title: DNase-seq, eWAT adipocytes

source_name: eWAT-derived primary adipocytes

value: epididymal white adipose tissus


title: Patient 127-EGFR.2435

status: Public on Nov 13 2018

type: RNA

city: Tokyo

first: Sophia

last: Subat

address: 3-8-31 Ariake, Koto-ward,

country: Japan

institute: Japanese Foundation for Cancer Research

description: One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

hyb_protocol: The cDNA was hybridized to the SurePrint G3 Human Gene Expression 8×60K Microarray (Design ID 028004, Agilent Technologies).

scan_protocol: After the hybridization, scanning of the arrays was carried out with the Agilent Micro Scanner System (G2565CA, Agilent Technologies)..

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.

molecule: total RNA

organism: Homo sapiens

source_name: lung adenocarcinoma

label_protocol: Total RNA was reverse transcribed into cDNA and labeled using the Low Input Quick Amp Labeling Kit (5190-2305, Agilent Technologies) following the manufacturer’s instructions.

extract_protocol: Total RNAs were extracted using miRNeasy Mini Kit and RNase-free (Qiagen, Hilden, Germany) according to the manufacturer’s instructions

tag: tissue

value: lung adenocarcinoma

tag: egfr status

value: EGFR mutation


title: DNase-seq, BAT adipocytes

type: SRA

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: genomic

data_processing:
DNase-seq data sets were mapped to the mm9 genome with STAR (Dobin et al., 2013) set to not map across splice junctions, and tag directory generation, peak calling/annotations and motif analyses were performed with HOMER (Heinz et al., 2010).
DNA hypersensitive sites were called using ”-style factor” setting with all other parameters set at default in eWAT-derived, iWAT-derived and BAT-derived adipocytes.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, peaks

molecule: genomic DNA

organism: Mus musculus

source_name: BAT-derived primary adipocytes

growth_protocol: Brown adipose tissue (pooled interscapular, cervical, and axillary depots) as well as the epididymal (eWAT) and inguinal (iWAT) adipose tissue were optained from 4-5wk old male NMRI mice.  Adipose tissues were carefully minced and treated with collagenase (type II; Sigma) to separate the SVF from mature adipocytes.

extract_protocol:
DNase I digestion was performed in eWAT, iWAT and BAT-derived adipocytes on ~10,000,000 million nuclei, essentially as previously described (Siersbæk et al., 2011, EMBO J, 30(8):1459-72), except that the mature adipocytes were harvested directly in Buffer A (15 mM Tris–HCl pH=8, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine) and 120 U/ml DNase I (Roche, cat# 11 284 932 001) was used for digestion.
DNase-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: The isolated SVF cells were cultured under differentiation-inducing conditions in a medium consisting of DMEM (Sigma), 10% newborn calf serum (NCS) (HyClone), 30 nM insulin, 25 μg/ml sodium ascorbate, 10 mM HEPES, pH 7.4, at 37°C, 4 mM l-glutamine (Invitrogen), 100 μg/ml streptomycin, 62.5 μg/ml penicillin, and 1 μM rosiglitazone (Novo Nordisk). The cultures were harvested 8 days after plating and for comparison between the in vitro differentiated adipocytes, only cultures with a >50% degree of differentiation were used.

tag: strain

value: NMRI

tag: Sex

value: male

tag: age

value: 4-5 weeks

value: brown adipose tissue

tag: cell type

value: Primary in vitro differentiated SVF cells


title: Patient 125-EGFR.2338


title: Patient 123-EGFR.2248


title: GSS0392_113_M_1800

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

country: USA

institute: Procter and Gamble

description: Gene expression data from LCM-separated epidermis from human forearm

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: ArrayPlates were scanned using the Affymetrix GeneTitan Instrument utilizing AGCC GeneTitan Instrument Control software version 4.2.0.1566

data_processing: The RMA algorithm was used as the processing protocol to normalize the data for subsequent analysis.

label: biotin

source_name: batch_subjectID_gender_sampling time

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

extract_protocol: Total RNA from LCM samples was isolated utilizing the Pico Pure RNA Isolation Kit (Life Technologies, Grand Island, NY) according to manufacturer's recommendations

treatment_protocol: Punch biopsy samples were frozen in OCT media. Laser capture microdissection (LCM) was performed to isolate the epidermal compartments for gene expression profiling.

value: Male

value: LCM-separated epidermis

tag: ancestry

tag: collection time


title: SAMPLE 131

city: Bethesda

first: Sai

last: Kanaparthi

state: MD

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

description: Gene expression data from Screening Visit

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v3) in R.3.2.1

source_name: Screening Visit_Cluster 3

label_protocol: Standard Affymetrix protocol

extract_protocol: TRIzol

value: Liver Biopsy

tag: histological clusters

value: Cluster 3

tag: interface activity

tag: perivenular fibrosis

tag: ishak fibrosis stage

tag: lobular inflammation

tag: portal inflammation

value: Mild


title: GSS0392_112_M_0


title: SAMPLE 133


title: SAMPLE 132


title: SAMPLE 129

source_name: Screening Visit_Cluster 1

value: Cluster 1

value: Moderate


title: GSS0392_112_M_1200


title: GSS0392_113_M_1200


title: SAMPLE 130


title: GSS0392_101_M_1800


title: GSS0392_113_M_0


title: Patient 121-EGFR.2101


title: GSS0392_104_M_1800


title: GSS0392_104_M_0


title: SAMPLE 126


title: GSS0392_113_M_600


title: SAMPLE 125


title: Patient 122-EGFR.2247


title: GSS0392_101_M_600


title: Patient 120-EGFR.2006


title: SAMPLE 124


title: SAMPLE 127


title: shHP1γ-17, biological rep1

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

description: Gene expression data from shHP1γ-17 infected H1792 cells.

hyb_protocol: according to manufacture protocol

scan_protocol: according to manufacture protocol

data_processing: Microarray data was processed by RAMA software using defalt analysis setting, Heat map was generated using MeV software.

source_name: shHP1γ-17 infected H1792 cell

label_protocol: according to manufacture protocol

growth_protocol: Cell were selected in 1ug/ml puromycin-containg medium

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

treatment_protocol: Cell were treated with lentivirus based shRNAs

value: H1792 lung adenocarcinoma cell line


title: GSS0392_104_M_600


title: GSS0392_104_M_1200


title: Patient 119-EGFR.1750


title: Patient 118-EGFR.1729


title: SAMPLE 128


title: shHP1γ-17, biological rep2


title: Patient 117-EGFR.1474


title: Patient 124-EGFR.2308


title: Patient 116-EGFR.1330


title: SAMPLE 121

source_name: Screening Visit_Cluster 2

value: Cluster 2


title: Patient 155-EGFR.5785

hyb_protocol: The labeled cRNAs were then hybridized to the Unrestricted Human miRNA 8×60K Microarray, release 19.0 (Design ID 046064, Agilent Technologies), which covers 2,042 human miRNAs.

scan_protocol: After the hybridization, the arrays were washed and scanned with a high resolution using the Agilent Microarray Scanner System (G2565CA, Agilent Technologies).

label_protocol: input RNA was used to generate Cyanine-3-pCp labeled cRNA using the miRNA Complete Labeling Reagent and Hyb Kit (5190-0456, Agilent Technologies) according to the manufacturer’s instructions


title: GSS0392_117_M_1800


title: SAMPLE 122


title: shHP1γ-16, biological rep2

description: Gene expression data from shHP1γ-16 infected H1792 cells.

source_name: shHP1γ-16 infected H1792 cell


title: shLuc-2, biological rep2

description: Gene expression data from shLuc infected H1792 cells.

