title: MCI_0019


title: MCI_0026

status: Public on Feb 26 2019

type: RNA

city: Obu

first: Daichi

last: Shigemizu

state: Aichi

address: 7-430 Morioka-cho

country: Japan

institute: National Center for Geriatrics and Gerontology

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.)

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

molecule: total RNA

organism: Homo sapiens

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: diagnosis

value: MCI

tag: age

tag: Sex

value: female


title: MCI_0025


title: MCI_0020


title: MCI_0014


title: MCI_0015

value: male


title: NC_0006

value: NC


title: MCI_0012


title: MCI_0013


title: MCI_0016


title: MCI_0018


title: MCI_0011


title: MCI_0010


title: MCI_0017


title: MCI_0009


title: MCI_0008


title: MCI_0002


title: DLB_0165

value: DLB


title: DLB_0168


title: DLB_0166


title: DLB_0169


title: MCI_0001


title: MCI_0004


title: DLB_0167


title: MCI_0007


title: MCI_0006


title: MCI_0003


title: DLB_0160


title: DLB_0161


title: DLB_0163


title: DLB_0162


title: DLB_0164


title: DLB_0157


title: DLB_0158


title: DLB_0159


title: MCI_0005


title: DLB_0155


title: DLB_0153


title: DLB_0156


title: DLB_0151


title: DLB_0150


title: DLB_0149


title: DLB_0148


title: DLB_0138


title: DLB_0140


title: DLB_0139


title: DLB_0143


title: DLB_0137


title: DLB_0142


title: DLB_0146


title: DLB_0144


title: DLB_0145


title: DLB_0136


title: DLB_0134


title: DLB_0131


title: DLB_0135


title: DLB_0128


title: DLB_0152


title: DLB_0129


title: DLB_0132


title: DLB_0133


title: DLB_0154


title: DLB_0147


title: DLB_0126


title: DLB_0127


title: DLB_0125


title: DLB_0124


title: DLB_0123


title: DLB_0122


title: DLB_0121


title: DLB_0130


title: DLB_0120


title: DLB_0115


title: DLB_0119


title: DLB_0118


title: DLB_0114


title: DLB_0117


title: DLB_0113


title: DLB_0111


title: DLB_0112


title: DLB_0116


title: DLB_0141


title: DLB_0110


title: DLB_0108


title: DLB_0103


title: DLB_0107


title: DLB_0109


title: DLB_0106


title: DLB_0102


title: DLB_0099


title: DLB_0104


title: DLB_0105


title: DLB_0101


title: DLB_0100


title: DLB_0098


title: DLB_0097


title: DLB_0096


title: DLB_0094


title: DLB_0092


title: DLB_0090


title: DLB_0087


title: DLB_0081


title: DLB_0089


title: DLB_0088


title: DLB_0079


title: DLB_0082


title: DLB_0086


title: DLB_0077


title: DLB_0085


title: DLB_0073


title: DLB_0072


title: DLB_0083


title: DLB_0078


title: DLB_0076


title: DLB_0095


title: DLB_0071


title: DLB_0091


title: DLB_0067


title: DLB_0066


title: DLB_0070


title: DLB_0069


title: DLB_0080


title: DLB_0093


title: DLB_0074


title: DLB_0068


title: DLB_0065


title: DLB_0063


title: DLB_0062


title: DLB_0064


title: DLB_0060


title: DLB_0058


title: DLB_0061


title: DLB_0053


title: DLB_0050


title: DLB_0056


title: DLB_0046


title: DLB_0051


title: DLB_0052


title: DLB_0045


title: DLB_0054


title: DLB_0055


title: DLB_0047


title: DLB_0044


title: DLB_0048


title: DLB_0042


title: DLB_0043


title: DLB_0040


title: DLB_0059


title: DLB_0039


title: DLB_0057


title: DLB_0049


title: DLB_0038


title: DLB_0031


title: DLB_0032


title: DLB_0041


title: DLB_0037


title: DLB_0034


title: DLB_0035


title: DLB_0026


title: DLB_0029


title: DLB_0028


title: DLB_0024


title: DLB_0036


title: DLB_0027


title: DLB_0023


title: DLB_0030


title: DLB_0025


title: DLB_0021


title: DLB_0022


title: DLB_0017


title: DLB_0016


title: DLB_0033


title: DLB_0015


title: DLB_0019


title: DLB_0013


title: DLB_0014


title: DLB_0020


title: DLB_0018


title: DLB_0009


title: DLB_0008


title: DLB_0010


title: DLB_0002


title: DLB_0003


title: DLB_0011


title: AD_1019

value: AD


title: AD_1020


title: DLB_0001


title: DLB_0004


title: DLB_0005


title: AD_1013


title: AD_1014


title: DLB_0012


title: AD_1017


title: AD_1012


title: AD_1011


title: AD_1016


title: AD_1021


title: AD_1015


title: DLB_0007


title: NC_0268


title: DLB_0006


title: AD_1009


title: AD_1018


title: AD_1008


title: AD_1006


title: AD_1007


title: AD_1010


title: AD_1004


title: AD_1002


title: AD_1000


title: AD_0998


title: AD_0997


title: AD_0995


title: AD_0987


title: AD_0984


title: AD_1005


title: AD_0989


title: AD_0994


title: AD_0993


title: AD_1003


title: AD_0991


title: AD_0992


title: AD_0990


title: AD_0985


title: AD_0986


title: AD_0988


title: AD_0999


title: AD_1001


title: AD_0982


title: AD_0978


title: AD_0981


title: AD_0980


title: AD_0996


title: AD_0976


title: AD_0973


title: AD_0972


title: AD_0959


title: AD_0977


title: AD_0960


title: AD_0971


title: AD_0958


title: AD_0963


title: AD_0970


title: AD_0979


title: AD_0962


title: AD_0966


title: AD_0968


title: AD_0983


title: AD_0975


title: AD_0964


title: DLB_0075


title: AD_0974


title: DLB_0084


title: AD_0961


title: AD_0952


title: AD_0957


title: AD_0955


title: AD_0956


title: AD_0953


title: AD_0954


title: AD_0950


title: AD_0949


title: AD_0942


title: AD_0948


title: AD_0947


title: AD_0951


title: AD_0932


title: AD_0930


title: AD_0934


title: AD_0940


title: AD_0936


title: AD_0939


title: AD_0928


title: AD_0946


title: AD_0941


title: AD_0933


title: AD_0937


title: AD_0944


title: AD_0943


title: AD_0938


title: AD_0945


title: AD_0929


title: AD_0931


title: AD_0926


title: AD_0925


title: AD_0927


title: AD_0923


title: AD_0919


title: AD_0918


title: AD_0922


title: AD_0967


title: AD_0920


title: AD_0921


title: AD_0903


title: AD_0905


title: AD_0916


title: AD_0935


title: AD_0908


title: AD_0907


title: AD_0913


title: AD_0915


title: AD_0912


title: AD_0909


title: AD_0924


title: AD_0914


title: AD_0911


title: AD_0899


title: AD_0900


title: AD_0902


title: AD_0906


title: AD_0898


title: AD_0895


title: AD_0917


title: AD_0896


title: AD_0904


title: AD_0897


title: AD_0888


title: AD_0893


title: AD_0887


title: AD_0889


title: AD_0890


title: AD_0882


title: AD_0881


title: AD_0891


title: AD_0878


title: AD_0886


title: AD_0880


title: AD_0884


title: AD_0883


title: AD_0879


title: AD_0885


title: AD_0877


title: AD_0892


title: AD_0875


title: AD_0874


title: AD_0873


title: AD_0901


title: AD_0872


title: AD_0869


title: AD_0868


title: AD_0867


title: AD_0910


title: AD_0866


title: AD_0865


title: AD_0860


title: AD_0861


title: AD_0864


title: AD_0876


title: AD_0855


title: AD_0859


title: AD_0856


title: AD_0857


title: AD_0863


title: AD_0862


title: AD_0854


title: AD_0871


title: AD_0852


title: AD_0853


title: AD_0851


title: AD_0969


title: AD_0965


title: AD_0870


title: AD_0847


title: AD_0848


title: AD_0850


title: AD_0849


title: AD_0858


title: AD_0894


title: AD_0846


title: AD_0845


title: AD_0844


title: AD_0834


title: AD_0840


title: AD_0838


title: AD_0839


title: AD_0836


title: AD_0842


title: AD_0843


title: AD_0841


title: AD_0835


title: AD_0837


title: AD_0833


title: AD_0832


title: AD_0831


title: AD_0830


title: AD_0829


title: AD_0819


title: AD_0828


title: AD_0827


title: AD_0821


title: AD_0826


title: AD_0818


title: AD_0825


title: AD_0817


title: AD_0822


title: AD_0820


title: AD_0824


title: AD_0823


title: AD_0816


title: AD_0813


title: AD_0814


title: AD_0809


title: AD_0807


title: AD_0812


title: AD_0815


title: AD_0810


title: AD_0808


title: AD_0799


title: AD_0806


title: AD_0800


title: AD_0802


title: AD_0801


title: AD_0804


title: AD_0805


title: AD_0811


title: AD_0796


title: AD_0797


title: AD_0793


title: AD_0792


title: AD_0791


title: AD_0789


title: AD_0803


title: AD_0794


title: AD_0788


title: AD_0798


title: AD_0790


title: AD_0787


title: AD_0786


title: AD_0779


title: AD_0782


title: AD_0784


title: AD_0783


title: AD_0795


title: AD_0781


title: AD_0780


title: AD_0775


title: AD_0776


title: AD_0778


title: AD_0777


title: AD_0774


title: AD_0785


title: AD_0771


title: AD_0772


title: AD_0773


title: AD_0770


title: AD_0766


title: AD_0768


title: AD_0765


title: AD_0769


title: AD_0759


title: AD_0767


title: AD_0761


title: AD_0763


title: AD_0762


title: AD_0757


title: AD_0754


title: AD_0753


title: AD_0752


title: AD_0760


title: AD_0755


title: AD_0764


title: AD_0756


title: AD_0750


