title: Sperm DNA from 11152

source_name: Semen Sample 11152


title: Sperm DNA from 11154

status: Public on Nov 01 2021

type: genomic

city: Provo

first: Tim

last: Jenkins

state: UT

address: 4005 Life Sciences Building

country: USA

institute: Brigham Young University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina's EPIC array using standard Illumina protocol

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

data_processing:
R (both Base R and the minfi software package in R)
Average Beta

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Semen Sample 11154

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from sperm samples following somatic cell lysis using Qiagen DNeasy Kit with sperm specific modifications

tag: treatment category

value: Placebo Arm

tag: age

tag: tissue

value: Somatic cell lysed sperm sample


title: Sperm DNA from 11151

source_name: Semen Sample 11151


title: Sperm DNA from 11149

source_name: Semen Sample 11149

value: Folic Acid


title: Sperm DNA from 11150

source_name: Semen Sample 11150


title: Sperm DNA from 11147

source_name: Semen Sample 11147


title: Sperm DNA from 11174

source_name: Semen Sample 11174


title: Sperm DNA from 11146

source_name: Semen Sample 11146


title: Sperm DNA from 11144

source_name: Semen Sample 11144


title: Sperm DNA from 11141

source_name: Semen Sample 11141


title: Sperm DNA from 11140

source_name: Semen Sample 11140


title: Sperm DNA from 11145

source_name: Semen Sample 11145


title: Sperm DNA from 11173

source_name: Semen Sample 11173


title: Sperm DNA from 11136

source_name: Semen Sample 11136


title: Sperm DNA from 11131

source_name: Semen Sample 11131


title: Sperm DNA from 11132

source_name: Semen Sample 11132


title: Sperm DNA from 11165

source_name: Semen Sample 11165


title: Sperm DNA from 11130

source_name: Semen Sample 11130


title: Sperm DNA from 11159

source_name: Semen Sample 11159


title: Sperm DNA from 11129

source_name: Semen Sample 11129


title: Sperm DNA from 11128

source_name: Semen Sample 11128


title: Sperm DNA from 11143

source_name: Semen Sample 11143


title: Sperm DNA from 11123

source_name: Semen Sample 11123


title: Sperm DNA from 11124

source_name: Semen Sample 11124


title: Sperm DNA from 11121

source_name: Semen Sample 11121


title: Sperm DNA from 11120

source_name: Semen Sample 11120


title: Sperm DNA from 11122

source_name: Semen Sample 11122


title: Sperm DNA from 11119

source_name: Semen Sample 11119


title: Sperm DNA from 11118

source_name: Semen Sample 11118


title: Sperm DNA from 11111

source_name: Semen Sample 11111


title: Sperm DNA from 11109

source_name: Semen Sample 11109


title: Sperm DNA from 11139

source_name: Semen Sample 11139


title: Sperm DNA from 11133

source_name: Semen Sample 11133


title: Sperm DNA from 11135

source_name: Semen Sample 11135


title: Sperm DNA from 11110

source_name: Semen Sample 11110


title: Sperm DNA from 11098

source_name: Semen Sample 11098


title: Sperm DNA from 11101

source_name: Semen Sample 11101


title: Sperm DNA from 11106

source_name: Semen Sample 11106


title: Sperm DNA from 11095

source_name: Semen Sample 11095


title: Sperm DNA from 11102

source_name: Semen Sample 11102


title: Sperm DNA from 11096

source_name: Semen Sample 11096


title: Sperm DNA from 11090

source_name: Semen Sample 11090


title: Sperm DNA from 11089

source_name: Semen Sample 11089


title: Sperm DNA from 11093

source_name: Semen Sample 11093


title: Sperm DNA from 11088

source_name: Semen Sample 11088


title: Sperm DNA from 11083

source_name: Semen Sample 11083


title: Sperm DNA from 11084

source_name: Semen Sample 11084


title: Sperm DNA from 11127

source_name: Semen Sample 11127


title: Sperm DNA from 11086

source_name: Semen Sample 11086


title: Sperm DNA from 11082

source_name: Semen Sample 11082


title: Sperm DNA from 11087

source_name: Semen Sample 11087


title: Sperm DNA from 11081

source_name: Semen Sample 11081


title: Sperm DNA from 11080

source_name: Semen Sample 11080


title: Sperm DNA from 11072

source_name: Semen Sample 11072


title: Sperm DNA from 11079

source_name: Semen Sample 11079


title: Sperm DNA from 11069

source_name: Semen Sample 11069


title: Sperm DNA from 11066

source_name: Semen Sample 11066


title: Sperm DNA from 11065

source_name: Semen Sample 11065


title: Sperm DNA from 11060

source_name: Semen Sample 11060


title: Sperm DNA from 11058

source_name: Semen Sample 11058


title: Sperm DNA from 11061

source_name: Semen Sample 11061


title: Sperm DNA from 11056

source_name: Semen Sample 11056


title: Sperm DNA from 11054

source_name: Semen Sample 11054


title: Sperm DNA from 11050

source_name: Semen Sample 11050


title: Sperm DNA from 11053

source_name: Semen Sample 11053


title: Sperm DNA from 11040

source_name: Semen Sample 11040


title: Sperm DNA from 11042

source_name: Semen Sample 11042


title: Sperm DNA from 11043

source_name: Semen Sample 11043


title: Sperm DNA from 11044

source_name: Semen Sample 11044


title: Sperm DNA from 11039

source_name: Semen Sample 11039


title: Sperm DNA from 11037

source_name: Semen Sample 11037


title: Sperm DNA from 11033

source_name: Semen Sample 11033


title: Sperm DNA from 11032

source_name: Semen Sample 11032


title: Sperm DNA from 11030

source_name: Semen Sample 11030


title: Sperm DNA from 11029

source_name: Semen Sample 11029


title: Sperm DNA from 11026

source_name: Semen Sample 11026


title: Sperm DNA from 11024

source_name: Semen Sample 11024


title: Sperm DNA from 11068

source_name: Semen Sample 11068


title: Sperm DNA from 11022

source_name: Semen Sample 11022


title: Sperm DNA from 11019

source_name: Semen Sample 11019


title: Sperm DNA from 11063

source_name: Semen Sample 11063


title: Sperm DNA from 11031

source_name: Semen Sample 11031


title: Sperm DNA from 11018

source_name: Semen Sample 11018


title: Sperm DNA from 11062

source_name: Semen Sample 11062


title: Sperm DNA from 11016

source_name: Semen Sample 11016


title: Sperm DNA from 11015

source_name: Semen Sample 11015


title: Sperm DNA from 11055

source_name: Semen Sample 11055


title: Sperm DNA from 11014

source_name: Semen Sample 11014


title: Sperm DNA from 11013

source_name: Semen Sample 11013


title: Sperm DNA from 11049

source_name: Semen Sample 11049


title: Sperm DNA from 11012

source_name: Semen Sample 11012


title: Sperm DNA from 11010

source_name: Semen Sample 11010


title: Sperm DNA from 11006

source_name: Semen Sample 11006


title: Sperm DNA from 11011

source_name: Semen Sample 11011


title: Sperm DNA from 11005

source_name: Semen Sample 11005


title: Sperm DNA from 10997

source_name: Semen Sample 10997


title: Sperm DNA from 11000

source_name: Semen Sample 11000


title: Sperm DNA from 10990

source_name: Semen Sample 10990


title: Sperm DNA from 10987

source_name: Semen Sample 10987


title: Sperm DNA from 10986

source_name: Semen Sample 10986


title: Sperm DNA from 10984

source_name: Semen Sample 10984


title: Sperm DNA from 11023

source_name: Semen Sample 11023


title: Sperm DNA from 10991

source_name: Semen Sample 10991


title: Sperm DNA from 10982

source_name: Semen Sample 10982


title: Sperm DNA from 10981

source_name: Semen Sample 10981


title: Sperm DNA from 10972

source_name: Semen Sample 10972


title: Sperm DNA from 10971

source_name: Semen Sample 10971


title: Sperm DNA from 10980

source_name: Semen Sample 10980


title: Sperm DNA from 10979

source_name: Semen Sample 10979


title: Sperm DNA from 10976

source_name: Semen Sample 10976


title: Sperm DNA from 10978

source_name: Semen Sample 10978


title: Sperm DNA from 10970

source_name: Semen Sample 10970


title: Sperm DNA from 10977

source_name: Semen Sample 10977


title: Sperm DNA from 10967

source_name: Semen Sample 10967


title: Sperm DNA from 10964

source_name: Semen Sample 10964


title: Sperm DNA from 10956

source_name: Semen Sample 10956


title: Sperm DNA from 10950

source_name: Semen Sample 10950


title: Sperm DNA from 10948

source_name: Semen Sample 10948


title: Sperm DNA from 11004

source_name: Semen Sample 11004


title: Sperm DNA from 10952

source_name: Semen Sample 10952


title: Sperm DNA from 10945

source_name: Semen Sample 10945


title: Sperm DNA from 10947

source_name: Semen Sample 10947


title: Sperm DNA from 10943

source_name: Semen Sample 10943


title: Sperm DNA from 10944

source_name: Semen Sample 10944


title: Sperm DNA from 10957

source_name: Semen Sample 10957


title: Sperm DNA from 10994

source_name: Semen Sample 10994


title: Sperm DNA from 10941

source_name: Semen Sample 10941


title: Sperm DNA from 10936

source_name: Semen Sample 10936


title: Sperm DNA from 10929

source_name: Semen Sample 10929


title: Sperm DNA from 10930

source_name: Semen Sample 10930


title: Sperm DNA from 10933

source_name: Semen Sample 10933


title: Sperm DNA from 10927

source_name: Semen Sample 10927


title: Sperm DNA from 10935

source_name: Semen Sample 10935


title: Sperm DNA from 10926

source_name: Semen Sample 10926


title: Sperm DNA from 10924

source_name: Semen Sample 10924


title: Sperm DNA from 10922

source_name: Semen Sample 10922


title: Sperm DNA from 10919

source_name: Semen Sample 10919


title: Sperm DNA from 10918

source_name: Semen Sample 10918


title: Sperm DNA from 10920

source_name: Semen Sample 10920


title: Sperm DNA from 10951

source_name: Semen Sample 10951


title: Sperm DNA from 10916

source_name: Semen Sample 10916


title: Sperm DNA from 10913

source_name: Semen Sample 10913


title: Sperm DNA from 10910

source_name: Semen Sample 10910


title: Sperm DNA from 10901

source_name: Semen Sample 10901


title: Sperm DNA from 10902

source_name: Semen Sample 10902


title: Sperm DNA from 10906

source_name: Semen Sample 10906


title: Sperm DNA from 10900

source_name: Semen Sample 10900


title: Sperm DNA from 10899

source_name: Semen Sample 10899


title: Sperm DNA from 10897

source_name: Semen Sample 10897


title: Sperm DNA from 10894

source_name: Semen Sample 10894


title: Sperm DNA from 10891

source_name: Semen Sample 10891


title: Sperm DNA from 10893

source_name: Semen Sample 10893


title: Sperm DNA from 10888

source_name: Semen Sample 10888


title: Sperm DNA from 10885

source_name: Semen Sample 10885


title: Sperm DNA from 10884

source_name: Semen Sample 10884


title: Sperm DNA from 10882

source_name: Semen Sample 10882


title: Sperm DNA from 10878

source_name: Semen Sample 10878


title: Sperm DNA from 10875

source_name: Semen Sample 10875


title: Sperm DNA from 10879

source_name: Semen Sample 10879


title: Sperm DNA from 10883

source_name: Semen Sample 10883


title: Sperm DNA from 10874

source_name: Semen Sample 10874


title: Sperm DNA from 10870

source_name: Semen Sample 10870


