Bowtie2 (version 2.2.5) with default parameters to remove rRNAs (Langmead and Salzberg, 2012). Unmapped reads were then mapped to the mm10 genome from the UCSC genome browser using STAR (version 020201) allowing up to 2 mismatch and up to 100 mapping locations (Dobin et al., 2013). We then calculated read density normalized by sequencing depth (bigWig) across the mouse genome.
Genome_build: mm10, rheMac8
Supplementary_files_format_and_content: bigWig

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Briefly, small pieces of frozen testis tissue were cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. We next crushed fixed tissues in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) by 40 strokes with a “B” pestle of Dounce homogenizer (Kimble-Chase, Vineland, USA). Thereafter, lysate was sonicated using Covaris ultrasonicator (Covaris, E220) to shear the chromatin to 150–200 bp. Lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl).  We performed immunoprecipitation using 6 µg rabbit polyclonal anti-H3K27Ac antibody (Abcam, ab4729). Following the immunoprecipitation, we extracted DNA with phenol:chloroform:isoamyl alcohol.
Libraries construction for anti-H3K27Ac, and input DNA were performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

value: Testis

tag: antibody

value: Input

value: adult


title: ChIPseq-H3K27ac-Rhesus-Testis

tag: Stage


title: Bcl6b KD -1

source_name: Bcl6b KD 2 days

value: mouse germline stem cells (GS cells)

value: Bcl6b KD


title: Nox1 KD -2

source_name: Nox1 KD 2 days

value: Nox1 KD


title: CHD-C38-1 [Heart]

first: Alejandro

last: Martin Trujillo

address: Hess Center for Science and Medicine at Mount Sinai,1470 Madison Avenue, 8th Floor

institute: Icahn school of medicine at mount sinai hospital

description: tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Raw Beta values were background and color corrected and quantile normalized using lumi and methylumi R packages. Finally, resulting Beta values were corrected for Infinium probe design biases
Processed data file includes: Average Beta and detection Pvalue
The file SignalIntensitiesData.GeoSubmission.AMT.txt includes Unmethylated, methylated signal intensities and detection P value for all Blood samples. Raw data for Heart samples are provided in the idat files.

label: Cy3, Cy5

source_name: Heart

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Heart

tag: diagnosis

value: congenital heart defect


title: CHD-C45-1 [Heart]

description: tissue


title: CHD-C49-1 [Heart]

description: tissue


title: CHD-C10-1 [Heart]

description: tissue


title: CHD-C50-1 [Heart]

description: tissue


title: Control KD -2

source_name: Control KD 2 days

value: Control KD


title: HCMEC 10319

description:
10319
Sample 8

value: fetal


title: CHD-C52-3 [Heart]

description: tissue


title: CHD-C55-1 [Heart]

description: tissue


title: ERK5 WT -2


title: Nox1 KD -1


title: HPMEC 11415

description:
11415
Sample 5

source_name: Human pulmonary microvascular endothelial cells


title: Bcl6b KD -2


title: HPMEC 11844

description:
11844
Sample 6


title: CHD-C58-2 [Heart]

description: tissue


title: CHD-L225-1 [Heart]

description: tissue


title: CHD-L280-1 [Heart]

description: tissue


title: CHD-L283-1 [Heart]

description: tissue


title: HCMEC 10299

description:
10299
Sample 7


title: CHD-L118-1 [Heart]

description: tissue


title: LSEC fetal 11605

description:
11605
Sample 3

source_name: Human hepatic sinusoidal endothelail cells


title: CHD-L216-1 [Heart]

description: tissue


title: CHD-C8-2 [Heart]

description: tissue


title: CHD-L302-1 [Heart]

description: tissue


title: CHD-L334-1 [Heart]

description: tissue


title: CHD-L306-1 [Heart]

description: tissue


title: HPMEC 10298

description:
10298
Sample 4


title: CHD-C9-1 [Heart]

description: tissue


title: CG0012-2040 [Blood]

description: tissue

source_name: Blood

value: Blood


title: LSEC fetal 11359

description:
11359
Sample 2


title: CG0011-8506 [Blood]

description: tissue


title: CG0012-1216 [Blood]

description: tissue


title: CG0018-6812 [Blood]

description: tissue


title: CG0011-8929 [Blood]

description: tissue


title: CG0010-0492 [Blood]

description: tissue


title: CG0012-2575 [Blood]

description: tissue


title: LSEC fetal 10691

description:
10691
Sample 1


title: CG0011-9158 [Blood]

description: tissue


title: CG0012-3513 [Blood]

description: tissue


title: CG0009-9892 [Blood]

description: tissue


title: CG0009-9531 [Blood]

description: tissue


title: CG0011-8317 [Blood]

description: tissue


title: CG0009-8565 [Blood]

description: tissue


title: CG0009-7979 [Blood]

description: tissue


title: CG0009-8816 [Blood]

description: tissue


title: CG0017-0473 [Blood]

description: tissue


title: CG0016-9655 [Blood]

description: tissue


title: CG0010-2264 [Blood]

description: tissue


title: CG0016-9262 [Blood]

description: tissue


title: CG0016-7474 [Blood]

description: tissue


title: CG0016-2267 [Blood]

description: tissue


title: CG0015-7195 [Blood]

description: tissue


title: CG0016-4718 [Blood]

description: tissue


title: CG0017-7915 [Blood]

description: tissue


title: Human islets 51 from non-diabetic donor

city: Bruxelles

first: Anthony

last: Piron

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

description:
ULB-CTL150711
processed data files:
de-t2d.tsv.gz

data_processing:
The sequencing reads were mapped to the human genome using Tophat v2.0.13 (https://ccb.jhu.edu/software/tophat/index.shtml)
The transcript quantification was done using flux-capacitor v1.2.4  (http://confluence.sammeth.net/display/FLUX/Home) which deconvolves the reads mapping into mutliple transcripts optimizing a linear equation system.
The paired differential analysis (metabolic stress conditions vs matched controls) was done using the R/Bioconductor package EdgeR v3.30.1 (http://bioconductor.org)
Genome_build: GRCh37/hg19
The quantification was done with salmon 0.13.2 (https://combine-lab.github.io/salmon/) for the DESeq2 and rank-rank hyper-geometric overlap analyses.
The differential analyses were done with DESeq 21.28.1 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) for the rank-rank hyper-geometric overlap analyses.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Treatment_vs_Control.tsv is tab separated EdgeR output ; RPKM is an excel file containing the RPKM converted expression matrix and some statistics ; de-* files contain the DESeq2 results.