title: AD_0751


title: AD_0749


title: AD_0748


title: AD_0758


title: AD_0745


title: AD_0746


title: AD_0744


title: AD_0742


title: AD_0743


title: AD_0738


title: AD_0739


title: AD_0740


title: AD_0733


title: AD_0731


title: AD_0747


title: AD_0735


title: AD_0734


title: AD_0737


title: AD_0741


title: AD_0730


title: AD_0725


title: AD_0724


title: AD_0723


title: AD_0729


title: AD_0727


title: AD_0732


title: AD_0722


title: AD_0718


title: AD_0717


title: AD_0736


title: AD_0716


title: AD_0721


title: AD_0728


title: AD_0726


title: AD_0711


title: AD_0712


title: AD_0710


title: AD_0715


title: AD_0709


title: AD_0713


title: AD_0704


title: AD_0703


title: AD_0714


title: AD_0719


title: AD_0720


title: AD_0708


title: AD_0698


title: AD_0701


title: AD_0697


title: AD_0700


title: AD_0706


title: AD_0705


title: AD_0696


title: AD_0702


title: AD_0695


title: AD_0707


title: AD_0692


title: AD_0690


title: AD_0694


title: AD_0699


title: AD_0688


title: AD_0691


title: AD_0689


title: AD_0693


title: AD_0687


title: AD_0683


title: AD_0680


title: AD_0678


title: AD_0685


title: AD_0686


title: AD_0684


title: AD_0677


title: AD_0668


title: AD_0667


title: AD_0673


title: AD_0666


title: AD_0669


title: AD_0672


title: AD_0670


title: AD_0665


title: AD_0664


title: AD_0663


title: AD_0676


title: AD_0682


title: AD_0679


title: AD_0681


title: AD_0674


title: AD_0662


title: AD_0659


title: AD_0660


title: AD_0661


title: AD_0671


title: AD_0656


title: AD_0675


title: AD_0655


title: AD_0657


title: AD_0654


title: AD_0651


title: AD_0653


title: AD_0650


title: AD_0648


title: AD_0652


title: AD_0647


title: AD_0646


title: AD_0658


title: AD_0643


title: AD_0642


title: AD_0644


title: AD_0639


title: AD_0638


title: AD_0645


title: AD_0640


title: AD_0637


title: AD_0633


title: AD_0636


title: AD_0635


title: AD_0632


title: AD_0631


title: AD_0634


title: AD_0630


title: AD_0649


title: AD_0628


title: AD_0629


title: AD_0624


title: AD_0627


title: AD_0622


title: AD_0641


title: AD_0626


title: AD_0620


title: AD_0616


title: AD_0619


title: AD_0618


title: AD_0617


title: AD_0615


title: AD_0614


title: AD_0609


title: AD_0610


title: AD_0611


title: AD_0607


title: AD_0612


title: AD_0606


title: AD_0608


title: AD_0605


title: AD_0623


title: AD_0625


title: AD_0599


title: AD_0598


title: AD_0601


title: AD_0600


title: AD_0602


title: AD_0604


title: AD_0594


title: AD_0593


title: AD_0596


title: AD_0603


title: AD_0592


title: AD_0588


title: AD_0587


title: AD_0585


title: AD_0586


title: AD_0591


title: AD_0590


title: AD_0613


title: AD_0580


title: AD_0595


title: AD_0597


title: AD_0579


title: AD_0578


title: AD_0577


title: AD_0583


title: AD_0584


title: AD_0582


title: AD_0581


title: AD_0574


title: AD_0573


title: AD_0572


title: AD_0575


title: AD_0571


title: AD_0565


title: AD_0567


title: AD_0568


title: AD_0566


title: AD_0589


title: AD_0621


title: AD_0564


title: AD_0563


title: AD_0562


title: AD_0576


title: AD_0561


title: AD_0558


title: AD_0557


title: AD_0556


title: AD_0560


title: AD_0554


title: AD_0570


title: AD_0569


title: AD_0553


title: AD_0545


title: AD_0546


title: AD_0552


title: AD_0549


title: AD_0544


title: AD_0548


title: AD_0559


title: AD_0551


title: AD_0547


title: AD_0550


title: AD_0543


title: AD_0538


title: AD_0555


title: AD_0541


title: AD_0542


title: AD_0536


title: AD_0535


title: AD_0534


title: AD_0531


title: AD_0530


title: AD_0537


title: AD_0539


title: AD_0529


title: AD_0533


title: AD_0532


title: AD_0526


title: AD_0527


title: AD_0525


title: AD_0528


title: AD_0522


title: AD_0523


title: AD_0521


title: AD_0520


title: AD_0517


title: AD_0519


title: AD_0540


title: AD_0518


title: AD_0515


title: AD_0513


title: AD_0514


title: AD_0510


title: AD_0524


title: AD_0506


title: AD_0512


title: AD_0507


title: AD_0511


title: AD_0508


title: AD_0502


title: AD_0504


title: AD_0516


title: AD_0509


title: AD_0501


title: AD_0503


title: AD_0505


title: AD_0499


title: AD_0495


title: AD_0490


title: AD_0497


title: AD_0498


title: AD_0500


title: AD_0492


title: AD_0491


title: AD_0493


title: AD_0494


title: AD_0488


title: AD_0489


title: AD_0484


title: AD_0496


title: AD_0480


title: AD_0483


title: AD_0485


title: AD_0478


title: AD_0487


title: AD_0486


title: AD_0479


title: AD_0476


title: AD_0482


title: AD_0466


title: AD_0475


title: AD_0470


title: AD_0469


title: AD_0468


title: AD_0472


title: AD_0471


title: AD_0467


title: AD_0474


title: AD_0465


title: AD_0461


title: AD_0481


title: AD_0464


title: AD_0477


title: AD_0462


title: AD_0460


title: AD_0473


title: AD_0458


title: AD_0459


title: AD_0454


title: AD_0452


title: AD_0450


title: AD_0456


title: AD_0453


title: AD_0451


title: AD_0455


title: AD_0463


title: AD_0441


title: AD_0457


title: AD_0435


title: AD_0448


title: AD_0433


title: AD_0447


title: AD_0442


title: AD_0449


title: AD_0445


title: AD_0437


title: AD_0434


title: AD_0443


title: AD_0440


title: AD_0444


title: AD_0446


title: AD_0438


title: AD_0436


title: AD_0431


title: AD_0423


title: AD_0424


title: AD_0439


title: AD_0430


title: AD_0429


title: AD_0432


title: AD_0427


title: AD_0426


title: AD_0425


title: AD_0420


title: AD_0428


title: AD_0421


title: AD_0422


title: AD_0412


title: AD_0411


title: AD_0414


title: AD_0416


title: AD_0419


title: AD_0417


title: AD_0413


title: AD_0415


title: AD_0408


title: AD_0409


title: AD_0404


title: AD_0407


title: AD_0406


title: AD_0402


title: AD_0400


title: AD_0401


title: AD_0399


title: AD_0403


title: AD_0418


title: AD_0398


title: AD_0397


title: AD_0396


title: AD_0394


title: AD_0405


title: AD_0410


title: AD_0393


title: AD_0392


title: AD_0390


title: AD_0391


title: AD_0389


title: AD_0395


title: AD_0383


title: AD_0382


title: AD_0384


title: AD_0388


title: AD_0387


title: AD_0385


title: AD_0379


title: AD_0378


title: AD_0377


title: AD_0372


title: AD_0380


title: AD_0376


title: AD_0366


title: AD_0368


title: AD_0386


title: AD_0370


title: AD_0375


title: AD_0371


title: AD_0364


title: AD_0369


title: AD_0367


title: AD_0381


title: AD_0363


title: AD_0365


title: AD_0360


title: AD_0361


title: AD_0374


title: AD_0362


title: AD_0373


title: AD_0358


title: AD_0359


title: AD_0357


title: AD_0354


title: AD_0353


title: AD_0352


title: AD_0356


title: AD_0346


title: AD_0348


title: AD_0350


title: AD_0342


title: AD_0343


title: AD_0341


title: AD_0339


title: AD_0355


title: AD_0351


title: AD_0340


title: AD_0338


title: AD_0336


title: AD_0335


title: AD_0334


title: AD_0331


title: AD_0332


title: AD_0327


title: AD_0345


title: AD_0328


title: AD_0330


title: AD_0329


title: AD_0324


title: AD_0325


title: AD_0323


title: AD_0326


title: AD_0347


title: AD_0349


title: AD_0337


title: AD_0333


title: AD_0322


title: AD_0319


title: AD_0317


title: AD_0316


title: AD_0315


title: AD_0314


title: AD_0344


title: AD_0312


title: AD_0318


title: AD_0313


title: AD_0311


title: AD_0309


title: AD_0320


title: AD_0310


title: AD_0321


title: AD_0308


title: AD_0302


title: AD_0303


title: AD_0306


title: AD_0305


title: AD_0307


title: AD_0300


title: AD_0301


title: AD_0304


title: AD_0296


title: AD_0295


title: AD_0294


title: AD_0297


title: AD_0293


title: AD_0291


title: AD_0292


title: AD_0287


title: AD_0289


title: AD_0298


title: AD_0290


title: AD_0288


title: AD_0286


title: AD_0285


title: AD_0282


title: AD_0280


title: AD_0281


title: AD_0279


title: AD_0283


title: AD_0278


title: AD_0299


title: AD_0277


title: AD_0276


title: AD_0273


title: AD_0274


title: AD_0271


title: AD_0272


title: AD_0284


title: AD_0268


title: AD_0270


title: AD_0269


title: AD_0266


title: AD_0265


title: AD_0264


title: AD_0263


title: AD_0267


title: AD_0260


title: AD_0259


title: AD_0275


title: AD_0261


title: AD_0262


title: AD_0256


title: AD_0258


title: AD_0251


title: AD_0253


title: AD_0250


title: AD_0252


title: AD_0254


title: AD_0248


title: AD_0249


title: AD_0247


title: AD_0246


title: AD_0240