title: Sperm DNA from 10861

source_name: Semen Sample 10861


title: Sperm DNA from 10859

source_name: Semen Sample 10859


title: Sperm DNA from 10857

source_name: Semen Sample 10857


title: Sperm DNA from 10864

source_name: Semen Sample 10864


title: Sperm DNA from 10858

source_name: Semen Sample 10858


title: Sperm DNA from 10854

source_name: Semen Sample 10854


title: Sperm DNA from 10852

source_name: Semen Sample 10852


title: Sperm DNA from 10856

source_name: Semen Sample 10856


title: Sperm DNA from 10866

source_name: Semen Sample 10866


title: Sperm DNA from 10842

source_name: Semen Sample 10842


title: Sperm DNA from 10889

source_name: Semen Sample 10889


title: Sperm DNA from 10851

source_name: Semen Sample 10851


title: Sperm DNA from 10840

source_name: Semen Sample 10840


title: Sperm DNA from 10833

source_name: Semen Sample 10833


title: Sperm DNA from 10835

source_name: Semen Sample 10835


title: Sperm DNA from 10836

source_name: Semen Sample 10836


title: Sperm DNA from 10892

source_name: Semen Sample 10892


title: Sperm DNA from 10853

source_name: Semen Sample 10853


title: Sperm DNA from 10832

source_name: Semen Sample 10832


title: Sperm DNA from 10872

source_name: Semen Sample 10872


title: Sperm DNA from 10873

source_name: Semen Sample 10873


title: Sperm DNA from 10830

source_name: Semen Sample 10830


title: Sperm DNA from 10829

source_name: Semen Sample 10829


title: Sperm DNA from 10824

source_name: Semen Sample 10824


title: Sperm DNA from 10827

source_name: Semen Sample 10827


title: Sperm DNA from 10869

source_name: Semen Sample 10869


title: Sperm DNA from 10819

source_name: Semen Sample 10819


title: Sperm DNA from 10823

source_name: Semen Sample 10823


title: Sperm DNA from 10818

source_name: Semen Sample 10818


title: Sperm DNA from 10816

source_name: Semen Sample 10816


title: Sperm DNA from 10817

source_name: Semen Sample 10817


title: Sperm DNA from 10814

source_name: Semen Sample 10814


title: Sperm DNA from 10811

source_name: Semen Sample 10811


title: Sperm DNA from 10839

source_name: Semen Sample 10839


title: Sperm DNA from 10808

source_name: Semen Sample 10808


title: Sperm DNA from 10805

source_name: Semen Sample 10805


title: Sperm DNA from 10804

source_name: Semen Sample 10804


title: Sperm DNA from 10799

source_name: Semen Sample 10799


title: Sperm DNA from 10803

source_name: Semen Sample 10803


title: Sperm DNA from 10792

source_name: Semen Sample 10792


title: Sperm DNA from 10798

source_name: Semen Sample 10798


title: Sperm DNA from 10791

source_name: Semen Sample 10791


title: Sperm DNA from 10783

source_name: Semen Sample 10783


title: Sperm DNA from 10787

source_name: Semen Sample 10787


title: Sperm DNA from 10788

source_name: Semen Sample 10788


title: Sperm DNA from 10782

source_name: Semen Sample 10782


title: Sperm DNA from 10786

source_name: Semen Sample 10786


title: Sperm DNA from 10789

source_name: Semen Sample 10789


title: Sperm DNA from 10781

source_name: Semen Sample 10781


title: Sperm DNA from 10775

source_name: Semen Sample 10775


title: Sperm DNA from 10779

source_name: Semen Sample 10779


title: Sperm DNA from 10774

source_name: Semen Sample 10774


title: Sperm DNA from 10780

source_name: Semen Sample 10780


title: Sperm DNA from 10767

source_name: Semen Sample 10767


title: Sperm DNA from 10772

source_name: Semen Sample 10772


title: Sperm DNA from 10771

source_name: Semen Sample 10771


title: Sperm DNA from 10768

source_name: Semen Sample 10768


title: Sperm DNA from 10766

source_name: Semen Sample 10766


title: Sperm DNA from 10764

source_name: Semen Sample 10764


title: Sperm DNA from 10765

source_name: Semen Sample 10765


title: Sperm DNA from 10759

source_name: Semen Sample 10759


title: Sperm DNA from 10756

source_name: Semen Sample 10756


title: Sperm DNA from 10752

source_name: Semen Sample 10752


title: Sperm DNA from 10763

source_name: Semen Sample 10763


title: Sperm DNA from 10748

source_name: Semen Sample 10748


title: Sperm DNA from 10762

source_name: Semen Sample 10762


title: Sperm DNA from 10737

source_name: Semen Sample 10737


title: Sperm DNA from 10739

source_name: Semen Sample 10739


title: Sperm DNA from 10749

source_name: Semen Sample 10749


title: Sperm DNA from 10727

source_name: Semen Sample 10727


title: Sperm DNA from 10740

source_name: Semen Sample 10740


title: Sperm DNA from 10730

source_name: Semen Sample 10730


title: Sperm DNA from 10745

source_name: Semen Sample 10745


title: Sperm DNA from 10734

source_name: Semen Sample 10734


title: Sperm DNA from 10777

source_name: Semen Sample 10777


title: Sperm DNA from 10728

source_name: Semen Sample 10728


title: Sperm DNA from 10773

source_name: Semen Sample 10773


title: Sperm DNA from 10732

source_name: Semen Sample 10732


title: Sperm DNA from 10725

source_name: Semen Sample 10725


title: Sperm DNA from 10726

source_name: Semen Sample 10726


title: Sperm DNA from 10723

source_name: Semen Sample 10723


title: Sperm DNA from 10721

source_name: Semen Sample 10721


title: Sperm DNA from 10714

source_name: Semen Sample 10714


title: Sperm DNA from 10720

source_name: Semen Sample 10720


title: Sperm DNA from 10713

source_name: Semen Sample 10713


title: Sperm DNA from 10722

source_name: Semen Sample 10722


title: Sperm DNA from 10715

source_name: Semen Sample 10715


title: Sperm DNA from 10710

source_name: Semen Sample 10710


title: Sperm DNA from 10701

source_name: Semen Sample 10701


title: Sperm DNA from 10698

source_name: Semen Sample 10698


title: Sperm DNA from 10704

source_name: Semen Sample 10704


title: Sperm DNA from 10691

source_name: Semen Sample 10691


title: Sperm DNA from 10705

source_name: Semen Sample 10705


title: Sperm DNA from 10692

source_name: Semen Sample 10692


title: Sperm DNA from 10686

source_name: Semen Sample 10686


title: Sperm DNA from 10689

source_name: Semen Sample 10689


title: Sperm DNA from 10709

source_name: Semen Sample 10709


title: Sperm DNA from 10693

source_name: Semen Sample 10693


title: Sperm DNA from 10702

source_name: Semen Sample 10702


title: Sperm DNA from 10681

source_name: Semen Sample 10681


title: Sperm DNA from 10682

source_name: Semen Sample 10682


title: Sperm DNA from 10703

source_name: Semen Sample 10703


title: Sperm DNA from 10674

source_name: Semen Sample 10674


title: Sperm DNA from 10678

source_name: Semen Sample 10678


title: Sperm DNA from 10677

source_name: Semen Sample 10677


title: Sperm DNA from 10684

source_name: Semen Sample 10684


title: Sperm DNA from 10673

source_name: Semen Sample 10673


title: Sperm DNA from 10672

source_name: Semen Sample 10672


title: Sperm DNA from 10695

source_name: Semen Sample 10695


title: Sperm DNA from 10671

source_name: Semen Sample 10671


title: Sperm DNA from 10663

source_name: Semen Sample 10663


title: Sperm DNA from 10668

source_name: Semen Sample 10668


title: Sperm DNA from 10662

source_name: Semen Sample 10662


title: Sperm DNA from 10661

source_name: Semen Sample 10661


title: Sperm DNA from 10660

source_name: Semen Sample 10660


title: Sperm DNA from 10712

source_name: Semen Sample 10712


title: Sperm DNA from 10664

source_name: Semen Sample 10664


title: Sperm DNA from 10654

source_name: Semen Sample 10654


title: Sperm DNA from 10657

source_name: Semen Sample 10657


title: Sperm DNA from 10653

source_name: Semen Sample 10653


title: Sperm DNA from 10656

source_name: Semen Sample 10656


title: Sperm DNA from 10647

source_name: Semen Sample 10647


title: Sperm DNA from 10648

source_name: Semen Sample 10648


title: Sperm DNA from 10646

source_name: Semen Sample 10646


title: Sperm DNA from 10650

source_name: Semen Sample 10650


title: Sperm DNA from 10639

source_name: Semen Sample 10639


title: Sperm DNA from 10627

source_name: Semen Sample 10627


title: Sperm DNA from 10643

source_name: Semen Sample 10643


title: Sperm DNA from 10626

source_name: Semen Sample 10626


title: Sperm DNA from 10645

source_name: Semen Sample 10645


title: Sperm DNA from 10633

source_name: Semen Sample 10633


title: Sperm DNA from 10637

source_name: Semen Sample 10637


title: Sperm DNA from 10623

source_name: Semen Sample 10623


title: Sperm DNA from 10629

source_name: Semen Sample 10629


title: Sperm DNA from 10667

source_name: Semen Sample 10667


title: Sperm DNA from 10632

source_name: Semen Sample 10632


title: Sperm DNA from 10621

source_name: Semen Sample 10621


title: Sperm DNA from 10625

source_name: Semen Sample 10625


title: Sperm DNA from 10618

source_name: Semen Sample 10618


title: Sperm DNA from 10614

source_name: Semen Sample 10614


title: Sperm DNA from 10612

source_name: Semen Sample 10612


title: Sperm DNA from 10616

source_name: Semen Sample 10616


title: Sperm DNA from 10619

source_name: Semen Sample 10619


title: Sperm DNA from 10613

source_name: Semen Sample 10613


title: Sperm DNA from 10610

source_name: Semen Sample 10610


title: Sperm DNA from 10652

source_name: Semen Sample 10652


title: Sperm DNA from 10603

source_name: Semen Sample 10603


title: Sperm DNA from 10602

source_name: Semen Sample 10602


title: Sperm DNA from 10635

source_name: Semen Sample 10635


title: Sperm DNA from 10601

source_name: Semen Sample 10601


title: Sperm DNA from 10596

source_name: Semen Sample 10596


title: Sperm DNA from 10600

source_name: Semen Sample 10600


title: Sperm DNA from 10594

source_name: Semen Sample 10594


title: Sperm DNA from 10592

source_name: Semen Sample 10592


title: Sperm DNA from 10588

source_name: Semen Sample 10588


title: Sperm DNA from 10578

source_name: Semen Sample 10578


title: Sperm DNA from 10580

source_name: Semen Sample 10580


title: Sperm DNA from 10577

source_name: Semen Sample 10577


title: Sperm DNA from 10570

source_name: Semen Sample 10570


title: Sperm DNA from 10599

source_name: Semen Sample 10599


title: Sperm DNA from 10573

source_name: Semen Sample 10573


title: Sperm DNA from 10566

source_name: Semen Sample 10566


title: Sperm DNA from 10574

source_name: Semen Sample 10574


title: Sperm DNA from 10565

source_name: Semen Sample 10565


title: Sperm DNA from 10563

source_name: Semen Sample 10563


title: Sperm DNA from 10562

source_name: Semen Sample 10562


title: Sperm DNA from 10560

source_name: Semen Sample 10560


title: Sperm DNA from 10609

source_name: Semen Sample 10609


title: Sperm DNA from 10556

source_name: Semen Sample 10556


title: Sperm DNA from 10558

source_name: Semen Sample 10558


title: Sperm DNA from 10555

source_name: Semen Sample 10555


title: Sperm DNA from 10548

source_name: Semen Sample 10548


title: Sperm DNA from 10546

source_name: Semen Sample 10546


title: Sperm DNA from 10549

source_name: Semen Sample 10549


