title: male_hypothalamus_12 months_1555150

description: Library name: 1555150


title: male_hypothalamus_24 months_1378835

status: Public on Mar 05 2026

type: SRA

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

country: USA

institute: Regeneron Pharmaceuticals

description: Library name: 1378835

library_source: transcriptomic

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: Tab-separated raw counts

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
Mice were sacrificed by CO2 asphyxiation. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

tag: strain

tag: tissue

value: hypothalamus

tag: Sex

value: male

tag: age

value: 24 months


title: male_cortex_12 months_1555147

description: Library name: 1555147

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: Rn7
Supplementary files format and content: Tab-separated raw counts

organism: Rattus norvegicus

source_name: cortex

extract_protocol:
Rats were anesthetized with 3.5% isoflurane and sacrificed by exsanguination and thoracotomy. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

value: Sprague Dawley

value: cortex

value: 12 months


title: male_hypothalamus_24 months_1378833

description: Library name: 1378833


title: male_hippocampus_9 months_1555143

description: Library name: 1555143

source_name: hippocampus

value: hippocampus

value: 9 months


title: male_hypothalamus_24 months_1378834

description: Library name: 1378834


title: female_hypothalamus_24 months_1378838

description: Library name: 1378838

value: female


title: male_hypothalamus_24 months_1378831

description: Library name: 1378831


title: male_hypothalamus_24 months_1378832

description: Library name: 1378832


title: male_hippocampus_12 months_1555139

description: Library name: 1555139


title: male_hippocampus_12 months_1555138

description: Library name: 1555138


title: male_hypothalamus_24 months_1378830

description: Library name: 1378830


title: male_hypothalamus_18 months_1378828

description: Library name: 1378828

value: 18 months


title: male_hypothalamus_12 months_1555154

description: Library name: 1555154


title: male_hippocampus_12 months_1555137

description: Library name: 1555137


title: male_cerebellum_24 months_1555136

description: Library name: 1555136

source_name: cerebellum

value: cerebellum


title: female_hypothalamus_18 months_1378827

description: Library name: 1378827


title: male_cerebellum_24 months_1555133

description: Library name: 1555133


title: male_cerebellum_24 months_1555134

description: Library name: 1555134


title: female_hypothalamus_18 months_1378826

description: Library name: 1378826


title: male_hippocampus_12 months_1555140

description: Library name: 1555140


title: male_cerebellum_12 months_1555130

description: Library name: 1555130


title: female_hypothalamus_12 months_1378823

description: Library name: 1378823


title: male_hypothalamus_12 months_1378824

description: Library name: 1378824


title: male_cerebellum_12 months_1555131

description: Library name: 1555131


title: male_hippocampus_12 months_1555132

description: Library name: 1555132


title: male_hypothalamus_12 months_1378825

description: Library name: 1378825


title: female_hypothalamus_12 months_1378822

description: Library name: 1378822


title: female_hypothalamus_6 months_1378820

description: Library name: 1378820

value: 6 months


title: male_cerebellum_12 months_1555129

description: Library name: 1555129


title: female_hypothalamus_6 months_1378821

description: Library name: 1378821


title: male_hippocampus_12 months_1555127

description: Library name: 1555127


title: male_cerebellum_12 months_1555128

description: Library name: 1555128


title: male_hypothalamus_6 months_1378819

description: Library name: 1378819


title: male_hypothalamus_6 months_1378818

description: Library name: 1378818


title: male_cerebellum_12 months_1555126

description: Library name: 1555126


title: male_cerebellum_12 months_1555125

description: Library name: 1555125


title: male_cerebellum_24 months_1555135

description: Library name: 1555135


title: male_cerebellum_12 months_1555124

description: Library name: 1555124


title: male_hypothalamus_27 months_1378817

description: Library name: 1378817

value: 27 months


title: male_cerebellum_12 months_1555123

description: Library name: 1555123


title: male_hypothalamus_27 months_1378815

description: Library name: 1378815


title: male_cerebellum_12 months_1555121

description: Library name: 1555121


title: male_hypothalamus_27 months_1378814

description: Library name: 1378814


title: male_hypothalamus_27 months_1378813

description: Library name: 1378813


title: male_hippocampus_12 months_1555122

description: Library name: 1555122


title: male_hippocampus_12 months_1555120

description: Library name: 1555120


title: male_hypothalamus_27 months_1378816

description: Library name: 1378816


title: male_hippocampus_6 months_1377914

description: Library name: 1377914


title: male_hippocampus_6 months_1377913

description: Library name: 1377913


title: male_hippocampus_12 months_1555118

description: Library name: 1555118


title: male_hippocampus_6 months_1377910

description: Library name: 1377910


title: male_hippocampus_12 months_1555117

description: Library name: 1555117


title: male_hypothalamus_24 months_1555114

description: Library name: 1555114


title: male_cerebellum_12 months_1555116

description: Library name: 1555116


title: male_hippocampus_6 months_1377912

description: Library name: 1377912


title: male_hippocampus_6 months_1377911

description: Library name: 1377911


title: female_hippocampus_12 months_1377907

description: Library name: 1377907


title: male_cerebellum_12 months_1555115

description: Library name: 1555115


title: female_hippocampus_12 months_1377908

description: Library name: 1377908


title: male_hippocampus_24 months_1555112

description: Library name: 1555112


title: male_hippocampus_6 months_1377909

description: Library name: 1377909


title: female_hippocampus_12 months_1377906

description: Library name: 1377906


title: male_hippocampus_24 months_1555113

description: Library name: 1555113


title: male_hippocampus_24 months_1555110

description: Library name: 1555110


title: male_hippocampus_12 months_1555119

description: Library name: 1555119


title: male_hypothalamus_24 months_1555108

description: Library name: 1555108


title: female_hippocampus_12 months_1377904

description: Library name: 1377904


title: male_hippocampus_24 months_1555111

description: Library name: 1555111


title: male_hippocampus_24 months_1555109

description: Library name: 1555109


title: female_hippocampus_12 months_1377903

description: Library name: 1377903


title: female_hippocampus_12 months_1377905

description: Library name: 1377905


title: male_hypothalamus_24 months_1555106

description: Library name: 1555106


title: male_hypothalamus_24 months_1555105

description: Library name: 1555105


title: male_hippocampus_12 months_1377901

description: Library name: 1377901


title: male_hippocampus_12 months_1377900

description: Library name: 1377900


title: male_hippocampus_12 months_1377899

description: Library name: 1377899


title: male_hippocampus_12 months_1377898

description: Library name: 1377898


title: male_hippocampus_12 months_1377897

description: Library name: 1377897


title: male_hippocampus_18 months_1377896

description: Library name: 1377896


title: male_hypothalamus_24 months_1555103

description: Library name: 1555103


title: male_hippocampus_12 months_1377902

description: Library name: 1377902


title: male_cerebellum_24 months_1555100

description: Library name: 1555100


title: male_cerebellum_24 months_1555102

description: Library name: 1555102


title: male_hypothalamus_24 months_1555099

description: Library name: 1555099


title: male_hippocampus_18 months_1377895

description: Library name: 1377895


title: male_hippocampus_18 months_1377893

description: Library name: 1377893


title: male_hypothalamus_24 months_1555098

description: Library name: 1555098


title: male_hippocampus_18 months_1377892

description: Library name: 1377892


title: male_hypothalamus_24 months_1555097

description: Library name: 1555097


title: male_cerebellum_24 months_1555096

description: Library name: 1555096


title: male_hypothalamus_24 months_1555107

description: Library name: 1555107


title: male_hippocampus_18 months_1377891

description: Library name: 1377891


title: male_hippocampus_21 months_1377889

description: Library name: 1377889

value: 21 months


title: male_cerebellum_24 months_1555093

description: Library name: 1555093


title: male_hippocampus_21 months_1377888

description: Library name: 1377888


title: male_cerebellum_24 months_1555094

description: Library name: 1555094


title: male_hippocampus_21 months_1377890

description: Library name: 1377890


title: male_hippocampus_21 months_1377887

description: Library name: 1377887


title: male_hypothalamus_24 months_1555104

description: Library name: 1555104


title: male_hippocampus_18 months_1377894

description: Library name: 1377894


title: female_hippocampus_24 months_1377885

description: Library name: 1377885


title: male_hippocampus_21 months_1377886

description: Library name: 1377886


title: male_cortex_24 months_1555090

description: Library name: 1555090


title: male_cerebellum_24 months_1555092

description: Library name: 1555092


title: male_cerebellum_24 months_1555095

description: Library name: 1555095


title: male_cerebellum_24 months_1555101

description: Library name: 1555101


title: male_cerebellum_21 months_1555089

description: Library name: 1555089


title: female_hippocampus_24 months_1377884

description: Library name: 1377884


title: female_hippocampus_6 months_1377881

description: Library name: 1377881


title: male_cerebellum_21 months_1555086

description: Library name: 1555086


title: female_hippocampus_24 months_1377883

description: Library name: 1377883


title: male_cerebellum_21 months_1555088

description: Library name: 1555088


title: female_hippocampus_21 months_1377882

description: Library name: 1377882


title: male_cortex_24 months_1555081

description: Library name: 1555081


title: female_hippocampus_6 months_1377880

description: Library name: 1377880


title: male_hippocampus_21 months_1377879

description: Library name: 1377879


title: male_cerebellum_21 months_1555085

description: Library name: 1555085


title: male_hippocampus_6 months_1377878

description: Library name: 1377878


title: male_cerebellum_21 months_1555087

description: Library name: 1555087


title: male_hippocampus_24 months_1555071

description: Library name: 1555071


title: male_hippocampus_24 months_1555070

description: Library name: 1555070


title: male_hippocampus_12 months_1377876

description: Library name: 1377876


title: male_hippocampus_24 months_1555072

description: Library name: 1555072


title: female_hippocampus_12 months_1377875

description: Library name: 1377875


title: female_hippocampus_12 months_1377874

description: Library name: 1377874


title: male_cortex_24 months_1555077

description: Library name: 1555077


title: male_hippocampus_18 months_1377877

description: Library name: 1377877


title: male_hippocampus_24 months_1377871

description: Library name: 1377871


title: male_hippocampus_24 months_1555078

description: Library name: 1555078


title: female_hippocampus_6 months_1377873

description: Library name: 1377873


title: male_hippocampus_24 months_1555067

description: Library name: 1555067


title: male_cortex_24 months_1555084

description: Library name: 1555084


title: male_hippocampus_24 months_1555069

description: Library name: 1555069


title: male_hippocampus_24 months_1377872

