title: AB12158

description:
28.2.21_D6_2_41BB_Endo
MARSseq


title: AB12156

status: Public on Mar 01 2024

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
28.2.21_D6_1_41BB_Endo
MARSseq

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

molecule: polyA RNA

organism: Mus musculus

source_name: tumor

growth_protocol: 8 to 10 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
mice were treated with 250ug of aPD1 or/and 200ug of a41BB.

tag: tissue

value: tumor

tag: cell type

value: endogenous CD8+

tag: experiment id

tag: days post_adoptive_transfer

tag: mouse number

tag: treatment


title: AB12160

description:
28.2.21_D6_2_41BB_Endo
MARSseq


title: AB11989

description:
Tumor8_PD1+41BB_Endo_5
MARSseq


title: AB11986

description:
Tumor1_Ctrl_Endo_1
MARSseq


title: AB11988

description:
Tumor9_PD1+41BB_Endo_4
MARSseq


title: AB12175

description:
28.2.21_D6_6_aPD1+41BB_Endo
MARSseq


title: AB12157

description:
28.2.21_D6_1_41BB_OT1
MARSseq

value: OT1 CD8+


title: AB11987

description:
Tumor6_41BB_Endo_2
MARSseq


title: AB11984

description:
Tumor7_41BB_Endo_5
MARSseq


title: AB11980

description:
Tumor9_PD1+41BB_Endo_2
MARSseq


title: AB11985

description:
Tumor8_PD1+41BB_Endo_4
MARSseq


title: AB12155

description:
28.2.21_D6_1_41BB_Endo
MARSseq


title: AB11982

description:
Tumor10_PD1+41BB_Endo_2
MARSseq


title: AB11979

description:
Tumor9_PD1+41BB_Endo_1
MARSseq


title: AB11977

description:
Tumor8_PD1+41BB_Endo_2
MARSseq


title: AB11976

description:
Tumor8_PD1+41BB_Endo_1
MARSseq


title: AB11978

description:
Tumor8_PD1+41BB_Endo_3
MARSseq


title: AB12162

description:
28.2.21_D6_2_41BB_OT1
MARSseq


title: AB11975

description:
Tumor7_41BB_Endo_3
MARSseq


title: AB11974

description:
Tumor7_41BB_Endo_2
MARSseq


title: AB11973

description:
Tumor7_41BB_Endo_1
MARSseq


title: AB11990

description:
Tumor9_PD1+41BB_Endo_3
MARSseq


title: AB11972

description:
Tumor6_41BB_Endo_1
MARSseq


title: AB11971

description:
Tumor5_41BB_Endo_2
MARSseq


title: AB13106

description:
30.6.21_MC38_5_Ctl_TCRb+
MARSseq

value: endogenous CD45+


title: AB11897

description:
Tumor10_PD1+41BB_Endo_3
MARSseq


title: AB11970

description:
Tumor5_41BB_Endo_1
MARSseq


title: AB11896

description:
Tumor9_PD1+41BB_Endo_5
MARSseq


title: AB11981

description:
Tumor10_PD1+41BB_Endo_1
MARSseq


title: AB11895

description:
Tumor8_PD1+41BB_Endo_5
MARSseq


title: AB11891

description:
Tumor6_41BB_Endo_3
MARSseq


title: AB11983

description:
Tumor7_41BB_Endo_4
MARSseq


title: AB11893

description:
Tumor7_41BB_Endo_6
MARSseq


title: AB11894

description:
Tumor7_41BB_Endo_7
MARSseq


title: AB11892

description:
Tumor6_41BB_Endo_4
MARSseq


title: AB11888

description:
Tumor4_pd1_Endo_1
MARSseq


title: AB11887

description:
Tumor2_Ctrl_Endo_2
MARSseq


title: AB11890

description:
Tumor5_41BB_Endo_3
MARSseq


title: AB11889

description:
Tumor4_pd1_Endo_2
MARSseq


title: AB11886

description:
Tumor2_Ctrl_Endo_1
MARSseq


title: AB11868

description:
Tumor_7_PD1-Syn_Pic
MARSseq


title: AB11867

description:
Tumor_10_PD1-XCR1_CD3
MARSseq


title: AB11869

description:
Tumor_7_PD1-Syn_CD11c
MARSseq


title: AB11863

description:
Tumor_2_PBS_CD11c
MARSseq


title: AB11864

description:
Tumor_2_PBS_CD3
MARSseq


title: AB11862

description:
Tumor_2_PBS_Pic
MARSseq


title: AB11861

description:
LN_7_PD1-Syn_CD3
MARSseq

source_name: LN

value: LN


title: AB11860

description:
LN_7_PD1-Syn_CD11c
MARSseq


title: AB11859

description:
LN_7_PD1-Syn_Pic
MARSseq


title: AB11858

description:
LN_12_PD1-XCR1_CD3
MARSseq


title: AB11857

description:
LN_12_PD1-XCR1_CD11c
MARSseq


title: AB11856

description:
LN_12_PD1-XCR1_Pic
MARSseq


title: AB11855

description:
LN_3_PBS_CD3
MARSseq


title: AB11854

description:
LN_3_PBS_CD11c
MARSseq


title: AB11853

description:
LN_3_PBS_Pic
MARSseq


title: AB11851

description:
LN_6_PD1-Syn_CD11c
MARSseq


title: AB11852

description:
LN_6_PD1-Syn_CD3
MARSseq


title: AB11850