source_name: shLuc infected H1792 cell


title: SAMPLE 119


title: Patient 115-EGFR.948


title: GSS0392_117_M_0


title: shHP1γ-16, biological rep1


title: GSS0392_117_M_600


title: Patient 114-EGFR.883


title: shLuc-1, biological rep1


title: GSS0392_117_M_1200


title: GSS0392_120_M_1200


title: Patient 154-EGFR.4480


title: SAMPLE 118


title: SAMPLE 120


title: Patient 143-EGFR.3888


title: Patient 152-EGFR.4412


title: SAMPLE 117


title: Patient 112-EGFR.553


title: SAMPLE 116


title: GSS0392_120_M_1800


title: Patient 113-EGFR.864


title: GSS0392_120_M_0


title: Patient 111-EGFR.521


title: SAMPLE 115


title: Patient 153-EGFR.4449


title: Patient 110-EGFR.204


title: Patient 151-EGFR.4384


title: Patient 150-EGFR.4364


title: GSS0392_120_M_600


title: Patient 109-EGFR.192


title: Patient 149-EGFR.4317


title: Patient 108-EGFR.118


title: Patient 148-EGFR.4286


title: Patient 147-EGFR.4276


title: SAMPLE 114


title: Patient 107-EGFR.111


title: Patient 106-EGFR.77


title: SAMPLE 111


title: SAMPLE 112


title: GSS0392_119_M_600


title: Patient 105-EGFR.71


title: GSS0392_119_M_1800


title: SAMPLE 110


title: GSS0392_119_M_0


title: GSS0392_103_M_1800


title: Patient 145-EGFR.4164


title: Patient 104-EGFR.66


title: SAMPLE 113


title: Patient 144-EGFR.3896


title: SAMPLE 109


title: Patient 143-EGFR.3888


title: GSS0392_103_M_600


title: GSS0392_103_M_1200


title: Patient 146-EGFR.4244


title: Patient 102-N.41554

value: EGFR-negative


title: Patient 142-EGFR.3863

value: lung adenocarcinoma


title: GSS0392_103_M_0


title: Patient 101-N.40310


title: Patient 141-EGFR.3836

value: EGFR mutation


title: Patient 100-N.39415


title: SAMPLE 107


title: Patient 103-N.42477


title: SAMPLE 108


title: SAMPLE 106


title: GSS0392_114_M_1200


title: SAMPLE 105


title: Patient 140-EGFR.3707


title: Patient 139-EGFR.3272


title: GSS0392_114_M_0


title: GSS0392_114_M_1800


title: SAMPLE 103


title: SAMPLE 104


title: SAMPLE 102


title: GSS0392_111_M_1800


title: Patient 98-N.36885


title: Patient 97-N.36567


title: Patient 137-EGFR.3067


title: GSS0392_119_M_1200


title: Patient 138-EGFR.3138


title: Patient 95-N.35648


title: Patient 136-EGFR.3042


title: Patient 94-N.33560


title: Patient 135-EGFR.2964


title: Patient 134-EGFR.2914


title: Patient 133-EGFR.2888


title: SAMPLE 101


title: Patient 99-N.38143


title: SAMPLE 100


title: GSS0392_111_M_1200


title: SAMPLE 99


title: SAMPLE 98


title: GSS0392_111_M_600


title: GSS0392_102_M_600


title: SAMPLE 97


title: Patient 96-N.35799


title: Patient 93-N.32659


title: Patient 92-N.32472


title: Patient 132-EGFR.2803


title: Patient 91-N.28571


title: GSS0392_102_M_0


title: GSS0392_111_M_0


title: Patient 131-EGFR.2787


title: SAMPLE 96


title: GSS0392_102_M_1800


title: SAMPLE 95


title: GSS0392_102_M_1200


title: Patient 130-EGFR.2780


title: Patient 90-N.27998


title: Patient 89-N.27265


title: Patient 88-N.26813


title: Patient 128-EGFR.2706


title: SAMPLE 123


title: Patient 129-EGFR.2773


title: Patient 87-N.26570


title: GSS0392_105_M_0


title: GSS0392_114_M_600


title: Patient 126-EGFR.2362


title: Patient 127-EGFR.2435


title: SAMPLE 93


title: Patient 86-N.26422


title: SAMPLE 92


title: Patient 85-N.26356


title: SAMPLE 90


title: GSS0392_105_M_1200


title: SAMPLE 91


title: SAMPLE 94


title: Patient 125-EGFR.2338


title: GSS0392_105_M_1800


title: GSS0392_105_M_600


title: Patient 124-EGFR.2308


title: Patient 84-N.26020


title: GSS0392_118_M_0


title: Patient 83-N.24642


title: SAMPLE 89


title: Patient 82-N.24461


title: SAMPLE 88


title: SAMPLE 87


title: Patient 123-EGFR.2248


title: Patient 122-EGFR.2247


title: Patient 81-N.22231


title: SAMPLE 86


title: GSS0392_118_M_1800


title: GSS0392_118_M_1200


title: SAMPLE 85


title: GSS0392_107_M_1200


title: Patient 121-EGFR.2101


title: Patient 80-N.21266


title: Patient 120-EGFR.2006


title: Patient 119-EGFR.1750


title: Patient 79-N.20653


title: Patient 118-EGFR.1729


title: Patient 78-N.19854


title: Patient 77-N.19408


title: SAMPLE 84

value: Severe


title: GSS0392_107_M_600


title: Patient 116-EGFR.1330


title: GSS0392_118_M_600


title: Patient 75-N.12872


title: Patient 117-EGFR.1474


title: SAMPLE 83


title: GSS0392_107_M_1800


title: GSS0392_115_M_600


title: GSS0392_107_M_0


title: Patient 115-EGFR.948


title: GSS0392_115_M_1800


title: Patient 114-EGFR.883


title: Patient 74-N.12727


title: Patient 73-N.12552


title: SAMPLE 81


title: SAMPLE 82


title: Patient 72-N.12215


title: GSS0392_108_M_1200


title: Patient 113-EGFR.864


title: SAMPLE 77


title: SAMPLE 80


title: SAMPLE 79


title: GSS0392_115_M_1200


title: GSS0392_108_M_0


title: Patient 76-N.19307


title: SAMPLE 76


title: Patient 70-N.10172


title: GSS0392_108_M_1800


title: Patient 71-N.10385


title: GSS0392_101_M_1200


title: Patient 110-EGFR.204


title: Patient 109-EGFR.192


title: Patient 112-EGFR.553


title: GSS0392_116_M_0


title: SAMPLE 75


title: SAMPLE 74


title: SAMPLE 78


title: Patient 69-N.10027


title: SAMPLE 73


title: GSS0392_108_M_600


title: GSS0392_116_M_1800


title: GSS0392_116_M_1200


title: GSS0392_116_M_600


title: Patient 111-EGFR.521


title: Patient 68-N.9968


title: Patient 108-EGFR.118


title: Patient 67-N.9034


title: Patient 66-N.8993


title: Patient 106-EGFR.77


title: Patient 65-N.8701


title: SAMPLE 71


title: GSS0392_110_M_1800


title: Patient 104-EGFR.66


title: Patient 64-N.8398


title: SAMPLE 70


title: Patient 103-N.42477


title: SAMPLE 69


title: Patient 62-N.6445


title: Patient 102-N.41554


title: Patient 61-N.6400


title: Patient 101-N.40310


title: GSS0392_110_M_600


title: Patient 105-EGFR.71


title: SAMPLE 72


title: GSS0392_110_M_1200


title: SAMPLE 66


title: SAMPLE 68


title: GSS_1414_293_F_NA

value: Female

value: African


title: SAMPLE 65


title: GSS0392_110_M_0


title: Patient 100-N.39415


title: SAMPLE 64


title: GSS_1414_232_F_NA


title: Patient 60-N.4940


title: GSS_1414_239_F_NA


title: GSS_1414_296_F_NA


title: Patient 63-N.7378


title: Patient 59-N.4808


title: Patient 58-N.4766


title: Patient 99-N.38143


title: SAMPLE 67


title: GSS_1414_325_F_NA


title: Patient 98-N.36885


title: Patient 57-N.4372


title: SAMPLE 62


title: Patient 96-N.35799


title: Patient 97-N.36567


title: Patient 56-N.4231


title: GSS_1414_104_F_NA


title: SAMPLE 63


title: SAMPLE 60


title: Patient 55-N.4189


title: SAMPLE 61


title: GSS_1414_303_F_NA


title: Patient 54-N.4180


title: GSS_1414_276_F_NA


title: Patient 95-N.35648


title: Patient 94-N.33560


title: Patient 53-N.3966


title: Patient 93-N.32659


title: SAMPLE 58


title: SAMPLE 57


title: Patient 92-N.32472


title: GSS_1414_253_F_NA


title: Patient 52-N.3947


title: Patient 51-N.3767


title: GSS_1414_291_F_NA


title: SAMPLE 56


title: SAMPLE 59


title: GSS_1414_263_F_NA


title: GSS_1414_270_F_NA


title: Patient 49-N.3455


title: Patient 48-N.3369


title: Patient 90-N.27998


title: Patient 91-N.28571


title: Patient 88-N.26813


title: SAMPLE 53


title: SAMPLE 52


title: Patient 47-N.3323


title: Patient 87-N.26570


title: SAMPLE 55


title: SAMPLE 51


title: SAMPLE 54


title: GSS_1414_246_F_NA


title: Patient 46-N.3236


title: Patient 107-EGFR.111


title: GSS_1414_327_F_NA


title: Patient 85-N.26356


title: GSS_1414_120_F_NA


title: Patient 86-N.26422


title: GSS_1414_316_F_NA


title: Patient 45-N.3221


title: GSS_1414_234_F_NA


title: Patient 89-N.27265


title: SAMPLE 50


title: GSS_1414_275_F_NA


title: Patient 44-N.3081


title: GSS_1414_287_F_NA


title: Patient 84-N.26020


title: Patient 43-N.2993


title: Patient 83-N.24642


title: Patient 42-N.2784


title: Patient 41-N.2766


title: Patient 82-N.24461


title: GSS_1414_217_F_NA


title: Patient 81-N.22231


title: SAMPLE 48


title: SAMPLE 47


title: SAMPLE 49


title: GSS_1414_323_F_NA


title: Patient 38-N.2532


title: Patient 39-N.2697


title: GSS_1414_202_F_NA


title: GSS_1414_301_F_NA


title: SAMPLE 44


title: Patient 37-N.2440


title: Patient 79-N.20653


title: Patient 40-N.2745


title: SAMPLE 45


title: SAMPLE 42


title: Patient 78-N.19854


title: Patient 77-N.19408


title: Patient 76-N.19307


title: SAMPLE 43


title: Patient 80-N.21266


title: SAMPLE 41


title: Patient 36-N.2374


title: SAMPLE 46


title: GSS_1414_304_F_NA


title: GSS_1414_197_F_NA


title: SAMPLE 40


title: GSS_1414_315_F_NA


title: GSS_1414_245_F_NA


title: GSS_1414_278_F_NA


title: GSS_1414_309_F_NA


title: SAMPLE 39


title: Patient 35-N.2335


title: GSS_1414_225_F_NA


title: Patient 33-N.2317


title: SAMPLE 38


title: Patient 73-N.12552


title: GSS_1414_256_F_NA


title: Patient 72-N.12215


title: Patient 32-N.2245


title: Patient 31-N.2231


title: Patient 30-N.2145


title: Patient 29-N.2088


title: Patient 75-N.12872


title: Patient 70-N.10172


title: Patient 71-N.10385


title: Patient 74-N.12727


title: Patient 34-N.2326


title: SAMPLE 35


title: Patient 69-N.10027


title: GSS_1414_149_F_NA


title: SAMPLE 34


title: SAMPLE 36


title: GSS_1414_280_F_NA


title: GSS_1414_319_F_NA


title: GSS_1414_331_F_NA


title: SAMPLE 33


title: Patient 28-N.2075


title: SAMPLE 32


title: SAMPLE 37


title: Patient 27-N.2001


title: Patient 67-N.9034


title: GSS_1414_292_F_NA


title: SAMPLE 31


title: Patient 26-N.1939


title: Patient 68-N.9968


title: GSS_1414_266_F_NA


title: SAMPLE 30


title: Patient 25-N.1547


title: GSS_1414_236_F_NA


title: GSS_1414_285_F_NA


title: Patient 65-N.8701


title: Patient 23-N.1452


title: Patient 64-N.8398


title: SAMPLE 29


title: Patient 22-N.1434


title: Patient 63-N.7378


title: SAMPLE 28


title: Patient 62-N.6445


title: SAMPLE 26


title: GSS_1414_193_F_NA


title: GSS_1414_229_F_NA


title: Patient 66-N.8993


title: GSS_1414_163_F_NA


title: Patient 61-N.6400


title: Patient 21-N.1360


title: SAMPLE 25


title: Patient 50-N.3479


title: SAMPLE 24


title: Patient 24-N.1515


title: Patient 20-N.1354


title: GSS_1414_305_F_NA


title: GSS_1414_326_F_NA


title: Patient 60-N.4940


title: Patient 59-N.4808


title: Patient 18-N.1078


title: Patient 19-N.1142


title: Patient 17-N.1001


title: SAMPLE 22


title: SAMPLE 23


title: Patient 58-N.4766


title: GSS_1414_299_F_NA


title: GSS_1414_330_F_NA


title: SAMPLE 27


title: GSS_1414_182_F_NA


title: Patient 57-N.4372


title: Patient 16-N.936


title: SAMPLE 21


title: Patient 15-N.866


title: Patient 56-N.4231


title: Patient 14-N.833


title: GSS_1414_332_F_NA


title: GSS_1414_257_F_NA


title: SAMPLE 20


title: Patient 55-N.4189


title: Patient 52-N.3947


title: SAMPLE 19


title: SAMPLE 18


title: SAMPLE 16


title: Patient 53-N.3966


title: SAMPLE 17


title: GSS_1414_306_F_NA


title: Patient 12-N.584


title: GSS_1414_264_F_NA


title: GSS_1414_240_F_NA


title: Patient 54-N.4180


title: SAMPLE 15


title: Patient 13-N.795


title: Patient 11-N.557


title: Patient 51-N.3767


title: GSS_1414_297_F_NA


title: Patient 50-N.3479


title: Patient 10-N.492


title: Patient 49-N.3455


title: SAMPLE 13


title: Patient 8-N.351


title: SAMPLE 12


title: Patient 48-N.3369


title: SAMPLE 14


title: GSS_1414_267_F_NA


title: Patient 7-N.321


title: GSS_1414_209_F_NA


title: GSS_1414_241_F_NA


title: SAMPLE 11


title: Patient 46-N.3236


title: GSS_1414_328_F_NA


title: Patient 6-N.231


title: Patient 47-N.3323


title: Patient 5-N.215


title: Patient 9-N.464


title: Patient 4-N.198


title: Patient 45-N.3221


title: GSS_1414_324_F_NA


title: Patient 44-N.3081


title: SAMPLE 8


title: Patient 3-N.174


title: Patient 2-N.165


title: Patient 43-N.2993


title: SAMPLE 7


title: Patient 41-N.2766


title: Patient 42-N.2784


title: GSS_1414_126_F_NA


title: SAMPLE 9


title: GSS_1414_261_F_NA


title: SAMPLE10


title: SAMPLE 6


title: GSS_1414_178_F_NA


title: GSS_1414_254_F_NA


title: GSS_1414_235_F_NA


title: SAMPLE 4


title: SAMPLE 5


title: GSS_1414_180_F_NA


title: Patient 40-N.2745


title: GSS_1414_204_F_NA


title: Adeno-Cre_H3K4me3_ChIP-Seq_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Total read numbers of ChIP-Seq samples are normalized to be 10 millions
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v1.1.2 with parameters -p 8 -m 1 --chunkmbs 512 --best
ChIP-Seq peaks for H3K4me1, H3K27ac and Mll4 were called using DANPOS2 v2.2.3 with the following parameters: --smooth_width 0  -ed 10000 --frsz 200 --extend 200 --pheight 1e-10 --extend_pheight 1e-3. And ChIP-Seq peaks for H3K4me3 were called with the following parameters: --smooth_width 0  -ed 15000 --frsz 200 --extend 200 --pheight 1e-5 --extend_pheight 1e-3.
Genome_build: mm9
Supplementary_files_format_and_content: wig files included in a tar archive on the series record.