description: Library name: 1377872


title: male_hippocampus_24 months_1555068

description: Library name: 1555068


title: female_hippocampus_6 months_1377868

description: Library name: 1377868


title: female_hippocampus_6 months_1377869

description: Library name: 1377869


title: female_hippocampus_6 months_1377867

description: Library name: 1377867


title: male_cerebellum_21 months_1555062

description: Library name: 1555062


title: male_cerebellum_21 months_1555063

description: Library name: 1555063


title: male_hippocampus_27 months_1377866

description: Library name: 1377866


title: male_cerebellum_21 months_1555066

description: Library name: 1555066


title: female_hippocampus_24 months_1377865

description: Library name: 1377865


title: female_hippocampus_6 months_1377870

description: Library name: 1377870


title: female_hippocampus_24 months_1377864

description: Library name: 1377864


title: male_cerebellum_21 months_1555061

description: Library name: 1555061


title: female_hippocampus_24 months_1377863

description: Library name: 1377863


title: female_hippocampus_24 months_1377862

description: Library name: 1377862


title: male_hippocampus_21 months_1555060

description: Library name: 1555060


title: male_hippocampus_21 months_1555059

description: Library name: 1555059


title: male_hippocampus_21 months_1555058

description: Library name: 1555058


title: male_cerebellum_21 months_1555065

description: Library name: 1555065


title: male_cerebellum_21 months_1555064

description: Library name: 1555064


title: male_cerebellum_21 months_1555057

description: Library name: 1555057


title: male_hippocampus_21 months_1555054

description: Library name: 1555054


title: male_hippocampus_24 months_1377861

description: Library name: 1377861


title: male_hippocampus_24 months_1377860

description: Library name: 1377860


title: female_hippocampus_24 months_1377857

description: Library name: 1377857


title: male_hippocampus_21 months_1555056

description: Library name: 1555056


title: female_hippocampus_24 months_1377856

description: Library name: 1377856


title: male_hippocampus_24 months_1377859

description: Library name: 1377859


title: male_hippocampus_21 months_1555055

description: Library name: 1555055


title: male_hippocampus_24 months_1377854

description: Library name: 1377854


title: male_hippocampus_21 months_1555052

description: Library name: 1555052


title: male_hippocampus_21 months_1555053

description: Library name: 1555053


title: male_hippocampus_21 months_1555050

description: Library name: 1555050


title: male_hippocampus_27 months_1377855

description: Library name: 1377855


title: male_hippocampus_21 months_1555051

description: Library name: 1555051


title: female_hippocampus_24 months_1377852

description: Library name: 1377852


title: male_hippocampus_24 months_1377850

description: Library name: 1377850


title: male_cortex_21 months_1555048

description: Library name: 1555048


title: male_hippocampus_24 months_1377849

description: Library name: 1377849


title: female_hippocampus_21 months_1377853

description: Library name: 1377853


title: male_hippocampus_21 months_1553288

description: Library name: 1553288


title: male_hypothalamus_21 months_1553279

description: Library name: 1553279


title: male_hypothalamus_21 months_1553282

description: Library name: 1553282


title: female_hippocampus_18 months_1377847

description: Library name: 1377847


title: male_hippocampus_18 months_1377846

description: Library name: 1377846


title: female_hippocampus_18 months_1377848

description: Library name: 1377848


title: male_hippocampus_6 months_1377845

description: Library name: 1377845


title: male_hypothalamus_21 months_1553276

description: Library name: 1553276


title: male_hypothalamus_21 months_1553281

description: Library name: 1553281


title: male_cortex_21 months_1553269

description: Library name: 1553269


title: male_hippocampus_24 months_1377851

description: Library name: 1377851


title: male_hippocampus_21 months_1555045

description: Library name: 1555045


title: male_hippocampus_12 months_1377843

description: Library name: 1377843


title: female_hippocampus_21 months_1377841

description: Library name: 1377841


title: female_hippocampus_21 months_1377842

description: Library name: 1377842


title: male_hypothalamus_21 months_1553277

description: Library name: 1553277


title: female_hippocampus_27 months_1377839

description: Library name: 1377839


title: female_hippocampus_6 months_1377844

description: Library name: 1377844


title: male_hypothalamus_21 months_1377838

description: Library name: 1377838


title: male_hypothalamus_21 months_1553275

description: Library name: 1553275


title: male_hypothalamus_27 months_1553268

description: Library name: 1553268


title: male_hippocampus_21 months_1377840

description: Library name: 1377840


title: male_hippocampus_21 months_1555049

description: Library name: 1555049


title: male_hypothalamus_18 months_1378829

description: Library name: 1378829


title: male_hypothalamus_27 months_1553267

description: Library name: 1553267


title: male_hypothalamus_21 months_1553278

description: Library name: 1553278


title: female_hippocampus_21 months_1377837

description: Library name: 1377837


title: male_hypothalamus_27 months_1553266

description: Library name: 1553266


title: male_hypothalamus_27 months_1553265

description: Library name: 1553265


title: female_hippocampus_27 months_1377836

description: Library name: 1377836


title: male_hypothalamus_27 months_1553264

description: Library name: 1553264


title: male_hippocampus_27 months_1377835

description: Library name: 1377835


title: male_hippocampus_27 months_1553263

description: Library name: 1553263


title: male_hypothalamus_27 months_1553262

description: Library name: 1553262


title: male_hypothalamus_27 months_1553261

description: Library name: 1553261


title: female_hippocampus_27 months_1377834

description: Library name: 1377834


title: male_hypothalamus_27 months_1553260

description: Library name: 1553260


title: male_hypothalamus_27 months_1553258

description: Library name: 1553258


title: male_hippocampus_21 months_1377831

description: Library name: 1377831


title: male_hippocampus_27 months_1377832

description: Library name: 1377832


title: male_hypothalamus_27 months_1553259

description: Library name: 1553259


title: female_hippocampus_27 months_1377829

description: Library name: 1377829


title: male_hippocampus_24 months_1377830

description: Library name: 1377830


title: female_hippocampus_21 months_1377826

description: Library name: 1377826


title: male_hypothalamus_27 months_1553257

description: Library name: 1553257


title: male_hippocampus_27 months_1377828

description: Library name: 1377828


title: male_cerebellum_27 months_1553256

description: Library name: 1553256


title: male_cerebellum_27 months_1553255

description: Library name: 1553255


title: male_cerebellum_27 months_1553252

description: Library name: 1553252


title: male_cerebellum_27 months_1553250

description: Library name: 1553250


title: female_hippocampus_27 months_1377823

description: Library name: 1377823


title: female_hippocampus_27 months_1377824

description: Library name: 1377824


title: female_hippocampus_27 months_1377822

description: Library name: 1377822


title: male_hippocampus_27 months_1377833

description: Library name: 1377833


title: male_cerebellum_27 months_1553249

description: Library name: 1553249


title: male_hippocampus_27 months_1377821

description: Library name: 1377821


title: male_cerebellum_27 months_1553248

description: Library name: 1553248


title: female_hippocampus_21 months_1377825

description: Library name: 1377825


title: female_hippocampus_27 months_1377819

description: Library name: 1377819


title: male_cerebellum_27 months_1553254

description: Library name: 1553254


title: female_hippocampus_27 months_1377820

description: Library name: 1377820


title: female_hippocampus_21 months_1377827

description: Library name: 1377827


title: male_cerebellum_27 months_1553245

description: Library name: 1553245


title: male_cerebellum_27 months_1553247

description: Library name: 1553247


title: male_cerebellum_27 months_1553246

description: Library name: 1553246


title: female_hypothalamus_27 months_1377817

description: Library name: 1377817


title: male_cortex_27 months_1553237

description: Library name: 1553237


title: male_hypothalamus_6 months_1377815

description: Library name: 1377815


title: male_hypothalamus_27 months_1553251

description: Library name: 1553251


title: female_hypothalamus_24 months_1377818

description: Library name: 1377818


title: male_hippocampus_27 months_1553232

description: Library name: 1553232


title: female_hypothalamus_27 months_1377816

description: Library name: 1377816


title: male_hypothalamus_6 months_1377814

description: Library name: 1377814


title: male_cortex_27 months_1553236

description: Library name: 1553236


title: male_cortex_27 months_1553233

description: Library name: 1553233


title: female_hypothalamus_21 months_1377812

description: Library name: 1377812


title: male_hippocampus_27 months_1553231

description: Library name: 1553231


title: female_hypothalamus_21 months_1377811

description: Library name: 1377811


title: male_hippocampus_27 months_1553229

description: Library name: 1553229


title: male_hypothalamus_24 months_1377813

description: Library name: 1377813


title: male_hippocampus_27 months_1553230

description: Library name: 1553230


title: male_hippocampus_27 months_1553228

description: Library name: 1553228


title: male_hippocampus_27 months_1553226

description: Library name: 1553226


title: female_hypothalamus_24 months_1377808

description: Library name: 1377808


title: male_hypothalamus_24 months_1377809

description: Library name: 1377809


title: male_hippocampus_27 months_1553225

description: Library name: 1553225


title: female_hypothalamus_21 months_1377807

description: Library name: 1377807


title: female_hypothalamus_24 months_1377806

description: Library name: 1377806


title: male_hippocampus_27 months_1553222

description: Library name: 1553222


title: male_hippocampus_27 months_1553224

description: Library name: 1553224


title: male_hippocampus_27 months_1553221

description: Library name: 1553221


title: male_hypothalamus_24 months_1377804

description: Library name: 1377804


title: male_hypothalamus_18 months_1553220

description: Library name: 1553220


title: male_hypothalamus_21 months_1377803

description: Library name: 1377803


title: male_hypothalamus_24 months_1377805

description: Library name: 1377805


title: male_hippocampus_27 months_1553223

description: Library name: 1553223


title: male_hypothalamus_18 months_1553218

description: Library name: 1553218


title: female_hypothalamus_21 months_1377799

description: Library name: 1377799


title: male_hypothalamus_18 months_1553219

description: Library name: 1553219


title: female_hypothalamus_24 months_1377801

description: Library name: 1377801


title: male_hypothalamus_6 months_1377810

description: Library name: 1377810


title: female_hypothalamus_21 months_1377800

description: Library name: 1377800


title: male_hippocampus_27 months_1377797

description: Library name: 1377797


title: male_hippocampus_18 months_1553215

description: Library name: 1553215


title: male_hypothalamus_18 months_1553208

description: Library name: 1553208


title: male_cortex_24 months_1377792

description: Library name: 1377792


title: male_hypothalamus_18 months_1553207

description: Library name: 1553207


title: male_hypothalamus_18 months_1553206

description: Library name: 1553206


title: male_cortex_21 months_1377794