molecule: polyA RNA

source_name: islets of Langerhans

growth_protocol: Human islet preparations were obtained from 26 non-diabetic organ donors. The islets were isolated using collagenase digestion and density gradient purification. They were cultured in M199 culture medium containing 5.5 mM glucose. After isolation, the human islets were cultured in M199 medium, containing 5.5 mmol/l glucose, for 2 days.

extract_protocol:
RNA from approximately 120 hand-picked islets per condition was prepared using the RNeasy MINI Kit + QIAshredder (Qiagen, Hilden, Germany) through lysing and homogenizing steps followed by DNA digestion using RNase-Free DNase Set (Qiagen) and washing steps. Total RNA concentration was measured using the NanoDrop™ 2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and RNA RIN values were obtained using Agilent Bioanalyzer 2100 (Agilent Technologies, Wokingham, UK) and Agilent RNA Nano Chips (Agilent Technologies). RIN values in the ND samples were: mean 8.9; SEM 0.1; median 8.8, range 7.9–9.7. The samples used for the T2D vs ND islet comparison had a RIN value of 7.5 and above, ensuring suitability for sequencing.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from 0.40 µg total RNA using poly-T oligo attached magnetic beads, and was then fragmented and primed with random hexamers for reverse transcription. Afterwards, second strand synthesis was performed by incorporating dUTP in place of dTTP to generate blunt-ended ds cDNA. Adenylation of the 3’ ends and adaptor ligation were then performed. Selective enrichment of DNA fragments with adapter molecules on both ends and DNA amplification were obtained by PCR. The generated libraries were quantified using qPCR and quality was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies) and Agilent DNA 1000 chips (Agilent Technologies).

treatment_protocol: Human islets from 26 non-diabetic donors were exposed to 0.5 mM palmitate (P), 22.2 mM glucose (G), P+G, 1 mM palmitate+oleate, (1:2 ratio, P+O) and P+O+G for 2 days (n=2-5/condition) (D4), followed by 4 days of washout (D8). Vehicle-treated islets from the same donor were collected as control condition at all different time points.

value: islets of Langerhans

tag: patient diagnosis

value: non-diabetic


title: Human islets 57 from non-diabetic donor

description:
ULB-CTL290114
processed data files:
de-t2d.tsv.gz


title: Human islets 49 from non-diabetic donor

description:
ULB-CTL101208
processed data files:
de-t2d.tsv.gz


title: CG0005-4217 [Blood]

description: tissue


title: Human islets 52 from non-diabetic donor

description:
ULB-CTL160606
processed data files:
de-t2d.tsv.gz


title: Human islets 56 from non-diabetic donor

description:
ULB-CTL220606
processed data files:
de-t2d.tsv.gz


title: Human islets 50 from non-diabetic donor

description:
ULB-CTL140912
processed data files:
de-t2d.tsv.gz


title: CG0016-6218 [Blood]

description: tissue


title: Human islets 54 from non-diabetic donor

description:
ULB-CTL190512
processed data files:
de-t2d.tsv.gz


title: CG0005-2984 [Blood]

description: tissue


title: CG0005-2821 [Blood]

description: tissue


title: Human islets 48 from non-diabetic donor

description:
ULB-CTL061011ab
processed data files:
de-t2d.tsv.gz


title: CG0004-1581 [Blood]

description: tissue


title: CG0005-3435 [Blood]

description: tissue


title: Human islets 58 from non-diabetic donor

description:
ULB-CTL300609
processed data files:
de-t2d.tsv.gz


title: CG0005-1440 [Blood]

description: tissue


title: Human islets 45 from non-diabetic donor

description:
PISA-L21708
processed data files:
de-t2d.tsv.gz


title: Human islets 55 from non-diabetic donor

description:
ULB-CTL220214
processed data files:
de-t2d.tsv.gz


title: Human islets 44 from non-diabetic donor

description:
PISA-L21707
processed data files:
de-t2d.tsv.gz


title: Human islets 53 from non-diabetic donor

description:
ULB-CTL190110
processed data files:
de-t2d.tsv.gz


title: CG0009-8206 [Blood]

description: tissue


title: Human islets 43 from non-diabetic donor

description:
PISA-L21704
processed data files:
de-t2d.tsv.gz


title: CG0009-8006 [Blood]

description: tissue


title: Human islets 42 from non-diabetic donor

description:
PISA-L21703
processed data files:
de-t2d.tsv.gz


title: CG0009-8912 [Blood]

description: tissue


title: CG0009-7117 [Blood]

description: tissue


title: CHD-C59-1 [Heart]

description: tissue


title: Human islets 46 from non-diabetic donor

description:
PISA-L21709
processed data files:
de-t2d.tsv.gz


title: CG0009-5746 [Blood]

description: tissue


title: CG0009-5307 [Blood]

description: tissue


title: Human islets 41 from non-diabetic donor

description:
PISA-L21702
processed data files:
de-t2d.tsv.gz


title: Control KD -1


title: Human islets 38 from non-diabetic donor

description:
PISA-L21699
processed data files:
de-t2d.tsv.gz


title: Human islets 36 from non-diabetic donor

description:
PISA-L21697
processed data files:
de-t2d.tsv.gz


title: Human islets 40 from non-diabetic donor

description:
PISA-L21701
processed data files:
de-t2d.tsv.gz


title: Human islets 47 from non-diabetic donor

description:
ULB-CTL010911
processed data files:
de-t2d.tsv.gz


title: Human islets 34 from non-diabetic donor

description:
PISA-L21695
processed data files:
de-t2d.tsv.gz


title: Human islets 37 from non-diabetic donor

description:
PISA-L21698
processed data files:
de-t2d.tsv.gz


title: Human islets 39 from non-diabetic donor

description:
PISA-L21700
processed data files:
de-t2d.tsv.gz


title: Human islets 35 from non-diabetic donor

description:
PISA-L21696
processed data files:
de-t2d.tsv.gz


title: Human islets 33 from non-diabetic donor

description:
PISA-L21694
processed data files:
de-t2d.tsv.gz


title: CG0023-9190 [Blood]

description: tissue


title: CG0005-1433 [Blood]

description: tissue


title: Human islets 32 from non-diabetic donor

description:
PISA-L21693
processed data files:
de-t2d.tsv.gz


title: CG0009-4093 [Blood]

description: tissue


title: CHD-L172-1 [Heart]

description: tissue


title: CG0014-9145 [Blood]

description: tissue


title: Human islets 31 from non-diabetic donor

description:
PISA-L21691
processed data files:
de-t2d.tsv.gz


title: CG0009-7354 [Blood]