title: Sperm DNA from 10544

source_name: Semen Sample 10544


title: Sperm DNA from 10586

source_name: Semen Sample 10586


title: Sperm DNA from 10545

source_name: Semen Sample 10545


title: Sperm DNA from 10587

source_name: Semen Sample 10587


title: Sperm DNA from 10541

source_name: Semen Sample 10541


title: Sperm DNA from 10533

source_name: Semen Sample 10533


title: Sperm DNA from 10595

source_name: Semen Sample 10595


title: Sperm DNA from 10572

source_name: Semen Sample 10572


title: Sperm DNA from 10529

source_name: Semen Sample 10529


title: Sperm DNA from 10528

source_name: Semen Sample 10528


title: Sperm DNA from 10526

source_name: Semen Sample 10526


title: Sperm DNA from 10568

source_name: Semen Sample 10568


title: Sperm DNA from 10518

source_name: Semen Sample 10518


title: Sperm DNA from 10515

source_name: Semen Sample 10515


title: Sperm DNA from 10514

source_name: Semen Sample 10514


title: Sperm DNA from 10524

source_name: Semen Sample 10524


title: Sperm DNA from 10512

source_name: Semen Sample 10512


title: Sperm DNA from 10511

source_name: Semen Sample 10511


title: Sperm DNA from 10519

source_name: Semen Sample 10519


title: Sperm DNA from 10535

source_name: Semen Sample 10535


title: Sperm DNA from 10510

source_name: Semen Sample 10510


title: Sperm DNA from 10551

source_name: Semen Sample 10551


title: Sperm DNA from 10521

source_name: Semen Sample 10521


title: Sperm DNA from 10509

source_name: Semen Sample 10509


title: Sperm DNA from 10507

source_name: Semen Sample 10507


title: Sperm DNA from 10502

source_name: Semen Sample 10502


title: Sperm DNA from 10505

source_name: Semen Sample 10505


title: Sperm DNA from 10504

source_name: Semen Sample 10504


title: Sperm DNA from 10532

source_name: Semen Sample 10532


title: Sperm DNA from 10500

source_name: Semen Sample 10500


title: Sperm DNA from 10497

source_name: Semen Sample 10497


title: Sperm DNA from 10503

source_name: Semen Sample 10503


title: Sperm DNA from 10499

source_name: Semen Sample 10499


title: Sperm DNA from 10525

source_name: Semen Sample 10525


title: Sperm DNA from 10496

source_name: Semen Sample 10496


title: Sperm DNA from 10501

source_name: Semen Sample 10501


title: Sperm DNA from 10493

source_name: Semen Sample 10493


title: Sperm DNA from 10491

source_name: Semen Sample 10491


title: Sperm DNA from 10487

source_name: Semen Sample 10487


title: Sperm DNA from 10486

source_name: Semen Sample 10486


title: Sperm DNA from 10513

source_name: Semen Sample 10513


title: Sperm DNA from 10495

source_name: Semen Sample 10495


title: Sperm DNA from 10485

source_name: Semen Sample 10485


title: Sperm DNA from 10481

source_name: Semen Sample 10481


title: Sperm DNA from 10483

source_name: Semen Sample 10483


title: Sperm DNA from 10480

source_name: Semen Sample 10480


title: Sperm DNA from 10482

source_name: Semen Sample 10482


title: Sperm DNA from 10477

source_name: Semen Sample 10477


title: Sperm DNA from 10478

source_name: Semen Sample 10478


title: Sperm DNA from 10475

source_name: Semen Sample 10475


title: Sperm DNA from 10469

source_name: Semen Sample 10469


title: Sperm DNA from 10471

source_name: Semen Sample 10471


title: Sperm DNA from 10468

source_name: Semen Sample 10468


title: Sperm DNA from 10467

source_name: Semen Sample 10467


title: Sperm DNA from 10463

source_name: Semen Sample 10463


title: Sperm DNA from 10451

source_name: Semen Sample 10451


title: Sperm DNA from 10453

source_name: Semen Sample 10453


title: Sperm DNA from 10449

source_name: Semen Sample 10449


title: Sperm DNA from 10452

source_name: Semen Sample 10452


title: Sperm DNA from 10455

source_name: Semen Sample 10455


title: Sperm DNA from 10450

source_name: Semen Sample 10450


title: Sperm DNA from 10458

source_name: Semen Sample 10458


title: Sperm DNA from 10479

source_name: Semen Sample 10479


title: Sperm DNA from 10441

source_name: Semen Sample 10441


title: Sperm DNA from 10442

source_name: Semen Sample 10442


title: Sperm DNA from 10446

source_name: Semen Sample 10446


title: Sperm DNA from 10476

source_name: Semen Sample 10476


title: Sperm DNA from 10444

source_name: Semen Sample 10444


title: Sperm DNA from 10432

source_name: Semen Sample 10432


title: Sperm DNA from 10437

source_name: Semen Sample 10437


title: Sperm DNA from 10434

source_name: Semen Sample 10434


title: Sperm DNA from 10439

source_name: Semen Sample 10439


title: Sperm DNA from 10447

source_name: Semen Sample 10447


title: Sperm DNA from 10426

source_name: Semen Sample 10426


title: Sperm DNA from 10429

source_name: Semen Sample 10429


title: Sperm DNA from 10424

source_name: Semen Sample 10424


title: Sperm DNA from 10423

source_name: Semen Sample 10423


title: Sperm DNA from 10420

source_name: Semen Sample 10420


title: Sperm DNA from 10461

source_name: Semen Sample 10461


title: Sperm DNA from 10418

source_name: Semen Sample 10418


title: Sperm DNA from 10417

source_name: Semen Sample 10417


title: Sperm DNA from 10416

source_name: Semen Sample 10416


title: Sperm DNA from 10415

source_name: Semen Sample 10415


title: Sperm DNA from 10454

source_name: Semen Sample 10454


title: Sperm DNA from 10409

source_name: Semen Sample 10409


title: Sperm DNA from 10407

source_name: Semen Sample 10407


title: Sperm DNA from 10406

source_name: Semen Sample 10406


title: Sperm DNA from 10405

source_name: Semen Sample 10405


title: Sperm DNA from 10431

source_name: Semen Sample 10431


title: Sperm DNA from 10404

source_name: Semen Sample 10404


title: Sperm DNA from 10410

source_name: Semen Sample 10410


title: Sperm DNA from 10430

source_name: Semen Sample 10430


title: Sperm DNA from 10401

source_name: Semen Sample 10401


title: Sperm DNA from 10399

source_name: Semen Sample 10399


title: Sperm DNA from 10398

source_name: Semen Sample 10398


title: Sperm DNA from 10396

source_name: Semen Sample 10396


title: Sperm DNA from 10397

source_name: Semen Sample 10397


title: Sperm DNA from 10400

source_name: Semen Sample 10400


title: Sperm DNA from 10394

source_name: Semen Sample 10394


title: Sperm DNA from 10386

source_name: Semen Sample 10386


title: Sperm DNA from 10388

source_name: Semen Sample 10388


title: Sperm DNA from 10385

source_name: Semen Sample 10385


title: Sperm DNA from 10393

source_name: Semen Sample 10393


title: Sperm DNA from 10390

source_name: Semen Sample 10390


title: Sperm DNA from 10384

source_name: Semen Sample 10384


title: Sperm DNA from 10381

source_name: Semen Sample 10381


title: Sperm DNA from 10382

source_name: Semen Sample 10382


title: Sperm DNA from 10380

source_name: Semen Sample 10380


title: Sperm DNA from 10378

source_name: Semen Sample 10378


title: Sperm DNA from 10411

source_name: Semen Sample 10411


title: Sperm DNA from 10376

source_name: Semen Sample 10376


title: Sperm DNA from 10375

source_name: Semen Sample 10375


title: Sperm DNA from 10374

source_name: Semen Sample 10374


title: Sperm DNA from 10373

source_name: Semen Sample 10373


title: Sperm DNA from 10369

source_name: Semen Sample 10369


title: Sperm DNA from 10371

source_name: Semen Sample 10371


title: Sperm DNA from 10368

source_name: Semen Sample 10368


title: Sperm DNA from 10367

source_name: Semen Sample 10367


title: Sperm DNA from 10365

source_name: Semen Sample 10365


title: Sperm DNA from 10362

source_name: Semen Sample 10362


title: Sperm DNA from 10389

source_name: Semen Sample 10389


title: Sperm DNA from 10361

source_name: Semen Sample 10361


title: Sperm DNA from 10357

source_name: Semen Sample 10357


title: Sperm DNA from 10359

source_name: Semen Sample 10359


title: Sperm DNA from 10355

source_name: Semen Sample 10355


title: Sperm DNA from 10356

source_name: Semen Sample 10356


title: Sperm DNA from 10353

source_name: Semen Sample 10353


title: Sperm DNA from 10354

source_name: Semen Sample 10354


title: Sperm DNA from 10350

source_name: Semen Sample 10350


title: Sperm DNA from 10348

source_name: Semen Sample 10348


title: Sperm DNA from 10351

source_name: Semen Sample 10351


title: Sperm DNA from 10347

source_name: Semen Sample 10347


title: Sperm DNA from 10345

source_name: Semen Sample 10345


title: Sperm DNA from 10346

source_name: Semen Sample 10346


title: Sperm DNA from 10343

source_name: Semen Sample 10343


title: Sperm DNA from 10334

source_name: Semen Sample 10334


title: Sperm DNA from 10341

source_name: Semen Sample 10341


title: Sperm DNA from 10342

source_name: Semen Sample 10342


title: Sperm DNA from 10332

source_name: Semen Sample 10332


title: Sperm DNA from 10331

source_name: Semen Sample 10331


title: Sperm DNA from 10336

source_name: Semen Sample 10336


title: Sperm DNA from 10363

source_name: Semen Sample 10363


title: Sperm DNA from 10325

source_name: Semen Sample 10325


title: Sperm DNA from 10324

source_name: Semen Sample 10324


title: Sperm DNA from 10327

source_name: Semen Sample 10327


title: Sperm DNA from 10322

source_name: Semen Sample 10322


title: Sperm DNA from 10321

source_name: Semen Sample 10321


title: Sperm DNA from 10330

source_name: Semen Sample 10330


title: Sperm DNA from 10320

source_name: Semen Sample 10320


title: Sperm DNA from 10319

source_name: Semen Sample 10319


title: Sperm DNA from 10316

source_name: Semen Sample 10316


title: Sperm DNA from 10317

source_name: Semen Sample 10317


title: Sperm DNA from 10311

source_name: Semen Sample 10311


title: Sperm DNA from 10307

source_name: Semen Sample 10307


title: Sperm DNA from 10305

source_name: Semen Sample 10305


title: Sperm DNA from 10306

source_name: Semen Sample 10306


title: Sperm DNA from 10333

source_name: Semen Sample 10333


title: Sperm DNA from 10300

source_name: Semen Sample 10300


title: Sperm DNA from 10303

source_name: Semen Sample 10303


title: Sperm DNA from 10295

source_name: Semen Sample 10295


title: Sperm DNA from 10297

source_name: Semen Sample 10297


title: Sperm DNA from 10293

source_name: Semen Sample 10293


title: Sperm DNA from 10292

source_name: Semen Sample 10292


title: Sperm DNA from 10290

source_name: Semen Sample 10290


title: Sperm DNA from 10288

source_name: Semen Sample 10288


title: Sperm DNA from 10287

source_name: Semen Sample 10287


title: Sperm DNA from 10284

source_name: Semen Sample 10284


title: Sperm DNA from 10283

source_name: Semen Sample 10283


title: Sperm DNA from 10279

source_name: Semen Sample 10279


title: Sperm DNA from 10281

source_name: Semen Sample 10281


title: Sperm DNA from 10315

source_name: Semen Sample 10315


title: Sperm DNA from 10276

source_name: Semen Sample 10276


title: Sperm DNA from 10278

source_name: Semen Sample 10278


title: Sperm DNA from 10273

source_name: Semen Sample 10273


