title: Tarca_008_P1A08


title: Tarca_066_P1F06

status: Public on May 24 2021

type: RNA

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

country: USA

institute: Wayne State University

hyb_protocol: Labeled cDNA were hybridized to the arrays in a GeneChip™ Hybridization Oven 640 by rotating at 60 rpm, 45°C for 16 hours.

scan_protocol: Arrays were then washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix 3000 7G GeneChip™ Scanner with Autoloader.

data_processing: Probeset definitions are based on Brainarray’s custom CDFs version 23 and represent ENTREZ IDs. Microarray raw gene expression data was background corrected, quantile normalized and summarized at ENTREZ ID level using Robust Multi-array Average (RMA) implemented in the oligo package of Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Biotinylated cDNA were prepared from 20 - 50 ng total RNA.

growth_protocol: Plasma samples were collected and stored in PAXgene® Blood RNA collection tube (BD 762165)

extract_protocol: RNA was isolated from PAXgene® Blood RNA collection tubes (BD Biosciences, San Jose, CA; Catalog #762165), as described in the PAXgene® Blood miRNA Kit Handbook. Purified RNA was quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean, Gentbrugge, Belgium), and quality was assessed by microfluidics using the RNA ScreenTape on the Agilent 2200 TapeStation (Agilent Technologies, Wilmington, DE, USA).