description: tissue


title: Human islets 30 from non-diabetic donor

description:
PISA-L21689
processed data files:
de-t2d.tsv.gz


title: CG0015-6226 [Blood]

description: tissue


title: CG0015-6294 [Blood]

description: tissue


title: CG0009-5543 [Blood]

description: tissue


title: Human islets 28 from non-diabetic donor

description:
PISA-L21687
processed data files:
de-t2d.tsv.gz


title: Human islets 29 from non-diabetic donor

description:
PISA-L21688
processed data files:
de-t2d.tsv.gz


title: CG0009-5294 [Blood]

description: tissue


title: CG0015-3882 [Blood]

description: tissue


title: Human islets 27 from non-diabetic donor

description:
PISA-L21686
processed data files:
de-t2d.tsv.gz


title: CG0014-6375 [Blood]

description: tissue


title: CG0016-1450 [Blood]

description: tissue


title: Human islets 24 from non-diabetic donor

description:
PISA-L16194
processed data files:
de-t2d.tsv.gz


title: CG0014-7306 [Blood]

description: tissue


title: CG0009-3593 [Blood]

description: tissue


title: CG0009-2031 [Blood]

description: tissue


title: CG0014-0937 [Blood]

description: tissue


title: Human islets 26 from non-diabetic donor

description:
PISA-L21685
processed data files:
de-t2d.tsv.gz


title: Human islets 25 from non-diabetic donor

description:
PISA-L21684
processed data files:
de-t2d.tsv.gz


title: CG0014-5181 [Blood]

description: tissue


title: Human islets 23 from non-diabetic donor

description:
PISA-L16193
processed data files:
de-t2d.tsv.gz


title: Human islets 20 from non-diabetic donor

description:
PISA-L16189
processed data files:
de-t2d.tsv.gz


title: Human islets 22 from non-diabetic donor

description:
PISA-L16192
processed data files:
de-t2d.tsv.gz


title: CG0009-1651 [Blood]

description: tissue


title: CG0009-1991 [Blood]

description: tissue


title: CG0009-1528 [Blood]

description: tissue


title: Human islets 19 from non-diabetic donor

description:
PISA-L16187
processed data files:
de-t2d.tsv.gz


title: Human islets 18 from non-diabetic donor

description:
PISA-L16186
processed data files:
de-t2d.tsv.gz


title: CG0009-1149 [Blood]

description: tissue


title: CG0009-2501 [Blood]

description: tissue


title: Human islets 16 from non-diabetic donor

description:
PISA-L13352
processed data files:
de-t2d.tsv.gz


title: CG0009-8259 [Blood]

description: tissue


title: Human islets 13 from non-diabetic donor

description:
PISA-L13347
processed data files:
de-t2d.tsv.gz


title: CG0003-6328 [Blood]

description: tissue


title: Human islets 14 from non-diabetic donor

description:
PISA-L13348
processed data files:
de-t2d.tsv.gz


title: CG0005-0456 [Blood]

description: tissue


title: CG0021-5802 [Blood]

description: tissue


title: Human islets 17 from non-diabetic donor

description:
PISA-L13354
processed data files:
de-t2d.tsv.gz


title: Human islets 15 from non-diabetic donor

description:
PISA-L13349
processed data files:
de-t2d.tsv.gz


title: CG0005-0590 [Blood]

description: tissue


title: Human islets 11 from non-diabetic donor

description:
PISA-L13345
processed data files:
de-t2d.tsv.gz


title: Human islets 10 from non-diabetic donor

description:
PISA-L13343
processed data files:
de-t2d.tsv.gz


title: Human islets 9 from non-diabetic donor

description:
PISA-L13342
processed data files:
de-t2d.tsv.gz


title: Human islets 21 from non-diabetic donor

description:
PISA-L16191
processed data files:
de-t2d.tsv.gz


title: Human islets 12 from non-diabetic donor

description:
PISA-L13346
processed data files:
de-t2d.tsv.gz


title: CG0004-8487 [Blood]

description: tissue


title: CG0003-3886 [Blood]

description: tissue


title: Human islets 8 from non-diabetic donor

description:
PISA-L13341
processed data files:
de-t2d.tsv.gz


title: CG0004-6956 [Blood]

description: tissue


title: Human islets 7 from non-diabetic donor

description:
PISA-L13340
processed data files:
de-t2d.tsv.gz


title: CG0009-1257 [Blood]

description: tissue


title: CG0002-4122 [Blood]

description: tissue


title: Human islets 5 from non-diabetic donor

description:
PISA-L13338
processed data files:
de-t2d.tsv.gz


title: Human islets 4 from non-diabetic donor

description:
PISA-L13337
processed data files:
de-t2d.tsv.gz


title: CG0004-5562 [Blood]

description: tissue


title: Human islets 3 from non-diabetic donor

description:
PISA-L13334
processed data files:
de-t2d.tsv.gz


title: CG0004-2664 [Blood]

description: tissue


title: CG0004-0926 [Blood]

description: tissue


title: Human islets 2 from non-diabetic donor

description:
PISA-L13333
processed data files:
de-t2d.tsv.gz


title: CG0003-6541 [Blood]

description: tissue


title: CG0023-9194 [Blood]

description: tissue


title: Human islets 1 from non-diabetic donor

description:
PISA-L13332
processed data files:
de-t2d.tsv.gz


title: Human islets 27 from type 2 diabetic donor

description:
ULB-T2D261010
processed data files:
de-t2d.tsv.gz

value: type 2 diabetes


title: CG0004-9629 [Blood]

description: tissue


title: Human islets 28 from type 2 diabetic donor

description:
ULB-T2D310311
processed data files:
de-t2d.tsv.gz


title: CG0003-6739 [Blood]

description: tissue


title: Human islets 26 from type 2 diabetic donor

description:
ULB-T2D230111
processed data files:
de-t2d.tsv.gz


title: CG0003-1087 [Blood]

description: tissue


title: CG0023-9809 [Blood]

description: tissue


title: CG0004-5692 [Blood]

description: tissue


title: CG0022-0495 [Blood]

description: tissue


title: Human islets 22 from type 2 diabetic donor

description:
ULB-T2D101208
processed data files:
de-t2d.tsv.gz


title: Human islets 25 from type 2 diabetic donor

description:
ULB-T2D180112
processed data files:
de-t2d.tsv.gz


title: CG0003-1450 [Blood]

description: tissue


title: Human islets 23 from type 2 diabetic donor

description:
ULB-T2D111110
processed data files:
de-t2d.tsv.gz


title: CG0003-0680 [Blood]