title: Sperm DNA from 10271

source_name: Semen Sample 10271


title: Sperm DNA from 10274

source_name: Semen Sample 10274


title: Sperm DNA from 10314

source_name: Semen Sample 10314


title: Sperm DNA from 10270

source_name: Semen Sample 10270


title: Sperm DNA from 10272

source_name: Semen Sample 10272


title: Sperm DNA from 10304

source_name: Semen Sample 10304


title: Sperm DNA from 10309

source_name: Semen Sample 10309


title: Sperm DNA from 10266

source_name: Semen Sample 10266


title: Sperm DNA from 10265

source_name: Semen Sample 10265


title: Sperm DNA from 10269

source_name: Semen Sample 10269


title: Sperm DNA from 10264

source_name: Semen Sample 10264


title: Sperm DNA from 10261

source_name: Semen Sample 10261


title: Sperm DNA from 10291

source_name: Semen Sample 10291


title: Sperm DNA from 10259

source_name: Semen Sample 10259


title: Sperm DNA from 10262

source_name: Semen Sample 10262


title: Sperm DNA from 10257

source_name: Semen Sample 10257


title: Sperm DNA from 10258

source_name: Semen Sample 10258


title: Sperm DNA from 10255

source_name: Semen Sample 10255


title: Sperm DNA from 10253

source_name: Semen Sample 10253


title: Sperm DNA from 10256

source_name: Semen Sample 10256


title: Sperm DNA from 10251

source_name: Semen Sample 10251


title: Sperm DNA from 10247

source_name: Semen Sample 10247


title: Sperm DNA from 10250

source_name: Semen Sample 10250


title: Sperm DNA from 10248

source_name: Semen Sample 10248


title: Sperm DNA from 10249

source_name: Semen Sample 10249


title: Sperm DNA from 10244

source_name: Semen Sample 10244


title: Sperm DNA from 10241

source_name: Semen Sample 10241


title: Sperm DNA from 10240

source_name: Semen Sample 10240


title: Sperm DNA from 10242

source_name: Semen Sample 10242


title: Sperm DNA from 10237

source_name: Semen Sample 10237


title: Sperm DNA from 10238

source_name: Semen Sample 10238


title: Sperm DNA from 10243

source_name: Semen Sample 10243


title: Sperm DNA from 10236

source_name: Semen Sample 10236


title: Sperm DNA from 10233

source_name: Semen Sample 10233


title: Sperm DNA from 10232

source_name: Semen Sample 10232


title: Sperm DNA from 10230

source_name: Semen Sample 10230


title: Sperm DNA from 10228

source_name: Semen Sample 10228


title: Sperm DNA from 10263

source_name: Semen Sample 10263


title: Sperm DNA from 10223

source_name: Semen Sample 10223


title: Sperm DNA from 10226

source_name: Semen Sample 10226


title: Sperm DNA from 10229

source_name: Semen Sample 10229


title: Sperm DNA from 10220

source_name: Semen Sample 10220


title: Sperm DNA from 10219

source_name: Semen Sample 10219


title: Sperm DNA from 10225

source_name: Semen Sample 10225


title: Sperm DNA from 10217

source_name: Semen Sample 10217


title: Sperm DNA from 10218

source_name: Semen Sample 10218


title: Sperm DNA from 10222

source_name: Semen Sample 10222


title: Sperm DNA from 10215

source_name: Semen Sample 10215


title: Sperm DNA from 10212

source_name: Semen Sample 10212


title: Sperm DNA from 10211

source_name: Semen Sample 10211


title: Sperm DNA from 10239

source_name: Semen Sample 10239


title: Sperm DNA from 10209

source_name: Semen Sample 10209


title: Sperm DNA from 10201

source_name: Semen Sample 10201


title: Sperm DNA from 10202

source_name: Semen Sample 10202


title: Sperm DNA from 10208

source_name: Semen Sample 10208


title: Sperm DNA from 10207

source_name: Semen Sample 10207


title: Sperm DNA from 10200

source_name: Semen Sample 10200


title: Sperm DNA from 10199

source_name: Semen Sample 10199


title: Sperm DNA from 10196

source_name: Semen Sample 10196


title: Sperm DNA from 10227

source_name: Semen Sample 10227


title: Sperm DNA from 10190

source_name: Semen Sample 10190


title: Sperm DNA from 10188

source_name: Semen Sample 10188


title: Sperm DNA from 10185

source_name: Semen Sample 10185


title: Sperm DNA from 10182

source_name: Semen Sample 10182


title: Sperm DNA from 10181

source_name: Semen Sample 10181


title: Sperm DNA from 10205

source_name: Semen Sample 10205


title: Sperm DNA from 10180

source_name: Semen Sample 10180


title: Sperm DNA from 10178

source_name: Semen Sample 10178


title: Sperm DNA from 10172

source_name: Semen Sample 10172


title: Sperm DNA from 10171

source_name: Semen Sample 10171


title: Sperm DNA from 10169

source_name: Semen Sample 10169


title: Sperm DNA from 10175

source_name: Semen Sample 10175


title: Sperm DNA from 10194

source_name: Semen Sample 10194


title: Sperm DNA from 10191

source_name: Semen Sample 10191


title: Sperm DNA from 10184

source_name: Semen Sample 10184


title: Sperm DNA from 10168

source_name: Semen Sample 10168


title: Sperm DNA from 10170

source_name: Semen Sample 10170


title: Sperm DNA from 10166

source_name: Semen Sample 10166


title: Sperm DNA from 10165

source_name: Semen Sample 10165


title: Sperm DNA from 10164

source_name: Semen Sample 10164


title: Sperm DNA from 10158

source_name: Semen Sample 10158


title: Sperm DNA from 10161

source_name: Semen Sample 10161


title: Sperm DNA from 10163

source_name: Semen Sample 10163


title: Sperm DNA from 10152

source_name: Semen Sample 10152


title: Sperm DNA from 10157

source_name: Semen Sample 10157


title: Sperm DNA from 10154

source_name: Semen Sample 10154


title: Sperm DNA from 10153

source_name: Semen Sample 10153


title: Sperm DNA from 10150

source_name: Semen Sample 10150


title: Sperm DNA from 10206

source_name: Semen Sample 10206


title: Sperm DNA from 10151

source_name: Semen Sample 10151


title: Sperm DNA from 10186

source_name: Semen Sample 10186


title: Sperm DNA from 10149

source_name: Semen Sample 10149


title: Sperm DNA from 10148

source_name: Semen Sample 10148


title: Sperm DNA from 10146

source_name: Semen Sample 10146


title: Sperm DNA from 10145

source_name: Semen Sample 10145


title: Sperm DNA from 10138

source_name: Semen Sample 10138


title: Sperm DNA from 10141

source_name: Semen Sample 10141


title: Sperm DNA from 10136

source_name: Semen Sample 10136


title: Sperm DNA from 10142

source_name: Semen Sample 10142


title: Sperm DNA from 10144

source_name: Semen Sample 10144


title: Sperm DNA from 10134

source_name: Semen Sample 10134


title: Sperm DNA from 10131

source_name: Semen Sample 10131


title: Sperm DNA from 10133

source_name: Semen Sample 10133


title: Sperm DNA from 10124

source_name: Semen Sample 10124


title: Sperm DNA from 10125

source_name: Semen Sample 10125


title: Sperm DNA from 10129

source_name: Semen Sample 10129


title: Sperm DNA from 10119

source_name: Semen Sample 10119


title: Sperm DNA from 10115

source_name: Semen Sample 10115


title: Sperm DNA from 10117

source_name: Semen Sample 10117


title: Sperm DNA from 10127

source_name: Semen Sample 10127


title: Sperm DNA from 10118

source_name: Semen Sample 10118


title: Sperm DNA from 10113

source_name: Semen Sample 10113


title: Sperm DNA from 10121

source_name: Semen Sample 10121


title: Sperm DNA from 10123

source_name: Semen Sample 10123


title: Sperm DNA from 10112

source_name: Semen Sample 10112


title: Sperm DNA from 10109

source_name: Semen Sample 10109


title: Sperm DNA from 10110

source_name: Semen Sample 10110


title: Sperm DNA from 10147

source_name: Semen Sample 10147


title: Sperm DNA from 10106

source_name: Semen Sample 10106


title: Sperm DNA from 10108

source_name: Semen Sample 10108


title: Sperm DNA from 10105

source_name: Semen Sample 10105


title: Sperm DNA from 10137

source_name: Semen Sample 10137


title: Sperm DNA from 10103

source_name: Semen Sample 10103


title: Sperm DNA from 10104

source_name: Semen Sample 10104


title: Sperm DNA from 10097

source_name: Semen Sample 10097


title: Sperm DNA from 10100

source_name: Semen Sample 10100


title: Sperm DNA from 10099

source_name: Semen Sample 10099


title: Sperm DNA from 10128

source_name: Semen Sample 10128


title: Sperm DNA from 10093

source_name: Semen Sample 10093


title: Sperm DNA from 10095

source_name: Semen Sample 10095


title: Sperm DNA from 10092

source_name: Semen Sample 10092


title: Sperm DNA from 10096

source_name: Semen Sample 10096


title: Sperm DNA from 10091

source_name: Semen Sample 10091


title: Sperm DNA from 10089

source_name: Semen Sample 10089


title: Sperm DNA from 10088

source_name: Semen Sample 10088


title: Sperm DNA from 10086

source_name: Semen Sample 10086


title: Sperm DNA from 10083

source_name: Semen Sample 10083


title: Sperm DNA from 10080

source_name: Semen Sample 10080


title: Sperm DNA from 10079

source_name: Semen Sample 10079


title: Sperm DNA from 10078

source_name: Semen Sample 10078


title: Sperm DNA from 10077

source_name: Semen Sample 10077


title: Sperm DNA from 10074

source_name: Semen Sample 10074


title: Sperm DNA from 10075

source_name: Semen Sample 10075


title: Sperm DNA from 10073

source_name: Semen Sample 10073


title: Sperm DNA from 10071

source_name: Semen Sample 10071


title: Sperm DNA from 10068

source_name: Semen Sample 10068


title: Sperm DNA from 10067

source_name: Semen Sample 10067


title: Sperm DNA from 10065

source_name: Semen Sample 10065


title: Sperm DNA from 10063

source_name: Semen Sample 10063


title: Sperm DNA from 10087

source_name: Semen Sample 10087


title: Sperm DNA from 10055

source_name: Semen Sample 10055


title: Sperm DNA from 10052

source_name: Semen Sample 10052


title: Sperm DNA from 10059

source_name: Semen Sample 10059


title: Sperm DNA from 10053

source_name: Semen Sample 10053


title: Sperm DNA from 10050

source_name: Semen Sample 10050


title: Sperm DNA from 10082

source_name: Semen Sample 10082


title: Sperm DNA from 10051

source_name: Semen Sample 10051


title: Sperm DNA from 10076

source_name: Semen Sample 10076


title: Sperm DNA from 10046

source_name: Semen Sample 10046


title: Sperm DNA from 10069

source_name: Semen Sample 10069


title: Sperm DNA from 10048

source_name: Semen Sample 10048


title: Sperm DNA from 10038

source_name: Semen Sample 10038


title: Sperm DNA from 10037

source_name: Semen Sample 10037


title: Sperm DNA from 10035

source_name: Semen Sample 10035


title: Sperm DNA from 10033

source_name: Semen Sample 10033


title: Sperm DNA from 10047

source_name: Semen Sample 10047


title: Sperm DNA from 10061

source_name: Semen Sample 10061


title: Sperm DNA from 10045

source_name: Semen Sample 10045


title: Sperm DNA from 10030

source_name: Semen Sample 10030


title: Sperm DNA from 10031

source_name: Semen Sample 10031


title: Sperm DNA from 10028

source_name: Semen Sample 10028


title: Sperm DNA from 10057

source_name: Semen Sample 10057


title: Sperm DNA from 10024

source_name: Semen Sample 10024


title: Sperm DNA from 10020

source_name: Semen Sample 10020