tag: individual

tag: tissue

value: Whole blood

tag: gestational age

tag: group

value: sPTD

tag: batch

tag: train

tag: lmp

tag: gadelivery

tag: diagnosisga

tag: subgroup


title: Tarca_042_P1D06

value: PPROM


title: Tarca_055_P1E07


title: Tarca_091_P1H07


title: Tarca_007_P1A07


title: Tarca_147_P2C07


title: Tarca_054_P1E06


title: Tarca_043_P1D07


title: Tarca_090_P1H06


title: Tarca_089_P1H05


title: Tarca_006_P1A06


title: Tarca_030_P1C06


title: Tarca_077_P1G05


title: Tarca_005_P1A05


title: Tarca_017_P1B05


title: Tarca_018_P1B06


title: Tarca_028_P1C04


title: Tarca_103_P2G01


title: Tarca_065_P1F05


title: Tarca_053_P1E05


title: Tarca_041_P1D05


title: Tarca_064_P1F04


title: Tarca_087_P1H03


title: Tarca_040_P1D04


title: Tarca_029_P1C05


title: Tarca_052_P1E04


title: Tarca_076_P1G04


title: Tarca_063_P1F03


title: Tarca_004_P1A04


title: Tarca_051_P1E03


title: Tarca_016_P1B04


title: Tarca_027_P1C03


title: Tarca_075_P1G03


title: Tarca_086_P1H02


title: Tarca_003_P1A03


title: Tarca_015_P1B03


title: Tarca_074_P1G02


title: Tarca_039_P1D03


title: Tarca_049_P1E01


title: Tarca_025_P1C01


title: Tarca_037_P1D01


title: Tarca_900_P10D05

description: re-analysis of GSM3452389

value: Control

value: TNL


title: Tarca_013_P1B01


title: Tarca_909_P10E06

description: re-analysis of GSM3452392


title: Tarca_001_P1A01


title: Tarca_896_P10H04

description: re-analysis of GSM3452387


title: Tarca_899_P10C05

description: re-analysis of GSM3452388

value: TL


title: Tarca_745_P08A10

description: re-analysis of GSM3452394


title: Tarca_903_P10G05

description: re-analysis of GSM3452390


title: Tarca_878_P10F02

description: re-analysis of GSM3452380


title: Tarca_744_P08H09

description: re-analysis of GSM3452393


title: Tarca_895_P10G04

description: re-analysis of GSM3452386


title: Tarca_892_P10D04

description: re-analysis of GSM3452385


title: Tarca_881_P10A03

description: re-analysis of GSM3452381


title: Tarca_891_P10C04

description: re-analysis of GSM3452384


title: Tarca_890_P10B04

description: re-analysis of GSM3452383


title: Tarca_876_P10D02

description: re-analysis of GSM3452379


title: Tarca_884_P10D03

description: re-analysis of GSM3452382


title: Tarca_859_P8C12

description: re-analysis of GSM3452374


title: Tarca_874_P10B02

description: re-analysis of GSM3452377


title: Tarca_875_P10C02

description: re-analysis of GSM3452378


title: Tarca_855_P8G11

description: re-analysis of GSM3452373


title: Tarca_847_P8G10

description: re-analysis of GSM3452370


title: Tarca_834_P9B09

description: re-analysis of GSM3452365


title: Tarca_849_P8A11

description: re-analysis of GSM3452371


title: Tarca_831_P9G08

description: re-analysis of GSM3452364


title: Tarca_829_P9E08

description: re-analysis of GSM3452362


title: Tarca_826_P9B08

description: re-analysis of GSM3452359


title: Tarca_864_P8H12

description: re-analysis of GSM3452376


title: Tarca_863_P8G12

description: re-analysis of GSM3452375


title: Tarca_850_P8B11

description: re-analysis of GSM3452372


title: Tarca_842_P8B10

description: re-analysis of GSM3452368


title: Tarca_838_P9F09

description: re-analysis of GSM3452366


title: Tarca_807_P9G05

description: re-analysis of GSM3452353


title: Tarca_817_P9A07

description: re-analysis of GSM3452355


title: Tarca_061_P1F01


title: Tarca_827_P9C08

description: re-analysis of GSM3452360


title: Tarca_821_P9E07

description: re-analysis of GSM3452357


title: Tarca_811_P9C06

description: re-analysis of GSM3452354


title: Tarca_830_P9F08

description: re-analysis of GSM3452363


title: Tarca_802_P9B05

description: re-analysis of GSM3452352


title: Tarca_841_P8A10

description: re-analysis of GSM3452367


title: Tarca_822_P9F07

description: re-analysis of GSM3452358


title: Tarca_820_P9D07

description: re-analysis of GSM3452356


title: Tarca_845_P8E10

description: re-analysis of GSM3452369


title: Tarca_828_P9D08

description: re-analysis of GSM3452361


title: Tarca_793_P9A04

description: re-analysis of GSM3452349


title: Tarca_794_P9B04

description: re-analysis of GSM3452350


title: Tarca_760_P8H11

description: re-analysis of GSM3452342


title: Tarca_778_P9B02

description: re-analysis of GSM3452346


title: Tarca_795_P9C04

description: re-analysis of GSM3452351


title: Tarca_782_P9F02

description: re-analysis of GSM3452347


title: Tarca_751_P8G10

description: re-analysis of GSM3452338


title: Tarca_784_P9H02

description: re-analysis of GSM3452348


title: Tarca_713_P8A06

description: re-analysis of GSM3452332


title: Tarca_720_P8H06

description: re-analysis of GSM3452334


title: Tarca_777_P9A02

description: re-analysis of GSM3452345


title: Tarca_759_P8G11

description: re-analysis of GSM3452341


title: Tarca_707_P8C05

description: re-analysis of GSM3452329


title: Tarca_721_P8A07

description: re-analysis of GSM3452335


title: Tarca_712_P8H05

description: re-analysis of GSM3452331


title: Tarca_764_P8D12

description: re-analysis of GSM3452343


title: Tarca_766_P8F12

description: re-analysis of GSM3452344


title: Tarca_752_P8H10

description: re-analysis of GSM3452339


title: Tarca_702_P8F04

description: re-analysis of GSM3452328


title: Tarca_688_P8H02

description: re-analysis of GSM3452325


title: Tarca_754_P8B11

description: re-analysis of GSM3452340


title: Tarca_699_P8C04

description: re-analysis of GSM3452327


title: Tarca_736_P8H08

description: re-analysis of GSM3452337


title: Tarca_088_P1H04


title: Tarca_718_P8F06

description: re-analysis of GSM3452333


title: Tarca_689_P8A03

description: re-analysis of GSM3452326


title: Tarca_709_P8E05

description: re-analysis of GSM3452330


title: Tarca_684_P8D02

description: re-analysis of GSM3452324


title: Tarca_730_P8B08

description: re-analysis of GSM3452336


title: Tarca_683_P8C02

description: re-analysis of GSM3452323


title: Tarca_668_P7D12

description: re-analysis of GSM3452317


title: Tarca_675_P8C01

description: re-analysis of GSM3452321


title: Tarca_667_P7C12

description: re-analysis of GSM3452316


title: Tarca_666_P7B12

description: re-analysis of GSM3452315


title: Tarca_672_P7H12

description: re-analysis of GSM3452320


title: Tarca_650_P7B10

description: re-analysis of GSM3452314


title: Tarca_670_P7F12

description: re-analysis of GSM3452318


title: Tarca_648_P7H09_2

description: re-analysis of GSM3452312


title: Tarca_647_P7G09

description: re-analysis of GSM3452311


title: Tarca_646_P7F09

description: re-analysis of GSM3452310


title: Tarca_637_P7E08

description: re-analysis of GSM3452306


title: Tarca_649_P7A10

description: re-analysis of GSM3452313


title: Tarca_623_P7G06

description: re-analysis of GSM3452303


title: Tarca_617_P7A06

description: re-analysis of GSM3452300


title: Tarca_671_P7G12

description: re-analysis of GSM3452319


title: Tarca_629_P7E07

description: re-analysis of GSM3452304


title: Tarca_638_P7F08

description: re-analysis of GSM3452307


title: Tarca_682_P8B02

description: re-analysis of GSM3452322


title: Tarca_639_P7G08

description: re-analysis of GSM3452308


title: Tarca_622_P7F06

description: re-analysis of GSM3452302


title: Tarca_615_P7G05

description: re-analysis of GSM3452298


title: Tarca_640_P7H08

description: re-analysis of GSM3452309


title: Tarca_616_P7H05

description: re-analysis of GSM3452299


title: Tarca_630_P7F07

description: re-analysis of GSM3452305


title: Tarca_611_P7C05

description: re-analysis of GSM3452296


title: Tarca_618_P7B06

description: re-analysis of GSM3452301


title: Tarca_592_P7H02

description: re-analysis of GSM3452293


title: Tarca_612_P7D05

description: re-analysis of GSM3452297


title: Tarca_591_P7G02

description: re-analysis of GSM3452292


title: Tarca_566_P6F11

description: re-analysis of GSM3452281


title: Tarca_557_P6E10

description: re-analysis of GSM3452277


title: Tarca_581_P7E01

description: re-analysis of GSM3452284


title: Tarca_576_P6H12

description: re-analysis of GSM3452282


title: Tarca_546_P6B09

description: re-analysis of GSM3452272


title: Tarca_556_P6D10

description: re-analysis of GSM3452276


title: Tarca_583_P7G01

description: re-analysis of GSM3452285


title: Tarca_584_P7H01_2

description: re-analysis of GSM3452286


title: Tarca_558_P6F10

description: re-analysis of GSM3452278


title: Tarca_547_P6C09

description: re-analysis of GSM3452273


title: Tarca_587_P7C02

description: re-analysis of GSM3452288


title: Tarca_544_P6H08

description: re-analysis of GSM3452271


title: Tarca_588_P7D02

description: re-analysis of GSM3452289


title: Tarca_542_P6F08

description: re-analysis of GSM3452269


title: Tarca_549_P6E09

description: re-analysis of GSM3452274


title: Tarca_559_P6G10

description: re-analysis of GSM3452279


title: Tarca_586_P7B02

description: re-analysis of GSM3452287


title: Tarca_543_P6G08

description: re-analysis of GSM3452270


title: Tarca_590_P7F02

description: re-analysis of GSM3452291


title: Tarca_551_P6G09

description: re-analysis of GSM3452275


title: Tarca_578_P7B01

description: re-analysis of GSM3452283


title: Tarca_607_P7G04

description: re-analysis of GSM3452295


title: Tarca_565_P6E11

description: re-analysis of GSM3452280


title: Tarca_589_P7E02

description: re-analysis of GSM3452290


title: Tarca_532_P6D07_2

description: re-analysis of GSM3452268


title: Tarca_523_P6C06

description: re-analysis of GSM3452266


title: Tarca_527_P6G06

description: re-analysis of GSM3452267


title: Tarca_514_P6B05

description: re-analysis of GSM3452265


title: Tarca_504_P6H03

description: re-analysis of GSM3452262


title: Tarca_499_P6C03

description: re-analysis of GSM3452258


title: Tarca_502_P6F03

description: re-analysis of GSM3452261


title: Tarca_498_P6B03

description: re-analysis of GSM3452257


title: Tarca_477_P5E12

description: re-analysis of GSM3452254


title: Tarca_447_P5G08

description: re-analysis of GSM3452247


title: Tarca_456_P5H09

description: re-analysis of GSM3452250


title: Tarca_472_P5H11

description: re-analysis of GSM3452253


title: Tarca_425_P5A06

description: re-analysis of GSM3452243


title: Tarca_450_P5B09

description: re-analysis of GSM3452249


title: Tarca_510_P6F04

description: re-analysis of GSM3452264


title: Tarca_458_P5B10

description: re-analysis of GSM3452251


title: Tarca_426_P5B06

description: re-analysis of GSM3452244


title: Tarca_501_P6E03

description: re-analysis of GSM3452260


title: Tarca_410_P5B04

description: re-analysis of GSM3452240


title: Tarca_446_P5F08

description: re-analysis of GSM3452246


title: Tarca_486_P6F01

description: re-analysis of GSM3452256


title: Tarca_480_P5H12

description: re-analysis of GSM3452255


title: Tarca_467_P5C11

description: re-analysis of GSM3452252


title: Tarca_509_P6E04

description: re-analysis of GSM3452263


title: Tarca_500_P6D03

description: re-analysis of GSM3452259


title: Tarca_409_P5A04

description: re-analysis of GSM3452239


title: Tarca_906_P10B06

description: re-analysis of GSM3452391


title: Tarca_448_P5H08

description: re-analysis of GSM3452248


title: Tarca_415_P5G04

description: re-analysis of GSM3452241


title: Tarca_402_P5B03

description: re-analysis of GSM3452236


title: Tarca_432_P5H06

description: re-analysis of GSM3452245


title: Tarca_404_P5D03

description: re-analysis of GSM3452237


title: Tarca_593_P7A03

description: re-analysis of GSM3452294


title: Tarca_384_P4H12

description: re-analysis of GSM3452232


title: Tarca_407_P5G03

description: re-analysis of GSM3452238


title: Tarca_389_P5E01

description: re-analysis of GSM3452233


title: Tarca_422_P5F05

description: re-analysis of GSM3452242


title: Tarca_379_P4C12

description: re-analysis of GSM3452229


title: Tarca_366_P4F10

description: re-analysis of GSM3452225


title: Tarca_381_P4E12

description: re-analysis of GSM3452230


title: Tarca_398_P5F02

description: re-analysis of GSM3452235


title: Tarca_348_P4D08

description: re-analysis of GSM3452221


title: Tarca_367_P4G10

description: re-analysis of GSM3452226


title: Tarca_395_P5C02

description: re-analysis of GSM3452234


title: Tarca_383_P4G12

description: re-analysis of GSM3452231


title: Tarca_357_P4E09

description: re-analysis of GSM3452223


title: Tarca_340_P4D07

description: re-analysis of GSM3452218


title: Tarca_345_P4A08

description: re-analysis of GSM3452219


title: Tarca_339_P4C07

description: re-analysis of GSM3452217


title: Tarca_334_P4F06

description: re-analysis of GSM3452216


title: Tarca_325_P4E05

description: re-analysis of GSM3452213


title: Tarca_378_P4B12

description: re-analysis of GSM3452228


title: Tarca_324_P4D05

description: re-analysis of GSM3452212


title: Tarca_360_P4H09

description: re-analysis of GSM3452224


title: Tarca_346_P4B08

description: re-analysis of GSM3452220


title: Tarca_317_P4E04

description: re-analysis of GSM3452211


title: Tarca_313_P4A04

description: re-analysis of GSM3452210


title: Tarca_329_P4A06

description: re-analysis of GSM3452215


title: Tarca_328_P4H05

description: re-analysis of GSM3452214


title: Tarca_351_P4G08

description: re-analysis of GSM3452222


title: Tarca_374_P4F11

description: re-analysis of GSM3452227


title: Tarca_312_P4H03

description: re-analysis of GSM3452209


title: Tarca_296_P4H01

description: re-analysis of GSM3452208


title: Tarca_252_P3D08

description: re-analysis of GSM3452204


title: Tarca_255_P3G08

description: re-analysis of GSM3452205


title: Tarca_250_P3B08

description: re-analysis of GSM3452202


title: Tarca_245_P3E07

description: re-analysis of GSM3452201


title: Tarca_258_P3B09

description: re-analysis of GSM3452206


title: Tarca_243_P3C07

description: re-analysis of GSM3452200


title: Tarca_275_P3C11

description: re-analysis of GSM3452207


title: Tarca_237_P3E06

description: re-analysis of GSM3452194


title: Tarca_235_P3C06

description: re-analysis of GSM3452192


title: Tarca_241_P3A07

description: re-analysis of GSM3452198


title: Tarca_238_P3F06

description: re-analysis of GSM3452195


title: Tarca_225_P3A05

description: re-analysis of GSM3452184


title: Tarca_242_P3B07

description: re-analysis of GSM3452199


title: Tarca_251_P3C08

description: re-analysis of GSM3452203


title: Tarca_219_P3C04

description: re-analysis of GSM3452182


title: Tarca_234_P3B06

description: re-analysis of GSM3452191


title: Tarca_223_P3G04

description: re-analysis of GSM3452183


title: Tarca_239_P3G06

description: re-analysis of GSM3452196


title: Tarca_229_P3E05

description: re-analysis of GSM3452186


title: Tarca_240_P3H06

description: re-analysis of GSM3452197


title: Tarca_236_P3D06

description: re-analysis of GSM3452193


title: Tarca_233_P3A06

description: re-analysis of GSM3452190


title: Tarca_232_P3H05

description: re-analysis of GSM3452189


title: Tarca_226_P3B05

description: re-analysis of GSM3452185


title: Tarca_230_P3F05

description: re-analysis of GSM3452187


title: Tarca_192_P2H12

description: re-analysis of GSM3452180


title: Tarca_189_P2E12

description: re-analysis of GSM3452179


title: Tarca_231_P3G05

description: re-analysis of GSM3452188


title: Tarca_173_P2E10

description: re-analysis of GSM3452174


title: Tarca_176_P2H10

description: re-analysis of GSM3452176


title: Tarca_188_P2D12

description: re-analysis of GSM3452178


title: Tarca_183_P2G11

description: re-analysis of GSM3452177


title: Tarca_175_P2G10

description: re-analysis of GSM3452175


title: Tarca_169_P2A10

description: re-analysis of GSM3452173


title: Tarca_165_P2E09

description: re-analysis of GSM3452172


title: Tarca_163_P2C09

description: re-analysis of GSM3452171


title: Tarca_127_P2G04

description: re-analysis of GSM3452162


title: Tarca_145_P2A07

description: re-analysis of GSM3452167


title: Tarca_136_P2H05

description: re-analysis of GSM3452164


title: Tarca_149_P2E07

description: re-analysis of GSM3452168


title: Tarca_137_P2A06

description: re-analysis of GSM3452165


title: Tarca_116_P2D03

description: re-analysis of GSM3452159


title: Tarca_117_P2E03

description: re-analysis of GSM3452160


title: Tarca_100_P2D01

description: re-analysis of GSM3452155


title: Tarca_144_P2H06

description: re-analysis of GSM3452166


title: Tarca_114_P2B03

description: re-analysis of GSM3452158


title: Tarca_108_P2D02

description: re-analysis of GSM3452156


title: Tarca_060_P1E12

description: re-analysis of GSM3452151


title: Tarca_048_P1D12

description: re-analysis of GSM3452150


title: Tarca_120_P2H03_2

description: re-analysis of GSM3452161


title: Tarca_218_P3B04

description: re-analysis of GSM3452181


title: Tarca_162_P2B09

description: re-analysis of GSM3452170


title: Tarca_084_P1G12

description: re-analysis of GSM3452153


title: Tarca_153_P2A08

description: re-analysis of GSM3452169


title: Tarca_132_P2D05

description: re-analysis of GSM3452163


title: Tarca_072_P1F12

description: re-analysis of GSM3452152


title: Tarca_012_P1A12

description: re-analysis of GSM3452147


title: Tarca_111_P2G02

description: re-analysis of GSM3452157


title: Tarca_096_P1H12

description: re-analysis of GSM3452154


title: Tarca_059_P1E11

description: re-analysis of GSM3452143


title: Tarca_083_P1G11

description: re-analysis of GSM3452145


title: Tarca_095_P1H11

description: re-analysis of GSM3452146


title: Tarca_035_P1C11

description: re-analysis of GSM3452142


title: Tarca_024_P1B12

description: re-analysis of GSM3452148


title: Tarca_071_P1F11

description: re-analysis of GSM3452144


title: Tarca_036_P1C12

description: re-analysis of GSM3452149


title: Tarca_011_P1A11

description: re-analysis of GSM3452140


title: Tarca_046_P1D10

description: re-analysis of GSM3452136


title: Sample_37_2

description: re-analysis of GSM3120098

hyb_protocol: 5.5ug sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.  200ul of labeled targets were hybridized to Affymetrix Human Transcriptome Arrays (HTA) 2.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip scanner 3000. Raw intensity data were generated from array images using Affymetrix AGCC software.

label_protocol: 100 ng of RNA was reverse transcribed and amplified using Affymetrix WT plus expression kit following manufacturer’s suggested protocol.

extract_protocol: RNA was isolated from  PAXgene® Blood RNA collection tube (BD 762165) as described in the PAXgene® Blood miRNA Kit Handbook (December, 2015). Purified RNA was quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean) and quality assessed by microfluidics using the RNA ScreenTape on the Agilent 2200 TapeStation.


title: Tarca_094_P1H10

description: re-analysis of GSM3452139


title: Tarca_034_P1C10

description: re-analysis of GSM3452135


title: Sample_21_2

description: re-analysis of GSM3120084


title: Sample_31_2

description: re-analysis of GSM3120094


title: Sample_36_2

description: re-analysis of GSM3120097


title: Sample_28_2

description: re-analysis of GSM3120091


title: Sample_24_2

description: re-analysis of GSM3120087


title: Sample_27_2

description: re-analysis of GSM3120090


title: Tarca_070_P1F10

description: re-analysis of GSM3452138


title: Sample_30_2

description: re-analysis of GSM3120093


title: Sample_26_2

description: re-analysis of GSM3120089


title: Sample_32_2

description: re-analysis of GSM3120095


title: Sample_20_2

description: re-analysis of GSM3120083


title: Sample_22_2

description: re-analysis of GSM3120085


title: Sample_15_2

description: re-analysis of GSM3120080


title: Sample_38_2

description: re-analysis of GSM3120099


title: Tarca_022_P1B10

description: re-analysis of GSM3452134


title: Sample_34_2

description: re-analysis of GSM3120096


title: Sample_23_2

description: re-analysis of GSM3120086


title: Sample_18_2

description: re-analysis of GSM3120081


title: Sample_29_2

description: re-analysis of GSM3120092


title: Sample_25_2

description: re-analysis of GSM3120088


title: Sample_14_2

description: re-analysis of GSM3120079


title: Tarca_023_P1B11

description: re-analysis of GSM3452141


title: Sample_19_2

description: re-analysis of GSM3120082


title: Sample_13_2

description: re-analysis of GSM3120078


title: Tarca_058_P1E10

description: re-analysis of GSM3452137


title: s385

type: protein

hyb_protocol: These SOMAmer reagents were then quantified by hybridization to custom DNA microarrays.

scan_protocol: The Cyanine-3 signal from the SOMAmer reagent was detected on microarrays. More details on all protocols are described in Gold L, et al. PLoS One. 2010;5(12):e15004 and Davies DR, et al. Proc Natl Acad Sci U S A. 2012;109(49):19971-6.

data_processing: The raw protein abundance data consisted of relative fluorescence units obtained from scanning the microarrays with a laser scanner. A sample-by-sample adjustment of the overall signal within a single plate (85 samples processed per plate/run) was performed in three steps: Hybridization Control Normalization, Median Signal Normalization, and Calibration, using the manufacturer’s protocol. Outlier protein abundance values above 2 × the 98th percentile of all samples, were replaced with 2 × the 98th percentile of all samples (data thresholding).