description:
LN_6_PD1-Syn_Pic
MARSseq


title: AB11849

description:
LN_10_PD1-XCR1_CD3
MARSseq


title: AB11848

description:
LN_10_PD1-XCR1_CD11c
MARSseq


title: AB11865

description:
Tumor_10_PD1-XCR1_Pic
MARSseq


title: AB11843

description:
Tumor_6_PD1-Syn_CD11c
MARSseq


title: AB11845

description:
LN_2_PBS_Pic
MARSseq


title: AB11866

description:
Tumor_10_PD1-XCR1_CD11c
MARSseq


title: AB11846

description:
LN_2_PBS_CD11c
MARSseq


title: AB11841

description:
Tumor_9_PD1-XCR1_CD3
MARSseq


title: AB11844

description:
Tumor_6_PD1-Syn_CD3
MARSseq


title: AB11839

description:
Tumor_1_PBS_CD3
MARSseq


title: AB11842

description:
Tumor_6_PD1-Syn_Pic
MARSseq


title: AB11837

description:
LN_5_PD1-Syn_CD3
MARSseq


title: AB11836

description:
LN_5_PD1-Syn_CD11c
MARSseq


title: AB11838

description:
Tumor_1_PBS_CD11c
MARSseq


title: AB11835

description:
LN_5_PD1-Syn_Pic
MARSseq


title: AB11833

description:
LN_9_PD1-XCR1_CD11c
MARSseq


title: AB11834

description:
LN_9_PD1-XCR1_CD3
MARSseq


title: AB11528

description:
Tumor9_ctrl_CD11c_1
MARSseq


title: AB11530

description:
Tumor9_ctrl_CD11c_2
MARSseq


title: AB11527

description:
Tumor9_ctrl_CD8+_1
MARSseq


title: AB11525

description:
Tumor8_ctrl_CD11c_2
MARSseq


title: AB11847

description:
LN_2_PBS_CD3
MARSseq


title: AB11523

description:
Tumor3_aPD1_CD11c_2
MARSseq


title: AB11522

description:
Tumor3_aPD1_CD11c_1
MARSseq


title: AB11521

description:
Tumor3_aPD1_CD8+_2
MARSseq


title: AB11840

description:
Tumor_9_PD1-XCR1_CD11c
MARSseq


title: AB11516

description:
Tumor3_aPD1_tPIC_1
MARSseq


title: AB11514

description:
Tumor1_aPD1_CD8+_1
MARSseq


title: AB11333

description:
Tumor8_ctrl_tPIC_1
MARSseq


title: AB11517

description:
Tumor1_aPD1_CD8+_2
MARSseq


title: AB11518

description:
Tumor1_aPD1_CD11c_2
MARSseq


title: AB11520

description:
Tumor3_aPD1_CD8+_1
MARSseq


title: AB11519

description:
Tumor3_aPD1_tPIC_2
MARSseq


title: AB11529

description:
Tumor9_ctrl_tPIC_1
MARSseq


title: AB11328

description:
Tumor5_aPD1_CD8+_2
MARSseq


title: AB11513

description:
Tumor1_aPD1_tPIC_1
MARSseq


title: AB11331

description:
Tumor8_ctrl_CD8+_1
MARSseq


title: AB11330

description:
Tumor5_aPD1_CD11c_2
MARSseq


title: AB11329

description:
Tumor5_aPD1_CD11c_1
MARSseq


title: AB11332

description:
Tumor8_ctrl_CD11c_1
MARSseq


title: AB11327

description:
Tumor5_aPD1_CD8+_1
MARSseq


title: AB11524

description:
Tumor8_ctrl_CD8+_2
MARSseq


title: AB11325

description:
Tumor5_aPD1_tPIC_1
MARSseq


title: AB11326

description:
Tumor5_aPD1_tPIC_2
MARSseq


title: AB11262

description:
D6_MC38_T_a41BB_5__3
MARSseq


title: AB11263

description:
D6_MC38_T_a41BB_7__1
MARSseq


title: AB11264

description:
D6_MC38_T_a41BB_7__2
MARSseq


title: AB11261

description:
D6_MC38_T_a41BB_5__2
MARSseq


title: AB11526

description:
Tumor8_ctrl_tPIC_2
MARSseq


title: AB11258

description:
D6_MC38_T_aPD1_4__2
MARSseq


title: AB11257

description:
D6_MC38_T_aPD1_4__1
MARSseq


title: AB11515

description:
Tumor1_aPD1_CD11c_1
MARSseq


title: AB11256

description:
D6_MC38_T_aPD1_3__1
MARSseq


title: AB11259

description:
D6_MC38_T_aPD1_4__3
MARSseq


title: AB11255

description:
D6_MC38_T_Ctrl2__2
MARSseq


title: AB11254

description:
D6_MC38_T_Ctrl2__1
MARSseq


title: AB11251

description:
D6_MC38_T1_aPD1+a41BB_5
MARSseq


title: AB11253

description:
D6_MC38_T_Ctrl1__2
MARSseq


title: AB11250

description:
D6_MC38_T1_aPD1+a41BB_4
MARSseq


title: AB11249

description:
D6_MC38_T1_aPD1+a41BB_3
MARSseq


title: AB11248

description:
D6_MC38_T1_aPD1+a41BB_2
MARSseq


title: AB11244

description:
D6_MC38_T3_aPD1+a41BB_1
MARSseq


title: AB11247

description:
D6_MC38_T1_aPD1+a41BB_1
MARSseq


title: AB11252

description:
D6_MC38_T_Ctrl1__1
MARSseq


title: AB11242

description:
021120_B16OVA/OT1/41BB_D2_aPD1_T3_1
MARSseq


title: AB11243

description:
021120_B16OVA/OT1/41BB_D2_Ctrl_T1_1
MARSseq


title: AB11260

description:
D6_MC38_T_a41BB_5__1
MARSseq