title: AD_0241


title: AD_0243


title: AD_0245


title: AD_0242


title: AD_0237


title: AD_0244


title: AD_0257


title: AD_0255


title: AD_0236


title: AD_0239


title: AD_0235


title: AD_0233


title: AD_0229


title: AD_0227


title: AD_0230


title: AD_0234


title: AD_0226


title: AD_0225


title: AD_0224


title: AD_0238


title: AD_0228


title: AD_0222


title: AD_0216


title: AD_0231


title: AD_0218


title: AD_0220


title: AD_0217


title: AD_0221


title: AD_0213


title: AD_0215


title: AD_0212


title: AD_0232


title: AD_0214


title: AD_0210


title: AD_0206


title: AD_0209


title: AD_0205


title: AD_0208


title: AD_0207


title: AD_0204


title: AD_0203


title: AD_0202


title: AD_0211


title: AD_0219


title: AD_0201


title: AD_0199


title: AD_0198


title: AD_0200


title: AD_0197


title: AD_0194


title: AD_0192


title: AD_0195


title: AD_0186


title: AD_0193


title: AD_0185


title: AD_0191


title: AD_0189


title: AD_0190


title: AD_0184


title: AD_0187


title: AD_0188


title: AD_0183


title: AD_0182


title: AD_0179


title: AD_0181


title: AD_0180


title: AD_0196


title: AD_0176


title: AD_0177


title: AD_0178


title: AD_0174


title: AD_0170


title: AD_0172


title: AD_0171


title: AD_0169


title: AD_0168


title: AD_0173


title: AD_0166


title: AD_0160


title: AD_0162


title: AD_0165


title: AD_0159


title: AD_0163


title: AD_0164


title: AD_0161


title: AD_0154


title: AD_0153


title: AD_0152


title: AD_0151


title: AD_0150


title: AD_0158


title: AD_0167


title: AD_0157


title: AD_0156


title: AD_0147


title: AD_0175


title: AD_0146


title: AD_0155


title: AD_0148


title: AD_0143


title: AD_0144


title: AD_0142


title: AD_0141


title: AD_0140


title: AD_0133


title: AD_0131


title: AD_0137


title: AD_0139


title: AD_0136


title: AD_0135


title: AD_0134


title: AD_0145


title: Sample_82561 HNSCC cell line

type: SRA

city: Ann Arbor

first: Chad

last: Brenner

state: Michigan

address: 1500 E Medical Center Drive / Cancer Center 6430

country: USA

institute: University of Michigan

description:
UMSCC_105
FPKM_ProcessedData.xlsx

library_source: transcriptomic

data_processing:
Read quality was assessed for each cohort using FastQC (v0.11.5)
Read alignment was performed using STAR (v2.5.3a)
Cufflinks (v2.2.1) was used to compute FPKM
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with FPKM values for each Cell line

source_name: RNA from Cell Lines

growth_protocol: Cell lines were in log phase growth

extract_protocol:
Qiagen Allprep Kit
Illumina TruSEQ Stranded Total RNA

treatment_protocol: 10% fetal bovine serum, 7µg/mL penicillin/streptomycin and 1% Non-essential amino acids in 5% CO2 incubator

tag: sample id

tag: cell line

value: HNSCC


title: Sample_82562 HNSCC cell line

description:
UMSCC_110
FPKM_ProcessedData.xlsx


title: Sample_82565 HNSCC cell line

description:
UMSCC_117
FPKM_ProcessedData.xlsx


title: Sample_82567 HNSCC cell line

description:
UMSCC_120
FPKM_ProcessedData.xlsx


title: Sample_82563 HNSCC cell line

description:
UMSCC_115
FPKM_ProcessedData.xlsx


title: Sample_82564 HNSCC cell line

description:
UMSCC_116
FPKM_ProcessedData.xlsx


title: Sample_85970 HNSCC cell line

description:
UMSCC_121
FPKM_ProcessedData.xlsx


title: Sample_79059 HNSCC cell line

description:
UMSCC_106
FPKM_ProcessedData.xlsx


title: Sample_82560 HNSCC cell line

description:
UMSCC_104
FPKM_ProcessedData.xlsx


title: Sample_82566 HNSCC cell line

description:
UMSCC_118
FPKM_ProcessedData.xlsx


title: AD_0132


title: AD_0138


title: Sample_82558 HNSCC cell line

description:
UMSCC_97
FPKM_ProcessedData.xlsx


title: AD_0130


title: AD_0127


title: AD_0125


title: AD_0129


title: Sample_60323 HNSCC cell line

description:
UMSCC_92
FPKM_ProcessedData.xlsx


title: Sample_102038 HNSCC cell line

description:
UMSCC_85
FPKM_ProcessedData.xlsx


title: Sample_82557 HNSCC cell line

description:
UMSCC_81B
FPKM_ProcessedData.xlsx


title: Sample_82556 HNSCC cell line

description:
UMSCC_81A
FPKM_ProcessedData.xlsx


title: Sample_82553 HNSCC cell line

description:
UMSCC_55
FPKM_ProcessedData.xlsx


title: AD_0121


title: AD_0122


title: Sample_82554 HNSCC cell line

description:
UMSCC_58
FPKM_ProcessedData.xlsx


title: AD_0119


title: Sample_82555 HNSCC cell line

description:
UMSCC_69
FPKM_ProcessedData.xlsx


title: Sample_60321 HNSCC cell line

description:
UMSCC_49
FPKM_ProcessedData.xlsx


title: AD_0126


title: AD_0120


title: Sample_82559 HNSCC cell line

description:
UMSCC_103
FPKM_ProcessedData.xlsx


title: Sample_82552 HNSCC cell line

description:
UMSCC_47
FPKM_ProcessedData.xlsx


title: AD_0123


title: AD_0116


title: AD_0118


title: AD_0115


title: AD_0117


title: Sample_82551 HNSCC cell line

description:
UMSCC_46
FPKM_ProcessedData.xlsx


title: Sample_82550 HNSCC cell line

description:
UMSCC_43
FPKM_ProcessedData.xlsx


title: AD_0124


title: Sample_82549 HNSCC cell line

description:
UMSCC_29
FPKM_ProcessedData.xlsx


title: AD_0113


title: AD_0114


title: AD_0128


title: Sample_79058 HNSCC cell line

description:
UMSCC_59
FPKM_ProcessedData.xlsx


title: Sample_82548 HNSCC cell line

description:
UMSCC_28
FPKM_ProcessedData.xlsx


title: AD_0112


title: Sample_82547 HNSCC cell line

description:
UMSCC_25
FPKM_ProcessedData.xlsx


title: AD_0111


title: Sample_102035 HNSCC cell line

description:
UMSCC_19
FPKM_ProcessedData.xlsx


title: Sample_85969 HNSCC cell line

description:
UMSCC_17B
FPKM_ProcessedData.xlsx


title: Sample_82545 HNSCC cell line

description:
UMSCC_14A
FPKM_ProcessedData.xlsx


title: AD_0110


title: Sample_85968 HNSCC cell line

description:
UMSCC_10B
FPKM_ProcessedData.xlsx


title: Sample_82544 HNSCC cell line

description:
UMSCC_12
FPKM_ProcessedData.xlsx


title: AD_0108


title: Sample_85967 HNSCC cell line

description:
UMSCC_10A
FPKM_ProcessedData.xlsx


title: AD_0106


title: AD_0105


title: AD_0107


title: AD_0103


title: AD_0104


title: AD_0109


title: Sample_82540 HNSCC cell line

description:
HSC4
FPKM_ProcessedData.xlsx


title: Sample_82542 HNSCC cell line

description:
UMSCC_1
FPKM_ProcessedData.xlsx


title: Sample_82543 HNSCC cell line

description:
UMSCC_8
FPKM_ProcessedData.xlsx


title: AD_0101


title: Sample_85971 HNSCC cell line

description:
UD2
FPKM_ProcessedData.xlsx


title: Sample_82539 HNSCC cell line

description:
HSC2
FPKM_ProcessedData.xlsx


title: Sample_82546 HNSCC cell line

description:
UMSCC_23
FPKM_ProcessedData.xlsx


title: Sample_82541 HNSCC cell line

description:
Detroit562
FPKM_ProcessedData.xlsx


title: AD_0100


title: AD_0099


title: AD_0098


title: Sample_82538 HNSCC cell line

description:
Cal33
FPKM_ProcessedData.xlsx


title: AD_0097


title: ChIPseq_Pax3_1day_dox_NIH3T3_rep1

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description:
processed data file:
NIH3T3_Pax3_1day_ChIP_peaks.bed
ChIP_Pax3_3T3_plusdox_01

library_source: genomic

data_processing:
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) or human (hg38) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. To identify the list of high confidence mouse Pax3 peaks we performed 3 independent Pax3 ChIP-seq experiments and, using the bedtools intersect function, only common regions between 2 experiments were further considered. In addition, the Pax3 peak list was filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse (or human) ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: processed files represent list of Pax3 peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input

molecule: genomic DNA

organism: Mus musculus

source_name: murine fibroblasts

growth_protocol: Mouse ES cell differentiation was achieved by diluting 40000 cells/ml in EB differentiation medium and incubation in an orbital shaker at 80 RPM. EB differentiation medium: IMDM supplemented with 15% FBS , 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol. For Serum-free differentiation, FBS was replaced with an equivalent amount of Knock-outTM Serum Replacement (Invitrogen). Trangene induction was achieved by adding doxycycline (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml), and then maintained throughout the differentiation protocol by replacing the media (including dox) every two days. At day 5, EBs were disgregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences) and replated on gelatin coated dishes using serum- or serum-free EB differentiation media supplemented with 1µg/ml doxycycline and 10ng/ml mouse basic-FGF.