molecule: protein

source_name: maternal plasma

label_protocol: The serum samples were diluted and then incubated with the respective SOMAmer mixes pre-immobilized onto streptavidin-coated beads. The beads were washed in order to remove all non-specifically bound proteins and other matrix constituents. Proteins that remained specifically bound to their cognate SOMAmer reagents were tagged using an NHS-biotin reagent. After the labeling reaction, the beads were exposed to an anionic competitor solution that prevents non-specific interactions from reforming after disruption. Using this approach, pure cognate-SOMAmer complexes and unbound (free) SOMAmer reagents are released from the streptavidin beads using ultraviolet light that cleaves the photo-cleavable linker used to quantitate protein. The photo-cleavage eluate, which contains all SOMAmer reagents (some bound to a biotin-labeled protein and some free), was separated from the beads and then incubated with a second streptavidin-coated bead that binds the biotin-labeled proteins and the biotin-labeled protein-SOMAmer complexes. The free SOMAmer reagents were then removed during subsequent washing steps. In the final elution step, protein-bound SOMAmer reagents were released from their cognate proteins using denaturing conditions.

value: maternal plasma


title: s469


title: s74


title: s522


title: s500


title: s532


title: s684


title: s693


title: s529


title: s460


title: s482


title: s475


title: s489


title: s239


title: s496


title: s488


title: s476


title: s479


title: Sample_11_2

description: re-analysis of GSM3120076


title: s503


title: Sample_10_2

description: re-analysis of GSM3120075


title: Sample_7_2

description: re-analysis of GSM3120104


title: Sample_6_2

description: re-analysis of GSM3120103


title: s513


title: Sample_8_2

description: re-analysis of GSM3120105


title: Sample_12_2

description: re-analysis of GSM3120077


title: s518


title: s495


title: s525


title: s492


title: s497


title: s243


title: s696


title: Sample_5_2

description: re-analysis of GSM3120102


title: Sample_4_2

description: re-analysis of GSM3120101


title: Sample_3_2

description: re-analysis of GSM3120100


title: s692


title: Sample_9_2

description: re-analysis of GSM3120106


title: s523


title: s699


title: s697


title: s486


title: s498


title: s686


title: s43


title: s702


title: s687


title: s685


title: s494


title: s49


title: s490


title: s44


title: s462


title: s531


title: s48


title: s478


title: s520


title: s689


title: s470


title: s499


title: s533


title: SC68

status: Public on May 20 2021

type: SRA

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
10X Genomics' Cell Ranger 3.0.2 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 3.0.2 software's cellranger count function
Cell Ranger output files included: raw_feature_bc_matrix.h5, possorted_genome_bam.bam, and possorted_genome_bam.bam.bai files (among others).  The raw_feature_bc_matrix.h5 files were utilized for further downstream analysis in R with the package Seurat 3.0 and sctransform, only cells expressing at least 200 genes were kept for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: .h5 files contain the UMI (transcript) counts assigned to each cell barcode for each gene; each .h5 file corresponds to one sample/biopsy

molecule: polyA RNA

source_name: dorsal, mid-forearm skin biopsy

extract_protocol:
Biopsies were finely diced using a scalpel and placed in a Miltenyi C tube.  The enzymes from the Miltenyi whole skin dissociation kit, human, were used to digest cells over a period of 2 hours at 37 degrees.  Biopsies were then further mechanically separated using the h_skin_01 program on the Miltenyi OctoDissociator.  The resulting single cell suspension was filtered twice through 70 micron filters and finally resuspended in PBS containing 0.04% BSA.  Cells were loaded into the the 10X Genomics Chromium instrument according to the manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v1 and v2 User Guides
single cell RNA-Seq

value: skin

tag: chemistry

value: 10X Genomics 3 Prime V2 chemistry

tag: condition

value: CONTROL


title: SC124


title: SC125


title: s481


title: SC33

value: 10X Genomics 3 Prime V1 chemistry


title: SC32


title: SC18


title: uterus_PBS_R4

status: Public on Mar 05 2021

data_processing:
Paired-end RNA-Seq sequence data were processed using Tophat2 aligner.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Count matrix was generated by summarizeOverlaps function from GenomicAlignments package, and saved in .csv format.

organism: Mus musculus

extract_protocol:
Pregnant C57BL/6 mice were euthanized at term delivery (18.5 days post coitum) and the myometrial and cervical tissues were collected, placed in RNAlater Stabilization Solution, and stored at -80°C until use. Approximately 30-50 mg of each tissue was homogenized in 750 µl of QIAzol Lysis Reagent (Qiagen, Hilden, Germany). Total RNA was purified using EZ1 Universal Tissue kit on the EZ1 Advanced as described by the manufacturer (Qiagen). The RNA-seq library was prepared using the TruSeq Stranded Total RNA kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: treatment

value: PBS

value: Myometrium


title: SC4


title: SC1


title: uterus_PBS_R3


title: s528


title: s471


title: uterus_PBS_8


title: s512


title: uterus_PBS_6


title: s691


title: uterus_PBS_5


title: uterus_hCG_9

value: human chorionic gonadotropin (hCG)


title: uterus_PBS_3


title: uterus_PBS_10


title: uterus_PBS_1


title: uterus_hCG_8


title: uterus_PBS_2


title: uterus_hCG_7


title: uterus_hCG_5


title: uterus_hCG_6


title: uterus_hCG_1


title: uterus_hCG_10


title: uterus_hCG_3


title: uterus_hCG_4


title: uterus_hCG_2


title: cervix_PBS_R3

value: Cervix


title: cervix_PBS_6


title: cervix_PBS_8


title: cervix_PBS_4


title: cervix_PBS_3


title: cervix_PBS_5


title: cervix_PBS_7


title: cervix_PBS_2


title: uterus_PBS_4


title: SC50


title: cervix_PBS_10


title: cervix_PBS_1


title: cervix_hCG_R3


title: cervix_hCG_7


title: cervix_hCG_9


title: 17454

status: Public on Feb 01 2021

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner in quasi-mapping-based mode.
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package.
Genome_build: Ensembl GRCh37 (hg19)
Supplementary_files_format_and_content: Count matrix was generated by tximport function with "scaledTPM" option, from tximport package (v. 1.10.1), and saved in .csv format.

source_name: Chorioamniotic Membranes

extract_protocol:
Chorioamniotic membrane samples were collected from the placenta within 30 min after delivery. A section of chorioamniotic membrane that extended the entire length of the membrane was cut, rolled, and snap-frozen using liquid nitrogen. Collected chorioamniotic membrane samples were stored at -80°C until use for RNA isolation. RNA was isolated from snap-frozen chorioamniotic membrane samples using the Qiagen RNeasy mini kit (Qiagen), following the manufacturer’s instructions. The RNAseq library was prepared using the TruSeq RNA library prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Chorioamniotic Membranes

value: PTL

tag: maternal inflammatory response

value: FALSE

tag: fetal inflammatory response


title: cervix_hCG_10


title: 16375


title: cervix_hCG_2


title: cervix_hCG_1


title: cervix_hCG_3


title: cervix_hCG_5


title: 12836


title: cervix_hCG_6


title: 18686


title: 14483

value: TRUE


title: 11179


title: 10655


title: 8764


title: 10043


title: 18163-1


title: 9174


title: 8035


title: 17866


title: 17909


title: cervix_hCG_4


title: 18405


title: 17122


title: 13342


title: 13914


title: 17539


title: 12736


title: 10522


title: 18345-1


title: 18238


title: 18457


title: 16523


title: 13060


title: 15396


title: 16399


title: 13028


title: 12412


title: 11906


title: 11854


title: 11455


title: 10285


title: 10240


title: 9704


title: 7620


title: Renca_nostim_rep3

status: Public on Nov 25 2020

city: Cambridge

first: Kathleen

middle: Brosnahan

last: Yates

state: MA

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

data_processing:
Read data were adapter and quality trimmed using Trimmomatic v0.36 (10.1093/bioinformatics/btu170).
Trimmed reads were quantified by pseudoalignment to mm10 using Kallisto v0.46.0 (https://doi.org/10.1038/nbt.3519).
A variance stabilizing transform was applied to the count matrix using the DESeq2 R package (https://doi.org/10.1186/s13059-014-0550-8).
Tximport v1.16.1 was used to generate transcript-level abundance estimates as TPM.
TPMs were then quantile between-sample normalized.
Genome_build: mm10
Supplementary_files_format_and_content: Quantile-normalized TPM, tab delimited text file

source_name: Renca renal cell carcinoma

growth_protocol: Cells were cultured in DMEM media supplemented with 10% heat-inactivated FBS.

extract_protocol:
QIAGEN Rneasy extraction with on-column Dnase digestion, according to manufacturer's instructions
NEBNext Ultra Directional RNA Library Prep Kit for Illumina, according to manufacturer's instructions and using the mRNA capture kit and 12 cycles of PCR enrichment.
Stranded libraries were sequenced on an Illumina NextSeq 500 instrument using paired-end 37-bp reads.

value: BALB/c

tag: cell line

value: Renca renal cell carcinoma


title: 16495


title: Renca_nostim_rep2


title: 11836


title: B16_nostim_rep3

source_name: B16 F10 melanoma

value: B16F10 melanoma


title: B16_nostim_rep1


title: B16_nostim_rep2


title: MCF10A-D4-2

status: Public on Nov 08 2020

city: Washington

first: Ghada

last: Sharif

state: DC

address: 3970 Reservoir Rd NW NRB E311

institute: Georgetown University

description:
CPM_invitro.csv
10A-17-2_S44_L006

data_processing:
Data was aligned to Hg19 by STAR; Gene Counts were generated with the following specifications: --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode TranscriptomeSAM GeneCounts
Count tables were merged with gawk (10A_Merged_reads, processed data files)
Counts per million were generated with EdgeR (CPM.csv, processed data files)
Genome_build: GRCh19
Supplementary_files_format_and_content: invitro_CPM.csv is a tab-separated values file containing the Counts Per Million of each cell line
Supplementary_files_format_and_content: invivo_CPM.csv is a tab-separated values file containing the Counts Per Million of each tumor pool

source_name: Mammary Epthelial Cells

growth_protocol: MCF10A  and MCFDCIS cell lines were maintained in DMEM:F12 (Invitrogen, Carlsbad, CA) with 5% horse serum, 20ng/ml EGF, 0.5mg/ml Hydrocortisone, 100ng/ml Cholera Toxin, and 10mg/mL Insulin. All cell lines were grown at 37C with 5% CO2.

extract_protocol:
RNA was isolated from cultured cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol and quantified by Nanodrop (Thermo Fisher, Waltham, MA).
RNA-sequencing used TruSeq total RNA with RiboZero Gold library preparation (Illumina, San Diego, CA, USA).

value: Normal Immortalized MCF10A Mammary Epithelial Cells

tag: passage


title: MCF10A-2

description:
CPM_invitro.csv
MCF10A-2_S37_L005

tag: tissue


title: MCF10A-3

description:
CPM_invitro.csv
MCF10A-3_S38_L005


title: 18534


title: MCF10A-1

description:
CPM_invitro.csv
MCF10A-1_S36_L005


title: MCF10A-D4-1

description:
CPM_invitro.csv
10A-17-1_S43_L006


title: MCF10A-D4-3

description:
CPM_invitro.csv
10A-17-3_S45_L006


title: H3K4me3 chipseq prep2

status: Public on Oct 31 2020

city: Darlinghurst

first: David

middle: Thomas

last: Humphreys

address: 405 Liverpool Street

department: Genome core

country: Australia

institute: Victor Chang Cardiac Research Institute

library_source: genomic

data_processing:
RNA-Seq was aligned to danRer10 using Rsubread (v 1.26.1)
ATAC-Seq was aligned to danRer10 genome using bowtie2 (v 2.2.8)
Chip-seq data was aligned to danRer10 using bowtie2 (c 2.2.8)
Bigwig files produced using Deeptools (bamCoverage v3.1.2)
Genome_build: danRer10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Danio rerio

source_name: heart

growth_protocol: adult zebrafish

extract_protocol:
RNA was purified using Qiagen miRNeasy miniprep kits
RNA-Seq libraries were constructed with Kapa stranded mRNA kits using 1ug of RNA input per sample. ChipSeq libraries were generated using Illumina ChipSeq library prep kits.