title: AB11240

description:
021120_B16OVA/OT1/41BB_D2_a41BB_T5_1
MARSseq


title: AB11238

description:
021120_B16OVA/OT1/41BB_D2_aPD1+a41BB_T7_2
MARSseq


title: AB11239

description:
021120_B16OVA/OT1/41BB_D2_a41BB_T6_1
MARSseq


title: AB11236

description:
021120_B16OVA/OT1/41BB_D2_aPD1+a41BB_T8_1
MARSseq


title: AB11235

description:
D2_MC38_T5_ctrl__2
MARSseq


title: AB11237

description:
021120_B16OVA/OT1/41BB_D2_aPD1+A41bb_T7_1
MARSseq


title: AB11233

description:
D2_MC38_T4_ctrl__1
MARSseq


title: AB11232

description:
D2_MC38_T3_ctrl__2
MARSseq


title: AB11234

description:
D2_MC38_T5_ctrl__1
MARSseq


title: AB11230

description:
D2_MC38_T2_ctrl__1
MARSseq


title: AB11229

description:
D2_MC38_T1_ctrl__1
MARSseq


title: AB11231

description:
D2_MC38_T3_ctrl__1
MARSseq


title: AB11228

description:
D2_MC38_T10_aPD1__1
MARSseq


title: AB11227

description:
D2_MC38_T9_aPD1__1
MARSseq


title: AB11226

description:
D2_MC38_T7_aPD1__2
MARSseq


title: AB11245

description:
D6_MC38_T2_aPD1+a41BB_1
MARSseq


title: AB11224

description:
D2_MC38_T15_A41bb__1
MARSseq


title: AB11225

description:
D2_MC38_T7_aPD1__1
MARSseq


title: AB11241

description:
021120_B16OVA/OT1/41BB_D2_aPD1_T4_1
MARSseq


title: AB11246

description:
D6_MC38_T2_aPD1+a41BB_2
MARSseq


title: AB11223

description:
D2_MC38_T13_A41bb__2
MARSseq


title: AB11221

description:
D2_MC38_T12_A41bb__1
MARSseq


title: AB11222

description:
D2_MC38_T13_A41bb__1
MARSseq


title: AB11219

description:
D2_MC38_T20_aPD1+A41bb__1
MARSseq


title: AB11218

description:
D2_MC38_T19_aPD1+A41bb__1
MARSseq


title: AB11217

description:
D2_MC38_T18_aPD1+A41bb__2
MARSseq


title: AB11216

description:
D2_MC38_T18_aPD1+A41bb__1
MARSseq


title: AB11220

description:
D2_MC38_T11_A41bb__1
MARSseq


title: AB11215

description:
D2_MC38_T17_aPD1+A41bb__3
MARSseq


title: AB11214

description:
D2_MC38_T17_aPD1+A41bb__2
MARSseq


title: AB11211

description:
D2_MC38_T16_aPD1+A41bb__2
MARSseq


title: AB10700

description:
20201001_S6_OT1_D6_Tumor1_Ctrl_1
MARSseq

value: OT1 CD8+_or_endogenous CD8+


title: AB10701

description:
20201001_S6_OT1_D6_Tumor1_Ctrl_2
MARSseq


title: AB11210

description:
D2_MC38_T16_aPD1+A41bb__1
MARSseq


title: AB11213

description:
D2_MC38_T17_aPD1+A41bb__1
MARSseq


title: AB10699

description:
20201001_S6_OT1_D6_Tumor2_Ctrl_4
MARSseq


title: AB10697

description:
081020_MC38_D2_a41bb15_1
MARSseq


title: AB10698

description:
20201001_S6_OT1_D6_Tumor2_Ctrl_3
MARSseq


title: AB10695

description:
081020_MC38_D2_a41bb14_1
MARSseq


title: AB10693

description:
081020_MC38_D2_aPD1_9_1
MARSseq


title: AB10696

description:
081020_MC38_D2_a41bb14_2
MARSseq


title: AB10694

description:
081020_MC38_D2_aPD1_10_1
MARSseq


title: AB10687

description:
081020_MC38_D2_a41bb13_3
MARSseq


title: AB10685

description:
081020_MC38_D2_a41bb13_1
MARSseq


title: AB10683

description:
081020_MC38_D2_a41bb11_2
MARSseq


title: AB10684

description:
081020_MC38_D2_a41bb12_1
MARSseq


title: AB10678

description:
081020_MC38_D2_aPD1_7_3
MARSseq


title: AB10680

description:
081020_MC38_D2_aPD1_8_2
MARSseq


title: AB10679

description:
081020_MC38_D2_aPD1_8_1
MARSseq


title: AB10677

description:
081020_MC38_D2_aPD1_7_2
MARSseq


title: AB11212

description:
D2_MC38_T16_aPD1+A41bb__3
MARSseq


title: AB10674

description:
081020_MC38_D2_aPD1+a41BB18_2
MARSseq


title: AB10681

description:
081020_MC38_D2_aPD1_8_3
MARSseq


title: AB10682

description:
081020_MC38_D2_a41bb11_1
MARSseq


title: AB10673

description:
081020_MC38_D2_aPD1+a41BB18_1
MARSseq


title: AB10672

description:
081020_MC38_D2_aPD1+a41BB17_3
MARSseq


title: AB10675

description:
081020_MC38_D2_aPD1+a41BB18_3
MARSseq


title: AB10671

description:
081020_MC38_D2_aPD1+a41BB17_2
MARSseq


title: AB10670

description:
081020_MC38_D2_aPD1+a41BB17_1
MARSseq


title: AB10669

description:
081020_MC38_D2_aPD1+a41BB16_3
MARSseq


title: AB10668

description:
081020_MC38_D2_aPD1+a41BB16_2