title: Sperm DNA from 10034

source_name: Semen Sample 10034


title: Sperm DNA from 10017

source_name: Semen Sample 10017


title: Sperm DNA from 10014

source_name: Semen Sample 10014


title: Sperm DNA from 10049

source_name: Semen Sample 10049


title: Sperm DNA from 10013

source_name: Semen Sample 10013


title: Sperm DNA from 10012

source_name: Semen Sample 10012


title: Sperm DNA from 10010

source_name: Semen Sample 10010


title: Sperm DNA from 10011

source_name: Semen Sample 10011


title: Sperm DNA from 10008

source_name: Semen Sample 10008


title: Sperm DNA from 10007

source_name: Semen Sample 10007


title: Sperm DNA from 10043

source_name: Semen Sample 10043


title: Sperm DNA from 10009

source_name: Semen Sample 10009


title: Sperm DNA from 10006

source_name: Semen Sample 10006


title: Sperm DNA from 10003

source_name: Semen Sample 10003


title: Sperm DNA from 10041

source_name: Semen Sample 10041


title: Sperm DNA from 10002

source_name: Semen Sample 10002


title: Gard-2_rep5

type: SRA

city: St. Louis

first: Nicole

last: Gilbert

state: MO

address: 425 S Euclid Ave

institute: Washington University School of Medicine

description:
Gard_2.txt
Raw_geneCPM_matrix.txt

library_source: transcriptomic

data_processing:
Illumina HiSeq 2500 reads demultiplexed using a custom demultiplexing script written in Python and then aligned to the Ensembl GRCm38.76 (Mus musculus) assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction, known junction saturation and read distribution over known gene models with RSeQC version 2.3.
All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM-normalized to adjust for differences in library size.
Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: bladder

extract_protocol:
Bladders were removed, flash frozen in liquid nitrogen, RNA was extracted using RNeasy Plus Mini kit (Qiagen). ds-cDNA was prepared from 10ng total RNA using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder

tag: strain

tag: genotype

value: wild type

tag: bladder exposure

value: G. vaginalis

tag: group


title: Gard-2_rep3

description:
Gard_2.txt
Raw_geneCPM_matrix.txt


title: Sperm DNA from 10005

source_name: Semen Sample 10005


title: PBS-2_rep5

description:
PBS_2.txt
Raw_geneCPM_matrix.txt

value: PBS


title: Gard-2_rep1

description:
Gard_2.txt
Raw_geneCPM_matrix.txt


title: Gard-2_rep2

description:
Gard_2.txt
Raw_geneCPM_matrix.txt


title: PBS-2_rep2

description:
PBS_2.txt
Raw_geneCPM_matrix.txt


title: PBS-2_rep3

description:
PBS_2.txt
Raw_geneCPM_matrix.txt


title: PBS-2_rep1

description:
PBS_2.txt
Raw_geneCPM_matrix.txt


title: Gard-1_rep4

description:
Gard_1.txt
Raw_geneCPM_matrix.txt


title: PBS-2_rep4

description:
PBS_2.txt
Raw_geneCPM_matrix.txt


title: Gard-1_rep5

description:
Gard_1.txt
Raw_geneCPM_matrix.txt


title: Gard-1_rep3

description:
Gard_1.txt
Raw_geneCPM_matrix.txt


title: PBS-1_rep1

description:
PBS_1.txt
Raw_geneCPM_matrix.txt


title: Gard-1_rep2

description:
Gard_1.txt
Raw_geneCPM_matrix.txt


title: Gard-1_rep1

description:
Gard_1.txt
Raw_geneCPM_matrix.txt


title: PBS-1_rep3

description:
PBS_1.txt
Raw_geneCPM_matrix.txt


title: PBS-1_rep2

description:
PBS_1.txt
Raw_geneCPM_matrix.txt


title: PBS-1_rep5

description:
PBS_1.txt
Raw_geneCPM_matrix.txt


title: LLC1_cell_line

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.7.0f).
Mapped reads were counted by FeatureCounts (version 1.6.4 ).
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: cell line

extract_protocol:
Total RNA was isolated from tumor tissues using TRIzol (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and RNeasy spin columns (Qiagen, Venlo, The Netherlands) according to the manufacturer's protocols.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep kit (Sample 1-20) or  NEBNext Ultra II RNA Library Prep Kit for Illumina (Sample 21-32) according to the manufacturer's protocols.

tag: treatment

value: CpG

tag: agent


title: LLC1_untreated_day_21_1

source_name: tumor tissue

value: untreated

tag: time point


title: LLC1_untreated_day_21_3


title: Gard-2_rep4

description:
Gard_2.txt
Raw_geneCPM_matrix.txt


title: ASB-XIV_cell_line

value: BALB/c

value: ASB-XIV


title: LLC1_untreated_day_14_3


title: LLC1_untreated_day_14_2


title: LLC1_untreated_day_14_1


title: Sperm DNA from 10001

source_name: Semen Sample 10001


title: LLC1_untreated_day_7_3


title: LLC1_untreated_day_7_2


title: LLC1_untreated_day_7_1


title: ASB-XIV_day_21_2


title: ASB-XIV_day_21_1


title: ASB-XIV_day_14_3


title: ASB-XIV_day_7_2


title: ASB-XIV_day_14_1


title: ASB-XIV_day_7_1


title: ASB-XIV_day_14_2


title: PBS-1_rep4

description:
PBS_1.txt
Raw_geneCPM_matrix.txt


title: ASB-XIV_day_7_3


title: LLC1_untreated_day_21_2


title: A159V-lung tumor

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description:
COHMM000012_D1.flt.txt
COHMM000012_D1

library_source: genomic

data_processing:
Library strategy: WES
The raw paired-end fastq files were mapped to mouse mm10 reference genome using the Burrows-Wheeler alignment (BWA) tool (version 0.7.17-r1188).
The output bam files were sorted and marked for duplicates and followed by indel realignment, base quality calibration, and left alignment of indels by using Genome Analysis Toolkit (version 4.1.9.0) analysis pipeline.
Pindel (version 0.2.5b9) was used to detect indels and structural variants in the tumor samples (D1) with the control of their corresponding normal lung samples (G1) using default parameters. The expected average insert size was set as 250bp in the Pindel bam-configuration file. The reported duplications, both somatic and germline, with the size between 10bp to 50bp were extracted for further analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text file mutation lists.

source_name: A159V/WT lung tumor tissue

extract_protocol:
Genomic DNA was isolated by cell lysis followed by protein digestion by proteinase K. After phenol/chloroform extraction, genomic DNA was isolated by ethanol precipitation and washed with 70% ethanol.
Follow standard mouse whole exons capture protocol.
Follow standard library preparation for WES.

treatment_protocol: FEN1 gene knock-in.

value: heterozygous for A159V FEN1 mutation

value: lung tumor


title: A159V-normal

description:
COHMM000012_D1.flt.txt
COHMM000012_G1

source_name: A159V/WT normal lung tissue

value: normal lung


title: WT-normal

description:
COHMM000011_D1.flt.txt
COHMM000011_G1

source_name: WT normal lung tissue

value: wildtype


title: eIF3-80S_Starv_rep1

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

description:
eIF3 associated 80S-seq 2h starvation replicate 1
Ribosome associated RNA

data_processing:
The adaptor and low quality bases of all sequencing data were removed by Cutadapt.
For all sequencing but not replicate 2 of Ribo-seq, the adaptor CTGTAGGCACCATCAAT was used. The first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428. For the replicate 2 of Ribo-seq, the adaptor was set as AAAAAAAAAA. The trimmed reads were aligned to mouse (human) transcriptome, using STAR with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed data files are tab separated rpkm values. The first column is gene name, and the second column is rpkm value.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
For cell lysates, at least four 10 cm dishes of cells were harvested in 400 µl ice-cold polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2). Cells were then disrupted by vortexing six times for 20s using lysing matrix D (Fisher), followed by a 40 s interval each time on ice, then centrifuged at 12,000g, 4 °C for 10 min. Samples were then subjected to sucrose gradient sedimentation. Sucrose solutions were prepared in polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2 and 2% Triton X-100). A 15%-45% (w/v) sucrose density gradients were freshly prepared in SW41 ultracentrifuge tubes (Backman) using a Gradient Master (BioComp Instruments). 500 µl of supernatant from cell lysates prepared as described above was loaded onto sucrose gradients followed by centrifugation for 2.5 hr at 32,000 rpm, 4 °C in a SW41 rotor. Separated samples were fractionated at 1.5 ml min-1 through an automated fractionation system (Isco) that continually monitors OD254 values. Ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 °C for 1 hr. SUPERase•In (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol LS reagent.
Fragmented RNAs were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 20-70 nt (for 40S-seq and eIF3-seq) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 µl RNA gel elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.1 U/µl SUPERase•In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.   Purified RNA fragments were re-suspended in Nuclease-free water, then dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase•In and 20 U T4 polynucleotide kinase). Dephosphorylated RNA fragments were precipitated using ethanol and re-suspended in Nuclease-free water. 0.15 μg linker (rApp/NNNNCTGTAGGCACCATCAAT/3ddC) then was added to the RNA fragments, heated at 70 °C for 90 s and then cooled to room temperature, followed by ligation for 3 hr at at 22 °C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase•In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 45-95 nt (for 40S-seq and eIF3-seq) or 60-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA gel elution buffer. RNA fragments were purified from RNA gel elution buffer as described earlier and re-suspended in Nuclease-free water. For reverse transcription, the following oligos containing barcodes were used:   (Phos)CTANNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  (Phos)AGCNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  (Phos)ATTNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  (Phos)CCGNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  where Phos represents phosphorylation, NNN represents random sequence, SpC18 represents Hexa-ethyleneglycol spacer.  The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75 ° C for 3 min, followed by incubation on ice for at least 1 min. The reaction master mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel. Corresponding region was excised, which was expected to be approximately 200 nt. The first-strand cDNA products were recovered in DNA gel elution buffer (300 mM NaCl, 1 mM EDTA), then purified and re-suspended in Nuclease-free water as described earlier.  cDNA products were circularized in 20 μl of reaction containing 1×CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr and the reaction was heat inactivated at 80 °C for 10 min.

treatment_protocol: For Ogt KO, cells were treated with 0.5uM of 4-OHT for 24 hrs, followed by fresh medium for 24hrs. For Thiamet-G treatment, cells were treated with 0.1uM of Thiamet-G for 16hrs. For Amino acid starvation, cells were treated with DMEM with DFBS for 2hrs.