value: whole heart

tag: developmental stage

value: adult

tag: genotype/variation

value: WT

tag: antibody


title: PolyA RNASeq prep4


title: H3K27Ac chipseq prep2


title: PolyA RNASeq prep3


title: H3K4me3 chipseq prep1


title: H3K27Ac chipseq prep4

value: klf1 overexpressing


title: PolyA RNASeq prep7


title: H3K27Ac chipseq prep3


title: H3K27Ac chipseq prep1


title: PolyA RNASeq prep1


title: H3K4me3 chipseq prep4


title: PolyA RNASeq prep6


title: H3K4me1 chipseq prep3


title: PolyA RNASeq prep2


title: PolyA RNASeq prep5


title: H3K4me1 chipseq prep4


title: H3K4me1 chipseq prep1


title: H3K4me1 chipseq prep2


title: HA tag pulldown prep4

value: HA tag


title: HA tag pulldown prep3


title: HA tag pulldown prep2


title: PolyA RNASeq prep8


title: HA tag pulldown prep1


title: chipseq input prep4


title: chipseq input prep1


title: chipseq input prep2


title: ATAC klf1 prep2


title: chipseq input prep3


title: ATAC klf1 prep1


title: H3K4me3 chipseq prep3


title: WGBS WT prep2


title: WGBS WT prep1


title: WGBS klf1 prep2


title: WGBS klf1 prep1


title: ATAC WT prep1


title: NT_UGI_HCT116_rep2_son

status: Public on Sep 20 2020

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description:
NT_UGI_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.bw
NT_UGI_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.0p33.region.bed

data_processing:
alignment of fastq files with bwa mem (version 0.7.17-r1194) using default parameters
SAM to BAM conversion and read sorting based on coordinates using samtools (version 1.9-50-g18be38a, and htslib version 1.9-90-ga80f5fd)
Marking duplicate reads in BAM files using picard-tools MarkDuplicates (version 2.18.5-SNAPSHOT)
Filtering out ambiguously mapped reads was done using samtools view (version 1.9): samtools view -b -h -q 1 NAME.sorted.dedup.bam -L list_of_chr_bam.bed -o NAME.MAPQfiltered.bam
Cell-type specific blacklists were defined as described in details in the Supplementary Material of the related publication. The corresponding blacklist was applied for each bam file using samtools view: samtools view -b -h NAME.MAPQfiltered.bam -L blacklist_HCT116.bed -o NAME.blacklist.bam -U NAME.filtered_blacklisted.bam
Filtered_blacklisted bam files of the corresponding replicates were merged using samtools merge (version 1.9). The following processing steps were performed on both individual replicates and the merged data also.
Scaled and smoothened coverage tracks were generated using the bamCoverage tool of the deepTools package (version 3.2.1). Bin size was set to 100bp, smoothening was performed with 5000 bases (--smoothLength 5000), reads were normalized to 1x sequencing coverage (--normalizeUsing RPGC), --effectiveGenomeSize 2793842910 --extendReads
Log2 ratio of treatment and input samples were calculated using the bigwigCompare tool of the deepTools package(version 3.2.1) and the genome scaled coverage track files of the enriched and the corresponding input samples. Binsize was set to 100bp. The resulting log2.bw files are uploaded to the GEO.
Interval files of the enriched regions were derived from the log2.bw files according to minor processing steps described in the Supplementary Material of the related publication.
Genome_build: GRCh38 (GRCh38.d1.vd1.fa from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)
Supplementary_files_format_and_content: BigWig files containing log2 ratio coverage signal of enriched vs input samples for 100bp bins, smoothened for 5000bp. Files are provided for individual replicates of each sample, as well as for merged data.
Supplementary_files_format_and_content: BED files containing regions of uracil enrichment derived from the log2.bw files. Files are provided for individual replicates of each sample, as well as for merged data.

source_name: HCT116 cells

growth_protocol: HCT116 and K562 cells were maintained in McCoy's 5A and RPMI media (Gibco), respectively. HCT116 cells were also stably transfected using retroviral transduction of EGFP-tagged UGI. Successfully transduced HCT116 cells were collected by FACS sorting using a BD FACSAria III Cell sorter.

extract_protocol:
Genomic DNA was purified by Quick-DNA Miniprep Plus Kit (Zymo Research) and sonicated with a BioRuptor (Diagenode). Immunoprecipitation was carried out by FLAG-tagged sensor protein binding to uracil residues in fragmented genomic DNA and was followed by purification with anti-FLAG beads (Sigma-Aldrich).
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 20 µM 5-fluoro-2'-deoxyuridine (5FdUR) or 100 nM raltitrexed (RTX) for 48 hours.

value: non-treated

tag: transgene

value: UGI

tag: sample type

value: input


title: NT_UGI_HCT116_rep1_son


title: WT_HCT116_rep2_son

description:
WT_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.bw
WT_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.0p27.region.bed

value: no transgene


title: RTX_UGI_HCT116_rep2_IP

description:
RTX_UGI_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.bw
RTX_UGI_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.0p25.region.bed

value: RTX

value: enriched


title: WT_HCT116_rep2_IP


title: RTX_UGI_HCT116_rep1_son


title: NT_UGI_HCT116_rep1_IP


title: NT_UGI_HCT116_rep2_IP


title: NT_UGI_HCT116MMR_rep2_IP

description: enriched

data_processing:
Alignment of fastq files with bwa mem (version 0.7.17-r1194) using default parameters
SAM to BAM conversion and read sorting based on coordinates using samtools (version 1.9-50-g18be38a, and htslib version 1.9-90-ga80f5fd)
Marking duplicated reads in BAM files using picard-tools MarkDuplicates (version 2.18.5-SNAPSHOT)
Filtering out ambiguously mapped reads was done using samtools view (version 1.9): samtools view -b -h -q 1 NAME.sorted.dedup.bam -L list_of_chr_bam.bed -o NAME.MAPQfiltered.bam
Cell-type specific blacklists were defined as described in details in the Supplementary Material of the related publication. The corresponding blacklist was applied for each bam file using samtools view: samtools view -b -h NAME.MAPQfiltered.bam -L blacklist_HCT116.bed -o NAME.blacklist.bam -U NAME.filtered_blacklisted.bam
Filtered_blacklisted bam files of the corresponding replicates were merged using samtools merge (version 1.9). The following processing steps were performed on both individual replicates and the merged data also.
Scaled and smoothened coverage tracks were generated using the bamCoverage tool of the deepTools package (version 3.2.1). Bin size was set to 100bp, smoothening was performed with 5000 bases (--smoothLength 5000), reads were normalized to 1x sequencing coverage (--normalizeUsing RPGC), --effectiveGenomeSize 2793842910 --extendReads
Log2 ratio of treatment and input samples were calculated using the bigwigCompare tool of the deepTools package(version 3.2.1) and the genome scaled coverage track files of the enriched and the corresponding input samples. Binsize was set to 100bp. The resulting log2.bw files are uploaded to the GEO.
In the case of the two control pull-down experiments, the genome scaled smoothed coverage tracks were calculated on the same way, then these were re-scaled according to the amount of the pulled-down DNA, and subtracted from the corresponding IP samples. Then log2 ratio tracks were calculated with the corrected IP and the corresponding input samples. For details, see the Supplementary file 3 of the corresponding publication.The resulting log2.bw files are uploaded to the GEO.
Interval files of the enriched regions were derived from the log2.bw files according to minor processing steps described in the Supplementary Material of the related publication.
Genome_build: GRCh38 (GRCh38.d1.vd1.fa from https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)
Supplementary_files_format_and_content: BigWig files containing log2 ratio coverage signal of enriched vs input samples for 100bp bins, smoothened for 5000bp. Files are provided for individual replicates of each sample, as well as for merged data.
Supplementary_files_format_and_content: BED files containing regions of uracil enrichment derived from the log2.bw files. Files are provided for individual replicates of each sample, as well as for merged data.
Supplementary_files_format_and_content: BigWig files containing log2 ratio coverage signal of enriched (that was corrected with a scaled coverage of control IP) vs input samples for 100bp bins, smoothened for 5000bp. Files are provided for replicate 2 of NT_UGI and 5FdUR_UGI samples.

source_name: HCT116 chr3+ (MMR proficient) cells

growth_protocol: HCT116 and HCT116 chr3+ cells were maintained in McCoy’s 5A and were stably transfected using retroviral transduction of EGFP-tagged UGI. Successfully transduced cells were collected by FACS sorting using a BD FACSAria III Cell sorter.

extract_protocol:
Genomic DNA was purified by Quick-DNA Miniprep Plus Kit (Zymo Research) and sonicated with a BioRuptor (Diagenode). Immunoprecipitation was carried out by FLAG-tagged sensor protein binding to uracil residues in fragmented genomic DNA and was followed by purification with anti-FLAG beads (Sigma-Aldrich). Control IP was done using anti-FLAG beads without the sensor construct.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For drug-treated samples, cells were treated with 20 µM 5-fluoro-2’-deoxyuridine (5FdUR) or 100 nM raltitrexed (RTX) for 48 hours.


title: RTX_UGI_HCT116MMR_rep2_IP

description: enriched


title: NT_UGI_HCT116MMR_rep1_IP

description: enriched


title: WT_HCT116_rep1_IP


title: RTX_UGI_HCT116MMR_rep1_son

description: input


title: RTX_UGI_HCT116MMR_rep2_son

description: input


title: NT_UGI_HCT116MMR_rep2_son

description: input


title: NT_UGI_HCT116MMR_rep1_son

description: input


title: 5FdUR_UGI_HCT116MMR_rep1_IP

description: enriched


title: RTX_UGI_HCT116MMR_rep1_IP

description: enriched


title: 5FdUR_UGI_HCT116MMR_rep2_son

description: input


title: RTX_UGI_HCT116_rep1_IP


title: RTX_UGI_HCT116_rep2_son


title: 5FdUR_UGI_HCT116_rep2_son

description:
5FdUR_UGI_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.bw
5FdUR_UGI_HCT116_merged_IP_vs_son.bin100bp.smooth5000.RPGC.log2.0p18.region.bed


title: 5FdUR_UGI_HCT116MMR_rep1_son

description: input


title: WT_HCT116_rep1_son


title: 5FdUR_UGI_HCT116MMR_rep2_IP

description: enriched


title: 5FdUR_UGI_HCT116_rep1_son


title: 5FdUR_UGI_HCT116_rep2_IP


title: 5FdUR_UGI_HCT116_rep1_IP


title: Tarca_084

status: Public on Jul 03 2020

description: From each woman, 5 ml of amniotic fluid were collected and processed according to recommended protocols (LARRABEE PB, JOHNSON KL, LAI C, et al. Global gene expression analysis of the living human fetus using cell-free messenger RNA in amniotic fluid. JAMA : the journal of the American Medical Association 2005;293:836-42).

hyb_protocol: see above

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: Microarray raw gene expression data was background corrected, quantile normalized and summarized at transcript clusters level using Robust Multi-array Average (RMA) implemented in the oligo package using probe annotation from   pd.hta.2.0_3.12.2 package of bioconductor.

source_name: Amniotic fluid

label_protocol: Ten ng of RNA was reverse-transcribed and amplified using the Affymetrix GeneChip® WT Pico Reagent Kit, following the manufacturer’s suggested protocol. Briefly, 5.5 ug sense–stranded cDNA was fragmented, labeled and hybridized in 200 ul to the Affymetrix GeneChip® Human Transcriptome Array 2.0 in an Affymetrix hybridization oven at 45°C, 60 rpm for 16 hours.

extract_protocol: Starting with 5 ml of amniotic fluid, we applied the Plasma/Serum RNA Purification Maxi Kit (# 56200) from Norgen Biotek following the manufacturer protocol, including the optional DNAse treatment. Following the RNA extraction, each sample was concentrated to a volume of 12 ul using the RNA Clean & Concentrator-5 kit (#R1015) from Zymo Research. The concentrates were then quantified by UV spectrophotometry on a DropSense (Trinean), and quality assessed on the Agilent 2200 TapeStation.