description: tissue


title: Human islets 24 from type 2 diabetic donor

description:
ULB-T2D150113
processed data files:
de-t2d.tsv.gz


title: Human islets 6 from non-diabetic donor

description:
PISA-L13339
processed data files:
de-t2d.tsv.gz


title: Human islets 21 from type 2 diabetic donor

description:
ULB-T2D080911
processed data files:
de-t2d.tsv.gz


title: Human islets 20 from type 2 diabetic donor

description:
PISA-L21714
processed data files:
de-t2d.tsv.gz


title: CG0023-0468 [Blood]

description: tissue


title: CG0003-0237 [Blood]

description: tissue


title: Human islets 19 from type 2 diabetic donor

description:
PISA-L21713
processed data files:
de-t2d.tsv.gz


title: CG0023-9188 [Blood]

description: tissue


title: Human islets 18 from type 2 diabetic donor

description:
PISA-L21712
processed data files:
de-t2d.tsv.gz


title: CG0008-9391 [Blood]

description: tissue


title: CG0008-8427 [Blood]

description: tissue


title: Human islets 17 from type 2 diabetic donor

description:
PISA-L21711
processed data files:
de-t2d.tsv.gz


title: Human islets 16 from type 2 diabetic donor

description:
PISA-L21710
processed data files:
de-t2d.tsv.gz


title: CG0008-8334 [Blood]

description: tissue


title: CG0023-9186 [Blood]

description: tissue


title: CG0008-8046 [Blood]

description: tissue


title: Human islets 14 from type 2 diabetic donor

description:
PISA-L21705
processed data files:
de-t2d.tsv.gz


title: Human islets 15 from type 2 diabetic donor

description:
PISA-L21706
processed data files:
de-t2d.tsv.gz


title: CG0008-6603 [Blood]

description: tissue


title: Human islets 12 from type 2 diabetic donor

description:
PISA-L21683
processed data files:
de-t2d.tsv.gz


title: CG0012-7402 [Blood]

description: tissue


title: Human islets 13 from type 2 diabetic donor

description:
PISA-L21692
processed data files:
de-t2d.tsv.gz


title: CG0008-6660 [Blood]

description: tissue


title: CG0008-3861 [Blood]

description: tissue


title: Human islets 11 from type 2 diabetic donor

description:
PISA-L16190
processed data files:
de-t2d.tsv.gz


title: Human islets 10 from type 2 diabetic donor

description:
PISA-L16188
processed data files:
de-t2d.tsv.gz


title: Human islets 9 from type 2 diabetic donor

description:
PISA-L16182
processed data files:
de-t2d.tsv.gz


title: CG0015-5110 [Blood]

description: tissue


title: Human islets 6 from type 2 diabetic donor

description:
PISA-L13355
processed data files:
de-t2d.tsv.gz


title: Human islets 8 from type 2 diabetic donor

description:
PISA-L16180
processed data files:
de-t2d.tsv.gz


title: CG0008-3244 [Blood]

description: tissue


title: CG0008-3884 [Blood]

description: tissue


title: Human islets 5 from type 2 diabetic donor

description:
PISA-L13353
processed data files:
de-t2d.tsv.gz


title: CG0002-9770 [Blood]

description: tissue


title: Human islets 4 from type 2 diabetic donor

description:
PISA-L13351
processed data files:
de-t2d.tsv.gz


title: Human islets 3 from type 2 diabetic donor

description:
PISA-L13350
processed data files:
de-t2d.tsv.gz


title: CG0002-8750 [Blood]

description: tissue


title: Human islets 2 from type 2 diabetic donor

description:
PISA-L13336
processed data files:
de-t2d.tsv.gz


title: CG0002-8551 [Blood]

description: tissue


title: CG0008-4700 [Blood]

description: tissue


title: CG0008-4825 [Blood]

description: tissue


title: CG0002-8289 [Blood]

description: tissue


title: Day13

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to ce10 whole genome using Tophat-2.0.9 with parameters --bowtie1 --segment-length 18
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks-2.2.1 with default parameters.
Genome_build: ce10
Supplementary_files_format_and_content: files with BigWig format that read counts are normalized to 10^7

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans CF512 at day 13

growth_protocol: Worms were propagated at 20 °C on solid high growth media seeded with E. coli OP50. Larvae were plated at the restrictive temperature 25 °C to block progeny production.

extract_protocol:
Total RNA from synchronized adult worms was extracted by using TRI-Solution (Bio Science Technology).
Sequencing libraries were manually generated for high-throughput sequencing. Poly(A) mRNA was purified using Oligotex Direct mRNA Mini Kit (Qiagen). Enriched mRNA was fragmented by incubating in 5X RNA Fragmentation Buffer (200 mM Tris-acetate (pH 8.1), 150 mM MgOAc, and 500 mM KOAc) at 82 °C for 5 min. cDNA was synthesized by using SuperScript III RT (Invitrogen) and random hexamers with incubation for 30 min at 55 °C. Approximately 500 ng of cDNA of each sample was repaired using the End-It DNA End-Repair Kit (Epicentre Biotechnologies), followed by addition of 3' A base for adaptor ligation. Overnight ligation of polished cDNA with Genomic DNA Adaptors (Illumina), amplification for 18 cycles, and isolation of about 200~500 bp from agarose gel were performed according to the manufacturer’s instructions.

value: Whole body

value: Day 13 adult

tag: strain


title: CG0002-7727 [Blood]

description: tissue


title: Day09

source_name: Caenorhabditis elegans CF512 at day 9

value: Day 9 adult


title: Day05

source_name: Caenorhabditis elegans CF512 at day 5

value: Day 5 adult


title: Human islets 7 from type 2 diabetic donor

description:
PISA-L16178
processed data files:
de-t2d.tsv.gz


title: Day01

source_name: Caenorhabditis elegans CF512 at day 1

value: Day 1 adult


title: CG0002-7853 [Blood]

description: tissue


title: CG0001-9605 [Blood]

description: tissue


title: Human islets 1 from type 2 diabetic donor

description:
PISA-L13331
processed data files:
de-t2d.tsv.gz


title: CG0007-9867 [Blood]

description: tissue


title: CG0008-0184 [Blood]

description: tissue


title: CG0007-9394 [Blood]

description: tissue


title: CG0007-9483 [Blood]

description: tissue


title: CG0007-9958 [Blood]