MARSseq


title: AB10665

description:
081020_MC38_D2_Ctrl3_2
MARSseq


title: AB10666

description:
081020_MC38_D2_Ctrl3_3
MARSseq


title: AB10667

description:
081020_MC38_D2_aPD1+a41BB16_1
MARSseq


title: AB10664

description:
081020_MC38_D2_Ctrl3_1
MARSseq


title: AB10663

description:
081020_MC38_D2_Ctrl2_2
MARSseq


title: AB10661

description:
081020_MC38_D2_Ctrl1_2
MARSseq


title: AB10659

description:
20200914_OT1-41BB_D6_Tumor10_aPD1+a41BB_1
MARSseq


title: AB10662

description:
081020_MC38_D2_Ctrl2_1
MARSseq


title: AB10656

description:
081020_MC38_D2_aPD1_7_5
MARSseq


title: AB10658

description:
20200914_OT1-41BB_D6_Tumor1_Ctrl_1
MARSseq


title: AB10657

description:
20200914_OT1-41BB_D6_Tumor6_a41BB_1
MARSseq


title: AB10676

description:
081020_MC38_D2_aPD1_7_1
MARSseq


title: AB10644

description:
20201001_S6_OT1_D6_Tumor2_Ctrl_2
MARSseq


title: AB10655

description:
081020_MC38_D2_aPD1_7_4
MARSseq


title: AB10641

description:
20201001_S6_OT1_D6_Tumor4_aPD1_3
MARSseq


title: AB10625

description:
20201001_S6_OT1_D6_Tumor5_aPD1_3
MARSseq


title: AB10629

description:
081020_MC38_D2_aPD1+a41BB18_4
MARSseq


title: AB10626

description:
20201001_S6_OT1_D6_Tumor5_aPD1_4
MARSseq


title: AB10628

description:
081020_MC38_D2_aPD1+a41BB17_5
MARSseq


title: AB10640

description:
20201001_S6_OT1_D6_Tumor4_aPD1_2
MARSseq


title: AB10642

description:
20201001_S6_OT1_D6_Tumor4_aPD1_4
MARSseq


title: AB10639

description:
20201001_S6_OT1_D6_Tumor4_aPD1_1
MARSseq


title: AB10623

description:
20201001_S6_OT1_D6_Tumor5_aPD1_1
MARSseq


title: AB10624

description:
20201001_S6_OT1_D6_Tumor5_aPD1_2
MARSseq


title: AB10482

description:
20200914_OT1-41BB_D6_Tumor2_Ctrl_1
MARSseq


title: AB10481

description:
20200914_OT1-41BB_D6_Tumor4_aPD1_1
MARSseq


title: AB10660

description:
081020_MC38_D2_Ctrl1_1
MARSseq


title: AB10368

description:
20200917_OT1-KO_D6_Tumor13_BFP_Ctrl_1
MARSseq


title: AB10370

description:
20200917_OT1-KO_D6_Tumor9_41BB_Ctrl_2
MARSseq


title: AB10478

description:
20200914_OT1-41BB_D6_Tumor8_aPD1+a41BB_2
MARSseq


title: AB10480

description:
20200914_OT1-41BB_D6_Tumor5_a41BB_1
MARSseq


title: AB10479

description:
20200914_OT1-41BB_D6_Tumor9_aPD1+a41BB_1
MARSseq


title: AB10363

description:
20200917_OT1-KO_D6_Tumor14_BFP_Ctrl_1
MARSseq


title: AB10361

description:
20200917_OT1-KO_D6_Tumor6_Zbdb32_PD1_1
MARSseq


title: AB10359

description:
20200917_OT1-KO_D6_Tumor5_Zbdb32_PD1_1
MARSseq


title: AB10357

description:
20200917_OT1-KO_D6_Tumor1_Zbdb32_Ctrl_1
MARSseq


title: AB10356

description:
20200914_OT1-41BB_D6_Tumor2_Ctrl
MARSseq


title: AB10477

description:
20200914_OT1-41BB_D6_Tumor8_aPD1+a41BB_1
MARSseq


title: AB10362

description:
20200917_OT1-KO_D6_Tumor2_Zbdb32_Ctrl_1
MARSseq


title: AB10355

description:
20200914_OT1-41BB_D6_Tumor4_aPD1
MARSseq


title: AB10367

description:
20200917_OT1-KO_D6_Tumor3_Zbdb32_Ctrl_1
MARSseq


title: AB10476

description:
20200914_OT1-41BB_D6_Tumor3_aPD1_2
MARSseq


title: AB10366

description:
20200917_OT1-KO_D6_Tumor10_41BB_PD1_1
MARSseq


title: AB10475

description:
20200914_OT1-41BB_D6_Tumor3_aPD1_1
MARSseq


title: AB10369

description:
20200917_OT1-KO_D6_Tumor9_41BB_Ctrl_1
MARSseq


title: AB10350

description:
20200914_OT1-41BB_D6_Tumor8_aPD1+a41BB
MARSseq


title: AB10282

description:
20200824_MC38_D10_Tumor7_41BB_1
MARSseq


title: AB10281

description:
20200824_MC38_D13_Tumor3_Ctrl_3
MARSseq


title: AB10283

description:
20200824_MC38_D13_Tumor4_aPD1_2
MARSseq


title: AB10278

description:
20200824_MC38_D13_Tumor2_Ctrl_2
MARSseq


title: AB10276

description:
20200824_MC38_D13_Tumor1_Ctrl_2
MARSseq


title: AB10630

description:
081020_MC38_D2_aPD1+a41BB18_5
MARSseq


title: AB10365

description:
20200917_OT1-KO_D6_Tumor15_BFP_PD1_1
MARSseq


title: AB10643

description:
20201001_S6_OT1_D6_Tumor2_Ctrl_1
MARSseq


title: day 4 INTa6+EpCAM+ cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME without Act A biol rep 2