tag: group

value: TNL

tag: gestational age

tag: bmi

tag: race

value: Black

tag: fetal sex

value: Male

tag: smoking status

value: No

tag: sample collection mode

value: CSection

tag: parity

value: Parous


title: Tarca_053

value: Female


title: Tarca_008


title: Tarca_194

value: Other


title: Tarca_206


title: Tarca_193


title: Tarca_067

value: White

value: Yes


title: Tarca_013


title: Tarca_211


title: Tarca_088

value: Hispanic


title: Tarca_120

value: Nulliparous


title: Tarca_060


title: Tarca_209


title: Tarca_185


title: Tarca_089


title: Tarca_162


title: Tarca_210


title: Tarca_200


title: Tarca_163


title: Tarca_031


title: Tarca_086


title: Tarca_016


title: Tarca_012

value: Transabdominal


title: Tarca_183


title: Tarca_152


title: Tarca_050


title: Tarca_028


title: Tarca_207


title: Tarca_029


title: Tarca_077


title: Tarca_117


title: Tarca_133


title: Tarca_161


title: Tarca_151


title: Tarca_106


title: Tarca_141


title: Tarca_208


title: Tarca_065


title: Tarca_074


title: Tarca_094


title: Tarca_105


title: Tarca_007


title: Tarca_062


title: Tarca_019


title: Tarca_204


title: Tarca_095


title: Tarca_032


title: Tarca_174


title: Tarca_020


title: Tarca_055


title: Tarca_041


title: Tarca_079


title: Tarca_072


title: Tarca_096


title: Tarca_004


title: Tarca_044


title: Tarca_040


title: Tarca_144


title: Tarca_129


title: Tarca_056


title: Tarca_123


title: Tarca_103


title: Tarca_155


title: Tarca_150


title: Tarca_076


title: Tarca_172


title: Tarca_171


title: Tarca_093


title: Tarca_188

value: Midtrimester


title: Tarca_037


title: Tarca_146


title: Tarca_100


title: Tarca_009


title: Tarca_010


title: Tarca_025


title: Tarca_052


title: Tarca_124


title: Tarca_118


title: Tarca_153


title: Tarca_127


title: Tarca_002


title: Tarca_107


title: Tarca_142


title: Tarca_132


title: Tarca_181


title: P14

status: Public on Jun 04 2020

description: Sample 14

data_processing:
Paired-end RNAseq sequence data in fastq format were processed using Salmon aligner v0.12.0 in quasi-mapping mode using a transcriptome index prepared from Mus musculus genome assembly GRCm38 (mm10).
Transcripts per million (TPM) values from Salmon output were scaled up to library size and imported into R (version 3.5.2) using the tximport package of Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each sample.

source_name: Placenta

growth_protocol: Foxp3DTR mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA). Mice were bred in the animal care facility at the C.S. Mott Center for Human Growth and Development (Wayne State University, Detroit, MI, USA) and housed under a circadian cycle (light:dark=12:12 h).

extract_protocol:
Total RNA was isolated from tissues using the RNeasy mini kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. RNA concentrations and purity were assessed with the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific), and RNA integrity was evaluated with the 2100 Bioanalyzer system (Agilent Technologies, Wilmington, DE) using the Agilent RNA 6000 Nano Kit (Agilent Technologies).
The RNAseq library was prepared by the Beijing Genomics Institute (BGI; Wuhan, China) using the MGIEasy RNA Library Prep kit (MGI Americas Inc., San Jose, CA, USA). Paired-end reads of 150 bp length were sequenced on the BGISEQ-500RS sequencer (BGI), and raw data were provided by BGI.

treatment_protocol: Foxp3DTR dams were injected i.p. with 25 µg/kg of diphtheria toxin from Corynebacterium diphtheria (partial depletion of Tregs) or 50 µg/kg of diphtheria toxin (total depletion of Tregs) dissolved in 200 μL of sterile 1X PBS using a 26-gauge needle on 14.5 dpc. Controls were injected with 200 μL of sterile 1X PBS alone. After 24 h, dams were injected with 5 µg/kg of DT or 50 µg/kg of DT in 200 μL of sterile 1X PBS, or with 200 μL of sterile 1X PBS alone respectively. Four hours later, dams were euthanized and the placental tissues were collected from implantation sites and placed in RNAlater Stabilization Solution (Life Technologies).

tag: treatment

value: Total Treg-depletion (50 microg DT)

value: Placenta


title: P13

description: Sample 13


title: P15

description: Sample 15


title: Tarca_157


title: Tarca_135


title: Tarca_184


title: P12

description: Sample 12


title: Tarca_191


title: Tarca_024


title: Tarca_021


title: P10

description: Sample 10

value: Partial Treg-depletion (25 microg DT)


title: Tarca_112


title: P11

description: Sample 11


title: Tarca_173


title: P8

description: Sample 8


title: P7

description: Sample 7


title: P9

description: Sample 9


title: Tarca_115


title: P6

description: Sample 6


title: Tarca_036


title: Tarca_119


title: Tarca_130


title: P5

description: Sample 5

value: Control (PBS)


title: P3

description: Sample 3


title: P4

description: Sample 4


title: P2

description: Sample 2


title: P1

description: Sample 1


title: Sample_260

status: Public on Dec 17 2019

data_processing: Microarray raw gene expression data was background corrected, quantile normalized and summarized at transcript clusters level using Robust Multi-array Average (RMA) implemented in the oligo package using probe to transcript cluster assignments from the hta20sttranscriptcluster.db package of Bioconductor.

tag: individual

tag: gestational age (wk)


title: Sample_252


title: Sample_250


title: Sample_261


title: Sample_245


title: Sample_257


title: Sample_256


title: Sample_255


title: Sample_243


title: Sample_259


title: Sample_253


title: Sample_258


title: Sample_244


title: Sample_248


title: Sample_238


title: Sample_242


title: Sample_239


title: Sample_246


title: Sample_249


title: Sample_237


title: Sample_234


title: Sample_254


title: Sample_235


title: Sample_251


title: Sample_247


title: Sample_241


title: Sample_226


title: Sample_231


title: Sample_218


title: Sample_233


title: Sample_225


title: Sample_236


title: Sample_214


title: Sample_240


title: Sample_211


title: Sample_227


title: Sample_213


title: Sample_219


title: Sample_232


title: Sample_220


title: Sample_221


title: Sample_224


title: Sample_215


title: Sample_217


title: Sample_229


title: Sample_223


title: Sample_216


title: Sample_222


title: Sample_228


title: Sample_209


title: Sample_210


title: Sample_208


title: Sample_212


title: Sample_201


title: Sample_205


title: Sample_207


title: Sample_192


title: Sample_204


title: Sample_196


title: Sample_206


title: Sample_198


title: Sample_200


title: Sample_203


title: Sample_193


title: Sample_195


title: Sample_199


title: Sample_184


title: Sample_202


title: Sample_186


title: Sample_190


title: Sample_194


title: Sample_187


title: Sample_197


title: Sample_185


title: Sample_191


title: Sample_230


title: Sample_182


title: Sample_180


title: Sample_189


title: Sample_183


title: Sample_181


title: Tarca_098

value: Black


title: Sample_188


title: Sample_178


title: Sample_179


title: Sample_177


title: Sample_172


title: Sample_171


title: Sample_164


title: Sample_167


title: Sample_173


title: Sample_166


title: Sample_161


title: Sample_176


title: Sample_170


title: Sample_165


title: Sample_162


title: Sample_168


title: Sample_163


title: Sample_157


title: Sample_169


title: Sample_158


title: Sample_175


title: Sample_156


title: Sample_154


title: Sample_160


title: Sample_155


title: Sample_151


title: Sample_150


title: Sample_152


title: Sample_159


title: Sample_149


title: Sample_143


title: Sample_140


title: Sample_132


title: Sample_142


title: Sample_136


title: Sample_146


title: Sample_134


title: Sample_147


title: Sample_153


title: Sample_139


title: Sample_130


title: Sample_129


title: Sample_124


title: Sample_144


title: Sample_131


title: Sample_127


title: Sample_148


title: Sample_128


title: Sample_138


title: Sample_126


title: Sample_141


title: Sample_145


title: Sample_135


title: Sample_137


title: Sample_125


title: Sample_123


title: Sample_122


title: Sample_120


title: Sample_113


title: Sample_117


title: Sample_111


title: Sample_115


title: Sample_119


title: Sample_116


title: Sample_114


title: Sample_110


title: Sample_104


title: Sample_105


title: Sample_103


title: Sample_112


title: Sample_95


title: Sample_118


title: Sample_99


title: Sample_108


title: Sample_133


title: Sample_109


title: Sample_100


title: Sample_102


title: Sample_121


title: Sample_98


title: Sample_96


title: Sample_94


title: Sample_106


title: Sample_107


title: Sample_101


title: Sample_97


title: Sample_92


title: Sample_91


title: Sample_93


title: Sample_87


title: Sample_88


title: Sample_89


title: Sample_81


title: Sample_90


title: Sample_86


title: Sample_84


title: Sample_80


title: Sample_85


title: Sample_83


title: Sample_68


title: Sample_76


title: Sample_77


title: Sample_70


title: Sample_72


title: Sample_66


title: Sample_78


title: Sample_82


title: Sample_75


title: Sample_79


title: Sample_73


title: Sample_71


title: Sample_67


title: Sample_74


title: Sample_174


title: Sample_69


title: Sample_61


title: Sample_63


title: Sample_65


title: Sample_64


title: Sample_59


title: Sample_62


title: Sample_54


title: Sample_55


title: Sample_51


title: Sample_45


title: Sample_50


title: Sample_58


title: Sample_60


title: Sample_57


title: Sample_44


title: Sample_40


title: Sample_53


title: Sample_56


title: Sample_47


title: Sample_52


title: Sample_48


title: Sample_46


title: Sample_49


title: Sample_39


title: Sample_38


title: Sample_42


title: Sample_43


title: Sample_30


title: Sample_37


title: Sample_27


title: Sample_24


title: Sample_32


title: Sample_31


title: Sample_34


title: Sample_41


title: Sample_28


title: Sample_36


title: Sample_35


title: Sample_26


title: Sample_25


title: Sample_16


title: Sample_18


title: Sample_29


title: Sample_13


title: Sample_33


title: Sample_12


title: Sample_17


title: Sample_22


title: Sample_20


title: Sample_15


title: Sample_14


title: Sample_23


title: Sample_19


title: EmbMNs_E12.5-2 (Single Cell)

status: Public on Jul 24 2019

first: Kate

middle: E

last: Galloway

department: Chemical Engineering

institute: Massachusetts Institute of Technology

data_processing:
We used the cellranger count pipeline (10x Genomics) to align and quantify single cell expression for each library.
Samples were combined into a single matrix via the aggr pipeline and normalized by read depth across the libraries.
scRNAseq datasets were imported into Monocle using cellrangerRkit in R to create a cellDataSet.
Data were normalized using estimateSizeFactors. Outliers were removed based on variance using estimateDispersion to remove 108 outlier cells. Clustering was performed using 10,300 genes with high dispersion and mean gene expression >= 0.1 on the first 10 PCs. Clusters of varying number were examined and clustering via 3 primary clusters was chosen to capture different populations (e. g. MEFs, converting cells, and iMNs). Pseudotemporal ordering was performed using identified clusters. Pseudotemporal ordering was rooted in the identified iMN endpoint.
Analysis of embryonic motor neurons and induced motor neurons from various conditions was performed using Seurat 2.2. Following alignment and processing in CellRanger, variable genes were identified using FindVariableGenes. Clustering was performed using FindClusters based on the number of PCs identified through the PCElbow plot function. Cluster markers were identified for each cluster using the FindMarkers function.
Genome_build: mm10

source_name: Induced motor neurons with 6FDDRR

growth_protocol: Cells were harvested at different points in conversion. Specific populations were identified and collected via FACS and all cells were sorted to obtain viable single cell suspensions. Fast-cycling cells were identified by low CFSE intensity at 4 dpi. Hb9::GFP+ at 8 dpi and 14 dpi cells were identified relative to Hb9::GFP negative control.

extract_protocol:
RNA from lysed cells was barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared using Single Cell 3′ Library Gel Bead Kit V2 (10x Genomics, 120237).
Sequencing was performed with using multiple NextSeq 500/550 High Output Kit v2 on an Illumina NextSeq with pair end 150bp (PE150). On average, sequencing generated 100-200K reads per cell on average over the libraries.

treatment_protocol: Cell suspensions were loaded into a chip and processed with the Chromium Single Cell Controller (10x Genomics). To generate single-cell gel beads in emulsion (GEMs), individual populations were assigned individual libraries using Single Cell 3′ Library and Gel Bead Kit V2 (10x Genomics, 120237). For each population, the target population size was between 1000-1500 cells. Cell suspensions were calibrated to capture the target number of cells. Fewer cells were captured at 8 dpi due to limited Hb9::GFP+ cells in 6F condition.