description: Library name: 1377794


title: male_hippocampus_18 months_1553210

description: Library name: 1553210


title: male_cortex_21 months_1377793

description: Library name: 1377793


title: male_cortex_18 months_1553212

description: Library name: 1553212


title: male_hippocampus_27 months_1377796

description: Library name: 1377796


title: male_cortex_21 months_1377791

description: Library name: 1377791


title: male_cortex_21 months_1377789

description: Library name: 1377789


title: male_hippocampus_18 months_1553216

description: Library name: 1553216


title: male_hippocampus_18 months_1553209

description: Library name: 1553209


title: male_hypothalamus_21 months_1377802

description: Library name: 1377802


title: male_cortex_18 months_1553213

description: Library name: 1553213


title: male_hypothalamus_21 months_1377798

description: Library name: 1377798


title: male_hippocampus_18 months_1553205

description: Library name: 1553205


title: female_hippocampus_27 months_1377795

description: Library name: 1377795


title: male_hippocampus_18 months_1553204

description: Library name: 1553204


title: male_hippocampus_18 months_1553203

description: Library name: 1553203


title: male_cortex_18 months_1553201

description: Library name: 1553201


title: male_cortex_21 months_1377790

description: Library name: 1377790


title: male_cortex_21 months_1377788

description: Library name: 1377788


title: female_cortex_21 months_1377787

description: Library name: 1377787


title: male_cortex_18 months_1553200

description: Library name: 1553200


title: male_hypothalamus_18 months_1553199

description: Library name: 1553199


title: male_cerebellum_18 months_1553198

description: Library name: 1553198


title: male_cerebellum_18 months_1553197

description: Library name: 1553197


title: male_hippocampus_6 months_1553196

description: Library name: 1553196


title: male_cerebellum_6 months_1553195

description: Library name: 1553195


title: female_hypothalamus_21 months_1377782

description: Library name: 1377782


title: male_cortex_21 months_1377784

description: Library name: 1377784


title: male_cortex_21 months_1377783

description: Library name: 1377783


title: male_hypothalamus_21 months_1377779

description: Library name: 1377779


title: male_hypothalamus_21 months_1377778

description: Library name: 1377778


title: male_cerebellum_18 months_1553190

description: Library name: 1553190


title: male_hippocampus_6 months_1553193

description: Library name: 1553193


title: male_hippocampus_6 months_1553191

description: Library name: 1553191


title: female_hypothalamus_21 months_1377781

description: Library name: 1377781


title: female_hypothalamus_21 months_1377777

description: Library name: 1377777


title: male_hippocampus_6 months_1553192

description: Library name: 1553192


title: male_hippocampus_6 months_1553187

description: Library name: 1553187


title: male_hippocampus_6 months_1553189

description: Library name: 1553189


title: female_cortex_21 months_1377780

description: Library name: 1377780


title: male_hippocampus_6 months_1553188

description: Library name: 1553188


title: female_hypothalamus_27 months_1377772

description: Library name: 1377772


title: female_hypothalamus_24 months_1377775

description: Library name: 1377775


title: female_cortex_21 months_1377786

description: Library name: 1377786


title: female_hypothalamus_27 months_1377773

description: Library name: 1377773


title: male_hypothalamus_21 months_1377774

description: Library name: 1377774


title: female_cortex_21 months_1377785

description: Library name: 1377785


title: male_hippocampus_6 months_1553186

description: Library name: 1553186


title: male_hippocampus_6 months_1553185

description: Library name: 1553185


title: female_hypothalamus_24 months_1377776

description: Library name: 1377776


title: male_cerebellum_18 months_1553194

description: Library name: 1553194


title: female_hypothalamus_24 months_1377771

description: Library name: 1377771


title: male_cortex_24 months_1377770

description: Library name: 1377770


title: male_cerebellum_18 months_1553184

description: Library name: 1553184


title: male_cerebellum_18 months_1553183

description: Library name: 1553183


title: male_cortex_24 months_1377769

description: Library name: 1377769


title: male_cerebellum_18 months_1553181

description: Library name: 1553181


title: male_cerebellum_18 months_1553182

description: Library name: 1553182


title: male_cortex_27 months_1377767

description: Library name: 1377767


title: male_cortex_27 months_1377766

description: Library name: 1377766


title: male_cortex_18 months_1377768

description: Library name: 1377768


title: male_cerebellum_18 months_1553179

description: Library name: 1553179


title: male_hippocampus_18 months_1553177

description: Library name: 1553177


title: pe25ppe41_KO_2

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

description: Library name: pe25ppe41_KO_2

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis culture

growth_protocol: Wild-type (WT) H37Rv and the ppe51, pe25/ppe41 and ppe42 deletion strains were cultured in 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% Tyloxapol, and 100 μM sodium propionate until an OD600 of 0.8 was reached. Cells were then pelleted, resuspended in buffered water, and incubated for an additional 5 hours.

extract_protocol:
The bacteria were harvested at the indicated timepoint and resuspended in Trizol, and lysed by bead beating for 30 seconds at 6 m/s for 3 cycles, with intermittent cooling on ice. Cell debris was pelleted at 20,000 g for 1 minute, and the supernatant was transferred to a heavy phase-lock gel tube containing 300 μL of chloroform. The tubes were inverted for 2 minutes and centrifuged at 20,000 g for 5 minutes. RNA in the aqueous phase was precipitated with 300 μL of isopropanol and 300 μL of high-salt solution (0.8 M sodium citrate, 1.2 M sodium chloride). RNA was purified using the QIAGEN RNeasy kit, and ribosomal RNA was depleted using a previously published protocol [Culviner, P. H. et al doi:10.1128/mBio.00010-20 (2020)]. Briefly, a biotinylated oligo mixture of 23S, 16S, and 5S was incubated with RNA to anneal to rRNA, followed by incubation with streptavidin beads. mRNA was purified from the supernatant using Ampure XP beads.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and the ppe51 and pe25/ppe41 deletion strains were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit while the ppe42 deletion strain along with corresponding wild type were sequenced at Fred Hutch with Illumina NovoSeqX+.

tag: cell type

value: M. tuberculosis culture

tag: treatment

value: pe25/ppe41 knockout mutant


title: pe25ppe41_KO_3

description: Library name: pe25ppe41_KO_3


title: male_hypothalamus_18 months_1553174

description: Library name: 1553174


title: male_hypothalamus_18 months_1553175

description: Library name: 1553175


title: male_hippocampus_18 months_1553176

description: Library name: 1553176


title: male_cerebellum_18 months_1553180

description: Library name: 1553180


title: female_cortex_27 months_1377764

description: Library name: 1377764


title: male_hypothalamus_6 months_1553172

description: Library name: 1553172


title: male_hypothalamus_18 months_1553178

description: Library name: 1553178


title: pe25ppe41_KO_1

description: Library name: pe25ppe41_KO_1


title: male_cortex_24 months_1377765

description: Library name: 1377765


title: ppe51_KO_2

description: Library name: ppe51_KO_2

library_source: other

molecule: other

growth_protocol: Wild-type (WT) H37Rv and the ppe51 deletion strain were cultured in 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% Tyloxapol, and 100 μM sodium propionate until an OD600 of 0.8 was reached. Cells were then pelleted, resuspended in buffered water, and incubated for an additional 5 hours.

extract_protocol:
The bacteria were harvested at the indicated timepoint and resuspended in Trizol, and lysed by bead beating for 30 seconds at 6 m/s for 3 cycles, with intermittent cooling on ice. Cell debris was pelleted at 20,000 g for 1 minute, and the supernatant was transferred to a heavy phase-lock gel tube containing 300 μL of chloroform. The tubes were inverted for 2 minutes and centrifuged at 20,000 g for 5 minutes. RNA in the aqueous phase was precipitated with 300 μL of isopropanol and 300 μL of high-salt solution (0.8 M sodium citrate, 1.2 M sodium chloride). RNA was purified using the QIAGEN RNeasy kit, and ribosomal RNA was depleted using a previously published protocol [Culviner, P. H. et al doi:10.1128/mBio.00010-20 (2020)]. Briefly, a biotinylated oligo mixture of 23S, 16S, and 5S was incubated with RNA to anneal to rRNA, followed by incubation with streptavidin beads. mRNA was purified from the supernatant using Ampure XP beads.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit.

value: ppe51 knockout mutant


title: ppe51_KO_3

description: Library name: ppe51_KO_3


title: male_cortex_27 months_1377763

description: Library name: 1377763


title: male_cortex_27 months_1377762

description: Library name: 1377762


title: male_hypothalamus_6 months_1553170

description: Library name: 1553170

value: hypothalamus


title: female_cortex_27 months_1377761

description: Library name: 1377761


title: male_hypothalamus_6 months_1553171

description: Library name: 1553171

value: male


title: ppe51_KO_1

description: Library name: ppe51_KO_1


title: male_hypothalamus_18 months_1553173

description: Library name: 1553173


title: male_cortex_6 months_1553168

description: Library name: 1553168


title: WT_3

description: Library name: WT_3

value: wild type


title: male_hypothalamus_6 months_1553167

description: Library name: 1553167

value: Sprague Dawley


title: female_cortex_27 months_1377760

description: Library name: 1377760

value: cortex


title: male_cerebellum_6 months_1553165

description: Library name: 1553165


title: male_cerebellum_6 months_1553166

description: Library name: 1553166


title: WT_2

description: Library name: WT_2


title: male_cerebellum_6 months_1553164

description: Library name: 1553164


title: female_cortex_21 months_1377758

description: Library name: 1377758


title: BT245 FTT treatment day 10 Neurocult, biol rep 8

city: Montréal

first: Jacek

last: Majewski

state: QC

address: 740 Av. du Docteur-Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: FTT_Neuro_2

data_processing:
Raw reads trimmed with Atropos
Trimmed reads mapped with STAR aligner
Feature counts extracted with featureCounts
TPM quantification with salmon
Assembly: hg38
Supplementary files format and content: raw counts (CSV)

organism: Homo sapiens

source_name: Brain

growth_protocol: BT245 pediatric glioma cells were cultured in NeuroCult NS-A media (StemCell Technologies) supplemented with bFGF (10 ng/mL), rhEGF (20 ng/mL), and heparin (0.0002%). Plates were pre-coated with poly-L-ornithine (0.01%) and laminin (0.01 mg/mL) to support adhesion. Cells were maintained in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
miRNeasy Mini Kit (QIAGEN) with DNase digest using RNase-free DNase Set (QIAGEN)
Library preparation was performed with ribosomal RNA (rRNA) depletion (done at the McGill Genome Center using NEBNextUltra II Directional RNA)

treatment_protocol: Cells were treated with either FID (Forskolin 10 µM, ISX9 10 µM, DAPT 5 µM, Laduviglusib 3 µM, IBET151 2 µM) or FTT (Fasudil 50 µM, Tranilast 100 µM, Temozolomide 50 µM) drug combinations. Stock solutions were prepared in DMSO and diluted into media to final concentrations, with the same DMSO volume administered in control conditions. Treatments were applied for 5–10 days depending on the group, in either standard NeuroCult or BrainPhys media.