extract_protocol:
ChIP-seq: D4 EBs (1-day induced and control Pax3 mouse cells) were trypsin-treated at 37°C for 1 minute with gentle shacking and reaction was inhibited by adding 10%FBS/PBS. 1-day induced Pax3 NIH3T3 cells and 6-day induced Pax3 mouse cells growing in monolayer were harvested by incubation with trypsin for 1-2 minutes. Human differentiating PAX3-inducible cells were collected at day 6 of differentiation (following 24h dox-mediated induction) by incubation with trypsin for 1-2 minutes. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with glycine and staining with PDGFRα-PE antibody. PDGFRα+ cells were sorted using FACSAriaII, snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated. Cells were sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF to achieve an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. For Pax3 ChIP, 25-40µg of chromatin (diluted to 500µl) were precleared for 4h at 4°C with 20µl of BSA-blocked Protein A (or Protein G)-conjugated sepharose beads (GE healthcare). Samples were supplemented with 1/10 volume of 10% Triton X-100 and incubated overnight with anti-Pax3 (Santa Cruz Biotechnology sc-34926) antibody. Immune complexes were recovered by incubation with 20µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. Libraries from iPax3 NIH3T3 cells were generated using the NEBNext DNA library prep kit (NEB).

tag: tissue

value: murine fibroblasts

tag: differentiation protocol

value: serum

tag: time

value: not applicable

tag: purification

value: unsorted

tag: doxycycline-treatment


title: ChIPseq_Pax3_1day_dox_NIH3T3_rep2

description:
processed data file:
NIH3T3_Pax3_1day_ChIP_peaks.bed
ChIP_Pax3_3T3_plusdox_02


title: ChIPseq_Pax3_nodox_NIH3T3_rep1

description:
processed data file:
NIH3T3_Pax3_1day_ChIP_peaks.bed
ChIP_Pax3_3T3_nodox_01

value: not treated


title: AD_0095


title: AD_0149


title: AD_0093


title: AD_0094


title: AD_0092


title: AD_0102


title: ChIPseq_Pax3_nodox_NIH3T3_rep2

description:
processed data file:
NIH3T3_Pax3_1day_ChIP_peaks.bed
ChIP_Pax3_3T3_nodox_02


title: FR3-3

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description:
FACS-sorted, tamoxifen at E12.5
Sample_106048

data_processing:
We downloaded the reads files and  concatenated those into a single .fastq.gz file for each sample.
We checked the quality of the raw reads data for each sample using FastQC [1] (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference genome including both mRNAs and lncRNAs (UCSC mm10)  [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We ran two different, popular techniques for differential expression analysis: Cufflinks/CuffDiff and HTSeq/DESeq2 [9], using UCSC mm10.fa as the reference genome sequence.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2: depth_normalized_counts, raw_counts, rlog_normalized_counts, Tuxedo: Fpkm, RawCounts, ScaledCounts

source_name: Bone/bone marrow (femur)

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2
Nextera XT DNA Library Preparation Kit

value: Bone/bone marrow (femur)

tag: genotype

tag: cell type

value: Fgfr3-derived CAR cells (GFP+tdTomato+)

value: Postnatal day 21


title: FR3-2

description:
FACS-sorted, tamoxifen at E12.5
Sample_106047


title: AD_0088


title: AD_0089


title: AD_0091


title: NICD rep2

city: Xi'an

first: Xian-Chun

last: Yan

address: Chang-Le Xi street #169

country: China

institute: fourth military medical university

data_processing:
Tophat2 software was used for basecalling
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150 bp) on HiSeq 3000.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: LLC tumor

extract_protocol:
To isolate primary tumor-associated endothelial cells (TECs), LLC inoculated in control and endothelial specific Notch signal activation mice (Cdh5 cre ERT2 and Rosa26 flox-stop-flox Notch1 ICD). Tumors were dissected on different days, minced mechanically and digested in 1mg/ml collagenase I (Sigma) and 10μg/ml DNase I (Sigma) for 45 min at 37°Cwith stirring. After passing through a 70μm tissue strainer, cell suspension was centrifuged for 4 min at 1200 rpm at 4°C, followed by erythrolysis with the Red-lysis buffer (Cwbio). Cell pelletes were resuspended in 90 μl of PBS containing 0.5% BSA and 2 mM EDTA, and mixed with 10 μl CD31-coated beads (Miltenyi Biotec, Bergisch Gladbach, Germany), and incubated at 4 °C for 30 min. Cells adhered to the beads were collected using a magnetic bead collector (Miltenyi),and washed three timeswithPBS containing 0.5% BSA and 2 mM EDTA. The sorted cells wereevaluated by flow cytometryafter staining with Endomucin (Santa Cruz Biotechnology, Santa Cruz, CA) and by Dil-Ac-LDL uptake assay using a kit (H7970, Solarbio, Beijing, China) according to the supplier’s instructions.TECs were more than 90% pure and were used for further experiments.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LLC tumor endothelial cells

tag: strain

value: LLC tumor

value: 8 weeks

value: NICeCA


title: Hes1-3

description:
FACS-sorted, tamoxifen at E12.5
Sample_106045

value: Hes1-derived CAR cells (GFP+tdTomato+)


title: NICD rep1


title: Hes1-1

description:
FACS-sorted, tamoxifen at E12.5
Sample_106043


title: FR3CECxcl12GFP

description:
tamoxifen injection at E12.5, FACS-sorted at P21
Sample_112397

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 500 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and t-SNE), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono

source_name: Femurs

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2
10X Genomic Chromium Single Cell 3' v2 Libraries

value: Femurs

value: GFP+ and tdTomato+ bone marrow mesenchymal cells cells

tag: developmental stage


title: NICD rep3


title: Ctrl rep2

value: wild type


title: AD_0096

value: AD

value: female


title: Ctrl rep1


title: Col2cre_E135

description:
FACS-sorted at E13.5
Sample_118945

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1500 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and t-SNE), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono

source_name: Hind limbs

extract_protocol:
Hind limbs were dissected and enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2
10X Genomic Chromium Single Cell 3' v2 Libraries

value: Hind limbs

value: Col2a1-cre; R26R(tdTomato/+)

value: tdTomato+ fetal growth plate chondrocytes and perichondrial cells

value: Embryonic day 13.5


title: Hes1CECxcl12GFP

description:
tamoxifen injection at E12.5, FACS-sorted at P21
Sample_112244

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal end swere cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2
10X Genomic Chromium Single Cell 3' v2 Libraries


title: AD_0086

value: male


title: AD_0087


title: IL-7+IL-1β

city: Seoul

first: Hong-Gyun

last: Lee

address: #527, Natural Science building, Hanyang Univ, Wangsimni-ro 222, Seondong-gu

country: South Korea

institute: Hanyang University

data_processing:
HCS 3.3.52 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: IL-7+IL-1β sitmulated memory-like CD4+ T cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).  total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

tag: genotype/variation

value: WT

value: mouse memory-like CD4 T cell

tag: treatment


title: IL-7+IL-23

source_name: IL-7+IL-23 sitmulated memory-like CD4+ T cell


title: Ctrl rep3

value: LLC tumor endothelial cells


title: IL-7+IL-23+IL-1β

source_name: IL-7+IL-23+IL-1β sitmulated memory-like CD4+ T cell


title: AD_0084


title: AD_0090


title: IL-7

source_name: IL-7 sitmulated memory-like CD4+ T cell


title: AD_0083


title: AD_0082


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 7

city: Delhi

first: Muzaffer

middle: Ahmed

last: Bhat

state: Delhi

address: ANSARI NAGAR NEW DELHI 110029

department: Physiology

country: India

institute: AIIMS

description:
SAMPLE 34
Homo sapiens whole genome expression microarray for human endometrium

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to 4 x 44k Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel was set to Green, and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1 and Design Id: 014850) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features were flagged in Feature Extraction and  Non-uniform Features and outliers were excluded.