source_name: Neurosphere-from cerebellum

growth_protocol: Cerebella from postnatal day 5 mice were used for the generation of neurospheres. The cerebella were washed gently with PBS and then placed in 60 mm dish with 2ml of the Neurobasal medium. Cerebellar tissues were chopped finely using sterile scalpels. Chopped pieces of cerebella were placed and slowly mashed in sterile 70  gm cell strainer and collected in 50 ml tube containing the Neurobasal medium. The dissociated cells were plated in 100 mm dishes density of 5 X10^5 cells per dish in Neurobasal medium supplemented with B27 supplement, 20ng/ml Epidermal Growth Factor (EGF), 20 ng/mL basic Fibroblast Growth Factor (bFGF) and 2  gg /mL heparin (Life Technologies, Waltham, MA). Within 3 V5 days, the cells propagated as free-floating neurospheres.

extract_protocol:
ChIP assays were performed as a modification of the previously described methods (Dhar et al., 2016; Dhar et al., 2012). In brief, cerebellar (4-month-old) tissues were isolated. DNA was purified from chromatin immunoprecipitates for MLL4 or IgG using the phenol/chloroform extraction. IgG was used as a negative control for ChIP. Then, DNA was amplified by quantitative PCR and normalized to input. To compare H3K4me1, H3K27ac, and H3K4me3 levels between Mll4f/f and Mll4 BSKO cerebellum, ChIP with reference exogenous genome (ChIP-Rx) was carried out as previously described (Li et al., 2016; Orlando et al., 2014). In brief, two biological replicates for Mll4f/f and Mll4 BSKO cerebellum were used for ChIP-Rx experiments. Drosophila melanogaster chromatin and Drosophila-specific H2Av antibody were added to each ChIP assay as a minor fraction. The following components for ChIP-Rx were purchased from Active Motif: the spike-in chromatin (53083), Drosophila-specific H2Av antibody (61686), spike-in ChIP positive control primer set (71037), and negative control primer set (71028). The immunoprecipitated DNAs were sequenced by Next-Generation Sequencing (NGS) (UCI GHTF).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neurosphere

value: neurosphere derived from cerebellum

tag: genotype

value: MLL4 KO

tag: chip antibody

value: H3K4me3 (Millipore, cat# 07-473)


title: Patient 38-N.2532


title: Adeno-Cre_H3K4me3_ChIP-Seq_rep1


title: Patient 1-N.148


title: Patient 39-N.2697


title: Adeno-Empty_H3K4me3_ChIP-Seq_rep2

value: wildtype


title: Patient 36-N.2374


title: Adeno-Empty_H3K4me3_ChIP-Seq_rep1


title: Patient 35-N.2335


title: Adeno-Cre_H3K4me1_ChIP-Seq_rep1

value: H3K4me1 (Abcam, cat# ab8895)


title: Patient 37-N.2440


title: SAMPLE 2

value: Liver Biopsy

value: Mild


title: Patient 34-N.2326


title: Adeno-Empty_H3K4me1_ChIP-Seq_rep2


title: SAMPLE 1


title: Patient 33-N.2317


title: SAMPLE 3

value: Cluster 3


title: Adeno-Empty_H3K4me1_ChIP-Seq_rep1


title: GSS_1414_279_F_NA

value: LCM-separated epidermis


title: GSS_1414_145_F_NA


title: aba2-2_8 h PEG plate_biological rep3

city: Yokohama

first: Shunsuke

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

hyb_protocol: 600 ng of cRNAs were hybridized to the microarray (GPL20796) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray chips were scanned by Agilent DNA Microarray Scanner G2505B and raw data was extracted using Feature Extraction program ver 9.1.

data_processing: Image data were normalized by RMA statistical algorithms for signals of microarray probes using limma package (Ritchie et al., 2015) on R 3.4.0. program.

organism: Arabidopsis thaliana

source_name: aba2-2, whole seedlings, 8 h PEG

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds were germinated and the seedlings were grown aseptically on solid 1/2MS media plus 1% sucrose at 23C under long-day (16 h light / 8 h darkness) photoperiodic conditions.

extract_protocol: Total RNA was extracted from three biological replicates by using the Plant RNA Purification Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions

treatment_protocol: For osmotic stress treatment, two-week old seedlings were transferred onto 1/2MS infused by PEG8000 (-1.2 MPa) for 8 h under continuous light conditions.

value: aba2-2 mutant

value: Whole seedlings

tag: developmental stage

value: 2 weeks after germination

tag: treatment

value: 8 h polyethylene glycol (PEG)


title: aba2-2_8 h PEG plate_biological rep2

tag: tissue


title: aba3-1_8 h PEG plate_biological rep3

source_name: aba3-1, whole seedlings, 8 h PEG

value: aba3-1 mutant


title: Adeno-Cre_H3K4me1_ChIP-Seq_rep2


title: Jurkat Negative Negative 1

city: Izmir

first: ipek

last: erdogan

address: Gulbahce

country: Turkey

institute: Izmir Institute of Technology

hyb_protocol: Samples were hybridized automatically over night (16 hours) at 42°C. To improve hybridization Argon pressure moved the samples within the Biochip resulting in 2-3x higher signal intensities than without movement

scan_protocol: Biotin and its detection with streptavidin-phycoerythrin (SAPE) in combination with Consecutive Signal Enhancement (CSE) procedure was used for maximum sensitivity. Feature recognition was done by using Cy3 filter set. Geniom RT Analyzer was used in this process.

data_processing: Local kNN background correction, Inter-array normalization

label: Biotin

source_name: Jurkat T cells_non-treated

label_protocol: mirVana™ microRNA labeling kit (Ambion) was used for total RNA labeling for miRNA analysis. 0.9 µg of total RNA were labeled for each array.

growth_protocol: Jurkat cell line, originated from human T cell leukemia, was maintained in RPMI 1640 supplemented with L-glutamine, 10% fetal bovine serum, 100 U/ml penicillin and 100 µg/ml streptomycin in an atmosphere of 5% CO2 at 37°C. Cells were passaged every 48 hours.

extract_protocol: Total RNA was extracted by phenol-chloroform

treatment_protocol: Cells were treated with 8 µM camptothecin for 4 hours

tag: cell line

value: T Lymphocytic Leukemia

value: Jurkat T Lymphocytes

tag: apoptosis inducer

tag: sorted subfraction

value: JNN (Jurkat Negative Negative)

tag: molecule type

value: miRNA


title: Jurkat Apoptotic Negative 2

source_name: Jurkat T cells_camptothecin_8 µM_4 hrs

tag: cell type

value: camptothecin

value: JAN (Jurkat Apoptotic Negative)


title: Jurkat Apoptotic Negative 3


title: Jurkat Apoptotic Negative 1


title: Patient 32-N.2245

value: lung adenocarcinoma

tag: egfr status

value: EGFR-negative


title: Jurkat Negative Negative 2


title: Jurkat Apoptotic Positive 3

value: JAP (Jurkat Apoptotic Positive)


title: Patient 31-N.2231


title: aba2-2_8 h PEG plate_biological rep1


title: Adeno-Cre_H3K27ac_ChIP-Seq_rep1

value: Neurosphere

value: neurosphere derived from cerebellum

value: MLL4 KO

value: H3K27ac (Abcam, cat# ab4729)


title: Jurkat Apoptotic Positive 2


title: aba3-1_8 h PEG plate_biological rep1

value: Whole seedlings


title: Adeno-Empty_H3K27ac_ChIP-Seq_rep2

value: wildtype


title: Patient 30-N.2145


title: aba3-1_8 h PEG plate_biological rep2

value: 2 weeks after germination

value: 8 h polyethylene glycol (PEG)


title: Patient 29-N.2088


title: Adeno-Cre_H3K27ac_ChIP-Seq_rep2


title: Jurkat Apoptotic Positive 1

value: T Lymphocytic Leukemia


title: Adeno-Empty_H3K27ac_ChIP-Seq_rep1


title: Col-0_8 h PEG plate_biological rep3

source_name: Col-0, whole seedlings, 8 h PEG

value: Col-0 wild-type


title: Patient 28-N.2075


title: Patient 27-N.2001


title: Patient 26-N.1939


title: Patient 25-N.1547


title: Mll4_WT_4month_RNA-Seq

description:
Sample25
Processed data file: genes.fpkm.xls

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Total read numbers of ChIP-Seq samples are normalized to be 10 million.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v1.1.2 with parameters -p 8 -m 1 --chunkmbs 512 --best
ChIP-Seq peaks for H3K4me1, H3K27ac and Mll4 were called using DANPOS2 v2.2.3 with the following parameters: --smooth_width 0 -ed 10000 --frsz 200 --extend 200 --pheight 1e-10 --extend_pheight 1e-3. ChIP-Seq peaks for H3K4me3 were called with the following parameters: --smooth_width 0 -ed 15000 --frsz 200 --extend 200 --pheight 1e-5 --extend_pheight 1e-3.
RNA-Seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 genome assembly using tophat v2.1.0 with parameters --mate-std-dev 200 -p 8 -r 203
The number of fragments that originated from each gene in each sample is estimated using cuffdiff with default parameters. Then, the differentially expressed genes based on P-value are inferred from the gene_exp.diff file.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: For ChIP-Seq data, wig files showing the average signal density across genome are generated using DANPOS2 v2.2.3.
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text files contain FPKM values for each gene of each sample.

source_name: mouse 4 month cerebellum, Mll4 WT

extract_protocol:
Total RNA was prepared from cerebellar tissues using Trizol reagent (Life Technologies). RNA samples were sequenced using the Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

value: Mll4 WT

value: cerebellum

tag: age

value: 4 months


title: Patient 24-N.1515


title: Mll4_WT_1month_RNA-Seq_Rep1

description:
Sample22
Processed data file: genes.fpkm.xls

source_name: mouse 1 month cerebellum, Mll4 WT

value: 1 month


title: Mll4_WT_1month_RNA-Seq_Rep2

description:
Sample23
Processed data file: genes.fpkm.xls


title: Col-0_8 h PEG plate_biological rep2


title: Col-0_8 h PEG plate_biological rep1


title: Mll4_KO_1month_RNA-Seq_Rep3

description:
Sample20
Processed data file: genes.fpkm.xls

source_name: mouse 1 month cerebellum, Mll4 KO

value: Mll4 KO


title: Patient 23-N.1452

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: EGFR-negative


title: Patient 22-N.1434


title: Mll4_WT_1month_RNA-Seq_Rep3

description:
Sample24
Processed data file: genes.fpkm.xls


title: Homeostatic epidermis IFE cells in G9a WT, replicate 3

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

country: Spain

institute: Institut for Research in Biomedicine (IRB-Barcelona)

hyb_protocol: Hybridisation mixture was prepared according to the Gene Atlas protocol (Affymetrix). Each sample target was hybridised to a Mouse Genome 430 PM array. After hybridisation for 16 hours at 45°C, washing and staining was performed in the GeneAtlas Fluidics Station (Affymetrix).

scan_protocol: The arrays were scanned in a GeneAtlas Imaging Station (Affymetrix). All processing was performed according to manufacturer’s recommendations.

data_processing: Overall array intensity was normalised between arrays and the probe intensity of all probes in a probe set summarised to a single value using RMA (Robust Multichip Average)

source_name: Homeostatic epidermis interfollicular cell in G9a WT

label_protocol: cDNA library preparation and amplification were performed from 25ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 8µg cDNA were subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

extract_protocol: RNA was extracted using TRizol (Sigma-Aldrich).