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

country: Germany

institute: University of Goettingen

description:
cjPGCLCs_pre-ME-ActA_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

library_source: transcriptomic

data_processing:
Quality check of the raw reads was done by FastQC v0.11.8, and subsequently mapped to the Callithrix jacchus reference genome assembly calJac4 using STAR 2.7.0a
Aligned reads were assigned to gene annotation using HTSeq-count version 0.11.
Differential gene expression was calculated using DESeq2. Genes were considered differentially expressed if they had an absolute log2FoldChange exceeding 2 and an adjusted p-value of less than 0.05
Reads were normalized by scale factor using DESeq2.
Assembly: calJac4
Supplementary files format and content: tab-delimited text files include counts normalized by DESeq2 size factor

organism: Callithrix jacchus

extract_protocol:
Total RNA was isolated using PicoPure RNA isolation kit or Qiagen RNeasy Plus Kit  kit. 40 ng of RNA were used for RNA-seq
NEBNext Ultra II Directional RNA library Prep Kit fro Illumina was used according to the manufacturer's instructions

tag: cell line

value: Culture in cjPSCM, induction without ActA, CXCR4+EpCAM+ FACS-sorted cells


title: AB10353

description:
20200914_OT1-41BB_D6_Tumor1_Ctrl
MARSseq


title: day 4 INTa6+EpCAM+ cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME without Act A biol rep 1

description:
cjPGCLCs_pre-ME-ActA_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: AB10274

description:
20200803_MC38_D10_Tumor12_aPD1+a41BB_2
MARSseq


title: day 4 INTa6-EpCAM- cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME without Act A biol rep 2

description:
soma_pre-ME-ActA_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Culture in cjPSCM, induction without ActA, CXCR4-EpCAM- FACS-sorted cells


title: AB10273

description:
20200803_MC38_D10_Tumor12_aPD1+a41BB_1
MARSseq


title: day 4 INTa6-EpCAM- cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME without Act A biol rep 1

description:
soma_pre-ME-ActA_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: AB10358

description:
20200917_OT1-KO_D6_Tumor4_Zbdb32_PD1_1
MARSseq


title: AB10627

description:
081020_MC38_D2_aPD1+a41BB17_4
MARSseq


title: AB10360

description:
20200917_OT1-KO_D6_Tumor5_Zbdb32_PD1_2
MARSseq


title: AB10364

description:
20200917_OT1-KO_D6_Tumor14_BFP_Ctrl_2
MARSseq


title: AB10272

description:
20200803_MC38_D10_Tumor11_aPD1+a41BB_2
MARSseq


title: AB10354

description:
20200914_OT1-41BB_D6_Tumor7_a41BB
MARSseq


title: AB10352

description:
20200914_OT1-41BB_D6_Tumor3_aPD1
MARSseq


title: AB10351

description:
20200914_OT1-41BB_D6_Tumor10_aPD1+a41BB
MARSseq


title: day 4 INTa6-EpCAM- cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME with Act A biol rep 2

description:
soma_pre-ME+ActA_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Culture in cjPSCM, induction with ActA, CXCR4-EpCAM- FACS-sorted cells


title: Pre-ME induced with Act A from iPSCs cultured in TESR biol rep 2

description:
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Precursor of mesendoderm

value: Culture in TESR, induction with ActA


title: AB10268

description:
20200803_MC38_D10_Tumor10_aPD1+a41BB_2
MARSseq


title: Pre-ME induced without Act A from iPSCs cultured in TESR biol rep 2

value: Culture in TESR, induction without ActA


title: AB10279

description:
20200824_MC38_D13_Tumor2_Ctrl_3
MARSseq


title: AB10277

description:
20200824_MC38_D13_Tumor1_Ctrl_3
MARSseq


title: Pre-ME induced without Act A from iPSCs cultured in TESR biol rep 1


title: AB10280

description:
20200824_MC38_D13_Tumor3_Ctrl_2
MARSseq


title: Pre-ME induced without Act A from cjiPSCs cultured in cjPSCM biol rep 1

description:
cjPSCM_pre-ME-ActA_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Culture in cjPSCM, induction without ActA


title: Pre-ME induced without Act A from cjiPSCs cultured in cjPSCM biol rep 2

description:
cjPSCM_pre-ME-ActA_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: Pre-ME induced with Act A from iPSCs cultured in TESR biol rep 1


title: AB10266

description:
20200803_MC38_D10_Tumor8_a41BB_3
MARSseq


title: AB10275

description:
20200803_MC38_D10_Tumor12_aPD1+a41BB_3
MARSseq


title: day 4 INTa6+EpCAM+ cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME with Act A biol rep 2

description:
cjPGCLCs_pre-ME+ActA_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Culture in cjPSCM, induction with ActA, CXCR4+EpCAM+ FACS-sorted cells


title: AB10271


title: AB10265

description:
Biomek MARS_03.09.20_H1_20200824_MC38_D13_Tumor8_a41BB_1
MARSseq


title: Pre-ME induced with Act A from cjiPSCs cultured in cjPSCM biol rep 2

description:
cjPSCM_pre-ME+ActA_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Culture in cjPSCM, induction with ActA


title: AB10264

description:
Biomek MARS_03.09.20_G1_20200824_MC38_D13_Tumor10_aPD1+a41BB_1
MARSseq


title: day 4 INTa6+EpCAM+ cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME with Act A biol rep 1

description:
cjPGCLCs_pre-ME+ActA_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: AB10263

description:
Biomek MARS_03.09.20_F1_20200824_MC38_D13_Tumor5_aPD1_1
MARSseq


title: day 4 INTa6-EpCAM- cells induced from cjiPSCs cultured in cjEPSCM and induced towards Pre-ME with Act A biol rep 1

description:
soma_pre-ME+ActA_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: AB10267

description:
20200803_MC38_D10_Tumor10_aPD1+a41BB_1
MARSseq


title: cjiPSCs cultured in cjPSCM biol rep 2

description:
cjiPSCs_cjPSCM_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: iPSCs

value: Culture in cjPSCM


title: cjiPSCs cultured in TESR biol rep 2

description:
cjiPSCs_TESR_R2
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Culture in TESR