source_name: human endometrium, Fertile Secretory with Stage IV Ovarian Endometriosis (Group 2B)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the One-Color Low Input TOTAL RNA Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol reagent.  The protocol included brief homogenisation using polytron homogeniser, followed by phase seperation by chloroform and precipitation using iso-propanol. This was followed by washing by 75% ethanol and elution in nuclease-free waster. Total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

tag: gender

value: Female

tag: sample group

value: Endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 8

description:
SAMPLE 35
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 9

description:
SAMPLE 36
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0081

tag: diagnosis

tag: age


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 5

description:
SAMPLE 32
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 6

description:
SAMPLE 33
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0080

tag: Sex


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 4

description:
SAMPLE 31
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0085


title: Disease free Endometrium of Infertile women, replicate 8

description:
SAMPLE 26
Homo sapiens whole genome expression microarray for human endometrium

source_name: human endometrium, Infertile Secretory without Endometriosis (Group 1B)


title: Disease free Endometrium of Infertile women, replicate 9

description:
SAMPLE 27
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0078


title: Disease free Endometrium of Infertile women, replicate 7

description:
SAMPLE 25
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 1

description:
SAMPLE 28
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of Infertile women, replicate 4

description:
SAMPLE 22
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0077


title: AD_0076


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 3

description:
SAMPLE 30
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0079


title: Disease free Endometrium of Infertile women, replicate 5

description:
SAMPLE 23
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of Infertile women, replicate 6

description:
SAMPLE 24
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of Infertile women, replicate 2

description:
SAMPLE 20
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of Infertile women, replicate 1

description:
SAMPLE 19
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of Infertile women, replicate 3

description:
SAMPLE 21
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0074


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 6

description:
SAMPLE 15
Homo sapiens whole genome expression microarray for human endometrium

source_name: human endometrium, Fertile Secretory with Stage IV Ovarian Endometriosis (Group 2A)


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 2

description:
SAMPLE 11
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 7

description:
SAMPLE 16
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of Infertile women, replicate 2

description:
SAMPLE 29
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 9

description:
SAMPLE 18
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 1

description:
SAMPLE 10
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0073


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 5

description:
SAMPLE 14
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 4

description:
SAMPLE 13
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0072


title: AD_0071


title: Disease free Endometrium of fertile women, replicate 9

description:
SAMPLE 9
Homo sapiens whole genome expression microarray for human endometrium

source_name: human endometrium, Fertile Secretory without Endometriosis (Group 1A)


title: AD_0069


title: Disease free Endometrium of fertile women, replicate 8

description:
SAMPLE 8
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 8

description:
SAMPLE 17
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0068


title: Disease free Endometrium of fertile women, replicate 5

description:
SAMPLE 5
Homo sapiens whole genome expression microarray for human endometrium


title: Endometrium  from Stage IV Ovarian Endometriosis of fertile women, replicate 3

description:
SAMPLE 12
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of fertile women, replicate 3

description:
SAMPLE 3
Homo sapiens whole genome expression microarray for human endometrium


title: Disease free Endometrium of fertile women, replicate 6

description:
SAMPLE 6
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0070


title: Disease free Endometrium of fertile women, replicate 4

description:
SAMPLE 4
Homo sapiens whole genome expression microarray for human endometrium


title: AD_0067


title: Disease free Endometrium of fertile women, replicate 2

description:
SAMPLE 2
Homo sapiens whole genome expression microarray for human endometrium


title: 10x_cip_d36

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

data_processing:
The cellranger-2.1.1 was used for mapping of the 10x single cell RNA-seq data.
The read1 data of pooled cells were split into single-cell data using the barcode sequences contained in the first 16 bp. The next 10 bp were recorded as unique molecular identifiers (UMIs). Read2 with 75 bp were aligned to the mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include UMI counts for each cell.

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: Mouse ESCs (mESCs) and iPS cell lines were cultured on feeder layers with mESC medium (high glucose DMEM, 15%FBS, NEAA, GlutaMAX, LIF) plus 2i (1 m PD0325901, 3 m CHIR99021). MEF cells were maintained in 10% FBS medium (high glucose DMEM supplemented with 10% FBS, GlutaMAX and NEAA).  The reprogramming cells at different days were cultured in iCD1 medium.

extract_protocol:
Cells in each day were isolated using 10x Genomics
The libraries were constructed using Chromium™ Single Cell 3' Reagent Kits v2

treatment_protocol: Stage 1 medium SFRM preparation: iCD1 medium (Chen et al., 2011a) which contains Vitamin C(50 mg/ml), bFGF(10 ng/ml) and CHIR99021(3 mM) supplemented with small molecules Brdu(10 mM), RepSox (5 mM), FSK(10 mM), VPA(0.1 mM), AM580(0.05 mM), EPZ5676(5 mM), DZNeP(0.05 mM), SGC0946(5 mM) and BMP4(10 ng/ml). For the CIP induction from mouse adult lung fibroblasts (MLFs) and tail tip fibroblasts (TTF), 5 mM Capmatinib and 5 mM EPZ6438 were recommended to enhance the induction efficiency. Stage 2 medium N2B27-2iL preparation: DMEM (high glucose, Hyclone), 1% N2 (GIBCO), 2% B27 (GIBCO), 1% GlutMax (GIBCO), 1% NEAA (GIBCO), 1% sodium pyruvate (GIBCO) 3 mM CHIR99021, 1 mM PD0325901 and 1000 U LIF.

tag: strain background

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: time point


title: AD_0064


title: AD_0065


title: 10x_cip_d40


title: 10x_cip_d22


title: 10x_cip_d18


title: AD_0061


title: AD_0062


title: AD_0063


title: 10x_cip_d26


title: 10x_cip_d32


title: 10x_cip_d12


title: Disease free Endometrium of fertile women, replicate 7

description:
SAMPLE 7
Homo sapiens whole genome expression microarray for human endometrium

tag: tissue


title: Disease free Endometrium of fertile women, replicate 1

description:
SAMPLE 1
Homo sapiens whole genome expression microarray for human endometrium


title: 10x_cip_d9


title: AD_0058


title: AD_0059


title: AD_0066


title: 10x_cip_d3


title: 10x_cip_d6


title: AD_0060


title: 10x_cip_d0


title: AD_0056


title: AD_0055


title: RNAseq_Pax3_6day_rep2

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_6day_plusdox_02

data_processing:
Mouse RNA-seq analysis: 150bp FastQ paired-end reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample were performed with FastQC. Read mapping was performed via Hisat2 (v2.0.2) using the mouse genome (mm10) as reference. Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Valencia, CA) using raw read counts. We filtered the generated list based on a minimum 2X Absolute Fold Change and FDR corrected p < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: processed files contain tab-delimited expression values following analysis using EdgeR (mouse RNA-seq) and RSEM (human RNA-seq)

source_name: differentiating mES cells

extract_protocol:
RNA-seq: sorted cells from murine and human differentiating ES cells were resuspended in Trizol. RNAs were extracted using the PureLink RNA mini prep kit following manufacturer's instruction (including in-column Dnase digestion).
RNA-seq libraries were generated using the TrueSeq stranded kit and dual-index adapter-barcodes following manufacturer's instructions.

value: differentiating mES cells

tag: differentiation protocol

value: serum

tag: time

value: day9 of differentiation

value: PDGFRα+FLK1- sorted


title: RNAseq_Pax3_6day_rep3

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_6day_plusdox_03

tag: purification

tag: doxycycline-treatment


title: 10x_cip_d16

tag: cell type


title: AD_0051

source_name: serum

value: AD


title: RNAseq_Pax3_6day_rep1

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_6day_plusdox_01


title: AD_0053

value: female


title: AD_0052


title: AD_0057


title: mRNA_OvarianCancer_rep57

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

data_processing:
Fastq files were generated by CASAVA-1.8.2 from Illumina Hiseq output.
Fastq files were mapped to hg19 reference genome by bowtie2 to generate bam files.
Expression level is quantified by RSEM-1.3.0.
Genome_build: hg19
Supplementary_files_format_and_content: Rsem.genes.results file has columns named TPM and FPKM. Each columns represent Transcripts Per Million mapped reads and Fragments Per Kilobase of transcript and Million mapped reads for each gene.

molecule: polyA RNA

source_name: mRNA from fresh frozen ovarian cancer

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
cDNA library was prepared with Illumina TruSeq Stranded mRNA Library Preparation Kit.

value: primary tumor from ovarian cancer patient


title: RNAseq_Pax3_1day_rep2

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_1day_plusdox_02

value: day4 of differentiation


title: mRNA_OvarianCancer_rep58


title: AD_0049


title: RNAseq_Pax3_1day_rep3

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_1day_plusdox_03


title: mRNA_OvarianCancer_rep55


title: RNAseq_Pax3_1day_rep1

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_1day_plusdox_01


title: SB28 replicate1

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

data_processing:
alignment with bowtie2/2.2.4,
raw counts calculated with htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: brain

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genetic background


title: SB28 replicate3


title: mRNA_OvarianCancer_rep54


title: SB28 replicate2


title: AD_0048


title: AD_0054


title: RNAseq_Ctrl_1day_rep3

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_1day_nodox_03

value: not treated


title: AD_0046


title: AD_0047


title: mRNA_OvarianCancer_rep56


title: RNAseq_Ctrl_1day_rep2

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_1day_nodox_02


title: mRNA_OvarianCancer_rep52


title: RNAseq_Ctrl_1day_rep1

description:
processed data file:
RNAseq_mouse_iPax3_1day_6day.xlsx
RNAseq_Pax3_1day_nodox_01


title: AD_0050


title: mRNA_OvarianCancer_rep51


title: AD_0045


title: mRNA_OvarianCancer_rep50


title: miR-19 replicate-1

city: Hangzhou

first: Jinghai

last: Chen

state: Zhejiang

address: 268 Kai-Xuan Road, North Central Building 540

department: Institute of Translational Medicine

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
Quantification of gene expression level: HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.  The file miR19_4dvsCtrl_4d_DEG_ALL.txt includes those genes identified with differential expression.