value: Brain

tag: cell line

value: Glioblastoma

value: FTT


title: male_cerebellum_6 months_1553159

description: Library name: 1553159


title: male_cortex_6 months_1553156

description: Library name: 1553156


title: male_cortex_6 months_1553155

description: Library name: 1553155


title: female_cortex_21 months_1377757

description: Library name: 1377757

value: female


title: WT_1

description: Library name: WT_1


title: female_cortex_27 months_1377759

description: Library name: 1377759


title: male_cerebellum_6 months_1553158

description: Library name: 1553158


title: male_cerebellum_6 months_1553153

description: Library name: 1553153


title: BT245 FTT treatment day 5, biol rep 7

description: Library name: FTT_1


title: BT245 FID treatment day 6, biol rep 6

description: Library name: FID_D6_1

value: FID


title: BT245 FID treatment day 10, biol rep 5

description: Library name: FID_2


title: male_cortex_6 months_1553152

description: Library name: 1553152


title: female_cortex_24 months_1377755

description: Library name: 1377755

value: 24 months


title: male_cerebellum_6 months_1553154

description: Library name: 1553154

value: cerebellum

value: 6 months


title: male_cerebellum_6 months_1553149

description: Library name: 1553149


title: male_hypothalamus_6 months_1553136

description: Library name: 1553136


title: male_cortex_6 months_1553157

description: Library name: 1553157


title: BT245 FID treatment day 10, biol rep 4

description: Library name: FID_1


title: male_hypothalamus_6 months_1553135

description: Library name: 1553135


title: female_cortex_21 months_1377754

description: Library name: 1377754

value: 21 months


title: female_cortex_21 months_1377753

description: Library name: 1377753


title: BT245 control Neurocult+DMSO, biol rep 3

description: Library name: Ctr_Neuro_2

value: DMSO


title: male_hypothalamus_6 months_1553130

description: Library name: 1553130


title: female_cortex_27 months_1377756

description: Library name: 1377756

value: 27 months


title: male_cerebellum_6 months_1553150

description: Library name: 1553150


title: male_hypothalamus_6 months_1553129

description: Library name: 1553129


title: male_hypothalamus_6 months_1553128

description: Library name: 1553128


title: BT245 control BrainPhys+DMSO, biol rep 2

description: Library name: Ctr_Brain_2


title: male_hypothalamus_6 months_1553127

description: Library name: 1553127


title: male_hypothalamus_6 months_1553125

description: Library name: 1553125


title: BT245 control BrainPhys+DMSO, biol rep 1

description: Library name: Ctr_Brain_1


title: female_cortex_24 months_1377750

description: Library name: 1377750


title: male_hypothalamus_6 months_1553126

description: Library name: 1553126


title: male_right atrium_12 months_1541872

description: Library name: 1541872

source_name: right atrium

value: right atrium

value: 12 months


title: HBE cells, CRE+VAF347 3

city: Baltimore

first: Wenjing

last: Gu

state: Maryland

address: 5501 Hopkins Bayview Circle, Asthma Allergy Center,FL 3A,RM4

institute: Johns Hopkins University

description:
Library name: Samples 6
RNA_seq counts.txt: ZC12

data_processing:
The library was sequenced using paired-end 2×150 bp sequencing on the Element AVITI system, and approximately 20 million paired-end reads were obtained for each sample.
Gene expression levels were defined as Salmon counts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include TPM values for each Sample

source_name: HBE cells

extract_protocol:
According to the manufacturer's instructions, the total RNA of each sample was processed using the Vazyme VAHTS Universal V10 RNA-seq Library Prep Kit, which selectively captures mRNA transcripts through poly(A) enrichment.
The enriched RNA was reverse-transcribed and constructed into a sequencing library following the manufacturer's protocol.

value: HBE cells

tag: genotype

value: WT


title: male_right atrium_12 months_1541871

description: Library name: 1541871

value: Sprague Dawley

value: male


title: female_cortex_24 months_1377752

description: Library name: 1377752

value: cortex


title: female_cortex_24 months_1377749

description: Library name: 1377749


title: HBE cells, CRE+VAF347 2

description:
Library name: Samples 5
RNA_seq counts.txt: ZC11


title: male_right atrium_12 months_1541870

description: Library name: 1541870


title: male_right atrium_12 months_1541866

description: Library name: 1541866


title: female_cortex_24 months_1377751

description: Library name: 1377751


title: female_cortex_24 months_1377748

description: Library name: 1377748


title: HBE cells, CRE+VAF347 1

description:
Library name: Samples 4
RNA_seq counts.txt: ZC10


title: male_right atrium_12 months_1541869

description: Library name: 1541869


title: female_cortex_24 months_1377747

description: Library name: 1377747


title: male_right atrium_12 months_1541865

description: Library name: 1541865


title: male_right atrium_12 months_1541868

description: Library name: 1541868


title: male_right atrium_12 months_1541864

description: Library name: 1541864


title: male_cortex_24 months_1377746

description: Library name: 1377746


title: male_right atrium_12 months_1541867

description: Library name: 1541867


title: male_right atrium_12 months_1541862

description: Library name: 1541862


title: HBE cells, CRE 2

description:
Library name: Samples 2
RNA_seq counts.txt: ZC5

value: CRE


title: HBE cells, CRE 3

description:
Library name: Samples 3
RNA_seq counts.txt: ZC6


title: female_cortex_24 months_1377745

description: Library name: 1377745


title: male_right atrium_12 months_1541863

description: Library name: 1541863


title: male_right ventricle_12 months_1541860

description: Library name: 1541860

source_name: right ventricle

value: right ventricle


title: male_cortex_24 months_1377743

description: Library name: 1377743


title: male_right ventricle_12 months_1541859

description: Library name: 1541859


title: male_cortex_24 months_1377742

description: Library name: 1377742


title: pole-3;pole-4, sRNA, rep2

city: Cambridge

first: Juan

middle: Carlos

last: Rueda Silva

address: 80 Tennis Ct Rd

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: Library name: pole-3pole-4_RppH_rep2

data_processing:
ChIP-Seq- Quality and Adaptor Trimming - Cutadapt
ChIP-Seq- Read aligment- BWA
ChIP-Seq- Peak calling and bdg generations- MACS3
ChIP-Seq- BigWig generation- bedGraphtoBigWig
ChIP-Seq- Differential enrichment analysis- DiffBind
RNA-Seq- Libraries were mapped, quality controlled, quantified and BigWigs were prepared using the standard Squire pipeline
sRNA-Seq- Quality and Adaptor Trimming - Cutadapt
sRNA-Seq- Mapping - STAR
sRNA-Seq- Count table generation - featureCounts
sRNA-Seq- Differential expression analysis - DeSEQ2
Assembly: Ensembl - WBCel235
Supplementary files format and content: .bw- library size normalized bigwigs for the sequencing tracks
Supplementary files format and content: .broadPeaks- MACS3 called broad peaks
Supplementary files format and content: .counts.tsv - raw gene and repeat RNA counts
Supplementary files format and content: .exon_norm_counts.txt - normalized 22G-RNA counts

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Worms were grown at 20C on HB101 Escherichia coli plates. Worms were synchronized by bleaching and synchronized young adults collected

extract_protocol:
RNA-Seq and sRNA-Seq samples were extracted with Trizol, in the case of sRNA-seq samples with treated with RppH. ChIP-Seq samples were crosslinked by 1% formalaldehyde and sonicated using a Diagenode Bioruptor Pico.
ChIP libraries were prepared using a standard paired ended DNA 150bp library. RNA libraries were prepared using a standard protocol with polyA enrichment. sRNA libraries were enriched for 22G-RNAs with RppH and sequenced using a standard sRNA library preparation protocol.