title: AB10270

description:
20200803_MC38_D10_Tumor11_aPD1+a41BB_1
MARSseq

value: tumor

value: endogenous CD8+


title: cjiPSCs cultured in cjPSCM biol rep 1

description:
cjiPSCs_cjPSCM_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: AB10269

description:
20200803_MC38_D10_Tumor10_aPD1+a41BB_3
MARSseq


title: AB10262

description:
Biomek MARS_03.09.20_E1_20200824_MC38_D13_Tumor4_aPD1_1
MARSseq


title: AB10261

description:
Biomek MARS_03.09.20_D1_20200824_MC38_D10_Tumor9_41BB_1
MARSseq


title: AB10259

description:
Biomek MARS_03.09.20_B1_20200824_MC38_D13_Tumor2_Ctrl_1
MARSseq


title: cjiPSCs cultured in TESR biol rep 1

description:
cjiPSCs_TESR_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt


title: AB10258

description:
Biomek MARS_03.09.20_A1_20200824_MC38_D13_Tumor1_Ctrl_1
MARSseq


title: PYMT_N_2

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

country: China

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample …

molecule: total RNA

source_name: mammary glands

growth_protocol: All animal experiments strictly complied with protocols approved by the Animal Welfare and Ethics Committee (AWEC) of China Pharmaceutical University. MiR-9-exon 1 knockout heterozygous (miR-9+/-) mice and MMTV-PyMT (stock No. 022974) transgenic mice were obtained from Shanghai Nanfang model Biotechnology Co., Ltd. All mice were on a mixed C57BL/6 background with littermate controls (females) used in all experiments. Mammary glands at hyperplastic stages were collected and total RNA was extracted.

extract_protocol:
RNA was harvested using TriZol Up (Cat # ET111-01, TransGen Biotech, Beijing, China). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mammary glands were collected and subjected to RNA extraction and deep sequencing, in parallel, using  Illumina NovaSeq 6000.

value: mammary glands

tag: genotype

value: without miR-9 knockout

tag: strain

value: MMTV-PyMT


title: PYMT_N_9ko_2

value: miR-9 knockout


title: PYMT_N_9ko_1


title: AB10229

description:
20200803_MC38_D10_Tumor6_aPD1_3
MARSseq


title: PYMT_T_9ko_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Excel files include RPKM values for each Sample.

source_name: tumors

growth_protocol: All animal experiments strictly complied with protocols approved by the Animal Welfare and Ethics Committee (AWEC) of China Pharmaceutical University. MiR-9-exon 1 knockout heterozygous (miR-9+/-) mice and MMTV-PyMT (stock No. 022974) transgenic mice were obtained from Shanghai Nanfang model Biotechnology Co., Ltd. All mice were on a mixed C57BL/6 background with littermate controls (females) used in all experiments. Tumours were collected and total RNA was extracted.

extract_protocol:
Tumours were collected and subjected to RNA extraction and deep sequencing, in parallel, using Illumina NovaSeq 6000.
RNA was harvested using TriZol Up (Cat # ET111-01, TransGen Biotech, Beijing, China).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: Sex

value: female

value: tumors


title: PYMT_T_9ko_1


title: AB10228

description:
20200803_MC38_D10_Tumor6_aPD1_2
MARSseq


title: PYMT_N_1


title: Pre-ME induced with Act A from cjiPSCs cultured in cjPSCM biol rep 1

description:
cjPSCM_pre-ME+ActA_R1
RNA_seq_raw_counts_new.geo.txt
RNA_seq_counts_normalized_by_sizefactor_new.geo.txt

value: Precursor of mesendoderm


title: AB10227

description:
20200803_MC38_D10_Tumor6_aPD1_1
MARSseq


title: AB10226

description:
20200803_MC38_D10_Tumor3_Ctrl_3
MARSseq


title: AB10225

description:
20200803_MC38_D10_Tumor3_Ctrl_2
MARSseq


title: PYMT_T_2


title: AB10224

description:
20200806_MC38_D13_Tumor6_aPD1_3
MARSseq


title: PYMT_T_1


title: AB10223

description:
20200806_MC38_D13_Tumor6_aPD1_2
MARSseq


title: AB10260

description:
Biomek MARS_03.09.20_C1_20200824_MC38_D13_Tumor3_Ctrl_1
MARSseq


title: AB10222

description:
20200806_MC38_D13_Tumor6_aPD1_1
MARSseq


title: AB10221

description:
20200806_MC38_D13_Tumor5_aPD1_3
MARSseq


title: AB10219

description:
20200806_MC38_D13_Tumor5_aPD1_1
MARSseq


title: S.griseus, with PQQ, rep2

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

description: sgpqq.csv

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the streptomyces rapamycinicus NRRL5491(CP085193.1) and streptomyces griesus DSM 40236 (GCA_900105705.1) genome assembly using bowtie2（version: 2-2.0.5）.
Gene expression level was calculated by DESeq2 R package (v.1.20.0), displaying as average values of three clones from each group.
Assembly: streptomyces rapamycinicus NRRL5491(CP085193.1) and streptomyces griseus DSM 40236 (GCA_900105705.1)
Supplementary files format and content: csv files include values as follows: BaseMean (the average of the normalized counts for samples with and without PQQ operon); log2FoldChange (The log2-transformed fold change of averaged gene expression with and without PQQ operon); lfcSE (The standard error associated with the log2FoldChange): stat (The Wald test statistic for testing the null hypothesis that the log2FoldChange is equal to zero (i.e., no differential expression)); pvalue (The p-value associated with the Wald test).