source_name: Heart

growth_protocol: Eight week-old male c57BL/6 mice

extract_protocol:
Total RNA was isolated from fresh ventricular tissue using Trizol. mRNA was then purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: Myocardial infarction was performed on eight week-old male c57BL/6 mice by ligation of the left anterior descending coronary artery, meanwhile, intra-cardiac injection of microRNA mimic miR-19a/miR-19b or control mimics (10 μg per mouse heart) respectively.

tag: strain

value: Heart

value: 8 weeks

tag: surgery

value: Myocardial infarction

value: intra-cardiac inject miR19a/b mimic

tag: harvest time

value: post myocardial infarction day 4


title: miR-19 replicate-3

value: male

tag: treatment


title: miR-19 replicate-2


title: PurR 3

city: London

first: Mariya

last: Goncheva

state: Ontario

address: Dental Services Building Room 3014, 1151 Richmond Street

department: Microbiology and Immunology

country: Canada

institute: The University of Western Ontario

data_processing:
Base calling was performed with Base Base software, using ISAC application
Alignment was performed using CLC genomics workbenck v 11.0.1 with the RNA-seq Analysis v 2.15 package
Genome_build: NC_007793
Supplementary_files_format_and_content: RPKM

organism: Staphylococcus aureus

source_name: Bacteria grown to OD of 1.0

growth_protocol: Cells grown in Tryptic soy broth to OD 1.0

extract_protocol:
Total RNA was extracted using an EZNA total RNA kit (Bio-Rad), according to the manufacturer's instructions, with the addition of 0.25 µg/ml lysostaphin to the lysis solution for 1h at 37˚C
The library was constructed using Illumina Script Seq RNA sequencing kit


title: Ctrl replicate-3

value: intra-cardiac inject control mimic


title: PurR 2


title: AD_0044


title: Ctrl replicate-2


title: mRNA_OvarianCancer_rep49

tag: gender


title: AD_0043

tag: diagnosis


title: Ctrl replicate-1

tag: age


title: mRNA_OvarianCancer_rep48


title: PurR 1


title: WT 3


title: mRNA_OvarianCancer_rep53


title: AD_0041

tag: Sex


title: whole newborn lenses_Le-Cre Rep3

city: Oxford

first: Michael

last: Robinson

state: Ohio

address: 700 E High St

department: Biology

institute: Miami University

data_processing:
Remove Truseq3-SE adapter sequence using Trimmomatic (version 0.36)
Single-end sequencing reads were aligned to the mouse genome (ENSEMBL 84 release, GRCm38) using RSEM (version 1.3.0)
Differential gene expression analysis was performed by DESeq2 (version 1.10.1) using the estimated gene-level counts from RSEM
Genome_build: RNA-Seq clean reads  were mapped to mouse genome (ENSEMBL 84 release, GRCm38)
Supplementary_files_format_and_content: Text files were generated using RSEM

source_name: Lens

growth_protocol: Newborn lenses from wild type FVB/N, hemizygous Le-Cre and hemizygous P0-3.9-GFPCre mice were collected at P0 and pooled into three biological replicates, each containing 6 lenses from 3 mice.

extract_protocol:
Total RNA, including mRNA, was extracted using the mirVana mRNA isolation kit (AM1560, ThermoFisher) according to the manufacturer’s recommendations. Total RNA samples with the RNA integrity number (RIN, Agilent 2100 Bioanalyzer) ≥8.0 were used to prepare a library of template molecules suitable for subsequent sequencing on an Illumina (St. Louis, MO) HiSeq platform.
Polyadenylated RNA was purified from the total RNA samples using Oligo dT conjugated magnetic beads and prepared for single-end sequencing according to the Illumina TruSeq RNA Sample Preparation Kit v3. The resultant library was sequenced for 50 cycles using the TruSeq SBS kit on an Illumina HiSeq 2000 system at the Genomics and Sequencing Core Laboratory at the University of Cincinnati.

tag: developmental stage

value: Newborn

value: whole lens

value: FVB/N

tag: genotype

value: Le-Cre transgenic


title: mRNA_OvarianCancer_rep47

tag: tissue


title: WT 2


title: whole newborn lenses_Le-Cre Rep2


title: AD_0039

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).


title: whole newborn lenses_Le-Cre Rep1


title: mRNA_OvarianCancer_rep44


title: AD_0042


title: AD_0038


title: whole newborn lenses_FVB/N Rep3

value: Wild-Type


title: mRNA_OvarianCancer_rep43


title: whole newborn lenses_FVB/N Rep2


title: AD_0037

value: AD


title: AD_0036


title: AD_0040


title: mRNA_OvarianCancer_rep42

value: female


title: Dusa plants 22hr following infection vs uninfected control, replicate 3

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

description: Raw data file in Genepix format

hyb_protocol: Hybridization was carried out according to the two-colour microarray-based gene expression analysis protocol (Agilent)

scan_protocol: Microarray slides were scanned using the Axon GenePix 4000B scanner (Molecular Devices)

data_processing: Axon GenePix 6.0 software was used for image analysis. Normalization and statistical analysis was carried out in the R environment using limma. Robust-spline and aquantile normalized log2 ratio (Cy5/Cy3) data in Series supplementary file.

organism: Persea americana

source_name: Root samples of susceptible plants infected with Rosellinia necatrix, 22hr post-infection

label_protocol: 4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dT) primers, using the Superscript III Reverse transcriptase. Samples and controls labelled with Cy3 and Cy5 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)

growth_protocol: BG83 explants were established in vitro and micropropagated according to Pliego-Alfaro F (2013), while plants of ‘Dusa’ were vegetatively propagated by Brokaw nursery (Spain) using a modified Frohlich method (Frolich EF, 1972). Plants of each rootstock (BG83 and ‘Dusa') were grown under controlled greenhouse conditions (~20ºC temperature and ~60% relative humidity) to carry out the inoculation assay with R. necatrix according to an established protocol (Sztejnberg A, 1980). From each rootstock, nine plants were used as non-inoculated (control plants) and eighteen plants were inoculated with R. necatrix. To ensure the spread of the inoculum, it was placed in eight points scattered around the stem (~3.5 cm apart) and introduced at two depths (~5cm and ~15 cm, respectively).

extract_protocol: Total RNA extracted using the CTAB extraction method

treatment_protocol: Plants were inoculated with 3.75 g of colonized wheat seeds per litter of substrate and monitored during disease progression until the appearance of aerial symptoms. The experiment was laid out in a randomized block design with three biological replicates per rootstock/time-point in which each biological replicate consisted in three plants.

tag: infection

value: Dusa

value: Root

source_name: Root samples of uninfected susceptible plants

value: uninfected


title: Dusa plants 8hr following infection vs uninfected control, replicate 3

description: Raw data file in Genepix format

source_name: Root samples of susceptible plants infected with Rosellinia necatrix, 8hr post-infection


title: whole newborn lenses_FVB/N Rep1


title: Dusa plants 22hr following infection vs uninfected control, replicate 1

description: Raw data file in Genepix format

value: infected with Rosellinia necatrix, 22hr post-infection


title: mRNA_OvarianCancer_rep41

value: primary tumor from ovarian cancer patient


title: AD_0035

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.


title: whole newborn lenses_P0-3.9GFPCre Rep3

value: P0-3.9GFPCre transgenic


title: mRNA_OvarianCancer_rep46


title: AD_0034


title: Dusa plants 8hr following infection vs uninfected control, replicate 2

description: Raw data file in Genepix format

value: infected with Rosellinia necatrix, 8hr post-infection


title: whole newborn lenses_P0-3.9GFPCre Rep2


title: AD_0033


title: mRNA_OvarianCancer_rep40


title: mRNA_OvarianCancer_rep45


title: Dusa plants 22hr following infection vs uninfected control, replicate 2

description: Raw data file in Genepix format


title: Dusa plants 8hr following infection vs uninfected control, replicate 1

description: Raw data file in Genepix format


title: whole newborn lenses_P0-3.9GFPCre Rep1


title: mRNA_OvarianCancer_rep38


title: WT 1


title: mRNA_OvarianCancer_rep39


title: BG83 plants 30hr following infection vs uninfected control, replicate 1

description: Raw data file in Genepix format

source_name: Root samples of tolerant plants infected with Rosellinia necatrix, 30hr post-infection

source_name: Root samples of uninfected tolerant plants


title: mRNA_OvarianCancer_rep37


title: BG83 plants 30hr following infection vs uninfected control, replicate 2

description: Raw data file in Genepix format

value: infected with Rosellinia necatrix, 30hr post-infection


title: mRNA_OvarianCancer_rep36


title: Lapins Fruit

city: Santiago

first: Jonathan

last: Maldonado

address: Av. Santa Rosa 1131, La Pintana

country: Chile

institute: Universidad de Chile

description: Fruit of Prunus avium var. Lapins

data_processing:
The software CLC Genome Workbench, version 11.0.1 (CLC Bio [http://www.clcbio.com]) was used to trim and quality filter the sequences following parameters: Q >= 20; no more than 2 ambiguities; final read length >= 50bp.
Coding sequences predicted from Prunus avium genome (Shirasawa et al., 2017) were used as reference set of transcripts for the RNAseq analysis
The sequences from each cultivar and tissue were separately mapped against the corresponding reference transcriptome using RNAseq function of the CLC Genome Workbench version 11.0.1 under the following parameters, similarity: 0.9; length fraction: 0.6; insertion/deletion cost: 3; mismatch cost: 3 and unspecific match limit: 10.
The relative transcript levels were obtained as the unique number of reads mapped to each gene. The identifiers in the processed data file are located at http://cherry.kazusa.or.jp/.
The expression levels among them were compared using a Z-Test (Kal et al., 1999). For visual inspection, original expression values were transformed by Log10 method and then normalized by the Quantile method that was the best to fits the result (Dillies et al., 2012; Hansen et al., 2012).
Genome_build: Shirasawa K, et al. DNA Res 2017 Oct 1 (PRJNA395588)
Supplementary_files_format_and_content: processed fastq files correspond to filtered sequences; tab-delimited text files include TPM, RPKM, unique gene reads and total gene reads for each Sample "without normalization"

organism: Prunus avium

source_name: Lapins

extract_protocol:
Total RNA was extracted using a modified protocol based in CTAB that yields high-quality total RNA from fruit mesocarps suitable for functional genomics analysis (Meisel et al., 2005).
Library construction and 454 FLX (454 Life Sciences, Roche) deep sequencing was performed by the Center for Integrated Biotechnology, Washington State University.