description: tissue


title: no trauma_no PTSD 8

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

description: Sample 24

data_processing: data processing miRge pipeline v1

source_name: no trauma_no PTSD_serum

extract_protocol:
Total RNA was isolated from 300 μl human serum using the mirVana PARIS kit (Ambion) according to the manufacturer’s instructions
Barcoded libraries (N=24, 8 per group) were prepared with an input of 25 ng total RNA using the Illumina Small RNA TruSeq kit

tag: phenotype

value: Healthy control

value: Male

value: Serum

tag: molecule subtype

value: Serum circulating miRNAs


title: no trauma_no PTSD 6

description: Sample 22

tag: tissue


title: no trauma_no PTSD 7

description: Sample 23


title: no trauma_no PTSD 5

description: Sample 21


title: CG0007-9423 [Blood]

description: tissue


title: SC53cis

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Seqeuncing reads were processed using Cell Ranger v2.0 pipeline (10x Genomics)
Genome_build: hg38
Supplementary_files_format_and_content: UMI reads count were calculated by Cell Ranger v2.0

growth_protocol: Tumors were grown in mice to between 500-800 mm3

extract_protocol:
Tumors were collected and RNA extracted using Trizol reagent and purified with a Qiagen RNeasy kit
Sequencing library were constructed following 10x Genomics Chromiun v2 library preparation protocol.

treatment_protocol: Mice were untreated

value: CDX flank

value: small cell lung cancer (SCLC)

tag: treatment

value: cisplatin, relapsed


title: SC53

value: vehicle-treated


title: CG0002-4574 [Blood]

description: tissue

value: Blood

value: congenital heart defect


title: CG0002-9246 [Blood]

description: tissue


title: no trauma_no PTSD 4

description: Sample 20

tag: gender


title: no trauma_no PTSD 3

description: Sample 19


title: CG0002-3570 [Blood]

description: tissue


title: CG0002-3471 [Blood]

description: tissue


title: no trauma_no PTSD 2

description: Sample 18


title: no trauma_no PTSD 1

description: Sample 17


title: trauma_no PTSD 8

description: Sample 16

source_name: trauma_no PTSD_serum

value: Resilient


title: CG0001-7693 [Blood]

description: tissue


title: CG0007-8752 [Blood]

description: tissue


title: CG0002-0377 [Blood]

description: tissue


title: CG0007-7105 [Blood]

description: tissue


title: CG0007-8071 [Blood]

description: tissue


title: trauma_no PTSD 6

description: Sample 14


title: trauma_no PTSD 5

description: Sample 13


title: CG0007-5380 [Blood]

description: tissue


title: CG0007-4747 [Blood]

description: tissue


title: trauma_no PTSD 4

description: Sample 12


title: Islet preparation 12 under control condition at D8

description:
PISA-2016-01-25-D8C
processed data files:
de-d8g.tsv.gz, de-d8g-d4g.tsv.gz

value: islets of Langerhans

value: non-diabetic


title: CG0007-4017 [Blood]

description: tissue


title: Islet preparation 11 under high glucose-exposed condition at D8

description:
PISA-2015-08-28-D8G
processed data files:
de-d8g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0003-0037 [Blood]

description: tissue


title: CG0001-6421 [Blood]

description: tissue


title: CG0007-4171 [Blood]

description: tissue


title: trauma_no PTSD 3

description: Sample 11


title: Islet preparation 12 under control condition at D4

description:
PISA-2016-01-25-D4C
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: Islet preparation 11 under control condition at D8

description:
PISA-2015-08-28-D8C
processed data files:
de-d8g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0001-6034 [Blood]

description: tissue


title: trauma_no PTSD 2

description: Sample 10


title: trauma_no PTSD 1

description: Sample 9


title: CG0002-3945 [Blood]

description: tissue


title: CG0023-9226 [Blood]

description: tissue


title: CG0022-8779 [Blood]

description: tissue


title: trauma_no PTSD 7

description: Sample 15


title: Islet preparation 11 under control condition at D4

description:
PISA-2015-08-28-D4C
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0021-5792 [Blood]

description: tissue


title: Islet preparation 12 under high glucose-exposed condition at D4

description:
PISA-2016-01-25-D4G
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0002-1021 [Blood]

description: tissue


title: trauma_PTSD 8

description: Sample 8

value: PTSD


title: Islet preparation 10 under control condition at D8

description:
PISA-2015-04-16-D8C
processed data files:
de-d8g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0016-7570 [Blood]

description: tissue


title: trauma_PTSD 7

description: Sample 7


title: CG0001-6465 [Blood]

description: tissue


title: CG0013-7387 [Blood]

description: tissue


title: Islet preparation 10 under high glucose-exposed condition at D4

description:
PISA-2015-04-16-D4G
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: Islet preparation 10 under control condition at D4

description:
PISA-2015-04-16-D4C
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: trauma_PTSD 5

description: Sample 5


title: Islet preparation 9 under high glucose-exposed condition at D8

description:
PISA-2015-02-09-D8G
processed data files:
de-d8g.tsv.gz, de-d8g-d4g.tsv.gz


title: trauma_PTSD 6

description: Sample 6


title: Islet preparation 11 under high glucose-exposed condition at D4

description:
PISA-2015-08-28-D4G
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0013-5874 [Blood]

description: tissue


title: CG0013-8532 [Blood]

description: tissue


title: CG0013-4840 [Blood]

description: tissue


title: Islet preparation 9 under control condition at D8

description:
PISA-2015-02-09-D8C
processed data files:
de-d8g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0013-2275 [Blood]

description: tissue


title: CG0013-9000 [Blood]

description: tissue


title: CG0012-9882 [Blood]

description: tissue


title: CG0012-8486 [Blood]

description: tissue


title: Islet preparation 9 under high glucose-exposed condition at D4

description:
PISA-2015-02-09-D4G
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0012-9421 [Blood]

description: tissue


title: trauma_PTSD 2

description: Sample 2


title: trauma_PTSD 3

description: Sample 3


title: CG0012-9664 [Blood]

description: tissue


title: CG0012-7826 [Blood]

description: tissue


title: CG0013-9325 [Blood]

description: tissue


title: Islet preparation 9 under control condition at D4

description:
PISA-2015-02-09-D4C
processed data files:
de-d4g.tsv.gz, de-d8g-d4g.tsv.gz


title: CG0012-4681 [Blood]

description: tissue


title: Islet preparation 8 under palmitate plus high glucose-exposed condition at D8

description:
PISA-2015-11-03-D8PG
processed data files:
de-d8pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0012-3381 [Blood]