organism: Streptomyces griseus

source_name: bacteria

extract_protocol:
The total RNA of each sample was extracted using Total RNA Extractor kit (B511311, Sangon, China) according to the manufacturer’s protocol. The extracted RNA was then sent to the Sangon Biotech (Shanghai) Co., Ltd. for library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacteria

value: with PQQ operon


title: S.griseus, without PQQ, rep3

description: sgpqq.csv

value: without PQQ operon


title: S.griseus, without PQQ, rep2

description: sgpqq.csv


title: S.griseus, without PQQ, rep1

description: sgpqq.csv


title: S.griseus, with PQQ, rep3

description: sgpqq.csv


title: AB10218

description:
20200806_MC38_D13_Tumor4_aPD1_3
MARSseq


title: AB10216

description:
20200806_MC38_D13_Tumor3_Ctrl_2
MARSseq


title: p46.S088.day7

city: Stanford

first: Hong

state: California

address: 240 Pasteur Dr

country: USA

institute: Stanford university

data_processing:
We used Trim Galore (v0.6.5) to trim Illumina adaptors from the raw fastq reads and removed reads that were too short after adaptor trimming (less than 20 nt). We then used Salmon (v1.2.1) to get transcript-level expression based on human transcriptome sequences from GENCODE site (v32). Gene-level expression was summarized using Tximport (v1.16.0).
Assembly: GRCh38
Supplementary files format and content: readcount.csv.gz: read count from Salmon; samplemeta.csv: sample meta data

organism: Homo sapiens

source_name: blood

extract_protocol:
RNA extraction was carried out using Thermo Fisher's MagMAX™ kit, specifically designed for PAXgene™ Blood RNA Tubes. Subsequently, sample quality control was conducted using the Agilent 2100 bioanalyzer, with a threshold set at RIN>7 to identify suitable samples. Qualified RNA from each sample was then subjected to non-stranded mRNAseq library preparation, which included globin depletion.
The library preparation process involved mRNA fragmentation, followed by the generation of first-strand cDNA using random hexamer-primed reverse transcription. This was followed by second-strand cDNA synthesis and adapter ligation reactions. The resulting libraries were PCR-enriched and purified using Ampure XP beads, with library quantification performed using the Agilent Technologies 2100 bioanalyzer. The subsequent steps included heat denaturation and circularization of double-stranded PCR products, leading to the formation of single-strand circular DNA (ssCir DNA) libraries. These libraries were then amplified with phi29 to create DNA nanoballs (DNBs), each containing more than 300 copies of a single molecular entity. These DNBs were loaded onto a patterned nanoarray, and sequencing was carried out to generate paired-end 150 base reads through sequenced by synthesis using the DNBSEQ-G400 platform.