tag: cell type

value: Mouse embryonic fibroblasts


title: eIF3-80S_Control_rep2

description:
Control cells eIF3 associated 80S-seq replicate 2
Ribosome associated RNA


title: eIF3-80S_Starv_rep2

description:
eIF3 associated 80S-seq 2h starvation replicate 2
Ribosome associated RNA


title: eIF3-80S_ThiametG

description:
eIF3 associated 80S-seq ThiametG treatment
Ribosome associated RNA


title: eIF3-80S_ThiametG_Starvation

description:
eIF3 associated 80S-seq ThiametG + Starvation
Ribosome associated RNA


title: eIF3-80S_OGT_KO_rep1

description:
eIF3 associated 80S-seq OGT knockout
Ribosome associated RNA


title: Ribo-seq_ThiametG_rep2

description:
Ribo-seq ThiametG treatment replicate 2
Ribosome associated RNA


title: eIF3-80S_OGT_KO_Starvation

description:
eIF3 associated 80S-seq OGT knockout + Starvation
Ribosome associated RNA


title: Ribo-seq_OGT_KO_Starvation_rep1

description:
Ribo-seq OGT knockout + Starvation replicate 1
Ribosome associated RNA


title: Ribo-seq_ThiametG_Starvation_rep1

description:
Ribo-seq ThiametG treatment + Starvation replicate 1
Ribosome associated RNA


title: Ribo-seq_OGT_KO_Starvation_rep2

description:
Ribo-seq OGT knockout + Starvation replicate 2
Ribosome associated RNA


title: Ribo-seq_OGT_KO_rep2

description:
Ribo-seq OGT knockout replicate 2
Ribosome associated RNA


title: ASB-XIV_day_21_3


title: Ribo-seq_ThiametG_Starvation_rep2

description:
Ribo-seq ThiametG treatment + Starvation replicate 2
Ribosome associated RNA


title: Ribo-seq_ThiametG_rep1

description:
Ribo-seq ThiametG treatment replicate 1
Ribosome associated RNA


title: Ribo-seq_OGT_KO_rep1

description:
Ribo-seq OGT knockout replicate 1
Ribosome associated RNA


title: Ribo-seq_Starvation_rep1

description:
Ribo-seq 2h Starvation replicate 1
Ribosome associated RNA


title: Ribo-seq_Starvation_rep2

description:
Ribo-seq 2h Starvation replicate 2
Ribosome associated RNA


title: Ribo-seq_Control_rep2

description:
Ribo-seq Control replicate 1
Ribosome associated RNA


title: Ribo-seq_Control_rep1


title: DN-8_S49

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
Tools were run via the RNAsik pipeline (https://monashbioinformaticsplatform.github.io/RNAsik-pipe/), with Picard used to mark PCR duplicates (http://broadinstitute.github.io/picard), STAR performing the alignment (Dobin et al. 2013) and unstranded read counts quantified by gene by featureCounts (subread v1.5.2) (Liao, Smyth, and Shi 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and cells

source_name: Oocyte

extract_protocol:
To perform single-cell RNA-seq analyses, GV-stage oocytes (18 oocytes/genotype) were individually placed in Eppendorf tube containing 10µL of nuclease-free water. Tubes were snap frozen in liquid nitrogen and stored at -80 o C until further experiment.
The whole lysate was supplied for cDNA synthesis and RNA-seq library preparation with, respectively, a SMARTer Ultra Low Input RNA Kit (Clontech, CA USA) and Nextera XT library prep kit (Illumina, CA, USA), each according to the manufacturer's instructions. Indexed libraries were pooled (10 nM each) and sequenced using an Illumina HiSeq 2500 System under single-end, 100-bp conditions.
single-cell RNAseq (SMART-seq)

tag: mouseid


title: WT-lung tumor

description:
COHMM000011_D1.flt.txt
COHMM000011_D1

source_name: WT lung tumor tissue


title: eIF3-80S_Control_rep1

description:
Control cells eIF3 associated 80S-seq replicate 1
Ribosome associated RNA


title: DN-7_S48


title: Rap1_IP_H4_shutoff_t0_R1

city: Buffalo

first: Michael

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

description: Rap1 Ips during histone H4 Shutoff

data_processing:
alignment with Bowtie       VN:1.0.0 bowtie sgd_r64/SacCer3 --best -l 32 -n 2
ChIP-seq replicates were merged with samtools merge -@ 8
Rap1 binding sites peaks called with MACS2  ---  -g 12157105 --nomodel --extsize 147

organism: Saccharomyces cerevisiae

source_name: cultured cells

growth_protocol: H4 shutoff (UKY403) and isogenic control (UKY412) strains of S. cerevisiae were obtained from the Grunstein lab. Cells were maintained on agar plates containing YPG media (1% yeast extract, 2% peptone, 2% galactose).

extract_protocol: Rap1p ChIPs were performed on whole cell extracts using a Rap1p antibody (Santa Cruz Biotechnology Rap1 Y-300, sc-20167) following established protocols. Two independent biological replicates from separate time-course experiments were performed for each experimental time-point

treatment_protocol: For time-course experiments, cells were initially inoculated in 5ml YPG liquid media and cultured at 30C. Logarithmically growing cells were then transferred and diluted into larger 1-1.5L YPG cultures for growth overnight at 30C while shaking in containers with 4x equivalent free-air volume. The following morning, mid-log phase cells (OD600 ~0.6-1.2) were collected by centrifugation, washed 2x within 5 minutes with ~250-500ml YP dextrose (YPD), and re-suspended in equivalent volume of YPD media for 0, 2, and 4 hours of continued growth at 30C.

tag: time point (hrs)

tag: antibody


title: Rap1_IP_H4_shutoff_t2_R2

description: Rap1 Ips during histone H4 Shutoff

value: Rap1p antibody (Santa Cruz Biotechnology Rap1 Y-300, sc-20167)


title: Rap1_IP_H4_shutoff_t4_R1

description: Rap1 Ips during histone H4 Shutoff


title: Rap1_IP_H4_shutoff_t0_R2

description: Rap1 Ips during histone H4 Shutoff


title: Rap1_IP_H4_shutoff_t4_R2

description: Rap1 Ips during histone H4 Shutoff


title: Rap1_IP_H4_shutoff_t2_R1

description: Rap1 Ips during histone H4 Shutoff


title: DN-6_S47


title: DN-5_S46


title: DN-3_S44


title: DN-30_S59


title: DN-4_S45


title: RNA-seq_Control_t4

description: RNA-seq during control histone H4 shutoff

data_processing:
TopHat       VN:1.4.1 sgd_r64/SacCer3 (genes.gtf from iGenomes build)
Genome_build: SacCer3
Supplementary_files_format_and_content: Bam Files where generated with Tophat (vn 1.4.1)
Supplementary_files_format_and_content: Abundance measurments contain FPKM measurements generated with cuffdiff VN:2.1.1 with saccer3 gene annotations

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using TRIzol Reagent following standard protocols. RNA was further purified using the RNEasy Mini Kit with on-column DNase digestion (Qiagen). Quality of extracted RNA was confirmed using an Agilent Bioanalyzer and samples with RIN > 8 were selected for sequencing. RNA from biological replicates for each control time-point and three biological replicates for each experimental (H4 Shutoff) time-point were collected.
RNA-seq was performed on all samples using the standard illumina protocol, which includes cDNA synthesis via random priming and ribosomal RNA depletion.


title: RNA-seq_H4_shutoff_t4_R3

description: RNA-seq during histone H4 shutoff


title: RNA-seq_Control_t2


title: RNA-seq_H4_shutoff_t4_R2

description: RNA-seq during histone H4 shutoff


title: RNA-seq_H4_shutoff_t4_R1

description: RNA-seq during histone H4 shutoff


title: DN-29_S58


title: DN-28_S57


title: RNA-seq_H4_shutoff_t2_R3

description: RNA-seq during histone H4 shutoff


title: DN-27_S56


title: DN-2_S43


title: RNA-seq_H4_shutoff_t2_R2

description: RNA-seq during histone H4 shutoff


title: DN-15_S55


title: RNA-seq_H4_shutoff_t2_R1

description: RNA-seq during histone H4 shutoff


title: RNA-seq_H4_shutoff_t0_R3

description: RNA-seq during histone H4 shutoff


title: RNA-seq_H4_shutoff_t0_R2

description: RNA-seq during histone H4 shutoff


title: DN-14_S54


title: RNA-seq_H4_shutoff_t0_R1

description: RNA-seq during histone H4 shutoff


title: DN-13_S53


title: DN-12_S52


title: RNA-seq_Control_t0


title: DN-11_S51


title: DN-10_S50


title: Mnase-seq Control_t2_R1

description: Mnase-seq of control strain for Histone H4 shutoff

data_processing:
alignment with Bowtie VN:0.12.7 parameters (bowtie --threads 32 -m 1 -S sgd_r64/SacCer3)
Genome_build: SacCer3
Supplementary_files_format_and_content: Processed data not available

extract_protocol:
Cross-linked chromatin–DNA complexes were extracted by mechanical disruption (bead beating; 4 1 min sessions, 2 min on ice between sessions).  An added level of standardization was achieved by quantifying the input of extracted chromatin loaded into each digest reaction; 1 mg total protein from whole-cell extracts per 200 ml digest reaction. Total protein concentration for whole cell extracts (chromatin extracts) was quantified using a Bradford assay (OD595). Following MNase treatment and cross-link reversal, DNA was phenol: chloroform precipitated, resuspended in 50 ml TE pH 8.0, and RNase treated. Small aliquots (20%,  10 ml) from each digest titration were then analyzed by gel electrophoresis. Gel intensity measurements for each lane were calculated using standard densitometry software provided by Biorad (Quantity OneTM) and exported to Microsoft ExcelTM for correlation analysis (Pearson). Correlation coefficients were calculated for digest titration levels no longer showing a visible di-nucleosome band (i.e. optimally digested samples) and spanning a region known to cover a size range of 0–400 bp of DNA. A 100-bp standard ladder (Qiagen) was analyzed on the same gel to calculate a relative front (i.e. separation relative to standard fragment sizes) for the migrating DNA population. ‘Matched’ digests were selected as two optimally digested samples having a correlation coefficient (r>0.9). Correlation coefficients r>0.9 were selected because these showed the most reproducible change in MNase protection data on single site real-time quantitative PCR (RT-qPCR) analysis (See Supplementary Methods section). The remaining sample from each optimal digest was column purified (Zymo Research), bypassing the need to gel excise mono-nucleosome DNA. Avoidance of gel extraction to isolate chromatin DNA at this stage is a key step to assure sampling of similar chromatin populations.
Matched DNA samples were prepared for sequencing using the standard Illumina protocol with additional care at the gel purification step to ensure that the same size range of DNA was selected.

tag: experiment type

value: Mnase-seq


title: DN-1_S42


title: DG-8_S66

value: b


title: DG-9_S67


title: DG-7_S65


title: Mnase-seq Control_t0_R1


title: Mnase-seq Control_t0_R2


title: Mnase-seq H4_shutoff_t2_R2

description: Mnase-seq of Histone H4 shutoff


title: DG-4_S63

value: a


title: DG-30_S77

value: d


title: Mnase-seq H4_shutoff_t2_R1

description: Mnase-seq of Histone H4 shutoff


title: Mnase-seq H4_shutoff_t0_R2

description: Mnase-seq of Histone H4 shutoff


title: Mnase-seq Control_t4_R1


title: Mnase-seq Control_t4_R2


title: Mnase-seq H4_shutoff_t4_R2

description: Mnase-seq of Histone H4 shutoff


title: DG-29_S76


title: WT-Gly-6

city: Wuhan

first: Haoran

last: Liu

state: Hubei

address: Jiefang avenue 1095

department: Urology

institute: Tongji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney

growth_protocol: All animals were raised in the Animal Facilities of Tongji Hospital under pathogen-free conditions according to the "NIH Guide for the Care and Use of Laboratory Animals".