tag: cell type

value: EmbMNs E12.5


title: 6FDDRR-iMN-1 (Single Cell)


title: 6FDDRR-iMN-2 (Single Cell)


title: MEFs (Single Cell)

description: MEFs

source_name: Mouse embryonic fibroblasts in N3 media at 4 dpi

value: MEFs


title: EmbMNs_E12.5-1 (Single Cell)


title: 4_A673_HCI_2509

status: Public on May 03 2019

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to GRCh38.p6 whole genome using STAR-2.5.1b using --outSAMunmapped within and otherwise default
Raw counts were generated for each sample using htseq-count with -t exon -i gene -r pos
Normalized counts were generated using default settings and blind = TRUE in the rlog package of DESeq2.
Genome_build: GRCh38.p6
Supplementary_files_format_and_content: csv, gene symbol and rlog (using DESeq2) normalized count data

source_name: A673 cells

growth_protocol: Ewing sarcoma cell lines were seeded at 20-25% confluency and left to adhere overnight. The following morning cells were treated with either DMSO or SP-2509 (2uM), and collected  48hrs post treament.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase digestion.  2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

tag: replicate

tag: sp-2509 sensitivity

value: Hypersensitive


title: 3_A673_DMSO

treatment_protocol: Ewing sarcoma cell lines were seeded at 20-25% confluency and left to adhere overnight. The following morning cells were treated with either DMSO or SP-2509 (2uM), and collected  48hrs post treament.

value: DMSO


title: Sample_8


title: Sample_10


title: Sample_6


title: Sample_5


title: 6_A673_HCI_2509


title: Sample_7


title: Sample_3


title: Sample_9


title: 8_A673_HCI_2509


title: 7_A673_DMSO


title: Sample_2


title: Sample_4


title: Sample_1


title: 5_A673_DMSO


title: Sample_9

status: Public on Feb 04 2019

source_name: Maternal Blood

value: TIL [Term in Labor (with labor)]


title: Sample_21


title: Sample_8


title: Sample_30

value: TNL [Term not in labor (without labor)]


title: Sample_32


title: Sample_5


title: Sample_6


title: Sample_27


title: Sample_20


title: Sample_7


title: Sample_26


title: Sample_3


title: Sample_4


title: Sample_19


title: Sample_23


title: Sample_14


title: Sample_36


title: Sample_22


title: Sample_21


title: Sample_34


title: Sample_25


title: Sample_31


title: Sample_24


title: Sample_18


title: Sample_37


title: Sample_38


title: Sample_29


title: Sample_15


title: Sample_28


title: Sample_7 [RNA-Seq 2]

data_processing:
Representation of gene-specific amplicons in amplified cDNA products was analyzed using a custom gene enumeration software developed at Cellecta, Inc. With this method, only reads that align to the gene specific amplicon are counted. The alignment uses only the 36 nucleotides started by forward primer position and 36 nucleotides region ended by reverse primer. Any reads from the middle portion of the amplicons are not counted. Alignment used the DriverMap Reference Database (hGWDv2) .
Supplementary_files_format_and_content: Raw count matrix in .csv format.

extract_protocol:
RNA was isolated from  PAXgene® Blood RNA collection tube (BD 762165) as described in the PAXgene® Blood miRNA Kit Handbook (December, 2015). Purified RNA was quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean) and quality assessed by microfluidics using the RNA ScreenTape on the Agilent 2200 TapeStation.
The DriverMap™ Human Genome-Wide Gene Expression Profiling Assay (hDM18Kv2) from Cellecta, Inc (Mountain View, CA) was used to measure the expression level of 18,559 protein coding genes by combining highly multiplexed RT-PCR amplification with Next-Generation Sequencing (NGS) quantitation. Sample processing was performed per manufacturer protocols available at https://www.cellecta.com/technology-portfolio/targeted-expression-profiling-driver-map-assay/. cDNA products amplified in the assay were analyzed on an Illumina NextSeq 500 sequencer using a NextSeq 500/550 High Output v2 kit (75 cycles).

value: TIL


title: Sample_6 [RNA-Seq 2]


title: Sample_3 [RNA-Seq 2]


title: Sample_9 [RNA-Seq 2]


title: Sample_4 [RNA-Seq 2]


title: Sample_37 [RNA-Seq 2]

value: TNL


title: Sample_38 [RNA-Seq 2]


title: Sample_8 [RNA-Seq 2]


title: Sample_36 [RNA-Seq 2]


title: Sample_34 [RNA-Seq 2]


title: Sample_32 [RNA-Seq 2]


title: Sample_13


title: Sample_11


title: Sample_10


title: Sample_5 [RNA-Seq 2]


title: Sample_31 [RNA-Seq 2]


title: Sample_28 [RNA-Seq 2]


title: Sample_26 [RNA-Seq 2]


title: Sample_12


title: Sample_30 [RNA-Seq 2]


title: Sample_29 [RNA-Seq 2]


title: Sample_25 [RNA-Seq 2]


title: Sample_22 [RNA-Seq 2]


title: Sample_24 [RNA-Seq 2]


title: Sample_23 [RNA-Seq 2]


title: Sample_11


title: Sample_19 [RNA-Seq 2]


title: Sample_20 [RNA-Seq 2]


title: Sample_21 [RNA-Seq 2]


title: Sample_15 [RNA-Seq 2]


title: Sample_13 [RNA-Seq 2]


title: Sample_10 [RNA-Seq 2]


title: Sample_12 [RNA-Seq 2]


title: Sample_11 [RNA-Seq 2]


title: Sample_14 [RNA-Seq 2]


title: Sample_7 [RNA-seq]

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner (version 0.9.1) in quasi-mapping-based mode using these command options: "--seqBias --gcBias --useVBOpt --vbPrior"
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package
Genome_build: Ensembl GRCh37.75 (hg19)
Supplementary_files_format_and_content: Count matrix from "scaledTPM" from tximport (v. 1.6.0) were save in .csv format

extract_protocol:
RNA was isolated from  PAXgene® Blood RNA collection tube (BD 762165) as described in the PAXgene® Blood miRNA Kit Handbook (December, 2015). Purified RNA was quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean) and quality assessed by microfluidics using the RNA ScreenTape on the Agilent 2200 TapeStation.
Starting with 500 ng of total RNA, cDNA library templates were synthesized using the Illumina TruSeq® Stranded Total RNA LT (Set A) Kit with Ribo-Zero Globin rRNA reduction, as described in the TruSeq® Stranded Total RNA Sample Preparation Guide (Rev. E, October 2013). Libraries were validated using the HS D1000 ScreenTape on the Agilent 2200 TapeStation, and quantified on the Qubit® 2.0 Fluorometer by the Qubit® dsDNA HS Assay (ThermoFisher). The Illumina HiSeq 2500 instrument was used to cluster the samples onto the flow cell.
The pools were put on at 10pM and run in rapid mode at 2×100 paired end. Illumina HiSeq Rapid PE Cluster kit V2 and HiSeq Rapid SBS kit v2 200 cycles was used.

tag: gestational age (weeks)


title: Sample_8 [RNA-seq]


title: Sample_9 [RNA-seq]


title: Sample_27 [RNA-Seq 2]


title: Sample_6 [RNA-seq]


title: Sample_5 [RNA-seq]


title: Sample_37 [RNA-seq]


title: Sample_38 [RNA-seq]


title: Sample_3 [RNA-seq]


title: Sample_18 [RNA-Seq 2]


title: Sample_36 [RNA-seq]


title: Sample_30 [RNA-seq]


title: Sample_31 [RNA-seq]


title: Sample_34 [RNA-seq]


title: Sample_32 [RNA-seq]


title: Sample_24 [RNA-seq]


title: Sample_26 [RNA-seq]


title: Sample_23 [RNA-seq]


title: Sample_21 [RNA-seq]


title: Sample_20 [RNA-seq]


title: Sample_14 [RNA-seq]


title: Sample_25 [RNA-seq]


title: Sample_15 [RNA-seq]


title: Sample_19 [RNA-seq]


title: Sample_18 [RNA-seq]


title: Sample_11 [RNA-seq]


title: Sample_13 [RNA-seq]


title: Sample_4 [RNA-seq]


title: Sample_10 [RNA-seq]


title: Sample_12 [RNA-seq]


title: Sample_29 [RNA-seq]


title: Sample_27 [RNA-seq]


title: Sample_28 [RNA-seq]


title: ctrl_36h_ns_2

status: Public on Dec 30 2018

description: adar.rawcount.txt

data_processing:
NextSeq raw data demultiplexed and converted to fastq files using the Illumina software Bcl2fastq v2.19.1
Fastq files were quality-trimmed and illumina adaptors removed using Trimmomatic v0.33
Fastq files were aligned to the mm10 genome assembly using Bowtie2 v2.2.4
Feature counts were aggregated into a single data matrix using HTSeq v0.6.1p1.
DESeq2 library size normalization by scale factor of normcounts. Differential expression performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Aggregated raw count matrix (output from HTSeq) in tab-delimited .txt file

source_name: B16 melanoma

growth_protocol: Cells were grown in DMEM supplemented with 10% heat-inactivated FBS and 2.5% Pen-Strep

extract_protocol:
Cells were trypsinized and lysed in QIAGEN RLT buffer and frozen at -80C. RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions.
Libraries were constructed using the NEB Ultra-Directional RNA kit using the ribosomal RNA depletion module, according to manufacturer's instructions.
Directional libraries were barcoded using NEB dual index barcodes and sequenced on the NextSeq (high output flowcell) by pair-end sequencing of 37bp.

treatment_protocol: Cells were treated with either 1000 U/mL IFNb, 100ng/mL IFNg, or an equivalent volume of vehicle control (PBS + 0.1% BSA) for 36 hours.

value: Control

tag: sgrna

value: Non-targeting sgRNA 5

value: Vehicle control


title: Sample_22 [RNA-seq]


title: ctrl_36h_ns_1

description: adar.rawcount.txt


title: ctrl_36h_ns_3

description: adar.rawcount.txt


title: ctrl_36h_ifnb_3

description: adar.rawcount.txt

value: IFNb


title: ctrl_36h_ifnb_2

description: adar.rawcount.txt


title: Preterm preeclampsia + HELLP syndrome placenta (3014)

description: sample was obtained from the chorionic plate

hyb_protocol: Cy3-RNAs were fragmented and hybridized on Agilent 44K Whole Human Genome Oligo Microarray Chips using Agilent Gene Expression Hybridization Kit.

scan_protocol: Images were scanned on an Agilent scanner and were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: The expression intensities were background-corrected using the minimum method in the backgroundCorrect function of the limma package available in Bioconductor. After log2 transformation, data were quantile-normalized using the preprocessCore package available in Bioconductor.

source_name: placenta

label_protocol: Total RNAs were reverse transcribed; cDNAs were transcripted into antisense cRNAs, which were labeled with One-Color Quick Amp Labeling Kit (Agilent Technologies Inc., USA) and purified with RNeasy Mini Kit (Qiagen).

growth_protocol: Human placental samples were obtained immediately after cesarean deliveries.

extract_protocol: Total RNA was isolated using RNeasy Fibrous Tissue Mini Kit (QIAGEN GmbH, Hilden, Germany), quantified with NanoDrop1000 (Thermo Scientific) and assessed by Agilent 2100 Bioanalyzer (Matriks AS, Oslo, Norway).

treatment_protocol: Villous tissues were dissected from the choriodecidua on dry ice and stored at -80C. Tissues were homogenized using a ThermoSavant FastPrep FP120 Homogenizer (Thermo Scientific, Wilmington, DE, USA) with Lysing MatrixD (MP Biomedicals, Illkirch, France).

tag: condition

tag: tissue

value: placenta

tag: gestational weeks

tag: baby gender

value: male


title: Preterm preeclampsia + HELLP syndrome placenta (3010)

value: female


title: Preterm preeclampsia + HELLP syndrome placenta (3013)


title: Preterm control placenta (kk06)

value: Preterm control placenta


title: Preterm preeclampsia + HELLP syndrome placenta (3024)


title: Preterm preeclampsia placenta (3025)

value: Preterm preeclampsia placenta


title: ctrl_36h_ifnb_1

description: adar.rawcount.txt


title: Preterm control placenta (kk04)


title: Preterm preeclampsia placenta (3019)


title: Preterm control placenta (3055)


title: adarsg1_36h_ns_3

description: adar.rawcount.txt

value: Adar KO

value: Adar sgRNA 1


title: adarsg1_36h_ns_2

description: adar.rawcount.txt


title: Preterm preeclampsia placenta (3047)


title: Preterm preeclampsia placenta (3020)


title: Preterm preeclampsia + HELLP syndrome placenta (3001)


title: adarsg1_36h_ns_1

description: adar.rawcount.txt


title: Preterm control placenta (3053)


title: Preterm preeclampsia placenta (3008)


title: Control HTR8/SVneo cells  replicate 3

description:
replicate 3
7754315051_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised and log transformed using the normaliseIllumina function from the beadarray package in Bioconductor, R.