value: Whole animal

tag: developmental stage

value: Young adult

tag: chip antibody

value: RppH

tag: batch


title: pole-3;pole-4, sRNA, rep3

description: Library name: pole-3pole-4_RppH_rep3


title: male_right ventricle_12 months_1541857

description: Library name: 1541857


title: male_right ventricle_12 months_1541856

description: Library name: 1541856


title: male_right ventricle_12 months_1541855

description: Library name: 1541855


title: male_cortex_24 months_1377741

description: Library name: 1377741

value: 24 months


title: pola-1, sRNA, rep3

description: Library name: pola-1_RppH_rep3


title: male_right ventricle_12 months_1541858

description: Library name: 1541858


title: male_right ventricle_12 months_1541854

description: Library name: 1541854


title: male_left atrium_12 months_1541848

description: Library name: 1541848

source_name: left atrium

value: left atrium


title: male_right atrium_12 months_1541861

description: Library name: 1541861


title: male_cortex_24 months_1377744

description: Library name: 1377744


title: male_right ventricle_12 months_1541852

description: Library name: 1541852


title: male_right ventricle_12 months_1541853

description: Library name: 1541853


title: male_left atrium_12 months_1541846

description: Library name: 1541846


title: female_cortex_24 months_1377740

description: Library name: 1377740

value: female


title: male_right ventricle_12 months_1541849

description: Library name: 1541849


title: pole-3;pole-4, sRNA, rep1

description: Library name: pole-3pole-4_RppH_rep1


title: male_right ventricle_12 months_1541850

description: Library name: 1541850


title: mcm-2, sRNA, rep3

description: Library name: mcm-2_RppH_rep3


title: HBE cells, CRE 1

description:
Library name: Samples 1
RNA_seq counts.txt: ZC4


title: mcm-2, sRNA, rep4

description: Library name: mcm-2_RppH_rep4


title: male_left atrium_12 months_1541847

description: Library name: 1541847


title: pola-1, sRNA, rep1

description: Library name: pola-1_RppH_rep1


title: pola-1, sRNA, rep2

description: Library name: pola-1_RppH_rep2


title: male_cortex_6 months_1377737

description: Library name: 1377737

value: 6 months


title: male_left atrium_12 months_1541845

description: Library name: 1541845


title: female_cortex_6 months_1377738

description: Library name: 1377738


title: male_right ventricle_12 months_1541851

description: Library name: 1541851


title: male_left atrium_12 months_1541844

description: Library name: 1541844


title: male_left atrium_12 months_1541842

description: Library name: 1541842


title: male_left atrium_12 months_1541843

description: Library name: 1541843


title: female_cortex_24 months_1377739

description: Library name: 1377739


title: mcm-2, sRNA, rep1

description: Library name: mcm-2_RppH_rep1


title: mcm-2, sRNA, rep2

description: Library name: mcm-2_RppH_rep2


title: male_left atrium_12 months_1541841

description: Library name: 1541841


title: female_cortex_18 months_1377734

description: Library name: 1377734

value: 18 months


title: male_left atrium_12 months_1541838

description: Library name: 1541838


title: N2, sRNA, rep4

description: Library name: N2_RppH_rep4


title: female_cortex_6 months_1377735

description: Library name: 1377735


title: N2, sRNA, rep2

description: Library name: N2_RppH_rep2


title: male_left ventricle_12 months_1541836

description: Library name: 1541836

source_name: left ventricle

value: left ventricle


title: male_left ventricle_12 months_1541832

description: Library name: 1541832

value: 12 months


title: female_cortex_18 months_1377733

description: Library name: 1377733


title: male_left atrium_12 months_1541837

description: Library name: 1541837


title: male_left ventricle_12 months_1541834

description: Library name: 1541834


title: female_cortex_18 months_1377732

description: Library name: 1377732


title: N2, sRNA, rep3

description: Library name: N2_RppH_rep3


title: N2, sRNA, rep1

description: Library name: N2_RppH_rep1


title: male_left ventricle_12 months_1541835

description: Library name: 1541835


title: male_cortex_18 months_1377730

description: Library name: 1377730


title: male_left ventricle_12 months_1541833

description: Library name: 1541833


title: female_cortex_18 months_1377731

description: Library name: 1377731


title: male_left ventricle_12 months_1541830

description: Library name: 1541830


title: male_cortex_18 months_1377729

description: Library name: 1377729


title: male_left ventricle_12 months_1541829

description: Library name: 1541829


title: pole-3;pole-4, RNA, rep4

description: Library name: pole-3pole-4_RNA_rep4

molecule: polyA RNA


title: male_left ventricle_12 months_1541828

description: Library name: 1541828


title: male_left ventricle_12 months_1541827

description: Library name: 1541827


title: male_left ventricle_12 months_1541831

description: Library name: 1541831


title: male_cortex_18 months_1377728

description: Library name: 1377728


title: male_left ventricle_12 months_1541826

description: Library name: 1541826


title: male_left atrium_12 months_1541839

description: Library name: 1541839


title: pole-3;pole-4, RNA, rep3

description: Library name: pole-3pole-4_RNA_rep3


title: pole-3;pole-4, RNA, rep2

description: Library name: pole-3pole-4_RNA_rep2


title: female_cortex_18 months_1377727

description: Library name: 1377727


title: female_cortex_18 months_1377726

description: Library name: 1377726


title: male_left ventricle_12 months_1541825

description: Library name: 1541825


title: pole-3;pole-4, RNA, rep1

description: Library name: pole-3pole-4_RNA_rep1


title: male_right atrium_6 months_1541822

description: Library name: 1541822

value: right atrium


title: male_right atrium_6 months_1541824

description: Library name: 1541824


title: male_right ventricle_6 months_1541820

description: Library name: 1541820


title: male_right atrium_6 months_1541818

description: Library name: 1541818


title: pola-1, RNA, rep4

description: Library name: pola-1_RNA_rep4


title: male_right atrium_6 months_1541823

description: Library name: 1541823


title: male_right atrium_6 months_1541819

description: Library name: 1541819


title: male_right atrium_6 months_1541816

description: Library name: 1541816


title: male_cortex_18 months_1377725

description: Library name: 1377725


title: male_right atrium_6 months_1541817

description: Library name: 1541817


title: male_cortex_6 months_1377736

description: Library name: 1377736


title: pola-1, RNA, rep3

description: Library name: pola-1_RNA_rep3


title: pola-1, RNA, rep2

description: Library name: pola-1_RNA_rep2


title: female_cortex_18 months_1377724

description: Library name: 1377724


title: female_cortex_27 months_1377722

description: Library name: 1377722

value: 27 months


title: male_cortex_24 months_1377723

description: Library name: 1377723


title: mcm-2, RNA, rep4

description: Library name: mcm-2_RNA_rep4


title: male_right atrium_6 months_1541815

description: Library name: 1541815

value: Sprague Dawley


title: male_right atrium_6 months_1541813

description: Library name: 1541813

value: male


title: male_right ventricle_6 months_1541812

description: Library name: 1541812


title: male_cortex_27 months_1377721

description: Library name: 1377721

value: cortex


title: pola-1, RNA, rep1

description: Library name: pola-1_RNA_rep1


title: mcm-2, RNA, rep3

description: Library name: mcm-2_RNA_rep3


title: female_cortex_27 months_1377720

description: Library name: 1377720


title: male_right ventricle_6 months_1541810

description: Library name: 1541810


title: male_right ventricle_6 months_1541809

description: Library name: 1541809


title: female_cortex_27 months_1377719

description: Library name: 1377719


title: male_right atrium_6 months_1541808

description: Library name: 1541808


title: male_right atrium_6 months_1541814

description: Library name: 1541814


title: male_right ventricle_6 months_1541807

description: Library name: 1541807


title: male_right ventricle_6 months_1541806

description: Library name: 1541806


title: female_cortex_6 months_1377718

description: Library name: 1377718


title: male_right ventricle_6 months_1541805

description: Library name: 1541805


title: N2, RNA, rep4

description: Library name: N2_RNA_rep4

value: WT


title: male_right ventricle_6 months_1541803

description: Library name: 1541803

value: right ventricle


title: male_right ventricle_6 months_1541801

description: Library name: 1541801


title: female_cortex_6 months_1377717

description: Library name: 1377717


title: N2, RNA, rep2

description: Library name: N2_RNA_rep2

value: Whole animal


title: mcm-2, RNA, rep1

description: Library name: mcm-2_RNA_rep1

value: Young adult


title: N2, RNA, rep3

description: Library name: N2_RNA_rep3


title: male_right ventricle_6 months_1541802

description: Library name: 1541802


title: male_right ventricle_6 months_1541811

description: Library name: 1541811


title: male_left atrium_6 months_1541800

description: Library name: 1541800


title: male_left atrium_6 months_1541799

description: Library name: 1541799


title: male_left atrium_6 months_1541798

description: Library name: 1541798


title: N2, RNA, rep1

description: Library name: N2_RNA_rep1


title: male_cortex_12 months_1377715

description: Library name: 1377715


title: male_cortex_12 months_1377714

description: Library name: 1377714


title: pole-3;pole-4, input, rep4

description: Library name: pole-3pole-4_rep4_input

library_source: genomic

molecule: genomic DNA


title: mcm-2, RNA, rep2

description: Library name: mcm-2_RNA_rep2


title: male_left atrium_6 months_1541796

description: Library name: 1541796


title: male_cortex_12 months_1377713

description: Library name: 1377713


title: male_right ventricle_6 months_1541804

description: Library name: 1541804


title: male_left atrium_6 months_1541797

description: Library name: 1541797


title: male_left atrium_6 months_1541795

description: Library name: 1541795


title: female_cortex_12 months_1377716

description: Library name: 1377716


title: pole-3;pole-4, input, rep3

description: Library name: pole-3pole-4_rep3_input


title: female_cortex_12 months_1377712

description: Library name: 1377712


title: male_left atrium_6 months_1541794

description: Library name: 1541794


title: pole-3;pole-4, input, rep2

description: Library name: pole-3pole-4_rep2_input


title: male_left atrium_6 months_1541793

description: Library name: 1541793


title: male_left atrium_6 months_1541792

description: Library name: 1541792


title: male_left atrium_6 months_1541791

description: Library name: 1541791


title: male_left atrium_6 months_1541790

description: Library name: 1541790


title: pola-1, input, rep4

description: Library name: pola-1_rep4_input


title: female_cortex_12 months_1377710

description: Library name: 1377710


title: male_left ventricle_6 months_1541787

description: Library name: 1541787


title: female_cortex_12 months_1377709

description: Library name: 1377709


title: male_left atrium_6 months_1541789

description: Library name: 1541789


title: male_left ventricle_6 months_1541786

description: Library name: 1541786


title: female_cortex_12 months_1377708

description: Library name: 1377708


title: pola-1, input, rep3

description: Library name: pola-1_rep3_input


title: male_left ventricle_6 months_1541788

description: Library name: 1541788


title: pola-1, input, rep2

description: Library name: pola-1_rep2_input


title: male_left ventricle_6 months_1541784