tag: cultivar

value: Lapins

value: fruit

value: Chile:Region Valparaiso, Los Andes


title: Rainier Fruit

description: Fruit of Prunus avium var. Rainier

source_name: Rainier

value: Rainier

value: Chile:Region O'Higgins, San Francisco de Mostazal


title: AD_0030

value: male


title: AD_0032


title: AD_0031


title: mRNA_OvarianCancer_rep35


title: AD_0029


title: Bing Fruit

description: Fruit of Prunus avium var. Bing

source_name: Bing

value: Bing

value: Chile:Region Valparaiso, Quillota


title: mRNA_OvarianCancer_rep34

value: female


title: SFR717m

city: Montreal

first: André

last: Veillette

state: Québec

address: 110 avenue des pins ouest

institute: Institut de Recherches Cliniques de Montréal

data_processing:
Basecalls performed using CASAVA version 1.8
Quality control with FASTQC
Alignment of reads was performed using TopHat v2
Quantification of transcript done with featureCounts v1.4
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCm38
Supplementary_files_format_and_content: Diff files with differential expression

source_name: SFR KO iNKT RNA

extract_protocol:
Total RNA was isolated from iNKT cells according to the manufacturer’s instructions using the RNeasy plus micro kit (Qiagen).
Illumina TruSeq RNA system; sequencing using PE50 on a HiSeq 2000 sequencer (Illumina technologies)

tag: strain background

tag: genotype/variation

value: SFR KO

value: thymic Invariant natural killer T (iNKT) cells


title: WT710m

source_name: WT iNKT cell RNA

value: wild type

tag: cell type


title: AD_0028

value: AD


title: SFR714f


title: Rainier Leaf

description: Leaves of Prunus avium var. Rainier

value: leaves


title: AD_0075


title: WT717m


title: mRNA_OvarianCancer_rep33

value: primary tumor from ovarian cancer patient


title: Lapins Leaf

description: Leaves of Prunus avium var. Lapins


title: mRNA_OvarianCancer_rep32


title: Bing Leaf

description: Leaves of Prunus avium var. Bing


title: mRNA_OvarianCancer_rep31


title: AD_0024


title: mRNA_OvarianCancer_rep29


title: P8_PZQ-selected4

city: Albuquerque

first: Charles

last: Cunningham

state: New Mexico

address: 1 University of New Mexico

institute: University of New Mexico

data_processing:
Raw reads were trimmed and filtered using Trimmomatic v0.36 with slide window of 4 nucleotides, average score above 20, and minimum length of 36 nucleotides.
Filtered high quality reads were mapped to the S. mansoni transcriptome annotated from assembly GCA_000237925.2 ASM23792v2 from NCBI
Expression levels were extimated using RSEM v1.2.31.
Differential gene analysis was performed using DESeq2 v1.18.1, EdgeR v3.20.8, and EBSeq v1.18.0.
Genome_build: NCBI assembly GCA_000237925.2 ASM23792v2
Supplementary_files_format_and_content: A matrix of the samples in a xlsx file with the raw and normalized count of the sequence reads.

organism: Schistosoma mansoni

source_name: whole parasites

extract_protocol:
Parasites were perfused on day 49, collected and rinsed with RPMI, then placed in RLT plus beta mercaptoethanol at -80. RNA was harvested using RNeasy Mini Kit (Qiagen #74104).  RNA was tested on nanodrop and Bioanalzer. Illumina platform KAPA Stranded mRNA-Seq Kit (KAPABIOSYSTEMS #KK8420) was used with 500 ng of total RNA for the construction of sequencing libraries.
Library consruction followed the workflow of Illumina platform KAPA Stranded mRNA-Seq Protocol v.3.15.

treatment_protocol: S. mansoni parasites were treated with either Vehicle (2% Cremophor EL), or praziquantel (300 mg/Kg) on 28, 35 and 37 days post infection by oral gavage.

value: whole organism

value: Puerto Rican-1 (PR-1)

value: pooled male and female

tag: days post infection

value: Praziquantel (900 mg/Kg)


title: P8_PZQ-selected3

tag: strain


title: P8_PZQ-selected2


title: RNAseq_Pax3_H9_1day_rep3

description:
processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_1day_dox_03

data_processing:
Human RNA-seq analysis: each sample’s reads were then processed using RSEM version 1.2.3 (with bowtie-0.12.9 for the alignment step) [103, 104]. Genes were filtered to select only those with median-normalized TPM (Transcripts Per Million mapped reads) greater than 10 in at least one sample, log2fold change greater than 1 and p<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq: processed files contain tab-delimited expression values following analysis using EdgeR (mouse RNA-seq) and RSEM (human RNA-seq)

source_name: differentiating hES cells

growth_protocol: Human ES cell differentiation was achieved by plating 10^6 cells in 6cm non-adherent Petri dishes and incubation at 37°C, 5% CO2 on a shaker at 60 RPM. After 2 days, mTeSR was replaced with EB Myogenic (EBM) Media supplemented with 10µM Y-27632 and 10µM GSK3 inhibitor (CHIR990217) [EB Myogenic media composition: IMDM supplemented with 15% FBS, 10% Horse Serum, 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol]. 2 days later, media was replaced to remove GSK3 inhibitor and the formed EBs were plated on gelatin-coated flasks using EBM + 10ng/ml human basic FGF (bFGF). 24h later, cultures were supplemented with 1µg/ml doxycycline (dox) for PAX3 induction. 24h later cells were harvested using Trypsin+EDTA solution and FACS sorted based on GFP expression.

value: differentiating hES cells

tag: differentiation protocol

value: serum

tag: time

value: day6 of differentiation

tag: purification

value: GFP-sorted

tag: doxycycline-treatment


title: AD_0027

city: Obu

first: Daichi

last: Shigemizu

institute: National Center for Geriatrics and Gerontology

source_name: serum

tag: diagnosis


title: RNAseq_Ctrl_H9_1day_rep3

description:
processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_nodox_03

value: unsorted

value: not treated


title: AD_0023

tag: age

value: female


title: RNAseq_Pax3_H9_1day_rep2

description:
processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_1day_dox_02


title: AD_0026

tag: Sex


title: AD_0019


title: P8_control4

tag: treatment

value: Vehicle (Cremophor EL)


title: AD_0025


title: AD_0021


title: AD_0022


title: mRNA_OvarianCancer_rep30

source_name: mRNA from fresh frozen ovarian cancer

tag: gender


title: AD_0020


title: RNAseq_Ctrl_H9_1day_rep2

description:
processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_nodox_02

tag: tissue


title: TmBER2-GS-4

first: Herbert

middle: Jimenez

last: Santos

address: 7−3−1, Hongo, Bunkyo-ku

department: School of International Health, Graduate School of Medicine

institute: The University of Tokyo

description: Gene expression data from TmBER2gs strain

hyb_protocol: cRNA was purified, fragmented and hybridized onto a custom-made probe array chip (Eh_Eia520620F) from Affymetrix for 16 h at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Hewlett-Packard Affymetrix Scanner 3000 . The probe intensities were extracted using the Affymetrix GeneChip Command Console.

data_processing: Raw probe intensities data were generated by the Command Console software and a GeneTitan Instrument. The resulting expression values were analyzed using Genespring GX 10.0.2 to identify genes that were differentially expressed between either TmBER1gs and pSAP2G or TmBER2gs and pSAP2G.

label: biotin

organism: Entamoeba histolytica

source_name: Entamoeba histolytica after TmBER2 gene silencing (biological replicate 4)

label_protocol: Following the manufacturer’s protocol, 5 μg of RNA was reverse transcribed to cDNA and used to synthesize biotin-labeled cRNA.

growth_protocol: E. histolytica G3 strain was transfected with appropriate gene silencing plasmids or empty vector. Transformants were selected by G418 treatment up to 10 μg/ml BIS medium. Confluent cultures after 3-4 days of incubation were collected for RNA extraction.