source_name: HTR8/SVneo cells

label_protocol: DNase-treated RNA was amplified and biotin-labeled with the Illumina TotalPrep RNA Amplification Kit (Ambion-Life Technologies).

growth_protocol: HTR8/SVneo trophoblastic cells were incubated with RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidified incubator at 37C until reaching 50% confluence.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quality control was performed with Agilent Bioanalyser 2100, RNA concentrations were measured with NanoDrop1000.

treatment_protocol: Cells were treated either with 100nM ZNF554 siRNA or 100nM scrambled (control) siRNA. Cells were collected for RNA isolation and microarray after 48h.

tag: cell line

value: immortalized extravillous trophoblast cells

value: control


title: ZNF554 siRNA-treated HTR8/SVneo cells  replicate 2

description:
replicate 2
7754315051_E

value: ZNF554 siRNA


title: Preterm preeclampsia placenta (3030)


title: ZNF554 siRNA-treated HTR8/SVneo cells  replicate 1

description:
replicate 1
7754315051_D


title: ZNF554 siRNA-treated HTR8/SVneo cells  replicate 3

description:
replicate 3
7754315051_F


title: Control HTR8/SVneo cells  replicate 1

description:
replicate 1
7754315051_A


title: adarsg1_36h_ifnb_3

description: adar.rawcount.txt


title: Control HTR8/SVneo cells  replicate 2

description:
replicate 2
7754315051_B


title: adarsg1_36h_ifnb_2

description: adar.rawcount.txt


title: Preterm preeclampsia + HELLP syndrome placenta (3018)


title: Preterm control placenta (3042)


title: ZNF554 siRNA-treated BeWo cells  replicate 3

description:
replicate 3
7754315051_L

source_name: BeWo cells

growth_protocol: BeWo trophoblast-like cells were incubated with Ham's F12-K medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidified incubator at 37C until reaching 50% confluence.

value: BeWo trophoblast-like choriocarcinoma cells


title: adarsg1_36h_ifnb_1

description: adar.rawcount.txt


title: ZNF554 siRNA-treated BeWo cells  replicate 1

description:
replicate 1
7754315051_J


title: Sth1_K4me3_2_(20170801_SB_ScDm_Sth_K4m30713)

status: Public on Dec 22 2018

city: Omaha

first: Sandipan

last: Brahma

state: NE

address: 985805 Nebraska Medical Center, DRCI 6054

institute: University of Nebraska Medical Center

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H3K4me3; replicate 2

data_processing:
Genome_build: UCSC sacCer3
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC sacCer3. 2. We extracted properly paired reads from the alignments. 3. We used mapped fragments in the length range of 121-200. 4. We computed the fraction of all aligned bases at each base pair and scaled it by the size of the sacCer3 genome = 121507105 (Supplementary file .121-200.bedgraph.gz).

organism: Saccharomyces cerevisiae

source_name: Chromatin immunocleavage and release followed by ChIP

extract_protocol:
CUT&RUN.ChIP_protocol.pdf
PMID 29651053

value: yeast

tag: experiment

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); Active Motif #39159 (ChIP)


title: Sth1_K36me3_1_(20180116_SB_ScDmSp_Sth1_K36m3)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H3K36me3; replicate 1

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); Active Motif #61021 (ChIP)


title: Sth1_K36me3_2_(20170801_SB_ScDm_SthK36m30713)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H3K36me3; replicate 2


title: Sth1_K4me3_1_(20180116_SB_ScDmSp_Sth1_K4m3)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H3K4me3; replicate 1


title: Sth1_input_2_(20170801_SB_ScDm_Sth_in_0713)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC); replicate 2

source_name: Chromatin immunocleavage and release

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN)


title: Sth1_input_1_(20180116_SB_ScDmSp_Sth1_input)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC); replicate 1


title: Sth1_H2B_2_(20170801_SB_ScDm_Sth_H2B_0713)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H2B; replicate 2

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); abcam #ab4626 (ChIP)


title: Sth1_IgG_2_(20170801_SB_ScDm_Sth_IgG_0713)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope IgG as non-specific-control; replicate 2

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); Antibodies-Online #ABIN101961 (ChIP)


title: Sth1_IgG_1_(20180116_SB_ScDmSp_Sth1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope IgG as non-specific-control; replicate 1


title: Sth1_H4ac_2_(20170801_SB_ScDm_Sth_H4ac0713)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H4ac; replicate 2

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); Millipore Sigma #06-598 (ChIP)


title: Sth1_H2AZ_2_(20170801_SB_ScDm_Sth_H2AZ0713)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H2AZ; replicate 2

value: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); Active Motif #39237 (ChIP)


title: Reb1_K4me3_2_(20180301_SB_ScDmSp_Reb1_K4m3)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H3K4me3; replicate 2


title: Sth1_H2B_1_(20180116_SB_ScDmSp_Sth1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H2B; replicate 1


title: Reb1_K4me3_1_(20180116_SB_ScDmSp_Reb1_K4m3)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H3K4me3; replicate 1


title: Reb1_K36me3_2_(20180301_SB_ScDmSp_Reb1_K36m3)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H3K36me3; replicate 2


title: ZNF554 siRNA-treated BeWo cells  replicate 2

description:
replicate 2
7754315051_K


title: Reb1_K36me3_1_(20180116_SB_ScDmSp_Reb1_K36m3)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H3K36me3; replicate 1


title: Reb1_input_1_(20180116_SB_ScDmSp_Reb1_input)

description: CUT&RUN with 3x FLAG-tagged protein Reb1; replicate 1


title: Reb1_input_2_(20180301_SB_ScDmSp_Reb1_in)

description: CUT&RUN with 3x FLAG-tagged protein Reb1; replicate 2


title: Reb1_IgG_1_(20180116_SB_ScDmSp_Reb1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope IgG as non-specific-control; replicate 1


title: Sth1_H4ac_1_(20180116_SB_ScDmSp_Sth1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H4ac; replicate 1


title: Reb1_IgG_2_(20180301_SB_ScDmSp_Reb1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope IgG as non-specific-control; replicate 2


title: Reb1_H2B_2_(20180301_SB_ScDmSp_Reb1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H2B; replicate 2


title: Reb1_H4ac_2_(20180301_SB_ScDmSp_Reb1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H4ac; replicate 2


title: Reb1_H4ac_1_(20180116_SB_ScDmSp_Reb1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H4ac; replicate 1


title: Reb1_H2AZ_2_(20180301_SB_ScDmSp_Reb1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H2AZ; replicate 2


title: Reb1_H2B_1_(20180116_SB_ScDmSp_Reb1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H2B; replicate 1


title: Htz1_K4me3_1_(20180301_SB_ScDmSp_Htz1K4m3_2)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H3K4me3; replicate 1


title: Control BeWo cells replicate 1

description:
replicate 1
7754315051_G


title: Control BeWo cells  replicate 2

description:
replicate 2
7754315051_H


title: Sth1_H2AZ_1_(20180116_SB_ScDmSp_Sth1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H2AZ; replicate 1


title: Htz1_K36me3_1_(20180301_SB_ScDmSp_Htz1_K36m3)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H3K36me3; replicate 1


title: Htz1_input_2_(20180116_SB_ScDmSp_Htz1_input)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ; replicate 2


title: Htz1_IgG_2_(20180116_SB_ScDmSp_Htz1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope IgG as non-specific-control; replicate 2


title: Htz1_H4ac_2_(20180116_SB_ScDmSp_Htz1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H4ac; replicate 2


title: Htz1_K36me3_2_(20170807_SB_ScDm_HtzK36m30713)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H3K36me3; replicate 2


title: Htz1_input_1_(20180301_SB_ScDmSp_Htz1_in)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ; replicate 1


title: Htz1_IgG_1_(20180301_SB_ScDmSp_Htz1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope IgG as non-specific-control; replicate 1


title: Htz1_H4ac_1_(20180301_SB_ScDmSp_Htz1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H4ac; replicate 1


title: Htb_K4me3_1_(20170807_SB_ScDm_Htb_K4m30713)

description: CUT&RUN with 3x FLAG-tagged protein H2B followed by ChIP with epitope H3K4me3; replicate 1


title: Htz1_H2B_1_(20180301_SB_ScDmSp_Htz1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H2B; replicate 1


title: Htb_K36me3_1_(20170807_SB_ScDm_HtbK36m30713)

description: CUT&RUN with 3x FLAG-tagged protein H2B followed by ChIP with epitope H3K36me3; replicate 1


title: Htz1_H2AZ_2_(20180116_SB_ScDmSp_Htz1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H2AZ; replicate 2


title: Htz1_H2B_2_(20180116_SB_ScDmSp_Htz1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H2B; replicate 2


title: Htz1_K4me3_2_(20170807_SB_ScDm_HtzK4m30713)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H3K4me3; replicate 2


title: Htb_input_1_(20170807_SB_ScDm_Htb_in_0713)

description: CUT&RUN with 3x FLAG-tagged protein H2B; replicate 1


title: Control BeWo cells  replicate 3

description:
replicate 3
7754315051_I


title: Htb_IgG_1_(20170807_SB_ScDm_Htb_IgG_0713)

description: CUT&RUN with 3x FLAG-tagged protein H2B followed by ChIP with epitope IgG as non-specific-control; replicate 1


title: Htz1_H2AZ_1_(20180301_SB_ScDmSp_Htz1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein H2AZ followed by ChIP with epitope H2AZ; replicate 1


title: Htb_H2B_1_(20170807_SB_ScDm_Htb_H2B_0713)

description: CUT&RUN with 3x FLAG-tagged protein H2B followed by ChIP with epitope H2B; replicate 1


title: Reb1_H2AZ_1_(20180116_SB_ScDmSp_Reb1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein Reb1 followed by ChIP with epitope H2AZ; replicate 1


title: Htb_H4ac_1_(20170807_SB_ScDm_Htb_H4ac0713)

description: CUT&RUN with 3x FLAG-tagged protein H2B followed by ChIP with epitope H4ac; replicate 1


title: Abf1_K36me3_2_(20180301_SB_ScDmSp_Abf1_K36m3)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H3K36me3; replicate 2


title: Abf1_K4me3_1_(20180116_SB_ScDmSp_Abf1_K4m3)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H3K4me3; replicate 1


title: Abf1_K36me3_1_(20180116_SB_ScDmSp_Abf1_K36m3)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H3K36me3; replicate 1


title: Abf1_input_2_(20180301_SB_ScDmSp_Abf1_in)

description: CUT&RUN with 3x FLAG-tagged protein Abf1; replicate 2


title: Abf1_H4ac_2_(20180301_SB_ScDmSp_Abf1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H4ac; replicate 2


title: Abf1_IgG_1_(20180116_SB_ScDmSp_Abf1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope IgG as non-specific-control; replicate 1


title: Htb_H2AZ_1_(20170807_SB_ScDm_Htb_H2AZ0713)

description: CUT&RUN with 3x FLAG-tagged protein H2B followed by ChIP with epitope H2AZ; replicate 1


title: Abf1_input_1_(20180116_SB_ScDmSp_Abf1_input)

description: CUT&RUN with 3x FLAG-tagged protein Abf1; replicate 1


title: Abf1_H2B_2_(20180301_SB_ScDmSp_Abf1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H2B; replicate 2


title: Abf1_H2B_1_(20180116_SB_ScDmSp_Abf1_H2B)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H2B; replicate 1


title: Abf1_H2AZ_1_(20180116_SB_ScDmSp_Abf1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H2AZ; replicate 1


title: Abf1_H4ac_1_(20180116_SB_ScDmSp_Abf1_H4ac)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H4ac; replicate 1


title: Abf1_H2AZ_2_(20180301_SB_ScDmSp_Abf1_H2AZ)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H2AZ; replicate 2


title: iEF-5

status: Public on Oct 22 2017

first: Kirsten

last: Johnson

state: Ohio

address: The Research Institute, WA5110, 700 Childrens Drive

department: Childhood Cancer and Blood Disorders

institute: Nationwide Childrens Hospital

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to hg19 whole genome using STAR-2.5.2b using --outSAMunmapped within and otherwise default parameters
Raw counts were generated for each sample using htseq-count with -m intersection-strict -s no -r pos
Normalized counts were generated using default settings  and blind = FALSE in the rlog package of DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: csv, Ensembl Gene Accession and normalized count data

source_name: iEF

extract_protocol:
Cells were trypsinized, counted, and 5 million cells were washed with PBS, pelleted, and flash-frozen. RNA was extracted using an Rneasy kit with on-column DNA digestion per kit instructions (Qiagen). 2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

value: A673 cells

tag: RNAi

value: EWS/FLI

tag: rescue

value: empty

tag: batch


title: iLuc-3

source_name: iLuc

value: Luciferase


title: iLuc-2


title: iLuc-5


title: iEF-3


title: iEF-1


title: iLuc-1


title: MelJuSo_Ptpn2_NS_rep1

status: Public on Jul 31 2017

data_processing:
NextSeq raw data demultiplexed and converted to fastq files using the Illumina software Bcl2fastq v2.17.1.14.
Fastq files were quality-trimmed and illumina adaptors removed using Trimmomatic v0.33
Fastq files were aligned to the relevant genome assembly (mm10 for mouse, hg19 for human) using Bowtie2 v2.2.4.
Feature counts were aggregated into a single data matrix using HTSeq v0.6.1p1.
DESeq2 library size normalization by scale factor of normcounts. Differential expression performed using DESeq2.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Aggregated raw count matrix (output from HTSeq) in tab-delimited .txt file

extract_protocol:
Cells were trypsinized and lysed in QIAGEN RLT buffer and frozen at -80C. RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions.
Libraries were constructed using the NEB Ultra-Directional RNA kit using the mRNA capture module, according to manufacturer's instructions.
Directional libraries were barcoded using NEB dual index barcodes and sequenced on the NextSeq (high output flowcell) by pair-end sequencing of 37bp.