description: tissue


title: trauma_PTSD 1

description: Sample 1


title: Islet preparation 8 under control condition at D8

description:
PISA-2015-11-03-D8CG
processed data files:
de-d8pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0012-3635 [Blood]

description: tissue


title: CG0007-4148 [Blood]

description: tissue


title: Mono_HFD3

city: La Jolla,

first: Inge

last: Holtman

state: California

address: 9500 Gilman Drive

department: CMM

institute: UCSD

data_processing:
Alignment with STAR_2.5.3a to the MM10 reference genome
Per gene quantification with HOMER (not normalized) using analyzeRepeats.pl
Genome_build: mm10
Supplementary_files_format_and_content: Tsv file from analyzeRepeats.pl with counts per gene (rows) per sample (column)

source_name: Sorter myeloid population

extract_protocol:
blood is collected by cardiac puncture on an EDTA coated syringe,  and lysed twice. Adipose tissue is collected in PBS, and incubated in 4mg/mL collagenase II,  supplemented with 2mmol/L flavopiridol and 0.25% BSA and 5mM Cacl2 for 20 min at  room temperature under agitation, before mechanical disruption with a 10mL pipette. Cell suspension were  centrifuged for 10min at 500g and the samples are resuspended in 70μL of Facs buffer  containing anti CD16/32 (FcRIII/II). 200 cells from each sample were directly sorted in a  96 wells plate (biorad) in 4μL H2O containing 0.2% Triton X-100 (sigma) and 0.8U/mL  RNase inhibitor (clontech).
Illumina hiseq libraries were prepared with 10ng amplified cDNA, using 8 cycles of PCR with Kapa library preparation chemistry kit (Kapa Biosystems).

tag: diet

value: high fat diet (HFD; 45% fat)

tag: population

value: Mono

tag: cell-sorting population

value: CD115 and Ly6C population


title: trauma_PTSD 4

description: Sample 4


title: Mono_HFD2


title: Islet preparation 8 under palmitate plus high glucose-exposed condition at D4

description:
PISA-2015-11-03-D4PG
processed data files:
de-d4pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0007-1945 [Blood]

description: tissue


title: CG0007-3637 [Blood]

description: tissue


title: CG0007-1757 [Blood]

description: tissue


title: Mono_HFD1


title: Mono_CD-CD8

value: control diet (CD; 10% fat)


title: CG0007-1343 [Blood]

description: tissue


title: CG0007-0296 [Blood]

description: tissue


title: Islet preparation 8 under control condition at D4

description:
PISA-2015-11-03-D4CG
processed data files:
de-d4pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0001-7181 [Blood]

description: tissue


title: Islet preparation 7 under palmitate plus high glucose-exposed condition at D8

description:
PISA-2015-09-16-D8PG
processed data files:
de-d8pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0000-4157 [Blood]

description: tissue


title: Mono_CD-CD7


title: CG0000-8257 [Blood]

description: tissue


title: CG0023-9182 [Blood]

description: tissue


title: Mono_CD1


title: Islet preparation 7 under control condition at D8

description:
PISA-2015-09-16-D8CG
processed data files:
de-d8pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: eWAT_pop4_HFD2

value: White adipose tissue (WAT)

value: eWAT_pop4 (gamma)

value: Tim4-CD11c+ and MHCII+ population


title: CG0001-9226 [Blood]

description: tissue


title: CG0002-4778 [Blood]

description: tissue


title: Islet preparation 7 under palmitate plus high glucose-exposed condition at D4

description:
PISA-2015-09-16-D4PG
processed data files:
de-d4pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0002-6323 [Blood]

description: tissue


title: Islet preparation 6 under palmitate plus high glucose-exposed condition at D8

description:
PISA-2015-07-21-D8PG
processed data files:
de-d8pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0006-9624 [Blood]

description: tissue


title: eWAT_pop3_CD-CD7

value: eWAT_pop3 (delta)

value: Tim4-CD11c- and MHCII high population


title: eWAT_pop2_HFD2

value: eWAT_pop2 (beta)

value: Tim4+ and MHCII high population


title: CG0006-8673 [Blood]

description: tissue

value: Blood


title: CG0006-7569 [Blood]

description: tissue

value: congenital heart defect


title: Islet preparation 6 under control condition at D8

description:
PISA-2015-07-21-D8C
processed data files:
de-d8pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: Islet preparation 6 under palmitate plus high glucose-exposed condition at D4

description:
PISA-2015-07-21-D4PG
processed data files:
de-d4pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0023-9255 [Blood]

description: tissue


title: Mono_CD-CD6


title: eWAT_pop1_HFD3

value: eWAT_pop1 (alpha)

value: Tim4+ and MHCII low population


title: Islet preparation 6 under control condition at D4

description:
PISA-2015-07-21-D4C
processed data files:
de-d4pg.tsv.gz, de-d8pg-d4pg.tsv.gz

value: islets of Langerhans

value: non-diabetic


title: eWAT_pop4_CD-CD8


title: CG0006-4820 [Blood]

description: tissue


title: CG0023-9802 [Blood]

description: tissue


title: Islet preparation 5 under palmitate-exposed condition at D8

description:
PISA-2015-02-16-D8P
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: Islet preparation 7 under control condition at D4

description:
PISA-2015-09-16-D4C
processed data files:
de-d4pg.tsv.gz, de-d8pg-d4pg.tsv.gz


title: CG0005-5376 [Blood]

description: tissue


title: CG0010-3195 [Blood]

description: tissue


title: CG0006-4458 [Blood]

description: tissue


title: Islet preparation 5 under palmitate-exposed condition at D4

description:
PISA-2015-02-16-D4P
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0006-3668 [Blood]

description: tissue


title: eWAT_pop3_HFD3

value: high fat diet (HFD; 45% fat)


title: eWAT_pop2_CD-CD8


title: Islet preparation 5 under control condition at D4

description:
PISA-2015-02-16-D4C
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0006-9122 [Blood]

description: tissue


title: CG0006-4278 [Blood]

description: tissue


title: eWAT_pop1_HFD2


title: CG0023-9250 [Blood]

description: tissue


title: CG0006-3505 [Blood]

description: tissue


title: CG0006-6459 [Blood]

description: tissue


title: CG0006-3142 [Blood]

description: tissue


title: Mono_CD3

value: Mono


title: CG0006-2885 [Blood]

description: tissue


title: CG0006-1333 [Blood]

description: tissue


title: Islet preparation 4 under control condition at D8

description:
PISA-2015-01-30-D8C
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: eWAT_pop4_CD-CD7


title: CG0002-5025 [Blood]