extract_protocol:
Kidney were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each mouse was intraperitoneally injected with saline or glyoxylate acid (Gly) (75 mg/kg/d, 200 μl) from day 1 to day 7. Animals were euthanized after 7 days, and kidney samples were collected at the time of euthanasia.

value: kidney

value: intraperitoneally injected with glyoxylate acid


title: Mnase-seq H4_shutoff_t0_R1

description: Mnase-seq of Histone H4 shutoff


title: DG-3_S62


title: WT-Gly-5


title: DG-28_S75


title: DG-27_S74


title: DG-2_S61


title: WT-Gly-4


title: WT-Gly-3


title: Mnase-seq Control_t2_R2


title: WT-Gly-2


title: DG-15_S73

value: c


title: Mnase-seq H4_shutoff_t4_R1

description: Mnase-seq of Histone H4 shutoff


title: DG-6_S64


title: WT-Gly-1


title: DG-13_S71


title: DG-12_S70


title: DG-10_S68


title: WT-Ctrl-5

value: intraperitoneally injected with saline


title: WT-Ctrl-6


title: DG-14_S72


title: WT-Ctrl-4


title: eWAT RNAseq, High Fat Diet, TET KO, Rep3

city: Ulsan

first: Sung Ho

last: Park

address: 50, UNIST-gil

country: South Korea

institute: UNIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR aligner version 2.7.3a with default parameters
Read counts for DESeq2 analysis were obtained using featureCounts v2.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was extracted from three biological replicates each of eWAT from CD- or HFD-fed WT or TKO mice using a Purelink RNA Micro kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: TET KO

value: eWAT

tag: diet

value: High Fat Diet


title: eWAT RNAseq, High Fat Diet, WT, Rep3

value: WT


title: DG-1_S60


title: WT

city: chengdu

first: ren

last: yafeng

address: NO.17，3th Section,Renmin South Road

institute: sichuan university

data_processing:
Illumina® software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Silane magnetic beads are used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction.
The Single Cell 3’ Protocol produces Illumina-ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sample index sequences are incorporated as the i7 index read. Read 1 and Read 2 are standard Illumina® sequencing primer sites used in paired-end sequencing.
Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells: 1) 500 < gene counts < 4000 per cell. 2) UMI counts < 8000 per cell. 3) the percentage of mitochondrial genes < 10%
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: liver nonparenchymal cells

extract_protocol:
For isolation of mouse hepatocytes or liver macrophages by magnetic beads, single-cell suspension of mice liver was centrifuged at 50g for 2 min. The cell pellet contained mainly hepatocytes and supernatant suspensions were nonparenchymal cells (NPCs).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A samples from three mice

tag: strain background

value: wild type

value: liver nonparenchymal cells

value: four times ccl4


title: DG-11_S69


title: yap1


title: WT-Ctrl-2


title: eWAT RNAseq, Normal Diet, TET KO, Rep3

value: Normal Diet


title: eWAT RNAseq, Normal Diet, TET KO, Rep2


title: WT-Ctrl-3


title: eWAT RNAseq, Normal Diet, TET KO, Rep1


title: eWAT RNAseq, High Fat Diet, WT, Rep2


title: eWAT RNAseq, High Fat Diet, TET KO, Rep2


title: WT-Ctrl-1


title: eWAT RNAseq, High Fat Diet, TET KO, Rep1


title: eWAT RNAseq, Normal Diet, WT, Rep3


title: Macrophage_Med16_IFNg_rep1

city: East Lansing

first: Andrew

last: Olive

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: Sample 16

data_processing:
Illumina software was used for Basecalls
FastQC (v0.11.5) was used to assess the quality of raw data.
Cutadapt (v2.9) was used to remove TruSeq adapter sequences with the parameters  --cores=15 -m 1 -a
Genome_build: A transcriptome was prepared with the rsem (v1.3.0) command rsem-prepare-reference using bowtie2 (v2.3.5.1) and the gtf and primary Mus musculus genome assembly from ENSEMBL release 99.
Trimmed sequencing reads were aligned and counts quantified using rsem-calculate-expression with standard bowtie2 parameters; fragment size and alignment quality for each sequencing library was assessed by estimating the read start position distribution (RSPD) via --estimate-rspd.
Gene counts as determined by rsem were used as input for differential expression analysis in DESeq2 according to standard protocols.
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Macrophage cell line (L3 clone)

growth_protocol: Macrophages were grown in DMEM with 10% FBS for the duration of the experiment

extract_protocol:
Cells were lysed directly in Trizol and total RNA was isolated using the Direct-zol RNA isolation kit from Zymogen
Libraries were constructed using poly-A tailed mRNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Macrophages were treated with 10ng/ul of IFN-gamma for 24 hours or were left untreated

value: Bone marrow

tag: derivation

value: Macrophage, J2 virus immortalized

value: IFN-gamma treated


title: eWAT RNAseq, Normal Diet, WT, Rep1

tag: tissue


title: Macrophage_Med16_IFNg_rep2

description: Sample 17

tag: strain


title: Macrophage_Med16_Untreated_rep3

description: Sample 15

tag: genotype

value: untreated


title: Macrophage_GSK3b_IFNg_rep3

description: Sample 12


title: eWAT RNAseq, Normal Diet, WT, Rep2


title: Macrophage_Med16_IFNg_rep3

description: Sample 18


title: Macrophage_Med16_Untreated_rep2

description: Sample 14


title: eWAT RNAseq, High Fat Diet, WT, Rep1


title: Macrophage_GSK3b_IFNg_rep1

description: Sample 10


title: Macrophage_GSK3b_IFNg_rep2

description: Sample 11


title: Macrophage_Med16_Untreated_rep1

description: Sample 13


title: Macrophage_GSK3b_Untreated_rep3

description: Sample 9


title: Macrophage_GSK3b_Untreated_rep1

description: Sample 7


title: Macrophage_GSK3b_Untreated_rep2

description: Sample 8


title: Liver_ApoE-/-_untreated_rep3

type: RNA

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: Replicate 3 of 5

hyb_protocol: ILLUMINA WG-6 V2 mouse BeadChips were used, with standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned using an Illumina iScan Reader

data_processing: Microarray data were extracted using Illumina GenomeStudio software (BeadStudio Gene Expression Analysis Module). Intensity data were normalized in R using the cubic spline algorithm.

source_name: Liver, ApoE-/- untreated mouse

label_protocol: Biotinylated cRNA were prepared with the Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit

growth_protocol: C57BL/6 were fed a high fat diet (HFD) (Western diet, Research Diets, New Brunswick, NJ) containing 35% (w/w) fat and 0.03% cholesterol or a normal diet (ND) (LabDiet, PMI Nutrition International LLC, St. Louis, MO) containing 5% fat and 200 ppm cholesterol from the age of week 6 to 14.  ApoE-/- mice were fed HFD (RD Western diet, Research Diets) containing 21% (w/w) fat and 0.15% cholesterol from week 6 to 14.  All mice were maintained in the animal facility of Idera Pharmaceuticals, Inc, housed under standard conditions with a 12 h light, 12-h dark cycle and had free access to food and water unless indicated otherwise.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed by Agilent 2100 Bioanalyzer

treatment_protocol: C57BL/6 and ApoE-/- mice were divided into two groups, group1 on HFD were treated with intraperitoneal (i.p.) injection of TLR antagonist at 15 mg/kg body weight 3 times per week from week 6 to 11.  Group 2 mice on HFD received no antagonist treatment. The experiment terminated at the week 14 when tissue samples were collected to evaluate the effects of TLR antagonist treatment.  All animal experiments were approved by Institutional Animal Care and Use Committee at Idera Pharmaceuticals.

value: ApoE-/-

tag: Sex

value: male

tag: age

value: 14 weeks

value: liver

value: high fat diet


title: Macrophage_NTC_IFNg_rep3

description: Sample 6

value: Control sgRNA (sgNTC)

tag: treatment


title: Liver_ApoE-/-_untreated_rep4

description: Replicate 4 of 5


title: Liver_ApoE-/-_treated_rep3

description: Replicate 3 of 5

source_name: Liver, ApoE-/- treated mouse

value: TLR7 and 9 antagonist


title: Liver_ApoE-/-_treated_rep4

description: Replicate 4 of 5


title: Liver_ApoE-/-_untreated_rep5

description: Replicate 5 of 5


title: Liver_ApoE-/-_untreated_rep2

description: Replicate 2 of 5


title: Liver_wt_untreated_rep2

description: Replicate 2 of 5

source_name: Liver, C57Bl/6 untreated mouse


title: Liver_wt_untreated_rep4

description: Replicate 4 of 5


title: Liver_ApoE-/-_treated_rep2

description: Replicate 2 of 5


title: Liver_wt_untreated_rep5

description: Replicate 5 of 5


title: Liver_ApoE-/-_treated_rep5

description: Replicate 5 of 5


title: Liver_ApoE-/-_untreated_rep1

description: Replicate 1 of 5


title: Macrophage_NTC_IFNg_rep1

description: Sample 4


title: Macrophage_NTC_IFNg_rep2

description: Sample 5


title: Macrophage_NTC_Untreated_rep3

description: Sample 3


title: Macrophage_NTC_Untreated_rep1

description: Sample 1


title: Macrophage_NTC_Untreated_rep2

description: Sample 2


title: mir139WT14d

city: Rotterdam

first: Stefan

middle: J.

last: Erkeland

state: Zuid-Holland

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

description: NGS of MLL-AF9-transformed HSPC-enriched WT bonemarrow cells, transduced with LentiCRISPRv2 gecko library

data_processing:
trim: inhouse script
zcat {input} | \              adapter_trim \                  --output "{output}" \                  -a GTTTTAGAGCT GTTTAGAGCT GTTTTTAGAGCT \                   --maximum-mismatches 2 \                   --minimum-matches 2 \                  --minimum-bases-remaining 2
alignment: hisat2:
hisat2 -p 6 \              -x gecko_v2.mmusculus.fasta \              --norc \              --no-spliced-alignment \              -U {input} | \                  samtools addreplacerg \                      -r "ID:{params.sampleid}" \          -r "CN:ECB" \          -r "LB:{params.sampleid}" \          -r "SM:{params.sampleid}" \          -r "PL:ILLUMINA" \          -r "DS:{params.fullpath}" \                      - | \                         samtools sort \                              -o {output} \                              -
merge: samtools merge
quantifications: samtools
samtools view  -F 0x0100 -F 0x0800 {input} | \              awk -F "\t" '{{print $3}}' | \              sort  | \              uniq -c | \              sed 's/^ *//' | \              awk '{{print $2 "," $1}}' > {output}
Genome_build: GeCKO v2 mouse library
Supplementary_files_format_and_content: CSV files

source_name: Bone marrow cells

growth_protocol: HSPCs were isolated from femur and tibiae from WT or Mir139KO C57BL/6 mice (8 – 20 wks) using the BD Mouse Hematopoietic Progenitor (Stem) Cell  Enrichment Set (cat 558451, Becton Dickinson). Cells were immediately resuspended in TRIzol or HPSCs were expanded in StemPro-34 SFM (Thermo Fisher Scientific, 10639011) supplemented with Interleukin (IL)-3 (1:1000 supernatant), IL-6 (10 ng/mL; SRP3330 Sigma Aldrich), Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) (10 ng/mL; CYT-222, Prospec Ltd) and Stem Cell Factor (SCF) (20 ng/mL; 5223SF, Cell Signaling Technology) and Penicillin-Streptomycin (P/S) (100U/mL; 15140163, Thermo Fisher Scientific) overnight, followed by retroviral transduction with pMSCV-MLL-AF9-neo or pMSCV-MLL-AF9-puro (Wong et al., 2007) with RetroNectin (T100A, Takara) according to manufacturer’s  protocol. Transduced cells were selected on Neomycin (800µg/mL; 10131035, Thermo Fisher Scientific) or Puromycin. After at least two re-platings in MethoCult (M3231, Stem Cell Technologies), MLL-AF9 cells were resuspended in TRIzol.