value: Epidermis

value: G9a WT

value: 15-week old


title: Mll4_KO_4month_RNA-Seq

description:
Sample21
Processed data file: genes.fpkm.xls

source_name: mouse 4 month cerebellum, Mll4 KO


title: aba3-1_8 h mock plate_biological rep3

source_name: aba3-1, whole seedlings, 8 h mock

value: aba3-1 mutant

value: 8 h mock (1/2MS)


title: aba2-2_8 h mock plate_biological rep2

source_name: aba2-2, whole seedlings, 8 h mock

value: aba2-2 mutant

value: Whole seedlings


title: Patient 21-N.1360


title: Homeostatic epidermis IFE cells in G9a cKO, replicate 4

source_name: Homeostatic epidermis interfollicular cell in G9a cKO

value: G9a cKO


title: Homeostatic epidermis IFE cells in G9a WT, replicate 1


title: aba2-2_8 h mock plate_biological rep1

value: 2 weeks after germination


title: Homeostatic epidermis IFE cells in G9a WT, replicate 2


title: aba3-1_8 h mock plate_biological rep2


title: Patient 20-N.1354


title: Mll4_KO_1month_RNA-Seq_Rep1

description:
Sample18
Processed data file: genes.fpkm.xls


title: aba3-1_8 h mock plate_biological rep1


title: aba2-2_8 h mock plate_biological rep3


title: Col-0_8 h mock plate_biological rep2

source_name: Col-0, whole seedlings, 8 h mock

value: Col-0 wild-type


title: Homeostatic epidermis bulge cells in G9a WT, replicate 3

source_name: Homeostatic epidermis bulge cell in G9a WT


title: Homeostatic epidermis IFE cells in G9a cKO, replicate 1


title: Input_KO_Rep2

source_name: mouse 4 month cerebellum, Mll4 KO, input

treatment_protocol: 1% formaldehyde for 20 min.


title: Homeostatic epidermis IFE cells in G9a cKO, replicate 3


title: Col-0_8 h mock plate_biological rep3


title: Patient 19-N.1142


title: Mll4_KO_1month_RNA-Seq_Rep2

description:
Sample19
Processed data file: genes.fpkm.xls


title: Patient 18-N.1078


title: Input_KO_Rep1


title: Input_WT_Rep2

source_name: mouse 4 month cerebellum, Mll4 WT, input

value: Mll4 WT


title: Patient 17-N.1001


title: Patient 16-N.936


title: Input_WT_Rep1

value: cerebellum


title: Homeostatic epidermis IFE cells in G9a cKO, replicate 2


title: H3K27ac_KO_ChIP-Seq_Rep2

source_name: mouse 4 month cerebellum, Mll4 KO, H3K27ac ChIP

value: 4 months

value: H3K27ac (Abcam, cat# ab4729)


title: Patient 15-N.866


title: H3K27ac_KO_ChIP-Seq_Rep1

value: Mll4 KO


title: Col-0_8 h mock plate_biological rep1


title: Homeostatic epidermis bulge cells in G9a WT, replicate 2


title: Homeostatic epidermis bulge cells in G9a WT, replicate 1


title: Patient 14-N.833

value: lung adenocarcinoma


title: aba2-2_3 h PEG solution_biological rep3

source_name: aba2-2, whole seedlings, 3 h PEG

value: 3 h polyethylene glycol (PEG)


title: Homeostatic epidermis bulge cells in G9a cKO, replicate 3

source_name: Homeostatic epidermis bulge cell in G9a cKO

value: Epidermis


title: Homeostatic epidermis bulge cells in G9a cKO, replicate 2


title: Homeostatic epidermis bulge cells in G9a cKO, replicate 1


title: H3K27ac_WT_ChIP-Seq_Rep2

source_name: mouse 4 month cerebellum, Mll4 WT, H3K27ac ChIP


title: H3K27ac_WT_ChIP-Seq_Rep1


title: aba3-1_3 h PEG solution_biological rep3

source_name: aba3-1, whole seedlings, 3 h PEG


title: Homeostatic epidermis bulge cells in G9a cKO, replicate 4


title: Patient 13-N.795

value: EGFR-negative


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 8

source_name: DMBA/TPA induced tumor in G9a cKO

treatment_protocol: DMBA and TPA (200 µl of 0.25 mg ml–1 or 0.02 mg ml–1 solution in acetone, respectively) were applied once weekly to the shaved back skin of 8-week-old mice for 6 weeks. For tumour formation studies, TPA treatment was continued twice weekly for up to 20 weeks

value: DMBA/TPA induced SCC tumor

tag: age in beginning of the experiment


title: aba3-1_3 h PEG solution_biological rep1

value: aba3-1 mutant


title: aba3-1_3 h PEG solution_biological rep2


title: aba2-2_3 h PEG solution_biological rep1


title: Patient 12-N.584


title: aba2-2_3 h PEG solution_biological rep2


title: H3K4me1_KO_ChIP-Seq_Rep2

source_name: mouse 4 month cerebellum, Mll4 KO, H3K4me1 ChIP

value: H3K4me1 (Abcam, cat# ab8895)


title: Patient 11-N.557

source_name: lung adenocarcinoma


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 5


title: Col-0_3 h PEG solution_biological rep3

source_name: Col-0, whole seedlings, 3 h PEG


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 9


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 3


title: Col-0_3 h PEG solution_biological rep2


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 6


title: H3K4me1_WT_ChIP-Seq_Rep2

source_name: mouse 4 month cerebellum, Mll4 WT, H3K4me1 ChIP


title: Patient 9-N.464


title: H3K4me1_KO_ChIP-Seq_Rep1


title: H3K4me1_WT_ChIP-Seq_Rep1


title: H3K4me3_KO_ChIP-Seq_Rep2

source_name: mouse 4 month cerebellum, Mll4 KO, H3K4me3 ChIP

value: H3K4me3 (Millipore, cat# 07-473)


title: Patient 8-N.351


title: Patient 6-N.231


title: H3K4me3_WT_ChIP-Seq_Rep2

source_name: mouse 4 month cerebellum, Mll4 WT, H3K4me3 ChIP


title: Patient 7-N.321


title: H3K4me3_KO_ChIP-Seq_Rep1


title: Patient 10-N.492


title: Patient 5-N.215


title: H3K4me3_WT_ChIP-Seq_Rep1


title: Mll4_WT_ChIP-Seq

source_name: mouse 4 month cerebellum, Mll4 WT, Mll4 ChIP

value: Mll4 (homemade)


title: Patient 3-N.174


title: aba2-2_3 h mock solution_biological rep3

source_name: aba2-2, whole seedlings, 3 h mock

value: aba2-2 mutant

value: Whole seedlings

value: 3 h mock (1/2MS)


title: DMBA/TPA induced tumor in G9a WT mouse, replicate 7

source_name: DMBA/TPA induced tumor in G9a WT

value: G9a WT


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 1

value: G9a cKO


title: DMBA/TPA induced tumor in G9a WT mouse, replicate 9


title: Patient 2-N.165


title: Col-0_3 h PEG solution_biological rep1

value: Col-0 wild-type

value: 2 weeks after germination


title: aba2-2_3 h mock solution_biological rep2


title: input-3450-1

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

country: France

institute: INSA

description: Total reads :  12 868 709 ; average fragment size : 174

data_processing:
Basecalls and alignment performed using Torrent_Suite 5.0.4
ChIP-seq reads were aligned to the N16961 genome
Genome_build: ASM674v1
Supplementary_files_format_and_content: The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the option –d and –fs

organism: Vibrio cholerae

source_name: bacteria

growth_protocol: Samples were prepared from exponential growing phase cultures at 37°C in LB media (OD = 0.5)

extract_protocol:
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBVc1 antibody
A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer’s instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA

treatment_protocol: Cells were treated with formalhedyde (1 %)

tag: strain

tag: dlt

tag: antibody

value: none, input


title: aba3-1_3 h mock solution_biological rep2

source_name: aba3-1, whole seedlings, 3 h mock

tag: genotype


title: aba2-2_3 h mock solution_biological rep1

tag: developmental stage


title: DMBA/TPA induced tumor in G9a WT mouse, replicate 8


title: DMBA/TPA induced tumor in G9a cKO mouse, replicate 2


title: DMBA/TPA induced tumor in G9a WT mouse, replicate 4


title: Col-0_3 h mock solution_biological rep2

source_name: Col-0, whole seedlings, 3 h mock

tag: treatment


title: DMBA/TPA induced tumor in G9a WT mouse, replicate 6

tag: tissue


title: Col-0_3 h mock solution_biological rep3


title: aba3-1_3 h mock solution_biological rep3


title: MumR+H2O2 replicate 3

city: Nashville

first: Lillian

last: Juttukonda

address: 1161 21st Avenue South

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

description: Normalized_expression_4615-JPZ-0010-0027_GEOupload

data_processing:
Quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK).
Alignment: Raw reads were imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA) and mapped to the reference Acinetobacter baumannii ATCC17978.
Filtering: After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates.
Generalization of normalized abundance measurements: Samples were grouped and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) (Robinson and Oshlack 2010) as the normalization method. Reference: Robinson MD, Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome biology 11:R25.
Supplementary_files_format_and_content: Comma separate values file containing gene symbol, chromosome, gene start and end, strand, and log2 normalized expression by sample

organism: Acinetobacter baumannii

source_name: Bacterial culture

growth_protocol: Acinetobacter baumannii cultures were prepared using colonies streaked to isolation from frozen stocks 2 days prior to the experiment. Overnight cultures in biological triplicate were started from a single colony and grown for sixteen hours in luria broth at 37C with shaking at 180 rpm. Overnight cultures were diluted 1:1000 into 10 mL LB in a 50 mL conical tube and grown to mid-exponential phase.

extract_protocol:
Cultures were thawed and centrifuged at 7,000 rpm for 10 minutes, supernatants were decanted, and pellets were dried on paper towels. Pellets were resuspended in LETS buffer (0.1 M LiCl, 10 mM EDTA, 10 mM Tris HCl pH 7.4, 1% SDS), homogenized in a bead beater (Fastprep-24, MP Biomedical, Santa Ana, CA) with Lysing Matrix B beads (MP Biomedicals, MP Biomedical, Santa Ana, CA) at a speed of 6 m/s for 45 seconds, heated at 55 °C for 5 minutes, and centrifuged for 10 minutes at 15,000 rpm. The upper phase was collected, mixed with 1 mL TRI Reagent (Sigma, St. Louis, MO), and incubated for 5 minutes at room temperature. Chloroform (0.2 mL, Acros Organics, Waltham, MA) was added, samples were vigorously shaken for 15 seconds, and samples were incubated at room temperature for 2 minutes. Following centrifugation at 4 °C for 15 minutes, 600 mL of the upper aqueous phase was collected and RNA was precipitated with 1 mL isopropanol (Sigma, St. Louis, MO). RNA was washed with 70% ethanol (Sigma, St. Louis, MO) and resuspended in 100 mL DNase-Free, RNase-Free water (ThermoFisher, Waltham, MA). DNA contamination was removed by treatment with 8 mL RQ1 enzyme (Promega, Madison, WI), 12 mL 10X RQ1 buffer, and 2 mL Ribolock RNase inhibitor (ThermoFisher, Waltham, MA) for 2 hours at 37 °C. DNase was removed and samples further purified by the RNEasy kit (Qiagen, Hilden, DE) using the manufacturer’s instructions and RNA was stored long-term at -80 °C.
Five hundred ng of total RNA was required for proceeding to downstream RNA-seq applications. First, ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Epidemiology) kit (Illumina, San Diego, CA) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house Genomic Services Lab (GSL) primers and amplified through 12 cycles of PCR. Library quantity was assessed by Qubit 2.0 Fluorometer, and the library quality was estimated by utilizing a DNA High Sense chip on an Caliper Gx (Perkin Elmer). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering.