description: tissue


title: eWAT_pop3_HFD2


title: Islet preparation 4 under control condition at D4

description:
PISA-2015-01-30-D4C
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0005-9901 [Blood]

description: tissue


title: eWAT_pop2_CD-CD7


title: CG0011-6905 [Blood]

description: tissue


title: Islet preparation 3 under control condition at D8

description:
PISA-2015-01-19-D8C
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0005-6846 [Blood]

description: tissue


title: Mono_CD2

value: CD115 and Ly6C population


title: Islet preparation 3 under palmitate-exposed condition at D8

description:
PISA-2015-01-19-D8P
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: Islet preparation 3 under palmitate-exposed condition at D4

description:
PISA-2015-01-19-D4P
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0011-7572 [Blood]

description: tissue


title: eWAT_pop1_CD-CD8

value: control diet (CD; 10% fat)


title: CG0011-2279 [Blood]

description: tissue


title: eWAT_pop4_HFD3

value: White adipose tissue (WAT)


title: Islet preparation 3 under control condition at D4

description:
PISA-2015-01-19-D4C
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0011-1956 [Blood]

description: tissue


title: CG0011-1714 [Blood]

description: tissue


title: Islet preparation 4 under palmitate-exposed condition at D8

description:
PISA-2015-01-30-D8P
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0011-1215 [Blood]

description: tissue


title: CG0011-1982 [Blood]

description: tissue


title: CG0010-8878 [Blood]

description: tissue


title: Islet preparation 2 under palmitate-exposed condition at D8

description:
PISA-2014-12-9-D8P
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: eWAT_pop3_CD-CD8


title: Islet preparation 2 under control condition at D8

description:
PISA-2014-12-9-D8C
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: Islet preparation 4 under palmitate-exposed condition at D4

description:
PISA-2015-01-30-D4P
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0006-0651 [Blood]

description: tissue


title: CG0006-1245 [Blood]

description: tissue


title: CG0010-7882 [Blood]

description: tissue


title: CG0019-0095 [Blood]

description: tissue


title: CG0005-7699 [Blood]

description: tissue


title: Islet preparation 2 under palmitate-exposed condition at D4

description:
PISA-2014-12-9-D4P
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: Islet preparation 2 under control condition at D4

description:
PISA-2014-12-9-D4C
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0023-9260 [Blood]

description: tissue


title: CG0021-7086 [Blood]

description: tissue


title: Islet preparation 1 under palmitate-exposed condition at D8

description:
PISA-2014-11-26-D8P
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: eWAT_pop2_HFD3


title: H0193_chip_D21_3

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Illumina base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422).
Sequence reads were trimmed using bbduk software (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6).
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93).
The expression levels of genes were determined with htseq-count 0.9.1 by using cellRanger pre-build genes annotations (Ensembl Assembly 93).
Genome_build: hg38 reference assembly obtained from cellRanger website (Ensembl 93).
Supplementary_files_format_and_content: raw_counts_hep_diff_chip_hiPS.txt: Tab-delimited raw counts for each sample.

source_name: hiPSC-derived hepatocytes

growth_protocol: hiPSCs were expanded in mTSR-1 (Stemcell Technologies) or StemMACS iPS-Brew XF (Miltenyi Biotech).

extract_protocol:
Total RNA was isolated with the RNeasy Micro kit (Qiagen). Briefly, MH cells were washed once with PBS 1x and collected in 350 μL of RLT buffer at room temperature. Three microfluidic channels were pooled for each biological replicate. RNA was then purified according to manufacturer’s instructions.
Total RNA was quantified using the Qubit 2.0 fluorometric Assay (Thermo Fisher Scientific). Libraries were prepared from 100 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH). Quality of libraries was assessed by using screen tape High sensitivity DNA D1000 (Agilent Technologies).

treatment_protocol: For differentiation to hepatocytes, endoderm commitment was performed in 6-well plates and completed in 24-well plates or in microfluidic channels upon single-cell splitting.

tag: passage

tag: derivation method

value: mmRNA reprogramming

tag: culture system

value: microfluidics

tag: differentiation stage

value: hepatocyte-like cells


title: CG0010-6964 [Blood]

description: tissue


title: H0193_chip_D21_1


title: H0193_chip_D21_2


title: CG0010-6402 [Blood]

description: tissue


title: CG0010-7969 [Blood]

description: tissue


title: Islet preparation 1 under palmitate-exposed condition at D4

description:
PISA-2014-11-26-D4P
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0010-6102 [Blood]

description: tissue


title: CG0010-5113 [Blood]

description: tissue


title: Islet preparation 1 under control condition at D4

description:
PISA-2014-11-26-D4C
processed data files:
de-d4p.tsv.gz, de-d8p-d4p.tsv.gz


title: H0193_well_D21_2

value: conventional culture condition


title: CG0010-6058 [Blood]

description: tissue


title: CG0010-4972 [Blood]

description: tissue


title: eWAT_pop1_CD-CD7


title: H0193_well_D21_1


title: CG0010-7214 [Blood]

description: tissue


title: YMR-2

city: Greater Noida

first: Anindita

last: Chakrabarty

state: UP

address: NH91 Tehsil Dadri

country: India

institute: Shiv Nadar University

data_processing:
Sequencing reads were first quality controlled using FastQC .
Adapters and low quality (Q20) reads were trimmed using fastq-mcf
Reads were then mapped against the hg19 (GRCh37) human reference genome using HISAT2  version 2.0.5
Read counts were first retrieved by exon (MAQ>10) and then summarized at gene level using featureCount  version v1.5.3. Read counts were subsequently normalized using EdgeR
Differential gene expression analysis was corrected for multiple testing using Benjamini-Hochberg method. Genes differentially expressed were defined if the False Discovery Rate is less than 5% (FDR<0.05).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: All DEGs (5%FDR) are be in the excel file: dge_5percFDR.xlsx. The file contains logFC, log CPM, P values, FDR, hgnc symbol.

source_name: MDA-MB-231 Cell Line (Mammary)

growth_protocol: 2X10^6 Cells were plated in 100mm dishes and harvested after 72hours of plating.

extract_protocol:
RNA was isolated using the Direct-zol RNA miniprep plus kit from Zymo-Research and processed as per manufacturer’s instructions.
NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) was used for library preparation. Amplification was done using paired-end primers on Illumina platform

treatment_protocol: Control was treated with DMSO and YMR with 15nM YM155 for 72 hrs after plating.