extract_protocol:
DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen, 69506) according to manufacturer’s protocol, with the addition of 400ug RNase A (Qiagen) per 5 million cells.
To determine over or under representation of sgRNAs, the integrated lentiviral sgRNA constructs were amplified by PCR followed by a nested PCR as described with modifications described below (Sanjana et al., 2014). Briefly, the first PCR reaction was performed for each sample in 13 separate 100 µl reactions. Each reaction contained 10 µg genomic DNA to get an estimated 300 times complexity using High Fidelity Herculase II Fusion DNA Polymerase (600675, Agilent Technologies), dNTPs (Invitrogen) and 0.5 µM of primers sgRNAlibF1 and sgRNAlibR1 (Table XX). The sequences encoding the sgRNAs were amplified using the following PCR conditions: 2 min at 95°C, 20 cycles of (30 sec at 95°C, 30 sec at 55°C, 1 min at 72°C) and fragments were extended for 10 min at 72°C. All PCR reactions were pooled and mixed. The second one-sided nested PCR reaction was performed for each sample in 6 separate 100 µl reactions. Each reaction contained 5 µl of the crude product from the first PCR, Fusion polymerase, dNTPs and 0.5 µM of primers sgRNAlibF2 and sgRNAlibR2. The concentration and quality of the libraries were determined by Agilent 2100 Bioanalyzer using a DNA1000 assay. Cluster generation was performed according to the Illumina TruSeq SR Rapid Cluster kit v2 (cBot) Reagents Preparation Guide (Illumina). Briefly, pooled libraries (10nM) were denaturated with NaOH, diluted to 10 pM and hybridized onto the flowcell. The hybridized products were sequentially amplified, linearized and end-blocked according to the Illumina Single Read Multiplex Sequencing user guide (Illumina). After hybridization with a custom-made sequencing primer (CGTTGTTCTTGTGGAAAGGACGAAACACCG), sequencing-by-synthesis was performed using the HiSeq 2500 (Illumina) using a single read 50-cycle protocol followed by single index sequencing.

treatment_protocol: The Mouse CRISPR Gecko v2 pooled library (Addgene, #1000000052, #1000000053) was amplified and lentivirus was generated according to protocols (Sanjana et al., 2014). MLL-AF9 and MLL-AF9-139KO cells were transduced with the pooled library with a 500 fold coverage. Cells were harvested to obtain reads for normalization purposes 24 hours after transduction. Puromycin (1µg/mL) was added to select transduced cells. Cells were expanded for 14 days.

tag: time post selection


title: Liver_wt_untreated_rep1

description: Replicate 1 of 5


title: WGBS_Bat8_wt

city: Grand Rapids

first: Piroska

middle: E

last: Szabó

address: 333 Bostwick ave NE

department: Epigenetics

institute: Van Andel Institute

description: WGBS 9.5 dpc wild type embryo DNA

data_processing:
Pair-end Reads were aligned to the mm10 genome using Biscuit(v 0.3.14.20200104)
Duplicated were removed using Picard MarkDuplicates.
DNA methylation and genetic information were extracted using Biscuit’s pileup
CpG beta values were extracted using vcf2bed.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary files format: cg.bw files contain the % CpG methylation at each CpG site
Supplementary_files_format_and_content: Bigwigs that contain methylation levels per CpG

source_name: embryo

extract_protocol:
DNA was isolated by using phenol -choloroform protocol followed by ethanol precipitation.
In order to generate the whole genome libraries with bisulfite converted DNA, embryo DNA was sonicated to approx. 150 bp DNA fragments. Further, DNA was end repaired by using End-It- DNA End-Repair Kit (Epicentre) and linker ligated with T4 ligase (NEB). The linked ligated DNA was bisulfite converted using EZ DNA Methylation-Gold™ Kit according to manufacturer's instructions (Zymo Research) and amplified with Pfu Turbo polymerase (Agilent). Sequencing was performed at the Integrative Genomic Core at the City of Hope Cancer Center.

treatment_protocol: An Ehmt2 conditional knockout mouse line (Ehmt2fl/fl) was generated by gene targeting in 129S1/SvImJ ES cells (Zeng, Han et al. PNAS 2019). The floxed SET domain was removed to generate the mutant allele by crossing the Ehmt2fl/+ male with 129S1/Sv-Hprttm1(CAGcre)Mann/J transgenic mouse female (Tang, Silva et al. 2002). Ehmt2-/- and WT embryos were obtained by natural mating of Ehmt2+/− females and males. Embryos were dissected at 9.5 dpc, and were genotyped for Ehmt2 mutation status and for sex by PCR using their allantois.

tag: age (days post coitum)

value: female

tag: background


title: Liver_ApoE-/-_treated_rep1

description: Replicate 1 of 5


title: Liver_wt_treated_rep4

description: Replicate 4 of 5

source_name: Liver, C57Bl/6 treated mouse


title: Liver_wt_treated_rep2

description: Replicate 2 of 5


title: Liver_wt_treated_rep5

description: Replicate 5 of 5


title: mir139WT24h

value: MLL-AF9-transformed HSPC-enriched WT bonemarrow cells

value: WT


title: mir139KO14d

description: NGS of MLL-AF9-transformed HSPC-enriched Mir139KO bonemarrow cells, transduced with LentiCRISPRv2 gecko library


title: 0W_LSK: control

city: Shanghai

first: Zhiwei

last: Chen

address: Room 807, Research and Education Plaza, 197 Ruijin 2nd Road, Luwan District, Shanghai, PRC

department: Shanghai Institute Of Hematology

institute: Shanghai Jiao Tong Universtiy School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat (version:2.0.9).
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using a protocol from Mortazavi A et al., Nat Methods, 2008.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Hematopoietic stem-progenitor cells

extract_protocol:
LSKs were sorted by BD FACSAria, total RNA was isolated from LSKs using the miRNeasy mini RNA isolation kit (Qiagen) according to the manual description.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Hematopoietic stem-progenitor cells

tag: time

value: 0 week after BCR/ABL expression induced

tag: sorting antibody

value: Lineage Cell Depletion Kit (Miltenyi Biotec). Lineage-negative cells were then stained with Biotin Mouse Lineage Panel (BD Pharmingen), Streptavidin APC-Cy7 (BD Pharmingen), Sca1-PE (BD Pharmingen) and c-Kit-APC (Biolegend)


title: Liver_wt_treated_rep3

description: Replicate 3 of 5

value: wild type


title: 3W_LSK: BCR/ABL expressing LSK cells

value: Bone marrow

value: 3 weeks after BCR/ABL expression induced


title: WGBS_Bat8_mut

description: WGBS 9.5 dpc Ehmt2 homozygous embryo DNA

value: homozygous mutant

value: pooled male and female


title: FaDu-shKLK6#2-2

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

hyb_protocol: Hybridization was performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 150 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner (Illumina Inc.). Data extraction was done for all beads individually, and the outliers are removed when the absolute difference to the median was greater than 2.5 times MAD(2.5 Hampelís method).

data_processing:
Raw data was read and normalized via lumi (R packages), processed was then analyzed by limma incorporating the technical replicate information.   The analysis is done with R on the bead-level data which is  found in the raw data produced by the scanner (e.g. in  5282035051.7z the file 5282035051_A.txt, which holds bead  level data for all probeIDs of sample A).    All analyses are done using the following mechanisms:  1) outlier removal (see below).  2) average values over beads are means (not median).  3) statistical tests are t-tests over all beads (e.g for one      probeID over all beads of all samples of a group) in original     scale (not log2 scale).     Example:      group x is sample A,B,C      control y is sample D,E,F      to test for significance of difference between group x       and control y, we use      t.test(all_beads_of_A_B_C, all_beads_D_E_F,         alternative = two.sided,        mu = 0 )       Example:      to check for significance against background (one specific       probeID):        t.test(all_beads_of_A, all_negative_of_A, alternative=greater)       Benjamini-Hochberg correction is applied over all p-values of     the differential expression analysis.         Calculation of GeneView data:  The calculations are also done on the set of beads which belong to  a given Gene Symbol (annotation column Symbol).         Outlier removal on bead level:    Outliers are removed by taking only beads with an expression value > 20 before  using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the   remaining beads.    The remaining bead level lists of different length for each sample are randomly  filled with NAs (NA=not available) and build the bead level matrix on which quantile  normalization is performed.    MAD rule:  mad = median absolute deviation  (<http://en.wikipedia.org/wiki/Median_absolute_deviation>)  x = one bead level expression value of some specific probeID  Than:  outliers are those x where abs((x-median)/mad) > 2.5
All remaining bead level data points are than quantile   normalized. As test for significance the studentís t-test is   used on the bead expression values of the two groups of interest.   In the case of significance of expression against background we   tested for greater than all negative beads for this sample and   in the case of comparing separate groups we tested for inequality   of the means of the groups. In both cases Benjamini-Hochberg   correction was applied to the complete set of p-values of   all ProbeIDs on the chip. The average expression value is   calculated as mean of the measured expressions of beads   together with the standard deviation of the beads.

source_name: cell line FaDu-shKLK6

label_protocol: Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina Inc.) were prepared according to manufacturer’s recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., Methods Enzymol, 216 (1992) 80-100). In brief, 300 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies, Germany).  Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality and quantity of cRNA was confirmed  using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany).

growth_protocol: FaDu cells were purchased from ATCC (HTB-43) and authentication was confirmed by the Multiplex Human Cell Line Authentication Test (Multiplexion, Germany). Generation of FaDu-mock and FaDu-shKLK6 clones was described elsewhere (Schrader et al., Mol Cancer. 2015 May 20;14:107). Stable clones were maintained in Dulbecco’ s Modified Eagle’ s Medium (Sigma, Germany) supplemented with 10 % fetal bovine serum (Sigma, Germany), 2 mM L-Glutamine (Sigma, Germany) and 50 μg/ml Penicillin-Streptomycin (Sigma, Germany) in a humidified atmosphere of 6-8 % CO2  at 37 °C.

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer’s instruction. DNA digestion was performed with RNase-free DNAse Set (Qiagen, Germany). Quantity and quality of isolated RNA was determined with the help of the Nanodrop Spectrophotometer ND-1000 (Peqlab, Germany).

treatment_protocol: As described in Schrader et al. (Mol Cancer. 2015 May 20;14:107) FaDu cells were transfected with either a control pRS vector encoding a non-effective Hush 29-mer scrambled shRNA cassette (TR30012, OriGene Technologies, USA) or a pRS-shKLK6 plasmid (TR316673, OriGene Technologies, USA) using FuGene HD Transfection Reagent (Promega, Germany) according to the manufacturer’ s instruction. Following selection with 1.5 μg/ml Puromycin (Gibco life technologies, Germany) for one week, stable clones were isolated and KLK6 silencing was confirmed on RNA level by RQ-PCR.

value: HNSCC derived cell line

tag: cell line

tag: technical replicates group


title: Liver_wt_untreated_rep3

description: Replicate 3 of 5

value: untreated

value: male

value: 14 weeks

tag: diet


title: FaDu-Mock#1-2

source_name: cell line FaDu-Mock

value: FaDu-Mock


title: FaDu-shKLK6#2-1


title: Liver_wt_treated_rep1

description: Replicate 1 of 5

value: TLR7 and 9 antagonist

value: liver

value: high fat diet


title: FaDu-Mock#3-2


title: FaDu-shKLK6#3-2


title: FaDu-shKLK6#1-1


title: FaDu-Mock#3-1


title: FaDu-Mock#2-1


title: FaDu-Mock#1-1