treatment_protocol: Cultures were removed from the incubator and treated with 5.65 microliters of 30% H2O2 (EMD Millipore, Darmstadt, DE), for a final concentration of 5 mM, or opened but not treated. After 10 minutes of incubation at 37C with shaking at 180 rpm, cultures were immediately mixed with 10 mL of a 1:1 mixture of ice-cold acetone (JT Baker, Center Valley, PA) and ethanol (Sigma, St. Louis, MO) and frozen at -70C.

tag: growth condition

value: mid-exponential growth in LB; 10 minute exposure to 5 mM H2O2

value: mumR-/- strain


title: IP-3450-2

description: Total reads : 13 070 887  ; average fragment size : 291

value: anti ParBVc1


title: DMBA/TPA induced tumor in G9a WT mouse, replicate 2


title: Patient 1-N.148

description: One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: lung adenocarcinoma

value: EGFR-negative


title: aba3-1_3 h mock solution_biological rep1

value: aba3-1 mutant


title: Fa3_rep2_sRNA_seq

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

data_processing:
For whole genome bisulfite sequencing analysis, paired-end sequencing reads were first trimmed with Trimmomatic for removal of Illumina adapters and low-quality bases (quality score < 20). The cleaned reads were then aligned to Fragaria vesca genome (Fragaria vesca v1.1, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Fvesca) using bsmap-2.87 with default settings. Uniquely and properly mapped paired-end reads (with options -u -p) were used to extract methylation ratios with the methratio.py (a script included in bsmap-2.87).
For RNA-seq data analysis, paired-end reads were aligned to Fragaria vesca genome (Fragaria vesca v1.1, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Fvesca) using STAR with default parameters. Uniquely mapped reads with MAPQ >20 were collected for further analysis.
For small RNA sequencing data analysis, sequenced reads were trimmed with Trimmomatic to remove Illumina adapters and low-quality bases (quality score < 20). Reads with length <18bp and length >30bp were discarded. Cleaned 24-nt reads were mapped to F. vesca genome and defined to siRNA cluster with Shortstack.
Genome_build: Fragaria vesca v1.1 (https://www.rosaceae.org/analysis/13)
Supplementary_files_format_and_content: bigWig were provided for Bisulfite-Seq, RNA-Seq and small-RNA-Seq

organism: Fragaria x ananassa

source_name: Strawberry fruit,  full red stage, approximately 35 days after bloom (DAB)

growth_protocol: Strawberries (Fragaria × ananassa Duch. cv. Hongjia) were grown in the scientific research innovation base at Zhejiang Academy of Agricultural Science at Haining (Zhejiang, China). Fruits at three developmental stages (Fa1, green stage, approximately 20 days after bloom (DAB); Fa2, intermediate red stage, 30 DAB; Fa3, full red stage, 35 DAB) were harvested. After being transferred to the lab on the day of harvest, fruits with uniform size and free of visible defects were selected.

extract_protocol:
For whole genome bisulfite sequencing, genomic DNA was extracted from leaves and fruits using a DNeasy Plant Maxi Kit (Qiagen) and then was used for library construction using Illumina’s standard DNA methylation analysis protocol and the NEB Ultra II DNA Library Prep Kit. For RNA-seq, total RNA was extracted with TRIzol reagent (Ambion) from fruits. For reverse transcription, 1 μg of RNA and oligo dT primers were used to synthesize cDNA in a 20-μL reaction using the qScript cDNA SuperMix kit (Quanta). For small-RNA sequencing, total RNA was extracted with TRIzol reagent (Ambion) from fruits. Total RNA was then separated on denaturing polyacrylamide gels and < 100-nt fractions were cut out and purified for standard small RNA library preparation. The samples were sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences using Illumina HiSeq2500.
The samples were sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences using Illumina HiSeq2500.
Bisulfite-Seq, RNA-Seq and small-RNA-Seq

treatment_protocol: No treatment applied.

tag: ecotype

value: Fragaria x ananassa Duch. cv. Hongjia

value: Strawberry fruit

tag: development stage


title: Fa3_rep1_sRNA_seq

value: full red stage, approximately 35 days after bloom (DAB)


title: MumR+H2O2 replicate 2


title: input-3450-2

description: Total reads :  2 749 374  ; average fragment size : 300


title: MumR+H2O2 replicate 1


title: Patient 4-N.198


title: MumR untreated replicate 3

value: mid-exponential growth in LB

value: MumR-/- strain


title: A549, irradiated (2.0 Gy) cells, biological replicate 4 (2Gy-24h-4)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: miRNA expression profiling of A549 irradiated cells (2Gy-24h-4)

hyb_protocol: Probes were hybridized with labelled RNA at 55°C for 22 hours using the Agilent’s Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes.

scan_protocol: Slides were washed by Agilent Gene expression wash buffer 1 and 2 and scanned using an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings. Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with cyclic Lowess for miRNA experiments and with quantile for gene expression profiling [Bolstad BM et al., Bioinformatics (2003), 19(2):185-93] to correct possible experimental distortions. Normalization function was applied to expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provides spot quality measures in order to evaluate the goodness and the reliability of hybridization. In particular flag ‘‘glsFound’’ (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as ‘‘null’’. So, in order to make more robust and unbiased statistical analysis, probes with a high proportion of ‘‘null’’ values were removed from the dataset. We decided to use about 40% of null as threshold in the filtering process obtaining a total of 333 available human miRNAs.

source_name: A549, irradiated (2.0 Gy) cells

label_protocol: total RNA (200 ng) was labeled with pCp Cy3, according to the Agilent Technologies protocol ( the miRNA Microarray System protocol v. 1.5) and unincorporated dyes were removed with MicroBioSpin6 columns (BioRad).

growth_protocol: All culture medium were from Life Technologies (Carlsbad, CA, USA) and were supplemented with heat inactivated fetal bovine serum (FBS, BIOCHROM, Berlin, Germany), 38 units/mL streptomycin, and 100 units/mL penicillin G. All cells were grown at 37◦C in a humidified atmosphere with 5% CO2. Non-small cell carcinoma cells were purchased from the American Type Culture Collection (ATCC, Manassas, VA). A549 cells derived from human alveolar type 2 primary lung adenocarcinoma cells (CCL-185™) and were cultured in Ham’s F12-K Nutrient Mixture. A549 cells were grown in a 1:1 mixture of DMEM and Ham’s F-12 medium (DMEM/F-12, Gibco, Life Technologies), HEPES 20 mM, 1% of MEM non-essential amino acids and 10% of heat-inactivated FCS. Cells were kept at 37 °C in a humidified atmosphere of 95% air and 5% CO2, and maintained in exponential and asynchronous phase of growth by repeated trypsinization and reseeding prior to reaching subconfluency.

extract_protocol: Total RNA was isolated from irradiated and non-irradiated cells by using Trizol® Reagent (Invitrogen, Life Technologies, Carlsbad, CA, USA), according to the manufacturer’s protocol. Total RNA quantification was performed using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA); RNA integrity and the content of miRNAs were assessed by capillary electrophoresis using the Agilent Bioanalyzer 2100, with the RNA 6000 Nano and the small RNA Nano chips, respectively (Agilent Technologies, Palo Alto, CA, USA). Only total RNA samples with RNA Integrity Number (RIN) values ≥ 6 were used for microarray analysis.

treatment_protocol: Cells were seeded on Petri dishes (35x15 or 60x15 mm), with or without glass coverslips, kept on ice before and after irradiation, and cultured at 37° C in fresh medium thereafter. Irradiation with gamma-rays was performed at the Department of Oncological and Surgical Sciences of Padova University with a 137Cs source (dose rate of 2.8 Gy/min) within the dose range 0-6 Gy. Except for irradiation, the control cells were subjected to the same experimental conditions.

tag: cell line

value: A549 cell line derived from human alveolar type 2 primary lung adenocarcinoma cells

value: IR

tag: time

value: 24 hr


title: Fa1_rep2_sRNA_seq

source_name: Strawberry fruit, green stage, approximately 20 days after bloom (DAB)


title: Fa1_rep1_sRNA_seq

value: green stage, approximately 20 days after bloom (DAB)


title: MumR untreated replicate 2


title: A549, irradiated (2.0 Gy) cells, biological replicate 3 (2Gy-24h-3)

description: miRNA expression profiling of A549 irradiated cells (2Gy-24h-3)


title: Fa3_rep2_mRNA_seq


title: Fa3_rep1_mRNA_seq


title: MumR untreated replicate 1


title: OxyR+H2O2 replicate 3

value: OxyR-/- strain


title: A549, irradiated (2.0 Gy) cells, biological replicate 2 (2Gy-24h-2)

description: miRNA expression profiling of A549 irradiated cells (2Gy-24h-2)


title: Fa2_rep2_mRNA_seq

source_name: Strawberry fruit, intermediate red stage, approximately 30 days after bloom (DAB)


title: DMBA treated IIFE cells in G9a WT animal, replicate4

source_name: DMBA/TPA pre-neoplastic epidermal interfollicular epidermis cell I G9a WT

treatment_protocol: DMBA (7,12-dimethylbenz[a]anthracene) / TPA (12-O-tetradecanoylphorbol-13-acetate)–based chemical skin carcinogenesis was performed as previously described1-3. Briefly, DMBA and TPA (200 µl of 0.25 mg ml–1 or 0.02 mg ml–1 solution in acetone, respectively) were applied once weekly to the shaved back skin of 8-week-old mice for 6 weeks, at which point animals were sacrificed for pre-neoplastic epidermis experiments.

value: epidermis

value: G9a WT

value: 15-week old mice


title: A549, irradiated (2.0 Gy) cells, biological replicate 1 (2Gy-24h-1)

description: miRNA expression profiling of A549 irradiated cells (2Gy-24h-1)


title: Col-0_3 h mock solution_biological rep1

value: Col-0 wild-type

value: Whole seedlings

value: 2 weeks after germination

value: 3 h mock (1/2MS)


title: A549, non-irradiated (0 Gy) cells, biological replicate 3 (0Gy-24h-3)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-24h-3)

source_name: A549, non-irradiated (0 Gy) cells

value: control


title: DMBA treated IFE cells in G9a WT animal, replicate3


title: DMBA treated IFE cells in G9a WT animal, replicate1


title: DMBA treated IFE cells in G9a cKO animal, replicate4

source_name: DMBA/TPA pre-neoplastic epidermal interfollicular epidermis cell I G9a cKO

value: G9a cKO


title: OxyR+H2O2 replicate 1

value: mid-exponential growth in LB; 10 minute exposure to 5 mM H2O2


title: DMBA treated IFE cells in G9a cKO animal, replicate2


title: DMBA treated IFE cells in G9a WT animal, replicate2


title: DMBA treated IFE cells in G9a cKO animal, replicate3


title: DMBA treated IFE cells in G9a cKO animal, replicate1


title: A549, non-irradiated (0 Gy) cells, biological replicate 2 (0Gy-24h-2)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-24h-2)


title: OxyR untreated replicate 3

value: mid-exponential growth in LB


title: A549, non-irradiated (0 Gy) cells, biological replicate 4 (0Gy-24h-4)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-24h-4)


title: Fa1_rep1_mRNA_seq

value: Fragaria x ananassa Duch. cv. Hongjia

value: Strawberry fruit


title: A549, non-irradiated (0 Gy) cells, biological replicate 1 (0Gy-24h-1)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-24h-1)

value: A549 cell line derived from human alveolar type 2 primary lung adenocarcinoma cells


title: OxyR+H2O2 replicate 2


title: DMBA treated Bulge cells in G9a WT animal, replicate3

source_name: DMBA/TPA pre-neoplastic epidermal bulge cell I G9a WT


title: DMBA treated Bulge cells in G9a WT animal, replicate4


title: Fa2_rep1_mRNA_seq

value: intermediate red stage, approximately 30 days after bloom (DAB)


title: OxyR untreated replicate 2


title: Leaf_BS_seq

source_name: Strawberry leaf

value: Strawberry leaf


title: Fa3_rep2_BS_seq

value: full red stage, approximately 35 days after bloom (DAB)


title: OxyR untreated replicate 1

value: OxyR-/- strain


title: A549, irradiated (2.0 Gy) cells, biological replicate 4 (2Gy-4h-4)

description: miRNA expression profiling of A549 irradiated cells (2Gy-4h-4)

data_processing: Inter-array normalization of expression levels was performed with cyclic Lowess for miRNA experiments and with quantile for gene expression profiling [Bolstad BM et al., Bioinformatics (2003), 19(2):185-93] to correct possible experimental distortions. Normalization function was applied to expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provides spot quality measures in order to evaluate the goodness and the reliability of hybridization. In particular flag ‘‘glsFound’’ (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as ‘‘null’’. So, in order to make more robust and unbiased statistical analysis, probes with a high proportion of ‘‘null’’ values were removed from the dataset. We decided to use about 40% of null as threshold in the filtering process obtaining a total of 311 available human miRNAs.