value: Resistant

tag: cell line

value: 15nM YM155 treated


title: H0193_well_D21_3


title: CG0010-7989 [Blood]

description: tissue

value: Blood


title: CG0010-7926 [Blood]

description: tissue

value: congenital heart defect


title: YMR-1


title: CG0013-5858 [Blood]

description: tissue


title: H0193_hiPS_2

source_name: hiPSC

value: pluripotent cells


title: Islet preparation 1 under control condition at D8

description:
PISA-2014-11-26-D8C
processed data files:
de-d8p.tsv.gz, de-d8p-d4p.tsv.gz


title: CG0010-2666 [Blood]

description: tissue


title: CG0010-1781 [Blood]

description: tissue


title: CG0023-9192 [Blood]

description: tissue


title: H0193_hiPS_3


title: Sensitive-2

value: Sensitive

value: untreated


title: CG0010-1067 [Blood]

description: tissue


title: CG0010-1300 [Blood]

description: tissue


title: CG0010-5830 [Blood]

description: tissue


title: CG0001-6459 [Blood]

description: tissue


title: CG0001-7753 [Blood]

description: tissue


title: OC37_TLOm1 25 nM decitabine

first: Owen

middle: A

last: O"Connor

address: 51 West 51st Street

department: enter for Lymphoid Malignancies

institute: Columbia University Medical Center

data_processing:
Alignment with STARv2.5.3
Gene-level raw counts summarization with STARTv2.5.3 quant-mode
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature generation with limma (R bioconductor package)
Genome_build: GRCh37.p2
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification

source_name: TLOm1 Adult T-cell leukemia

growth_protocol: The cells grown in logarithomic phase during treatment

extract_protocol:
RNAs were extracted with using Qiagen Rneasy mini kit
Strand specific sequencing libraries were generated from rRNA depleted total RNAs using the TruSeq Stranded mRNA kit by Illumina

treatment_protocol: All the samples were treated with indicated concentration of drugs for 96 hours with drug addition every 24 hours.

value: 25 nM decitabine


title: H0193_hiPS_1


title: Sensitive-1


title: CG0002-5928 [Blood]

description: tissue


title: CG0001-5726 [Blood]

description: tissue


title: OC36_TLOm1 12.5 nM decitabine

value: 12.5 nM decitabine


title: CG0001-9113 [Blood]

description: tissue


title: CG0001-5056 [Blood]

description: tissue


title: OC35_TLOm1 5 nM decitabine

value: 5 nM decitabine


title: CG0023-9230 [Blood]

description: tissue


title: OC33_TLOm1 untreated


title: CG0002-2669 [Blood]

description: tissue


title: CG0023-9235 [Blood]

description: tissue


title: CG0002-4184 [Blood]

description: tissue


title: OC28_PF82 12.5 nM decitabine

source_name: PF382 T-cell Acute Lymphoblastic Leukemia


title: OC27_PF382 5 nM decitabine


title: CG0023-9240 [Blood]

description: tissue


title: CG0024-1352 [Blood]

description: tissue


title: CG0001-3591 [Blood]

description: tissue


title: CG0001-7905 [Blood]

description: tissue


title: OC25_PF382 untreated


title: OC5_HH 25 nM decitabine

source_name: HH Cutaneous T cell Lymphoma

value: HH


title: E. coli 042 hns2

city: Barcelona

first: Mario

last: Huttener Queiroz

address: Av. Diagonal 643

country: Spain

institute: Universitat de Barcelona

data_processing:
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1.
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina.
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters.
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters.
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr
Genome_build: NCBI reference sequence (NC_017626 for the E. coli 042 chromosome) and (NC_017627 for the pAA plasmid).
Supplementary_files_format_and_content: The expression_0_NC_017626_7_gene_GEO.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample.

organism: Escherichia coli 042

source_name: cells

growth_protocol: LB medium at 25ºC with 200rpm agitation.

extract_protocol:
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina).
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

tag: genotype

value: mutant hns2


title: E. coli 042 hns

value: mutant hns


title: CG0000-2064 [Blood]

description: tissue

tag: diagnosis


title: AsPC-1_PRLR-SF_biological rep1

city: Shanghai

first: PeiQi

last: Huang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

description: Gene expression data from biological replicate 1 of AsPC-1 cells infected with shRNA targeting PRLR

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0/RMA algorithm, Affy packages in R.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) / Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) / Ovation® Pico WTA System V2(Cat#3302， NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were cultured accroding to American Type Culture Collection (ATCC, Manassas, VA) protocols.

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

treatment_protocol: Wildtype AsPC-1 cells were infected with reconstructed lentivirus overexpressing Ctrl or PRLR-SF and treated with 1 μg/ml puromycin for more than 7 days.

value: pancreas; Derived from metastatic site:ascites

value: infected with shRNA targeting PRLR


title: E. coli 042 wt

value: wild type


title: CG0023-9181 [Blood]

description: tissue


title: OC4_HH 12.5 nM decitabine


title: AsPC-1_PRLR-SF_biological rep3

description: Gene expression data from biological replicate 3 of AsPC-1 cells infected with shRNA targeting PRLR


title: AsPC-1_PRLR-SF_biological rep2

description: Gene expression data from biological replicate 2 of AsPC-1 cells infected with shRNA targeting PRLR


title: CG0000-5330 [Blood]

description: tissue


title: AsPC-1_Ctrl_biological rep3

description: Gene expression data from biological replicate 3 of AsPC-1 cells infected with scrambles shRNA

value: infected with scrambles shRNA


title: OC29_PF382 25 nM decitabine


title: CG0023-9184 [Blood]

description: tissue


title: OC3_HH 5 nM decitabine


title: CG0023-9800 [Blood]

description: tissue


title: CG0023-9246 [Blood]

description: tissue


title: CG0001-3807 [Blood]

description: tissue


title: CG0023-9216 [Blood]

description: tissue


title: OC1_HH untreated

source_name: HH Cutaneous T-cell Lymphoma


title: CG0023-9180 [Blood]

description: tissue

source_name: Blood


title: CG0023-9207 [Blood]

description: tissue


title: AsPC-1_Ctrl_biological rep1

description: Gene expression data from biological replicate 1 of AsPC-1 cells infected with scrambles shRNA


title: CG0023-9211 [Blood]

description: tissue


title: OLC48_TLOm1 500 nM azacitidine

value: 500 nM azacitidine


title: AsPC-1_Ctrll_biological rep2

description: Gene expression data from biological replicate 2 of AsPC-1 cells infected with scrambles shRNA


title: CG0003-5265 [Blood]

description: tissue


title: CG0000-5745 [Blood]

description: tissue


title: CG0001-1314 [Blood]

description: tissue