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

treatment_protocol: Cells were maintained in BIS culture medium supplemented with 10 μg/ml G418.

tag: transfected with

value: TmBER2gs plasmid


title: AD_0018

address: 7-430 Morioka-cho

value: male


title: pSAP2G-4

description: Gene expression data from mock control transformant

source_name: Entamoeba histolytica transfected with empty vector pSAP2G (biological replicate 4)

value: pSAP2G empty vector


title: TmBER2-GS-3

source_name: Entamoeba histolytica after TmBER2 gene silencing (biological replicate 3)


title: pSAP2G-3

source_name: Entamoeba histolytica transfected with empty vector pSAP2G (biological replicate 3)


title: pSAP2G-1

source_name: Entamoeba histolytica transfected with empty vector pSAP2G (biological replicate 1)


title: TmBER2-GS-2

source_name: Entamoeba histolytica after TmBER2 gene silencing (biological replicate 2)


title: P8_PZQ-selected1


title: pSAP2G-2

source_name: Entamoeba histolytica transfected with empty vector pSAP2G (biological replicate 2)


title: P8_control2


title: AD_0017

value: AD


title: RNAseq_Pax3_H9_1day_rep1

first: Alessandro

last: Magli

institute: University of Minnesota

description:
processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_1day_dox_01


title: TmBER1-GS-2

description: Gene expression data from TmBER1gs strain

source_name: Entamoeba histolytica after TmBER1 gene silencing (biological replicate 2)

value: TmBER1gs plasmid


title: P8_control3

value: whole organism


title: TmBER2-GS-1

source_name: Entamoeba histolytica after TmBER2 gene silencing (biological replicate 1)


title: AD_0016


title: RNAseq_Ctrl_H9_1day_rep1

description:
processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_nodox_01


title: P7_PZQ-selected4

value: Puerto Rican-1 (PR-1)


title: ChIPseq_Pax3_1day_dox_H9

description:
processed data file:
human_PAX3_1day_ChIP_peaks.bed
ChIP_H9_PAX3_1day_plusdox

data_processing:
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) or human (hg38) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. To identify the list of high confidence mouse Pax3 peaks we performed 3 independent Pax3 ChIP-seq experiments and, using the bedtools intersect function, only common regions between 2 experiments were further considered. In addition, the Pax3 peak list was filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse (or human) ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: processed files represent list of Pax3 peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input

extract_protocol:
ChIP-seq: D4 EBs (1-day induced and control Pax3 mouse cells) were trypsin-treated at 37°C for 1 minute with gentle shacking and reaction was inhibited by adding 10%FBS/PBS. 1-day induced Pax3 NIH3T3 cells and 6-day induced Pax3 mouse cells growing in monolayer were harvested by incubation with trypsin for 1-2 minutes. Human differentiating PAX3-inducible cells were collected at day 6 of differentiation (following 24h dox-mediated induction) by incubation with trypsin for 1-2 minutes. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with glycine and staining with PDGFRα-PE antibody. PDGFRα+ cells were sorted using FACSAriaII, snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated. Cells were sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF to achieve an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. For Pax3 ChIP, 25-40µg of chromatin (diluted to 500µl) were precleared for 4h at 4°C with 20µl of BSA-blocked Protein A (or Protein G)-conjugated sepharose beads (GE healthcare). Samples were supplemented with 1/10 volume of 10% Triton X-100 and incubated overnight with anti-Pax3 (Santa Cruz Biotechnology sc-34926) antibody. Immune complexes were recovered by incubation with 20µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. Libraries from iPax3 NIH3T3 cells were generated using the NEBNext DNA library prep kit (NEB).


title: HA-ChIPseq_SD_180

city: Cambridge

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
QC and trimming (Sickle Version 1.33)
Adapter removal (Trim Galore version 0.4.2 )
Alligment ( Bowtie2 2.2.6)
Samtools Version 0.1.19-96b5f2294a
Read processing and normalisation ( Deeptools Version 3.1.2)
Genome_build: LYZE00000000
Supplementary_files_format_and_content: Reads alligned to complete W303 genome

organism: Saccharomyces cerevisiae

source_name: Cse4-6HA SD

growth_protocol: G1 arrested Mid log phase yeast culture in were grown in standard medium (YPD) and released in to S-phase

extract_protocol:
standart (phenol/cholorofrom based) yeast genomic extraction method is used
Home made reagents are used with 1:100 dilution of adapters
Chip_Seq and DNA_seq

treatment_protocol: ChIP samples where threated with Hyroxyurea and cells were crosslinked with EGS and Formaldehyde

tag: genotype

value: Cse4-6HA SD

tag: antibody

value: Pierce catno:88837


title: P7_PZQ-selected3

value: pooled male and female

value: Praziquantel (900 mg/Kg)


title: Input_1day_dox_H9

city: Minneapolis

address: 2231 6th St SE

description:
processed data file:
mouse_Pax3_6day_ChIP_peaks.bed
Input_H9_1day_plusdox

value: differentiating hES cells

value: serum

value: day6 of differentiation


title: P7_PZQ-selected2


title: TmBER1-GS-1

source_name: Entamoeba histolytica after TmBER1 gene silencing (biological replicate 1)


title: AD_0015


title: P7_PZQ-selected1


title: RepPro_SD_cdc45-2A

source_name: Cse4-6HA SD Cdc45-2A

value: Cse4-6HA SD Cdc45-2A


title: RepPro_SD


title: AD_0014

value: female


title: AD_0013


title: AD_0012


title: P8_control1

value: Vehicle (Cremophor EL)


title: P7_control4


title: RepPro_Pol1HA_cdc45-2A

source_name: Cse4-6HA 3HA-Rad54 cdc45-2A

value: Cse4-6HA 3HA-Rad54 cdc45-2A


title: P7_control1

source_name: whole parasites


title: P7_control2


title: P7_control3


title: RepPro_Pol1HA

source_name: Cse4-6HA 3HA-Rad53

value: Cse4-6HA 3HA-Rad53


title: HA-ChIPseq_wt

value: Cse4-HA HA-Rad53


title: AD_0010

source_name: serum

value: AD


title: AD_0011


title: HA-ChIPseq_SD_60


title: HA-ChIPseq_negative control


title: AD_0008


title: P6_PZQ-selected3


title: AD_0007

value: male


title: AD_0009


title: AD_0006


title: P6_PZQ-selected4

value: whole organism


title: PolyIC-stimulated MPs - 6 days + Gardiquimod 24 h [DC_pIC-G-2]

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with  GenePix 4100A microarray scanner

data_processing: Assessment of spot quality was done with aid of GenePix flags. After filtration of low quality spots, Lowess normalization of log2-expression ratios was performed.

organism: Salmo salar

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Primary salmon mononuclear phagocytes (MPs) isolated from head kidney and cultured in vitro in L-15 medium supplemented with 5% FBS for up to 7 days

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

source_name: control macriphages - 1 day

value: Control


title: HA-ChIPseq_cdc45-2A

value: Cse4-HA HA-Rad54 cdc45-2A


title: PolyIC-stimulated MPs - 7 days [DC_pIC-D6-2]

source_name: PolyIC-stimulated MPs - 7 days

value: PolyIC 7 days


title: P6_PZQ-selected2

value: Puerto Rican-1 (PR-1)

value: pooled male and female


title: PolyIC-stimulated MPs - 24 h [DC_pIC-D1]

source_name: PolyIC-stimulated MPs - 24 h

value: PolyIC 24 h


title: PolyIC-stimulated MPs - 6 days + Gardiquimod 24 h [DC_pIC-G-1]


title: P6_PZQ-selected1

value: Praziquantel (900 mg/Kg)


title: P6_control4


title: AD_0005


title: PolyIC-stimulated MPs - 7 days [DC_pIC-D6-1]


title: P6_control2


title: P6_control3


title: CpG-stimulated MPs - 6 days + Gardiquimod 24 h [DC_CpG-G-1]

value: CpG 6 days, Gardiquimod 24 h


title: CpG-stimulated MPs - 6 days + Gardiquimod 24 h [DC_CpG-G-2]


title: AD_0003


title: AD_0004


title: P6_control1


title: AD_0001


title: MG_2_5_1_H3K9me3-116180169

city: Athens

first: Mary

last: Goll

state: Select State

address: 120 E. Green Street

department: Genetics

institute: University of Georgia

data_processing:
Sequenced reads were trimmed using Trimgalore version 4.0 and only reads greater than 20bp were retained. Parameters used trimgalore --length 20 --fastqc --gzip
Reads aligned using BWA version 0.7.15 algorithms algn and samse
Samtools 1.3.1 used to sort and index bam files
IGVtools 2.3.81 to create tdf files viewable in Integrated Genome Viewer. Parameters igvtools count -z 7 -w 100
HOMER version 4.8 create Tag Directories for downstream data analysis
HOMER version 4.8 call peaks using findpeaks style histone size 1000 against input file
HOMER version 4.8 annotatePeaks for metaplot and heatmap generation annotatePeaks parameters -hist 50 -ghist - size 10000
Rstudio for heatmap s
Genome_build: GCF_000002035.6_GRCz10_genomic

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Cells lysed using lysis buffer followed by chromatin shearing in Diagenode Bioruptor and histone-DNA complexes were isolated with antibody.
Illumina TruSeq ChIP

tag: hours post fertilization

tag: developmental stage

value: embryo

tag: chip antibody


title: AD_0002

value: female


title: CpG-stimulated MPs - 7 days [DC_CpG-D6-2]

source_name: CpG-stimulated MPs - 7 days

value: CpG 6 days


title: Non-stimulated MPs - 6 days + Gardiquimod 24 h [DC_C-G-1]

value: Gardiquimod 24 h


title: MG_2_5_1_Input-116188128


title: Non-stimulated MPs - 7days [DC_C-D6-2]

source_name: Non-stimulated MPs - 7days


title: Non-stimulated MPs - 7days [DC_C-D6-1]