value: IR

value: 4 hr


title: DMBA treated Bulge cells in G9a WT animal, replicate1

value: epidermis

value: G9a WT

value: 15-week old mice


title: A549, irradiated (2.0 Gy) cells, biological replicate 3 (2Gy-4h-3)

description: miRNA expression profiling of A549 irradiated cells (2Gy-4h-3)


title: WT+H2O2 replicate 3

value: WT parental strain


title: A549, irradiated (2.0 Gy) cells, biological replicate 2 (2Gy-4h-2)

description: miRNA expression profiling of A549 irradiated cells (2Gy-4h-2)


title: Fa1_rep2_mRNA_seq

value: green stage, approximately 20 days after bloom (DAB)


title: Fa3_rep1_BS_seq


title: Fa2_rep2_BS_seq


title: WT+H2O2 replicate 1


title: WTsample untreated replicate 3


title: A549, non-irradiated (0 Gy) cells, biological replicate 4 (0Gy-4h-4)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-4h-4)

value: control


title: A549, non-irradiated (0 Gy) cells, biological replicate 3 (0Gy-4h-3)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-4h-3)


title: A549, irradiated (2.0 Gy) cells, biological replicate 1 (2Gy-4h-1)

description: miRNA expression profiling of A549 irradiated cells (2Gy-4h-1)


title: Fa1_rep2_BS_seq


title: Fa2_rep1_BS_seq


title: T2

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Science

institute: Cornell University

data_processing:
Reads were aligned using Tophat (version 2.0.9) (Kim et al 2013) using parameters -p -o -G –no-novel-juncs
Raw count for each gene was estimated with Bioconductor ( EdgeR version 3.18.1) using bam files
Differentially expressed genes were identified using DESeq package ( Anders and Huber 2010)
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited/xls files include FPKM values/counts for each Sample

organism: Bos taurus

source_name: Blastocyst derived trophoblast cultures

growth_protocol: Primary trophoblast outgrowths were grown on irradiated mouse embryonic fibroblasts and passaged

extract_protocol:
Trophoblast colonies were collected and total RNA was extracted using RNAqueous micro kit (Thermo Fisher Scientific). After Poly-A mRNA isolation, Illumina TruSeq RNA Sample Prep Kit  was used with for the construction of sequencing libraries.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell type source

value: Blastocyst derived trophoblast culture

tag: cell type

value: Primary trophoblast cells

tag: passage


title: Fa1_rep1_BS_seq

value: Fragaria x ananassa Duch. cv. Hongjia


title: WTsample untreated replicate 2

description: Normalized_expression_4615-JPZ-0010-0027_GEOupload

value: mid-exponential growth in LB


title: T1


title: WTsample untreated replicate 1


title: A549, non-irradiated (0 Gy) cells, biological replicate 2 (0Gy-4h-2)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-4h-2)

value: A549 cell line derived from human alveolar type 2 primary lung adenocarcinoma cells


title: DMBA treated Bulge cells in G9a cKO animal, replicate3

source_name: DMBA/TPA pre-neoplastic epidermal bulge cell I G9a cKO

value: G9a cKO

tag: age


title: DMBA treated Bulge cells in G9a WT animal, replicate2


title: DMBA treated Bulge cells in G9a cKO animal, replicate4


title: WT+H2O2 replicate 2

value: mid-exponential growth in LB; 10 minute exposure to 5 mM H2O2


title: DMBA treated Bulge cells in G9a cKO animal, replicate2


title: A549, non-irradiated (0 Gy) cells, biological replicate 1 (0Gy-4h-1)

description: miRNA expression profiling of A549 non-irradiated cells (0Gy-4h-1)


title: DMBA treated Bulge cells in G9a cKO animal, replicate1


title: T3


title: 66 ADC patient, low PAEP expression

status: Public on Nov 12 2018

city: Heidelberg

first: Michael

last: Meister

state: Select One

address: Roentgenstr. 1

department: STF

country: Germany

institute: Thoraxklinik-Heidelberg

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at 45 °C on GeneChip Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific, Carlsbad (USA)) Gene Chip Hybridization Oven 640 (Thermo Fisher Scientific, Carlsbad (USA)). Washing and staining of the GeneChips was done by utilizing the GeneChip Fluidics Station 450 (Thermo Fisher Scientific, Carlsbad (USA)).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Thermo Fisher Scientific, Carlsbad (USA)).

data_processing:
The raw data generated by the microarray analysis was normalized with the software Expression Console (Thermo Fisher Scientific, Carlsbad (USA)) (RMA algorithm). For further evaluation the software Transcriptome Analysis Console (Thermo Fisher Scientific, Carlsbad (USA)) was used.
3' Expression Arrays - RMA

source_name: ADC patient, low PAEP expression

label_protocol: Biotinylated cRNA was prepared from 5µM with a GeneChip 3' IVT PLUS Reagent Kit  (Thermo Fisher Scientific, Carlsbad (USA)) according to manufaturer's protocol.

extract_protocol: For RNA isolation 10 - 15 cryo sections (10 - 15 µm each)  were prepared for each patient. The corresponding first and the last section were stained with hematoxylin as well as eosin and afterwards they were reviewed by a lung pathologist to determine the proportions of viable tumor cells, stromal cells, normal lung cells, infiltrating lymphocytes and necrotic areas. RNA was extracted using an AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden (Germany)) according to manufacturer's instructions.

treatment_protocol: Tumor tissues were snap-frozen within 30 minutes after resection and stored at -80°C unitl subsequent processing.

tag: gender

value: female

value: lung

value: human non-small cell lung cancer cells

tag: histology

value: adenocarcinoma

tag: tumor stage 7th edition tnm

tag: paep expression

value: low


title: IP-3450-1

description: Total reads : 13 483 693 ; average fragment size : 242

tag: strain

tag: dlt

tag: antibody

value: anti ParBVc1


title: 57 ADC patient, low PAEP expression

value: male

tag: tissue


title: 69 ADC patient, low PAEP expression


title: 64 ADC patient, low PAEP expression


title: 63 ADC patient, low PAEP expression


title: 70 ADC patient, low PAEP expression


title: 58 ADC patient, low PAEP expression


title: 62 ADC patient, low PAEP expression


title: 56 ADC patient, low PAEP expression


title: 68 ADC patient, low PAEP expression


title: 67 ADC patient, low PAEP expression


title: 65 ADC patient, low PAEP expression


title: 61 ADC patient, low PAEP expression


title: 55 ADC patient, low PAEP expression


title: 49 ADC patient, high PAEP expression

source_name: ADC patient, high PAEP expression

value: high


title: 59 ADC patient, low PAEP expression


title: 60 ADC patient, low PAEP expression


title: 53 ADC patient, low PAEP expression


title: 54 ADC patient, low PAEP expression


title: 48 ADC patient, high PAEP expression


title: 51 ADC patient, low PAEP expression


title: 47 ADC patient, high PAEP expression


title: 45 ADC patient, high PAEP expression


title: 50 ADC patient, high PAEP expression


title: 46 ADC patient, high PAEP expression


title: ΔlftR rep1

city: Wernigerode

first: Samuel

last: Hauf

address: Burgstr. 37

department: Division of Enteropathogenic Bacteria and Legionella (FG11)

institute: Robert Koch-Institute

description:
depletion of bacterial rRNA using Illumina Ribo-ZeroTM
Sample 4

data_processing:
Quantification of transcript abundancy via quasi-mapping of raw reads using salmon-0.8.2_linux_x86_64 (https://github.com/COMBINE-lab/salmon)
For statistical significance a two-sided t-test was performed on log-transformed TPM values obtained from salmon output (quant.sf files) assuming heteroscedastic data
Significant hits were selected as having p < 0.01, an expression ratio > 2 and at least 10 TPM detected in all three replicates for wildtype or mutant
Genome_build: L. monocytogenes EGDe cDNA (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-38/fasta/bacteria_0_collection/listeria_monocytogenes_egd_e/cdna/Listeria_monocytogenes_egd_e.ASM19603v1.cdna.all.fa.gz)
Supplementary_files_format_and_content: The *_quant.sf.txt files contain the quantification output of salmon as tab delimited txt, the csv file contains a summary of the raw data as well as the statistics calculated from it.

organism: Listeria monocytogenes EGD-e

source_name: bacterial cells

growth_protocol: Strains were grown in BHI broth to an OD600 of ~0.5 (mid exponential phase).

extract_protocol:
RNA extraction followed the protocol of Völker et al. 1995 (01 April 1994, Microbiology 140: 741-752, doi: 10.1099/00221287-140-4-741) with modifications. Cell pellets were resuspended in 1 ml Lysis Buffer I (25% sucrose; 20 mM Tris-HCl pH 8, 0.25 mM EDTA) and 2 µl of lysozyme (100 mg/ml) was added. After incubation for 5 min on ice, the samples were pelleted (15,000 x g for 30 s at 4°C) and resuspended in 300 µl Lysis Buffer II (3 mM EDTA, 200 mM NaCl). This solution was then mixed with 300 µl Lysis Buffer III (3 mM EDTA, 200 mM NaCl, 1% SDS) that had been pre-incubated at 95°C and the mixture was incubated at 95°C for five more minutes. 600 µl phenol/chloroform/isoamylalcohol (25:24:1) was added and vigorously mixed at room temperature for 5 min. Phases were separated by centrifugation (15,000 x g, 5 min), the aqueous upper phase was collected and the phenol/chloroform extraction was repeated. Afterwards, the aqueous phase was mixed with 600 µl chloroform/isoamylalcohol (25:1), shaken vigorously for 5 min and phases were separated by centrifugation (5 min at 15,000 x g). The chloroform extraction was repeated. Finally, RNA was precipitated by addition of 0.1 x volume 3 M sodium acetate (pH 5.2) and 1.5 volumes 96% ethanol and incubation at -20°C overnight and pelleted by centrifugation (15,000 x g for 15 min at 4°C). The pellet was washed with 70% ethanol and resuspended in 100 µl DEPC treated water. 10 µg total RNA were digested with DNAse using the RNase-Free DNase Set (Qiagen). RNA was then purified using RNA clean & concentrator columns (Zymo Research) for purification for RNA molecules longer than 200 nucleotides. RNA quality was assessed using Agilent Bioanalyzer RNA Nano chips.
rRNA depletion was performed using the Ribo-Zero Bacteria Kit (Illumina) following the manufacturer's instructions. A total of approximately 2 µg purified RNA was trestedtreated with 10 µl Ribo-ZeroRemoval Solution and RNA concentrations were determined using a Qubit® fluorometer. After rRNA removal the remaining RNA was pelleted by ethanol precipitation following the recommendations in the Ribo-Zero protocol. RNA libraries were prepared using the TruSeq® Stranded mRNA Kit, starting with 19.5 µl Fragment, Prime, Finish Mix being added to the dried RNA pellet after rRNA depletion and ethanol precipitation. From this point on the manufacturers protocol was strictly followed (Illumina Part # 15031047 Rev. E). The RNA libraries were sequenced in paired-end mode with 2 times 76 cycles on the Illumina MiSeq (MiSeq® Reagent Kit v3; 150 cycles).