description: Library name: 1541784


title: pola-1, input, rep1

description: Library name: pola-1_rep1_input


title: female_cortex_12 months_1377707

description: Library name: 1377707


title: male_left ventricle_6 months_1541785

description: Library name: 1541785


title: male_left ventricle_6 months_1541783

description: Library name: 1541783


title: male_cortex_18 months_1377706

description: Library name: 1377706


title: pole-3;pole-4, input, rep1

description: Library name: pole-3pole-4_rep1_input


title: mcm-2, input, rep4

description: Library name: mcm-2_rep4_input


title: male_left ventricle_6 months_1541781

description: Library name: 1541781


title: mcm-2, input, rep3

description: Library name: mcm-2_rep3_input


title: male_left ventricle_6 months_1541780

description: Library name: 1541780


title: male_cortex_18 months_1377705

description: Library name: 1377705


title: male_left ventricle_6 months_1541779

description: Library name: 1541779


title: male_left ventricle_6 months_1541778

description: Library name: 1541778


title: mcm-2, input, rep1

description: Library name: mcm-2_rep1_input


title: female_cortex_18 months_1377703

description: Library name: 1377703


title: male_left atrium_21 months_1541775

description: Library name: 1541775

value: 21 months


title: male_cortex_12 months_1377702

description: Library name: 1377702


title: male_left atrium_21 months_1541776

description: Library name: 1541776


title: male_left ventricle_6 months_1541777

description: Library name: 1541777


title: N2, input, rep4

description: Library name: N2_rep4_input


title: female_cortex_12 months_1377700

description: Library name: 1377700


title: male_left ventricle_6 months_1541782

description: Library name: 1541782


title: mcm-2, input, rep2

description: Library name: mcm-2_rep2_input


title: male_left atrium_21 months_1541774

description: Library name: 1541774


title: male_left atrium_21 months_1541770

description: Library name: 1541770


title: male_left atrium_21 months_1541771

description: Library name: 1541771


title: N2, input, rep3

description: Library name: N2_rep3_input


title: male_cortex_12 months_1377701

description: Library name: 1377701


title: male_cortex_18 months_1377704

description: Library name: 1377704


title: male_left atrium_21 months_1541769

description: Library name: 1541769


title: N2, input, rep2

description: Library name: N2_rep2_input


title: male_left atrium_21 months_1541773

description: Library name: 1541773


title: male_left atrium_21 months_1541768

description: Library name: 1541768


title: N2, input, rep1

description: Library name: N2_rep1_input


title: male_left atrium_21 months_1541766

description: Library name: 1541766


title: female_hippocampus_18 months_1377698

description: Library name: 1377698

value: hippocampus


title: male_left atrium_21 months_1541772

description: Library name: 1541772

value: left atrium


title: pole-3;pole-4, H3K27me3 ChIP, rep4

description: Library name: pole-3pole-4_H3K27me3_rep4


title: female_hypothalamus_27 months_1377697

description: Library name: 1377697

value: hypothalamus

value: female


title: male_left atrium_21 months_1541767

description: Library name: 1541767


title: male_left atrium_21 months_1541765

description: Library name: 1541765


title: pole-3;pole-4, H3K27me3 ChIP, rep3

description: Library name: pole-3pole-4_H3K27me3_rep3


title: female_cortex_12 months_1377699

description: Library name: 1377699


title: male_right atrium_21 months_1541764

description: Library name: 1541764


title: male_right atrium_21 months_1541761

description: Library name: 1541761


title: pole-3;pole-4, H3K27me3 ChIP, rep2

description: Library name: pole-3pole-4_H3K27me3_rep2


title: male_right atrium_21 months_1541760

description: Library name: 1541760


title: pole-3;pole-4, H3K27me3 ChIP, rep1

description: Library name: pole-3pole-4_H3K27me3_rep1


title: male_cortex_27 months_1377694

description: Library name: 1377694


title: female_hippocampus_18 months_1377695

description: Library name: 1377695

value: 18 months


title: male_right atrium_21 months_1541757

description: Library name: 1541757


title: female_hippocampus_18 months_1377693

description: Library name: 1377693


title: male_right atrium_21 months_1541755

description: Library name: 1541755


title: male_right atrium_21 months_1541759

description: Library name: 1541759


title: male_right atrium_21 months_1541758

description: Library name: 1541758


title: male_right atrium_21 months_1541756

description: Library name: 1541756


title: male_right atrium_21 months_1541762

description: Library name: 1541762


title: male_right atrium_21 months_1541754

description: Library name: 1541754


title: pola-1, H3K27me3 ChIP, rep3

description: Library name: pola-1_H3K27me3_rep3


title: female_cortex_27 months_1377692

description: Library name: 1377692


title: male_cortex_27 months_1377691

description: Library name: 1377691


title: male_right ventricle_21 months_1541751

description: Library name: 1541751


title: male_right ventricle_21 months_1541752

description: Library name: 1541752


title: male_right atrium_21 months_1541753

description: Library name: 1541753


title: pola-1, H3K27me3 ChIP, rep2

description: Library name: pola-1_H3K27me3_rep2


title: male_right ventricle_21 months_1541750

description: Library name: 1541750


title: female_hippocampus_18 months_1377696

description: Library name: 1377696


title: male_right ventricle_21 months_1541749

description: Library name: 1541749


title: pola-1, H3K27me3 ChIP, rep4

description: Library name: pola-1_H3K27me3_rep4


title: male_cortex_27 months_1377690

description: Library name: 1377690


title: mcm-2, H3K27me3 ChIP, rep4

description: Library name: mcm-2_H3K27me3_rep4


title: male_right ventricle_21 months_1541748

description: Library name: 1541748


title: female_cortex_6 months_1377689

description: Library name: 1377689

value: 6 months


title: pola-1, H3K27me3 ChIP, rep1

description: Library name: pola-1_H3K27me3_rep1


title: mcm-2, H3K27me3 ChIP, rep3

description: Library name: mcm-2_H3K27me3_rep3


title: male_right ventricle_21 months_1541745

description: Library name: 1541745


title: male_right ventricle_21 months_1541744

description: Library name: 1541744


title: female_cortex_6 months_1377688

description: Library name: 1377688


title: female_cortex_6 months_1377687

description: Library name: 1377687


title: female_cortex_27 months_1377686

description: Library name: 1377686


title: mcm-2, H3K27me3 ChIP, rep2

description: Library name: mcm-2_H3K27me3_rep2


title: male_right ventricle_21 months_1541743

description: Library name: 1541743


title: male_right ventricle_21 months_1541741

description: Library name: 1541741


title: male_left ventricle_21 months_1541740

description: Library name: 1541740

value: left ventricle


title: male_right ventricle_21 months_1541742

description: Library name: 1541742


title: male_cortex_27 months_1377685

description: Library name: 1377685


title: N2, H3K27me3 ChIP, rep4

description: Library name: N2_H3K27me3_rep4


title: male_left ventricle_21 months_1541738

description: Library name: 1541738


title: male_left ventricle_21 months_1541739

description: Library name: 1541739


title: N2, H3K27me3 ChIP, rep2

description: Library name: N2_H3K27me3_rep2


title: TSB3

city: wuhan

first: hongrong

last: hong

state: hubei province

address: Huazhong Agricultural University, Lion Street, Hongshan District

department: preventive veterinary medicine

country: China

institute: Huazhong Agricultural University

description: Library name: sample6

data_processing:
After sequencing on an Illumina sequencer, image analysis, and base identification, the raw reads were harvested after quality control. Q30 was used for QC. The raw reads were de-joined using cutadapt [2] software (v1.9.3) to remove low-quality reads and retain reads >=16 nt in length. The original reads were de-joined using cutadapt software (v1.9.3) to remove low-quality reads and retain reads >=16 nt in length to obtain trimmed reads.
Assembly: Then, tDRmapper software to identify the tRFs and tiRNAs in each sample and the corresponding counts, and then use the edgeR software (v3.16.1) to identify the tRFs and tiRNAs in each sample. (v3.16.5) was used to normalize and calculate the P-value and Fold Change between the two groups of samples (with replicates), and screen for differentially expressed tRF&tiRNA.
Supplementary files format and content: excle and fastq

organism: Brucella melitensis M5-90

source_name: bacteria

extract_protocol:
Different samples used for RNA extraction require different treatments: For cultured adherent cells: Remove the culture medium and add 1 mL of Trizol per well for six-well plates or 0.5 mL per well for 12-well plates. Pipette the solution up and down 3–5 times to ensure complete lysis, then transfer the lysate into a centrifuge tube.
Sequencing library was determined by Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kit (Agilent, part # 5067-1504)

value: bacteria


title: male_cortex_6 months_1377684

description: Library name: 1377684


title: male_left ventricle_21 months_1541737

description: Library name: 1541737


title: male_left ventricle_21 months_1541736

description: Library name: 1541736


title: TSB2

description: Library name: sample5


title: male_right ventricle_21 months_1541747

description: Library name: 1541747


title: male_left ventricle_21 months_1541735

description: Library name: 1541735


title: male_cortex_6 months_1377682

description: Library name: 1377682


title: TSB1

description: Library name: sample4


title: mcm-2, H3K27me3 ChIP, rep1

description: Library name: mcm-2_H3K27me3_rep1


title: pole-3;pole-4, H3 ChIP, rep4

description: Library name: pole-3pole-4_H3_rep4


title: male_cortex_6 months_1377681

description: Library name: 1377681


title: pole-3;pole-4, H3 ChIP, rep3

description: Library name: pole-3pole-4_H3_rep3


title: female_cortex_6 months_1377683

description: Library name: 1377683


title: male_left ventricle_21 months_1541733

description: Library name: 1541733


title: male_left ventricle_21 months_1541732

description: Library name: 1541732


title: GW3

description: Library name: sample3


title: male_cortex_6 months_1377680

description: Library name: 1377680


title: pole-3;pole-4, H3 ChIP, rep2

description: Library name: pole-3pole-4_H3_rep2


title: male_left ventricle_21 months_1541731

description: Library name: 1541731


title: GW2

description: Library name: sample2


title: male_left ventricle_21 months_1541734

description: Library name: 1541734


title: male_cortex_6 months_1377679

description: Library name: 1377679


title: GW1

description: Library name: sample1


title: N2, H3K27me3 ChIP, rep1

description: Library name: N2_H3K27me3_rep1


title: pole-3;pole-4, H3 ChIP, rep1

description: Library name: pole-3pole-4_H3_rep1


title: male_cortex_6 months_1377678

description: Library name: 1377678


title: pola-1, H3 ChIP, rep4

description: Library name: pola-1_H3_rep4


title: pola-1, H3 ChIP, rep3

description: Library name: pola-1_H3_rep3


title: male_left ventricle_21 months_1541729

description: Library name: 1541729


title: male_cortex_12 months_1377677

description: Library name: 1377677

value: 12 months


title: male_cortex_12 months_1377676

description: Library name: 1377676


city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: Library name: Ogataea-polymorpha_insitu-HiC-DpnII_rep2_initial-sequencing