treatment_protocol: Cells were treated with either 1000 U/mL IFNb, 100ng/mL IFNg, 10ng/mL TNFa, alone or in combination, or an equivalent volume of vehicle control (PBS + 0.1% BSA) for 48 hours.

value: MelJuSo

value: melanoma

tag: genotype/variation

tag: infected with lentivirus containing sgrna against

tag: treated with

value: NS


title: MelJuSo_Ptpn2_NS_rep3

tag: cell type


title: iEF-2


title: MelJuSo_Ptpn2_IFNg_rep3

value: IFNg


title: Abf1_K4me3_2_(20180301_SB_ScDmSp_Abf1_K4m3)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope H3K4me3; replicate 2


title: MelJuSo_Ptpn2_IFNg_rep2


title: MelJuSo_Ptpn2_IFNg_rep1


title: MelJuSo_Ctrl_NS_rep3

value: Control

value: non-targeting sequence Bro4


title: MelJuSo_Ctrl_NS_rep1


title: Abf1_IgG_2_(20180301_SB_ScDmSp_Abf1_IgG)

description: CUT&RUN with 3x FLAG-tagged protein Abf1 followed by ChIP with epitope IgG as non-specific-control; replicate 2

value: yeast


title: MelJuSo_Ctrl_NS_rep2


title: MelJuSo_Ctrl_IFNg_rep2


title: MelJuSo_Ctrl_IFNg_rep3


title: HT29_Ptpn2_NS_rep2

value: colon cancer


title: HT29_Ptpn2_IFNg_rep2


title: HT29_Ptpn2_NS_rep1


title: HT29_Ctrl_NS_rep2


title: HT29_Ptpn2_IFNg_rep1


title: HT29_Ctrl_IFNg_rep1

value: lung cancer cells


title: HT29_Ctrl_NS_rep1


title: MelJuSo_Ptpn2_NS_rep2


title: A549_Ptpn2_NS_rep2


title: A549_Ctrl_IFNg_rep2


title: A549_Ptpn2_NS_rep1


title: A549_Ptpn2_IFNg_rep1


title: A549_Ctrl_NS_rep1


title: A375_Ptpn2_NS_rep2


title: A549_Ctrl_IFNg_rep1


title: A375_Ptpn2_IFNg_rep3


title: A549_Ptpn2_IFNg_rep2


title: A375_Ptpn2_NS_rep3


title: A549_Ctrl_NS_rep2


title: A375_Ptpn2_IFNg_rep2


title: A375_Ptpn2_NS_rep1


title: A375_Ctrl_NS_rep3


title: A375_Ptpn2_IFNg_rep1


title: A375_Ctrl_IFNg_rep2


title: A375_Ctrl_IFNg_rep1


title: A375_Ctrl_IFNg_rep3


title: Ptpn2sg3_IFNbTNFa_rep3

value: IFNbTNFa


title: Ptpn2sg3_IFNbTNFa_rep2


title: Ptpn2sg3_IFNbTNFa_rep1


title: A375_Ctrl_NS_rep2


title: Ptpn2sg3_IFNg_rep3


title: HT29_Ctrl_IFNg_rep2


title: Bro3_IFNg_rep2

value: non-targeting sequence Bro3


title: Bro3_IFNg_rep1


title: Ptpn2sg3_NS_rep3


title: Ptpn2sg3_NS_rep1


title: Bro3_NS_rep2


title: Ptpn2sg3_NS_rep2


title: Bro3_IFNgTNFa_rep3

value: IFNgTNFa


title: Bro3_NS_rep1


title: Bro3_IFNgTNFa_rep1


title: Bro3_IFNgTNFa_rep2


title: MelJuSo_Ctrl_IFNg_rep1


title: Bro3_NS_rep3


title: Bro3_IFNbIFNg_rep3

value: IFNbIFNg


title: Ptpn2sg3_IFNgTNFa_rep2


title: Ptpn2sg3_IFNbIFNg_rep3


title: Ptpn2sg3_IFNg_rep1


title: Ptpn2sg3_IFNgTNFa_rep1


title: Ptpn2sg3_IFNbIFNg_rep1


title: Bro3_IFNg_rep3


title: Ptpn2sg3_TNFa_rep3

value: TNFa


title: Bro3_TNFa_rep1


title: Bro3_IFNbIFNg_rep2


title: Bro3_TNFa_rep2


title: Ptpn2sg3_TNFa_rep1


title: Bro3_IFNb_rep3

value: IFNb


title: Bro3_TNFa_rep3


title: Bro3_IFNbIFNg_rep1


title: Ptpn2sg3_IFNg_rep2


title: Bro3_IFNb_rep2


title: Ptpn2sg3_IFNgTNFa_rep3


title: Ptpn2sg3_TNFa_rep2


title: Bro3_IFNb_rep1


title: Ptpn2sg3_IFNb_rep2


title: Bro3_IFNbTNFa_rep3


title: Ptpn2sg3_IFNb_rep3


title: Ptpn2sg3_IFNb_rep1


title: Bro3_IFNbTNFa_rep1


title: Ptpn2sg3_IFNbIFNg_rep2


title: Bro3_IFNbTNFa_rep2


title: Subject_1_LABOR_Visceral [gene-level]

status: Public on Dec 31 2015

hyb_protocol: Standard Affymetrix Exon Array hyb protocol.

scan_protocol: Standard Affymetrix Exon Array scan protocol.

data_processing:
Probe intensities were summarized and processed with RMA implemented in arroma.affymetrix package in R-3.2.2. For transcript level summaries ExonRmaPlm function from arroma.affymetrix was used (option mergeGroups=TRUE), while for probeset (exon) level summaries the option mergeGroups=FALSE was used.
probe group file: HuEx-1_0-st-v2.na30.hg19.probeset.csv
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.transcript.csv
Log2 transformed probeset (exon) and transcript (group) level expression summaries for core transcripts based on NetAffx Nov. 12, 2007 (R3) (HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) .

label_protocol: Standard Affymetrix Exon Array labeling protocol.

growth_protocol: Paired visceral and subcutaneous adipose tissue samples were obtained after an eight-hour fast. Subcutaneous adipose tissue samples were collected at the site of a transverse lower abdominal incision, in the middle of the Pfannenstiel incision, from the deeper strata of subcutaneous fat. Visceral samples were obtained from the most distal portion of the greater omentum.(Visceral and subcutaneous adipose tissues were collected using Metzenbaum scissors and measured approximately 1.0 cm3. Tissues were snap-frozen in liquid nitrogen, and were kept at –80°C until use.

extract_protocol: Total RNA was isolated from snap-frozen adipose tissue samples using TRI Reagent® (Ambion®, Life Technologies Corporation, Austin, TX, USA) combined with the Qiagen RNeasy Lipid Tissue Kit protocol (Qiagen, Valencia, CA, USA), according to the manufacturers’ recommendations. The RNA concentrations and the A260 nm/A280 nm ratios were assessed using a NanoDrop® 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA integrity numbers were determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: No treatments were involved.

tag: subject id

value: Subject 1

tag: subject status

value: labor

value: adipose

tag: region

value: Visceral


title: Subject_18_NOLABOR_Visceral [gene-level]

source_name: no labor_Visceral

value: Subject 18

value: no labor


title: Subject_32_NOLABOR_Subcutaneous [gene-level]

source_name: no labor_Subcutaneous

value: Subject 32

value: Subcutaneous


title: Subject_30_NOLABOR_Subcutaneous [gene-level]

value: Subject 30


title: Subject_26_LABOR_Subcutaneous [gene-level]

value: Subject 26


title: Subject_22_NOLABOR_Visceral [gene-level]

value: Subject 22


title: Subject_31_NONPREGNANT_Subcutaneous [gene-level]

source_name: non pregnant_Subcutaneous

value: Subject 31

value: non pregnant


title: Subject_5_NOLABOR_Subcutaneous [gene-level]

value: Subject 5


title: Subject_13_NOLABOR_Visceral [gene-level]

value: Subject 13


title: Subject_9_NOLABOR_Subcutaneous [gene-level]

value: Subject 9


title: Subject_50_NOLABOR_Subcutaneous [gene-level]

value: Subject 50


title: Subject_25_LABOR_Visceral [gene-level]

value: Subject 25


title: Subject_48_NOLABOR_Visceral [gene-level]

value: Subject 48


title: Subject_35_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 35

value: adipose


title: Subject_2_LABOR_Visceral [gene-level]

value: Subject 2

value: labor

value: Visceral


title: Subject_51_LABOR_Subcutaneous [gene-level]

value: Subject 51

value: Subcutaneous


title: Subject_42_LABOR_Visceral [gene-level]

value: Subject 42


title: Subject_16_NOLABOR_Visceral [gene-level]

value: Subject 16

value: no labor


title: Subject_36_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 36

value: non pregnant


title: Subject_17_NOLABOR_Visceral [gene-level]

value: Subject 17


title: Subject_28_NOLABOR_Subcutaneous [gene-level]

value: Subject 28


title: Subject_13_NOLABOR_Subcutaneous [gene-level]

value: Subject 13


title: Subject_38_NONPREGNANT_Visceral [gene-level]

source_name: non pregnant_Visceral

value: Subject 38


title: Subject_21_NOLABOR_Visceral [gene-level]

value: Subject 21


title: Subject_44_NOLABOR_Subcutaneous [gene-level]

value: Subject 44


title: Subject_4_LABOR_Subcutaneous [gene-level]

value: Subject 4

value: adipose


title: Subject_3_LABOR_Subcutaneous [gene-level]

value: Subject 3

value: labor


title: Subject_2_LABOR_Subcutaneous [gene-level]

value: Subject 2


title: Subject_21_NOLABOR_Subcutaneous [gene-level]

value: Subcutaneous


title: Subject_18_NOLABOR_Subcutaneous [gene-level]

value: Subject 18


title: Subject_35_NONPREGNANT_Visceral [gene-level]

value: Subject 35

value: Visceral


title: Subject_44_NOLABOR_Visceral [gene-level]

value: no labor


title: Subject_49_LABOR_Subcutaneous [gene-level]

value: Subject 49


title: Subject_6_LABOR_Subcutaneous [gene-level]

value: Subject 6


title: Subject_7_NOLABOR_Subcutaneous [gene-level]

value: Subject 7


title: Subject_41_NONPREGNANT_Visceral [gene-level]

value: Subject 41

value: non pregnant


title: Subject_12_NOLABOR_Visceral [gene-level]

value: Subject 12


title: Subject_19_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 19


title: Subject_22_NOLABOR_Subcutaneous [gene-level]

value: Subject 22


title: Subject_34_NOLABOR_Subcutaneous [gene-level]

value: Subject 34

value: adipose


title: Subject_40_NONPREGNANT_Visceral [gene-level]

value: Subject 40


title: Subject_24_NOLABOR_Visceral [gene-level]

value: Subject 24


title: Subject_39_NONPREGNANT_Visceral [gene-level]

value: Subject 39