treatment_protocol: 25 ml of the culture was collected and quenched by adding of 25 ml ice cold killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3). After 5 min incubation on ice, cells were harvested by centrifugation.

tag: genotype

tag: background strain

value: EGDe


title: ΔlftR rep2

description:
depletion of bacterial rRNA using Illumina Ribo-ZeroTM
Sample 5


title: 52 ADC patient, low PAEP expression


title: 43 ADC patient, high PAEP expression


title: ΔlftR rep3

description:
depletion of bacterial rRNA using Illumina Ribo-ZeroTM
Sample 6


title: 33 ADC patient, high PAEP expression


title: 37 ADC patient, high PAEP expression


title: 41 ADC patient, high PAEP expression


title: 35 ADC patient, high PAEP expression


title: 39 ADC patient, high PAEP expression


title: 36 ADC patient, high PAEP expression


title: WT rep2

description:
depletion of bacterial rRNA using Illumina Ribo-ZeroTM
Sample 2

value: wildtype


title: 42 ADC patient, high PAEP expression


title: 38 ADC patient, high PAEP expression


title: 30 SCC patient, low PAEP expression

source_name: SCC patient, low PAEP expression

value: squamous cell carcinoma


title: 32 ADC patient, high PAEP expression


title: 28 SCC patient, low PAEP expression


title: 31 ADC patient, high PAEP expression


title: WT rep3

description:
depletion of bacterial rRNA using Illumina Ribo-ZeroTM
Sample 3


title: 34 ADC patient, high PAEP expression


title: 44 ADC patient, high PAEP expression


title: WT rep1

description:
depletion of bacterial rRNA using Illumina Ribo-ZeroTM
Sample 1


title: 29 SCC patient, low PAEP expression


title: 27 SCC patient, low PAEP expression


title: 40 ADC patient, high PAEP expression


title: 25 SCC patient, low PAEP expression


title: lamina propria macrophages of LysMCre mice, biological rep5

city: Philadelphia

first: Celeste

last: Simon

state: PA

address: 421 Curie Blvd. BRBII/II, Room 438

institute: University of Pennsylvania

description: Gene expression data from lamina propria macrophages of LysMCre mice with DSS-induced acute colitis

hyb_protocol: 5.5µg of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Hybridized chips were scanned with GeneChipTM Scanner 3000 7G (Affymetrix).  Affymetrix Command Console and Expression Console (Thermo Fisher Scientific) were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

data_processing: Probe intensity (.cel) files were normalized with RMA in Partek Genomics Suite v6.6

source_name: lamina propria macrophages sorted from LysMCre mice with DSS-induced acute colitis

label_protocol: 1.5ng of total RNA were converted to first-strand cDNA using low cycle PCR followed by linear amplification using T7 in vitro transcription (IVT) technology. The cRNA was then converted to biotinylated sensestrand cDNA, fragmented and assessed by Bioanalyzer.

growth_protocol: Mice were given 3% dextran sodium sulfate (DSS) in drinking water for 5 days, followed by 3 days on regular drinking water. Lamina propria macrophages (CD45+, CD11b+, F4/80+) were isolated by flow sorting on Day 8.

extract_protocol: Trizol LS extraction of total RNA was performed according to the manufacturer's protocol

value: LysMCre

value: macrophages

tag: cell markers


title: 22 SCC patient, low PAEP expression


title: 23 SCC patient, low PAEP expression


title: 21 SCC patient, low PAEP expression


title: lamina propria macrophages of LysMCre;Arntfl/fl mice, biological rep4

description: Gene expression data from lamina propria macrophages of LysMCre;Arntfl/fl mice with DSS-induced acute colitis

source_name: lamina propria macrophages sorted from LysMCre;Arntfl/fl mice with DSS-induced acute colitis

value: LysMCre;Arntfl/fl


title: lamina propria macrophages of LysMCre;Arntfl/fl mice, biological rep3


title: 24 SCC patient, low PAEP expression


title: 26 SCC patient, low PAEP expression


title: JURKAT_INPUT

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

data_processing:
RNAseq: The sequenced reads were aligned to the mouse genome (UCSC mm9) with STAR aligner using gene annotations from Ensembl 72, and intronic reads were discarded
RNAseq: Sequencing result was normalized to ERCC spike in and differential gene expression performed with EdgeR (Empirical analysis of digital gene expression data in R) version 3.08 (Robinson et al., 2010). Adjusted p values were computed using the Benjamini-Hochburg method. Protein coding genes, long non-coding RNA and pseudogenes with adjusted p values less than 0.01 were used for the downstream analysis with DAVID.
ChIPseq: Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm).
ChIPseq: For histone marks, ChIP-seq in MLL-AF9 cells peak detection was performed with MACS (model-based analysis of ChIP-Seq) version 1.4.2 using default parameters (Zhang et al., 2008). The average coverage (calculated using rpm tracks described above) across the entire region is shown in the boxplots where p values were calculated with the Wilcoxon signed-rank test. Heatmaps depict log2 fold change of coverage profiles in a 4 kb window around the merged peak center in 25 bp binned averages and sorted by total coverage in this window. Heatmaps and metagene plots of the genes with changed H3K27ac read coverage around the TSS (±3kb) after Chaf1b knockout were plotted with ngs.plot 2.47 and ranked by read intensity. The CHAF1B read coverage at these sites was plotted with the same order.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: anno.txt: Locations of ChIP-seq peaks, as called by MACS, with extra column describing the genomic context of the peak.
Supplementary_files_format_and_content: EdgeR.txt: Normalized counts from EdgeR along with statistics on the degree to which a given gene or accessible region varies between sample sets.

source_name: Human ALL Cell Line

growth_protocol: MLL-AF9 murine leukemic cells were grown in RPMI-1640 supplemented with 10% FBS, 100 ng/mL SCF, 50 ng/mL IL6, 20 ng/mL IL3. MOLM13/U937/JURKAT cells were grown in RPMI-1640 supplemented with 10% FBS

extract_protocol:
RNA was extracted from MLL-AF9 murine leukemic cells lysed in TRI, and collected on Direct-Zol miniprep columns with on-column DNAse digestion.
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 ¬µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: To induce deletion, MLL-AF9 murine leukemic cells were treated with 10-7M B-estradiol daily for two days (48 hours)

tag: cell line

value: JURKAT

tag: chip antibody


title: lamina propria macrophages of LysMCre;Arntfl/fl mice, biological rep1


title: 15 SCC patient, high PAEP expression

source_name: SCC patient, high PAEP expression


title: lamina propria macrophages of LysMCre mice, biological rep1


title: lamina propria macrophages of LysMCre mice, biological rep4


title: lamina propria macrophages of LysMCre;Arntfl/fl mice, biological rep2


title: 16 SCC patient, low PAEP expression


title: 19 SCC patient, low PAEP expression


title: Control soybean roots [-AMF-Fv]

city: Córdoba

first: Nathalie

last: Marquez

state: Córdoba

address: Camino 60 cuadras Km 5,5

country: Argentina

institute: INTA

description:
-AMF-Fv
3 Biological replicates. Rep 3 has two technical replicates

hyb_protocol: Labelled cDNA targets were then hybridized (competitive hybridization) to the oligonucleotide arrays at 65 °C for 17 hours.

scan_protocol: Slides were scanned using the scanner Agilent G2505B at high resolution of 5 μm at 532 (Cy3) and 633 nm (Cy5) wavelengths (Agilent Technologies, Santa Clara, USA).

data_processing:
Data pre-processing was performed using the limma library (Smyth, 2005) from the R-package (R Core Team, 2012). Background correction was performed using background Correct function, using the “rma” algorithm. Between arrays normalization was performed using normalize Between Array function using “quantile” method. Finally, gene expressions were transformed to log2 scale and summarization of technical replicates was done calculating the median.
Estimated contrasts were expressed in log2 fold change scale. To express the contrasts differences as “fold change”, the following transformation was applied: FC= 2contrast when the contrast was ≥ 0 and − 2 –contrast when the contrast was < 0. This way, fold-changes have positive as well as negative value. A fold-change of 4 means a 4 times increase of gene expression, meanwhile a value of -4 means a 4 times decrease.

organism: Glycine max

source_name: Control soybean roots

label_protocol: Synthesis of cDNA and labelling was performed with Quick Amp Labeling Kit as described in the protocol (Agilent Technologies Inc., USA). A two-colour microarray-based gene expression analysis protocol was used. Labelled cDNA targets (Cy3- and Cy5) were fragmented at 60 °C for 30 minutes.

growth_protocol: Soybean plantlets were cultivated in vitro conditions in a growth chamber set at 20/18°C (day/night), 70 % relative humidity, with a photoperiod of 16 h d-1 and a photosynthetic photon flux (PPF) of 225 µmol m−2 s−1.

extract_protocol: Total RNA extracted RNeasy plant mini kit (Qiagen, Valencia, USA) according to the manufacturer’s instructions.

value: whole root

source_name: pooled whole control soybean roots


title: lamina propria macrophages of LysMCre mice, biological rep3


title: U937_INPUT

source_name: Human AML Cell Line


title: lamina propria macrophages of LysMCre mice, biological rep2


title: 18 SCC patient, low PAEP expression


title: 17 SCC patient, low PAEP expression


title: 13 SCC patient, high PAEP expression


title: MOLM13_INPUT


title: 20 SCC patient, low PAEP expression


title: Pre-mycorrhized soybean roots [+AMF-Fv]

description:
+AMF-Fv
3 Biological replicates. Rep 3 has two technical replicates

source_name: Pre-mycorrhized soybean roots


title: Soybean roots inoculated with F. virguliforme [-AMF+Fv]

description:
-AMF+Fv
3 Biological replicates.

source_name: Soybean roots inoculated with F virguliforme


title: Pre-mycorrhized soybean roots inoculated with F. virguliforme [+AMF+Fv]

description:
+AMF+Fv
3 Biological replicates.

source_name: Pre-mycorrhized soybean roots inoculated with F virguliforme


title: 11 SCC patient, high PAEP expression


title: 14 SCC patient, high PAEP expression


title: 12 SCC patient, high PAEP expression


title: JURKAT_GATA3

value: Cell Signaling:5852


title: JURKAT_CHAF1B


title: U937_CHAF1B_SH2


title: U937_CHAF1B_SH1


title: U937_CHAF1B


title: MOLM13_CEBPA

value: Cell Signaling:8178


title: MOLM13_CHAF1A


title: MOLM13_CHAF1B


title: MA9LC_C1BKO_Pol2

source_name: MLL-AF9 Leukemic Cells

tag: genotype/variation

value: knock out

value: Cell Signaling:14958


title: MA9LC_C1BKO_Runx2

value: Cell Signaling:12556


title: MA9LC_C1BWT_Runx2

value: wild type


title: U937_CEBPA


title: 9 SCC patient, high PAEP expression

value: lung

tag: cell type

value: human non-small cell lung cancer cells


title: 10 SCC patient, high PAEP expression

value: male

value: high


title: 7 SCC patient, high PAEP expression


title: MA9LC_C1BKO_FliRep2


title: 6 SCC patient, high PAEP expression


title: MA9LC_C1BKO_FliRep1


title: U937_CHAF1B_CONTROL


title: 1 SCC patient, high PAEP expression


title: 5 SCC patient, high PAEP expression


title: MA9LC_C1BWT_Pol2


title: 26 2106T control 2

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at 45 °C on GeneChip Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific, Carlsbad (USA)) in a Gene Chip Hybridization Oven 640 (Thermo Fisher Scientific, Carlsbad (USA)). Washing and staining of the GeneChips was done by utilizing the GeneChip Fluidics Station 450 (Thermo Fisher Scientific, Carlsbad (USA)).