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.7+ for all analyses. Briefly, raw fastq files were mapped to either NCBI RefSeq assembly GCF_001664045.1 reference genome for data from Ogataea polymorpha, or the newly constructed "Ohag_RefGenome_v1.fasta" reference genome detailed in this manuscript for data from Ogataea haglerorum using bowtie2 (version 2.5+), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings (with DpnII [GATC] restriction sites, as defined in the .bed files produced by the hicFindRestSites command in hicexplorer), and resulting images of the contact matrix images were made with hicPlotMatrix; (total) merged matrices were constructed by first merging all replicates using the cat command and processing them n an identical manner. Contact map images are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012), performed with the hicCorrectMatrix program, to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA. The command hicCorrelate was used to plot scatterplots and to calculate the Pearson correlation values of Hi-C replicates, while the commands hicFindTADs (with flags --correctForMultipleTesting fdr [false discovery rate], --thresholdComparisons 0.3, and --delta 0.15) and hicPlotTADs visualized TAD-like structures across Ogataea chromosomes.
Assembly: Assembly: NCBI RefSeq assembly GCF_001664045.1 for data from Ogataea polymorpha, or the newly constructed "Ohag_RefGenome_v1.fasta" detailed in this manuscript for data from Ogataea haglerorum.
Supplementary files format and content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins of a defined size (the resolution of the Hi-C contact matrix), and the interactions between the bins is reported - either raw contact counts or Knight-Ruiz corrected contact counts.

organism: Ogataea polymorpha

source_name: log phase cells

growth_protocol: Ogataea strains were grown from freezer stocks on YPD plates (1% w/v yeast extract, 2% w/v peptone, 2% w/v glucose, 2% w/v agar) at 30°C. Individual colonies were used to inoculate liquid cultures of YPD broth, which were grown for 16 hours (overnight) with shaking at 30oC. New Ogataea cultures were inoculated by backdiluting the overnight culture into fresh YPD medium and cultures were grown to log-phase (OD600 0.8 to 1.2) at 30oC with shaking.

extract_protocol:
First, the concentration of genomic DNA per cell pellet was determined by resuspending one cell pellet 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 ug proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 ug RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Using a fresh cell pellet, the approximate amount of that cell pellet containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x DpnII restriction enzyme buffer and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Cells were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used eight and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon on either an Illumina Hiseq 4000 as 100 nucleotide (nt) paired-end (PE100) reads or an Illumina Novaseq 6000 as 59 nt paired-end (PE59) reads.

treatment_protocol: Log-phase Ogataea cultures were then crosslinked 10 min in 1% formaldehyde (w/v) at room temperature, with shaking at 100 rpm, and then quenched with 0.3M glycine for 10 minutes at room temperature. Crosslinked cells were pelleted by centrifugation at 1,800xg, the supernatant was decanted, and cell pellets were stored at -80oC

value: SH4330 (NCYC495 MATa ura3)

value: log phase cells

value: wild type


title: pola-1, H3 ChIP, rep1

description: Library name: pola-1_H3_rep1


description: Library name: Ogataea-polymorpha_insitu-HiC-DpnII_rep1_initial-sequencing


description: Library name: Ogataea-haglerorum_insitu-HiC-DpnII_rep2_reseq

organism: Ogataea haglerorum


title: male_cortex_12 months_1377675

description: Library name: 1377675

value: cortex

value: male


title: male_right atrium_24 months_1541713

description: Library name: 1541713

value: Sprague Dawley

value: right atrium

value: 24 months


title: mcm-2, H3 ChIP, rep4

description: Library name: mcm-2_H3_rep4

value: Whole animal

value: Young adult


title: male_left ventricle_21 months_1541730

description: Library name: 1541730

value: 21 months


description: Library name: Ogataea-haglerorum_insitu-HiC-DpnII_rep1_reseq


title: male_right atrium_24 months_1541712

description: Library name: 1541712


title: mcm-2, H3 ChIP, rep3

description: Library name: mcm-2_H3_rep3


title: female_hypothalamus_12 months_1377674

description: Library name: 1377674

value: hypothalamus

value: female


title: male_right atrium_24 months_1541714

description: Library name: 1541714


title: Ogataea-haglerorum_polyA-mRNAseq_rep5

description: Library name: Ogataea-haglerorum_polyA-mRNAseq_rep5

data_processing:
Raw fastq files were mapped to the newly constructed "Ohag_RefGenome_v1.fasta" reference genome detailed in this manuscript for data from Ogataea haglerorum with hisat2 v2.2.1 (Kim et al., 2019), output sam files were converted to bam files, sorted, and indexed with samtools (Li et al., 2009), and Bins Per Million (BPM; the equivalent of Transcripts per Million [TPM])-normalized bigwig files were made by deeptools (Ramírez et al. 2016) for display on IGV (Robinson et al. 2011). For making quintile or top/bottom 5% expressed gene files, each RNA-seq replicate was separately mapped to the respective genome using hisat2 and gene count files for each replicate were generated by htseq (Putri et al. 2022) using the “count” subprogram. The resulting gene count files for each gene were normalized for gene length by TPM counts, and the TPM values for each replicate were averaged, in Microsoft Excel.
Assembly: Assembly: the newly constructed "Ohag_RefGenome_v1.fasta" detailed in this manuscript for data from Ogataea haglerorum.
Supplementary files format and content: htseq-count files are two column files with the first column being the gene name and the second column being the count value of that gene; the bigwig files are generated by Deeptools (Ramírez et al. 2016); briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin; the bigwig file format is a single column with the enrichment per bin displayed, and the seven headers indicate the chromosome and bin size.

source_name: log growth cells

extract_protocol:
One volume of acid phenol (Invitrogen) was added prior to incubation for 60 minutes at 65°C, with vortexing every 10 minutes. Samples were centrifuged for 5 minutes at 16,000 x g at 4°C, and one additional round of acid phenol and one round of chloroform extraction were performed, followed by ethanol precipitation. Samples were treated with DNase I (Sigma-Aldrich) for 15 minutes at room temperature, followed by incubation with 2mM EDTA at 65°C for 10 minutes. Samples were purified using the RNA Clean and Concentrator-25 kit (Zymo Research) according to manufacturer’s instructions. Sample quantity was evaluated with a Qubit 3.0 using the RNA Broad Range kit (ThermoFisher) and integrity was evaluated by TapeStation (Agilent)
Polyadenylated messenger RNA (polyA mRNA) was selected for high-throughput sequencing with the Universal Plus mRNA-Seq library preparation kit by Tecan per the manufacturer’s protocols; triple polyA mRNA-seq replicate libraries were constructed for each strain. All polyA mRNA-seq libraries were Illumina sequenced at the GC3F on a NovaSeq 6000 as SR150 reads.

treatment_protocol: Cells were harvested by centrifugation prior to the RNA isolation protocol

value: log growth cells

value: haploid yeast cells


title: mcm-2, H3 ChIP, rep1

description: Library name: mcm-2_H3_rep1


title: Ogataea-haglerorum_polyA-mRNAseq_rep4

description: Library name: Ogataea-haglerorum_polyA-mRNAseq_rep4


title: male_hypothalamus_12 months_1377672

description: Library name: 1377672


title: male_right atrium_24 months_1541708

description: Library name: 1541708


title: Ogataea-haglerorum_H4K16ac_ChIPseq_rep4

description: Library name: Ogataea-haglerorum_H4K16ac_ChIPseq_rep4

data_processing:
Raw ChIP-seq data files, as fastq files, were mapped to the appropriate Ogataea species genome with bowtie2 (version 2.5.4), and output sam files were converted to sorted bam files using samtools (version 1.14), which were used by Deeptools (version 3.5.0) to produce bigwig files with 25 basepair bin resolution, normalized by Reads per Kilobase Per Million Reads (RPKM), for display on the Integrative Genomics Viewer (IGV)
Assembly: Assembly: NCBI RefSeq assembly GCF_001664045.1 for data from Ogataea polymorpha, or the newly constructed "Ohag_RefGenome_v1.fasta" detailed in this manuscript for data from Ogataea haglerorum.
Supplementary files format and content: the bigwig files are generated by Deeptools (Ramírez et al. 2016); briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin; the bigwig file format is a single column with the enrichment per bin displayed, and the seven headers indicate the chromosome and bin size.

extract_protocol:
Pellets were resuspended in ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + 1x Halt proteinase inhibitor cocktail [ThermoFisherScientific, cat #78441]) and cells were disrupted by sonication, which simultaneously sheared chromatin, using a Bioruptor Pico (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 2uL) and samples were nutated overnight at 4oC. The next day, equilibrated protein A/G magnetic agarose beads (Pierce/Thermo Scientific; cat # PI78609) was added to bind the antibody, incubated for 2 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were RNaseA treated for two hours at 50oC, then proteinase K treated for 2 hours at 50oC, the DNA was extracted with phenol:chloroform:IAA (25:24:1), and DNA was precipitated with ethanol, sodium acetate, and glycogen, and allowed to precipitate overnight at -80oC. The next day, samples were precipitated by centrifugation, washed, dried in a Speedvac and resuspended in 30uL TE. ChIP DNA was quantified with a Qubit 3.0 using the HS method.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the NEB Next Ultra II Library Preparation Kit (New England Biolabs, #E7645L) with the adapters from the NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1 [E7335L] or 2 [E7500L]) according to the manufacturer’s instructions, except that final libraries were only PCR-amplified using eight cycles for amplification.

tag: chipseq antibody

value: ActiveMotif anti-H4K16ac antibody, cat# 39167, lot# 08719003


title: male_hypothalamus_12 months_1377673

description: Library name: 1377673

value: 12 months


title: male_right atrium_24 months_1541707

description: Library name: 1541707


title: male_right atrium_24 months_1541711

description: Library name: 1541711


title: pola-1, H3 ChIP, rep2

description: Library name: pola-1_H3_rep2


title: female_hypothalamus_12 months_1377669

description: Library name: 1377669


title: Ogataea-haglerorum_H4K16ac_ChIPseq_rep3

description: Library name: Ogataea-haglerorum_H4K16ac_ChIPseq_rep3


title: male_hypothalamus_12 months_1377671

description: Library name: 1377671


title: N2, H3 ChIP, rep4

description: Library name: N2_H3_rep4

value: WT


title: Ogataea-haglerorum_H4K16ac_ChIPseq_rep2

description: Library name: Ogataea-haglerorum_H4K16ac_ChIPseq_rep2

value: log phase cells


title: female_hypothalamus_12 months_1377670

description: Library name: 1377670


title: N2, H3 ChIP, rep2

description: Library name: N2_H3_rep2


title: male_right atrium_24 months_1541709

description: Library name: 1541709


title: male_right atrium_24 months_1541706

description: Library name: 1541706


title: Ogataea-haglerorum_polyA-mRNAseq_rep1

description: Library name: Ogataea-haglerorum_polyA-mRNAseq_rep1


title: N2, H3 ChIP, rep3

description: Library name: N2_H3_rep3


title: Ogataea-haglerorum_H4K16ac_ChIPseq_rep1

description: Library name: Ogataea-haglerorum_H4K16ac_ChIPseq_rep1

value: wild type


title: female_hypothalamus_12 months_1377667

description: Library name: 1377667


title: male_hypothalamus_18 months_1377668

description: Library name: 1377668

value: 18 months


title: zebrafish anal fin, xantho-leucophore, rep5

city: Charlottesville

first: Delai

last: Huang

state: VA

address: 2071 Winterfield Circle

institute: University of Virginia

description: Library name: XL5

data_processing:
Raw data was demultiplexed using bcl2fastq with default setting.
Data cleaned using fastp with default setting.
Quantified using kallisto with default setting.
Assembly: GRCz11
Supplementary files format and content: tsv files contains target id, full length of the transcripts, effective length, estimated number of fragments and tpm.