source_name: 2106T control 2

growth_protocol: NSCLC cell lines were seeded into a 12-well-plate at 1.6 x 10^5 cells per well.

extract_protocol: Cells were washed, detached and frozen prior to RNA extraction with a RNeasy Mini Kit (Qiagen, Hilden (Germany)) according to manufacturer's instructions.

treatment_protocol: The next day after seeding the cells, they were serum-starved for about 16 h. H1975 cells (lung adenocarcinoma cell line, ATCC, Manassas (USA)) were then incubated with PMA and the corresponding control at 37 °C and 5 % CO2 for 24 h. 2106T (lung squamous cell carcinoma cell line, [Gottschling et al., Lung Cancer 2012]) cells were treated with LPA, PMA, EGF and HB-EGF under the same conditions, respectively. Three independent experiments were performed (named with 1, 2 and 3).

tag: treatment

value: control


title: 28 2106T HB-EGF 1

source_name: 2106T HB-EGF 1

value: squamous cell carcinoma

value: HB-EGF


title: 3 SCC patient, high PAEP expression

tag: age


title: 27 2106T control 3

source_name: 2106T control 3


title: old-RSV-d5-#58

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

description:
lung RNA
common reference
FTR files: Cy3 #1, Cy5 #2

hyb_protocol: Samples were hybridized to NimbleGen 12x135 k Mus musculus microarrays, containing probes for 44,170 genes with 3 spots per target probe. Each microarray corresponded to labeled RNA from one individual mouse.

scan_protocol: Slides were scanned in an ozone-free room with a Agilent G2565CA microarray scanner. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen) resulting in a table containing individual probe signal intensities for both dyes.

data_processing: Data for gene-coding probes were normalized in R by using a four step approach consisting of: (1) natural log-transformation, (2) quantile normalization of all scans, (3) correcting the sample spot signal for its corresponding reference spot signal and (4) averaging data from replicate probe spots. This resulted in normalized data for 44170 probes, which was used for further statistical analysis in R and Microsoft Excel.

source_name: Lung

label_protocol: Per sample, 500 ng of RNA was amplified and labeled using the Agilent QuickAmp kit. Samples were labeled with Cy3 and the common reference (made by pooling equimolar amounts of antisense RNA from individual samples) was labeled with Cy5.

growth_protocol: We used adult (6-8 weeks) and old (62-72 weeks) C57BL/6JRccHsd mice. Mice were kept in a 12-hour light/dark cycle under SPF and temperature-controlled conditions, and were fed ad libitum.

extract_protocol: RNA was extracted from homogenized lung tissue using the Qiagen RNeasy kit. RNA concentrations were measured using a NanoDrop spectrophotometer and RNA quality was measured using a Agilent Bioanalyzer.

treatment_protocol: Mice were inoculated intranasally with 50 µl containing an infectious dose of 10^6 TCID50 RSV type A2 or mock as control, under anesthesia by isoflurane. At day 2 and 5 after inoculation, mice were anesthetized with Ketamine/Xylazine, bled and sacrificed to collect lungs. Lungs were perfused with PBS to eliminate blood cells prior to collection of the tissue, immersed in RNAlater RNA stabilization agent (Ambion) and subsequently stored at -80ᵒC until further processing.

value: old

tag: infection

value: RSV

tag: day

tag: animal number

tag: sample type

value: common reference


title: adult-mock-d0-#27

value: adult

value: mock


title: 30 2106T HB-EGF 3

source_name: 2106T HB-EGF 3

tag: histology


title: 25 2106T control 1

source_name: 2106T control 1


title: old-RSV-d2-#49


title: MA9LC_C1BWT_Fli1Rep2

tag: strain


title: 4 SCC patient, high PAEP expression

tag: gender

value: female

tag: tumor stage 7th edition tnm

tag: paep expression


title: 2 SCC patient, high PAEP expression

tag: tissue


title: adult-RSV-d2-#34


title: 8 SCC patient, high PAEP expression


title: MA9LC_C1BWT_Fli1Rep1


title: adult-RSV-d5-#38


title: 29 2106T HB-EGF 2

source_name: 2106T HB-EGF 2


title: MA9LC_C1BKO_CebpaRep2

value: knock out

value: Cell Signaling:8178


title: 23 2106T EGF 2

value: EGF


title: old-RSV-d5-#60


title: old-mock-d0-#46


title: 24 2106T EGF 3


title: adult-RSV-d2-#33


title: MA9LC_C1BKO_CebpaRep1


title: MA9LC_C1BWT_CebpaRep1

value: wild type


title: MA9LC_C1BWT_CebpaRep2


title: 22 2106T EGF 1

value: lung


title: 20 2106T control 2

value: human non-small cell lung cancer cells


title: adult-RSV-d5-#39


title: 21 2106T control 3


title: s_27T high backfat  thickness

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (Sscrofa11.1) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: raw.genes.fat.csv.gz: raw genes counts
Supplementary_files_format_and_content: res.genes.fat.csv.gz: DESeq2 results for differential expressed gene analysis

organism: Sus scrofa

source_name: fat tissue

extract_protocol:
The total RNA was isolated using by TriReagent (Ambion, Life Technologies). The fat samples were collected immediately after slaughter and stored in tubes with RNAlater (Ambion). The fat samples were homogenized with the use of zirconium oxide beads (diameter 0.5 mm) in BulletBlender homogenizer (Next Advance Inc., USA).The concentration and quality of RNA were estimated on TapeStation 2200 (Agilent Technologies, Warsaw, Poland) using RNA Screen Tape (Agilent Technologies). The RNA samples with RIN (RNA integrity number) above 8.0 were used to further analyses.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

value: Subcutaneous fat

tag: phenotype

value: high backfat  thickness

value: 17 months

value: Pulawska breed


title: s_28T high backfat  thickness

value: 18 months


title: adult-RSV-d2-#35


title: adult-mock-d0-#28


title: s_26T high backfat  thickness

value: 16 months


title: old-RSV-d2-#50

value: old

value: RSV


title: 18 2106T PMA 3

tag: cell line

value: squamous cell carcinoma

value: PMA


title: adult-RSV-d5-#40

value: adult

value: common reference


title: s_25T high backfat  thickness

value: 15 months

value: female


title: MA9LC_C1BWT_H3K27ac

value: wild type

tag: chip antibody

value: Cell Signaling:8173


title: old-mock-d0-#47

value: mock


title: old-RSV-d2-#53


title: adult-RSV-d5-#41


title: 17 2106T PMA 2

value: lung

value: human non-small cell lung cancer cells


title: s_24T high backfat  thickness

value: Subcutaneous fat

value: high backfat  thickness

value: 14 months


title: s_22T low backfat  thickness

value: low backfat  thickness

value: 13 months

value: Pulawska breed


title: s_21T low backfat  thickness

value: 12 months


title: MA9LC_MSCV_CHAF1B


title: MA9LC_MSCV


title: 16 2106T PMA 1

value: squamous cell carcinoma

value: PMA


title: 15 2106T control 3

value: control


title: s_20T low backfat  thickness

value: 11 months


title: MA9LC_H3K4me3

value: Cell Signaling:9751


title: MA9LC_Input


title: s_19T low backfat  thickness

value: 10 months

value: female


title: old-RSV-d2-#52

value: old

value: RSV

value: common reference


title: adult-RSV-d2-#31

value: adult


title: MA9LC_C1BKO_ATACrep2

tag: genotype/variation

value: knock out


title: MA9LC_C1BKO_ATACrep1


title: adult-mock-d0-#29

value: mock


title: s_18T low backfat  thickness

value: Subcutaneous fat

value: low backfat  thickness

value: 9 months


title: adult-mock-d0-#26


title: adult-RSV-d2-#32


title: 13 2106T control 1

value: lung

tag: cell type

value: human non-small cell lung cancer cells


title: old-RSV-d5-#56


title: 14 2106T control 2

value: squamous cell carcinoma

tag: treatment


title: 12 2106T LPA 3

value: LPA


title: MA9LC_C1BWT_ATACrep2

value: wild type


title: 11 2106T LPA 2


title: s_17T low backfat  thickness

tag: age

value: 8 months

value: Pulawska breed


title: old-RSV-d2-#51

tag: infection


title: MA9LC_PCNA

value: Cell Signaling:13110


title: MA9LC_C1BWT_ATACrep1


title: MA9LC_C1BKO_RNArep5


title: s_14T high backfat  thickness

value: high backfat  thickness

value: 7 months

value: female


title: old-mock-d0-#45

value: old

tag: day

value: common reference


title: s_8T high backfat  thickness

value: 6 months


title: old-RSV-d5-#59

value: RSV

tag: animal number


title: s_5T high backfat  thickness

value: Subcutaneous fat

value: 4 months


title: s_6T low backfat  thickness

value: low backfat  thickness

value: 5 months


title: s_3T low backfat  thickness

value: 3 months


title: 9 2106T control 3

value: lung

value: human non-small cell lung cancer cells

value: squamous cell carcinoma

value: control


title: 10 2106T LPA 1

value: LPA


title: 8 2106T control 2


title: MA9LC_C1BKO_RNArep3

value: knock out


title: MA9LC_C1BKO_RNArep4


title: MA9LC_C1BKO_RNArep2


title: 7 2106T control 1


title: adult-RSV-d5-#37

value: adult

tag: sample type


title: MA9LC_C1BKO_RNArep1


title: 6 H1975 PMA 3

tag: histology

value: adenocarcinoma

value: PMA


title: ΔsigCDE_standard_biol.rep2 [re-analysis]

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

country: Finland

institute: University of Turku

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing: The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using  protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.

organism: Synechocystis sp. PCC 6803

source_name: cells from mutant ΔsigCDE, standard growth conditions, biological replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).

treatment_protocol: Cells were grown in standard growth conditions (A730=1, 40 mL). Thre were no treatment for the cells.

value: glucose tolerant


title: ΔsigCDE_standard_biol.rep1 [re-analysis]

source_name: cells from mutant ΔsigCDE, standard growth conditions, biological replicate 1


title: 5 H1975 PMA 2


title: MA9LC_C1BWT_RNArep4

tag: strain

value: wild type


title: 4 H1975 PMA 1


title: s_16 high feed conversion ratio

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (Sscrofa11.1) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: raw.genes.pituitary.csv.gz: raw gene counts
Supplementary_files_format_and_content: res.genes.pituitary.csv.gz: DESeq2 results for differential expressed gene analysis

source_name: pituitary

value: pituitary

tag: group

value: high feed conversion ratio

value: Pulawska breed

tag: gender

value: female


title: Triple expressor

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

institute: Scuola Superiore Sant'Anna

description: Gene expression data from 7-day old seedlings expressing AD-HIFCOOD, GBD-pVHL and PHD3

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: RMA algorithm using RobinA (PMID:22684630)

label_protocol: Affymetrix standard labeling protocol

growth_protocol: seeds were surface sterilized using ethanol 10% and commercial bleach 10%, rinsed several times with sterile water, sowed in 1/2 strength agarized MS medium supplemented wth 1% sucrose and germinated for 7 days before sampling.

extract_protocol: Total RNA was extracted using the Spectrum RNA isolation Kit (Sigma-Aldrich)

treatment_protocol: no treament

tag: developmental stage

value: seedling

tag: ecotype

tag: genotype

value: triple transgenic


title: 3 H1975 control 3

source_name: H1975 control 3

tag: tissue

value: lung

tag: cell line