organism: Danio rerio

source_name: anal fin

extract_protocol:
Tissue from 20 fish was dissociated into a single-cell suspension, and healthy EGFP⁺ cells were isolated by fluorescence-activated cell sorting. Total mRNA was then extracted using RNAqueous™-Micro Total RNA Isolation Kit.
Libraries were constructed using the SMART-Seq mRNA LP kit following manufacturer's protocol.

value: anal fin

value: xantho-leucophore


title: Ogataea-haglerorum_H3K9ac_ChIPseq_rep4

description: Library name: Ogataea-haglerorum_H3K9ac_ChIPseq_rep4

value: ActiveMotif anti-H3K9ac antibody, cat# 39137, lot# 28720002


title: zebrafish anal fin, xantho-leucophore, rep4

description: Library name: XL4


title: zebrafish anal fin, xantho-leucophore, rep1

description: Library name: XL1


title: zebrafish anal fin, xantho-leucophore, rep3

description: Library name: XL3


title: male_right atrium_24 months_1541704

description: Library name: 1541704

value: Sprague Dawley

value: right atrium

value: male

value: 24 months


title: male_right ventricle_24 months_1541700

description: Library name: 1541700

value: right ventricle


title: male_right ventricle_24 months_1541699

description: Library name: 1541699


title: Ogataea-haglerorum_H3K9ac_ChIPseq_rep3

description: Library name: Ogataea-haglerorum_H3K9ac_ChIPseq_rep3


title: male_right atrium_24 months_1541703

description: Library name: 1541703


title: Ogataea-haglerorum_H3K9ac_ChIPseq_rep2

description: Library name: Ogataea-haglerorum_H3K9ac_ChIPseq_rep2


title: Ogataea-haglerorum_H3K9ac_ChIPseq_rep1

description: Library name: Ogataea-haglerorum_H3K9ac_ChIPseq_rep1


title: female_hypothalamus_27 months_1377666

description: Library name: 1377666

value: hypothalamus

value: female

value: 27 months


title: male_right atrium_24 months_1541710

description: Library name: 1541710


title: zebrafish anal fin, xantho-leucophore, rep2

description: Library name: XL2


title: zebrafish anal fin, xanthophore, rep5

description: Library name: X5

value: xanthophore


title: female_hypothalamus_12 months_1377664

description: Library name: 1377664

value: 12 months


title: male_hypothalamus_27 months_1377665

description: Library name: 1377665


title: male_hypothalamus_18 months_1377662

description: Library name: 1377662


title: male_right ventricle_24 months_1541701

description: Library name: 1541701


title: Ogataea-haglerorum_H3K4me3_ChIPseq_rep2

description: Library name: Ogataea-haglerorum_H3K4me3_ChIPseq_rep2

value: ActiveMotif anti-H3K4me3 antibody, cat# 39159, lot# 31420006


title: zebrafish anal fin, xanthophore, rep4

description: Library name: X4


title: male_right atrium_24 months_1541705

description: Library name: 1541705


title: male_right ventricle_24 months_1541698

description: Library name: 1541698


title: male_hypothalamus_18 months_1377661

description: Library name: 1377661


title: female_hypothalamus_12 months_1377663

description: Library name: 1377663


title: pJ23106_timP, Mutazyme, Phusion, replicate 3

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

country: France

institute: University of Bordeaux

description: Library name: P_TimP_EP3_P

data_processing:
Raw FASTQ files were generated by the sequencing platform.
(I) Quality control. Read quality was assessed using FastQC v0.11.9 and aggregated with MultiQC v1.22.1. Illumina adapter sequences were removed using Cutadapt v4.8  with the parameters “-e 0.10 -O 20 -m 30 --match-read-wildcards -n 2”. Low-quality bases at the 3′ end and low-quality reads were removed using Prinseq-lite v0.20.4 with “-trim_qual_right 28 -min_qual_mean 28”.
(II) Assembly of paired-end reads. Read pairs were recovered with cmpfastq and assembled into single sequences using PANDAseq v2.11 with parameters “-N -o 20 -O 0 -t 0.6 -A simple_bayesian -C empty”.
(III) Mapping to the reference. Assembled reads were aligned to the timP mRNA amplicon reference sequence (“promoter” or “no promoter” depending on the sample) using BWA-MEM (BWA v0.7.17) with parameters “-A 1 -B 4 -O 6 -E 1 -L 10,10”.
(IV) Extraction of mutated sequences. Reads containing a single nucleotide substitution and matching the expected length (330 or 308 nt for “promoter” and “no promoter”, respectively) were extracted using BamTools v2.5.2. Among those, sequences containing no substitutions in the promoter region (positions 1-35 or 1-13 for “promoter” and “no promoter”, respectively) and a single nucleotide substitution in the TimP mRNA sequence (295 nt) compared to the reference were retrieved using utilities from the GenomicAlignments 1.38.2, Rsamtools 2.18.0, and dplyr 1.1.4 packages in R 4.3.2.
(V) Statistical analysis. Differential expression analysis was performed to compare single substitution frequencies at each position between “no promoter” and “promoter” constructs using Trinity 2.15.1 and the R package DESeq2 1.42.1. Samples amplified with DreamTaq and Mutazyme II were analyzed independently, and in both cases, replicates amplified by KAPA and Phusion were pooled, and biological “no promoter” and “promoter” replicates paired. Substitutions were considered significantly over- or under-represented when the adjusted P-value (Padj, corresponding to the False Discovery Rate) was ≤ 0.05 and the absolute log2 fold change (|log2FC|) was ≥ 1.
Assembly: NC_016810.1 (positions 2672651-2672945)
Supplementary files format and content: format: Excel spreadsheet; content: normalized counts, log2 fold-changes, and p-values of combined replicates (statistical analysis of single substitutions by sequence)

organism: Escherichia coli str. K-12 substr. MG1655

extract_protocol:
The genomic DNA of bacterial colonies was extracted using the EasyPure Bacteria Genomic DNA Kit (Transgen Biotech).
Two DNA sequences encoding timP mRNA of S. enterica under the control of the PJ23106 promoter (“promoter” library) or the native timP -10 box (“no promoter” library) and flanked with homology region for homologous recombination in E. coli chromosome were synthesized by Eurofins. These two DNA sequences were amplified by 30 cycles of PCR using the Dream Taq DNA polymerase (Thermo Fisher Scientific) and purified. One hundred ng of the purified DNA samples were further mutagenized using the GeneMorph II Random Mutagenesis kit (Mutazyme II DNA polymerase, Agilent) as per the manufacturer’s instructions with 30 PCR cycles. The PCR reactions were purified and 200 ng of the DreamTaq and the Mutazyme II PCR samples were introduced and recombined into the E. coli XTL632 chromosome. Recombinant bacteria were selected on Tet/SacB counter-selection plates at 42°C. Colonies were harvested from the plates and the DNA was extracted using the EasyPure Bacteria Genomic DNA Kit (Transgen Biotech). The experiment, including the PCR and mutagenesis steps, was repeated 3 times. The extracted DNA was amplified to add the Illumina adapters using the KAPA HiFi HotStart ReadyMix (Roche) as well as using the Phusion Hot Start polymerase (ThermoScientific). The amplicons were sequenced at the Bordeaux Transcriptome Genome Platform (PGBT, Cestas-Pierroton, France) using Illumina NextSeq 2000 P1 instrument in paired-end mode 2x300 nt (overlapping reads).


title: Ogataea-haglerorum_H3K4me3_ChIPseq_rep1

description: Library name: Ogataea-haglerorum_H3K4me3_ChIPseq_rep1

value: log phase cells


title: female_hypothalamus_18 months_1377659

description: Library name: 1377659


title: zebrafish anal fin, xanthophore, rep1

description: Library name: X1


title: pJ23106_timP, Mutazyme, Phusion, replicate 1

description: Library name: P_TimP_EP1_P


description: Library name: Ogataea-haglerorum_insitu-HiC-DpnII_rep2_initial-sequencing

value: wild type


title: male_right ventricle_24 months_1541696

description: Library name: 1541696


title: male_right ventricle_24 months_1541697

description: Library name: 1541697


title: mcm-2, H3 ChIP, rep2

description: Library name: mcm-2_H3_rep2

value: Whole animal

value: Young adult


title: pJ23106_timP, Mutazyme, Phusion, replicate 2

description: Library name: P_TimP_EP2_P


title: zebrafish anal fin, xanthophore, rep2

description: Library name: X2

value: anal fin


title: female_hypothalamus_18 months_1377657

description: Library name: 1377657

value: 18 months


title: female_hypothalamus_18 months_1377656

description: Library name: 1377656


title: male_right ventricle_24 months_1541695

description: Library name: 1541695

value: Sprague Dawley


title: pJ23106_timP, Mutazyme, KAPA, replicate 1

description: Library name: P_TimP_EP1_K


title: female_hypothalamus_18 months_1377660

description: Library name: 1377660


title: male_right ventricle_24 months_1541694

description: Library name: 1541694


title: male_right ventricle_24 months_1541692

description: Library name: 1541692


description: Library name: Ogataea-polymorpha_insitu-HiC-DpnII_rep2_reseq

value: SH4330 (NCYC495 MATa ura3)


title: female_hypothalamus_18 months_1377658

description: Library name: 1377658


description: Library name: Ogataea-haglerorum_insitu-HiC-DpnII_rep1_initial-sequencing


title: zebrafish anal fin, xanthophore, rep3

description: Library name: X3