value: blood

tag: patient

value: F

tag: condition

value: SLE

tag: responder

value: R

tag: time point


title: p46.S090.day28


title: AB10217

description:
20200806_MC38_D13_Tumor4_aPD1_1
MARSseq


title: p46.S087.day1or2


title: AB10214

description:
20200806_MC38_D13_Tumor2_Ctrl_3
MARSseq


title: p46.S086.day0


title: AB10213

description:
20200806_MC38_D13_Tumor2_Ctrl_2
MARSseq


title: AB10212

description:
20200806_MC38_D13_Tumor2_Ctrl_1
MARSseq


title: p44.S083.day7

value: NR


title: p41.S080.day28


title: AB10211

description:
20200806_MC38_D13_Tumor1_Ctrl_3
MARSseq

value: tumor


title: AB10210

description:
20200806_MC38_D13_Tumor1_Ctrl_2
MARSseq

value: endogenous CD8+


title: p41.S077.day1or2


title: AB10220

description:
20200806_MC38_D13_Tumor5_aPD1_2
MARSseq


title: AB10209

description:
20200806_MC38_D13_Tumor1_Ctrl_1
MARSseq


title: p41.S078.day7


title: S.griseus, with PQQ, rep1

description: sgpqq.csv


title: p41.S076.day0


title: AB10207

description:
20200803_MC38_D10_Tumor7_a41BB_3
MARSseq


title: p40.S075.day28


title: p40.S074.day23


title: AB10206

description:
20200803_MC38_D10_Tumor7_a41BB_2
MARSseq


title: p40.S073.day7


title: AB10205

description:
20200803_MC38_D10_Tumor7_a41BB_1
MARSseq


title: p40.S072.day1or2


title: p40.S071.day0


title: p44.S085.day28


title: AB10203

description:
20200803_MC38_D10_Tumor5_aPD1_2
MARSseq


title: AB10215

description:
20200806_MC38_D13_Tumor3_Ctrl_1
MARSseq


title: p44.S081.day0


title: p38.S070.day28


title: AB10202

description:
20200803_MC38_D10_Tumor5_aPD1_1
MARSseq


title: p38.S068.day7


title: AB10201

description:
20200803_MC38_D10_Tumor4_aPD1_3
MARSseq


title: AB10200

description:
20200803_MC38_D10_Tumor4_aPD1_2
MARSseq


title: p38.S069.day23


title: AB10208

description:
20200803_MC38_D10_Tumor8_a41BB_1
MARSseq


title: AB10198

description:
20200803_MC38_D10_Tumor2_Ctrl_3
MARSseq


title: AB10199

description:
20200803_MC38_D10_Tumor4_aPD1_1
MARSseq


title: AB10196

description:
20200803_MC38_D10_Tumor2_Ctrl_1
MARSseq


title: AB10197

description:
20200803_MC38_D10_Tumor2_Ctrl_2
MARSseq


title: p38.S066.day0


title: p38.S067.day1or2


title: p35.S064.day23


title: p35.S065.day28


title: p35.S063.day7


title: AB10195

description:
20200803_MC38_D10_Tumor1_Ctrl_3
MARSseq


title: AB10204

description:
20200803_MC38_D10_Tumor5_aPD1_3
MARSseq


title: p35.S062.day1or2


title: AB10194

description:
20200803_MC38_D10_Tumor1_Ctrl_2
MARSseq


title: p35.S061.day0


title: AB10193

description:
20200803_MC38_D10_Tumor1_Ctrl_1
MARSseq


title: AB10121

description:
20200724_D6_T1_aPD1_CD25-
MARSseq

value: OT1 CD8+


title: p34.S060.day28


title: Penis, tdTom, rep1

city: Solna

first: Anais

last: Julien

state: non-US Resident

address: Solnavagen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

data_processing: none provided

source_name: penis

extract_protocol: none provided

value: penis


title: p34.S058.day7


title: p34.S056.day0


title: p34.S057.day1or2


title: VDJ-seq_Old_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

library_source: genomic

data_processing:
Hi-C, H3K27ac HiChIP,and capture Hi-C raw reads were processed to the mouse reference genome mm10 by HiCUP (v0.7.2) with the settings of Arima. High-quality and unique paired-end tags (PETs) from HiCUP were further processed to the HIC file through Juicer (v1.6.0) for visualization with Juicebox. These PETs were also processed with cLoops2 (v0.0.2) for quantifications. Chromosome X was excluded from the analysis.Replicates from H3K27ac HiChIP samples were combined and down-sampling equally to 39 million PETs for all following analysis.
ChIP-Seq raw reads were mapped to the mouse reference genome mm10 by Bowtie2 (v2.3.5) . Only non-redundant reads with MAPQ >=10 were saved as BED files for the following analysis. Bigwig tracks were generated by bamCoverage in deepTools (v3.3.0) with parameters of --ignoreDuplicates --minMappingQuality 10 --normalizeUsing CPM for visualization and quantification aggregation analysis.Visualization of ChIP-Seq tracks were performed by IGV or the cLoops2 plot module (v0.0.2) .ChIP-Seq peaks were identified using the cLoops2 callPeaks module. For transcription factor data, the key parameters -eps 150 -minPts 20,50 were employed. For H3K27ac data, the parameters -eps 150,300 -minPts 20,50 -sen were used. Peak identification was performed on each replicate individually, followed by the compilation of a union set encompassing both conditions (young and old) and overlapping replicates. Differential peaks were identified for young and old conditions using a Poisson test. The test utilized average counts from replicates for each peak and considered normalized total reads of 30 million. A p-value cutoff of <1e-5 and a fold change cutoff of >=2 were used to identify significant differential peaks. ChIP-seq peak or domain regions aggregation analyses, including heatmaps and average profile plots, were generated using the computeMatrix and plotHeatmap commands from the deepTools (v3.3.0) package.Quantification of ChIP-seq signals in Hi-C compartments was performed by the cLoops2 quant module. H3K27ac peak annotations were performed by the anoPeaks.py script in cLoops2 package. H3K27ac peaks within a 2 kb range upstream or downstream of the transcription start site (TSS) are annotated as promoters, while those outside this range are labeled as enhancers for the downstream analysis.
RNA-seq raw reads were mapped to mm10 by STAR (v2.7.3a) and quantified into RPKM with Cufflinks (v2.2.1).
VDJ-Seq analysis was performed using HTGTS-Rep.
Assembly: mm10
Supplementary files format and content: BEDPE files for capture Hi-C, Hi-C, HiChIP samples were provided for valid interactions.BED (BEDPE) files for single-end (paired-end) ChIP-seq samples were provided for processed high quality unqiue reads. TEXT files for processed VDJ-seq were provided. TEXT files for processed gene expression in FPKM from RNA-seq data were also provided.
Library strategy: VDJ-seq

molecule: genomic DNA

source_name: progenitor B cells

growth_protocol:
Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines are cultured as previous described (Ramamoorthy et al., 2020).  The D345 cell line was maintained in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gemini) and a 1ⅹ penicillin-streptomycin solution (Gibco).  293T human embryonic kidney cells used for lentiviral expression was purchased from ATCC (Cat# CRL-3216) and cultured in DMEM (Gibco) with 10% FBS (Gemini) and 1ⅹ penicillin-streptomycin solution (Gibco).
The Platinum-E (Plat-E) cell line used for retroviral expression was purchased from Cell Biolabs (Cat# RV-101) and cultured in DMEM (Gibco) with 10% FBS (Gemini), 1ⅹpenicillin-streptomycin solution (Gibco), 10mM Hepes and 0.3 μg/mL L-glutamine. All cells were cultured at 37C in a humidified atmosphere with 5% CO2.

extract_protocol:
For Rag2-/- mice, total bone marrow was extracted from tibia and femurs and erythrocytes are lysed. Pro-B cells were purified by combining positive selection using CD19+ selective beads (Stem Cell Technology, Cat #18954) and sorting by CD19+ and B220+ markers.
For C57BL/6J mice, total bone marrow was extracted from tibia and femurs and erythrocytes are lysed. Cells were pre-purified using CD19+ selective beads (Stem Cell Technology, Cat#18954) and sorted with IgM-B220+CD43+ markers. Flow cytometry experiments were performed on BD FACSAria II Cell Sorter. Flowjo software was used for data analysis.
For the Hi-C libraries. Genome-wide in situ Hi-C was performed with Rag2-/- young and old primary pro-B cells, and Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+, Rag2-/-Ebf1+/−Pax5+/−, D345-BFP and D345-Wapl-BFP pro-B cell lines, using the Arima Hi-C Kit (Arima Genomics), including KAPA Hyper Prep indexing and library amplification (catalog no. KK8500, Roche Molecular Systems Inc) according to the manufacturer’s instructions. For each assay, 1-2×106 cells were used as the input materials and two biological replicates were performed for each group. Samples were sequenced 2×150 bp on an Illumina NovaSeq instrument at the Single Cell & Transcriptomics Core at Johns Hopkins University.
For the capture Hi-C libraries, whole genome Hi-C libraries were first generated as previously described. To enrich the IgH locus (mm10, chr12: 113,201,001 - 116,030,000), SureSelect Target Enrichment probes with 2× tiling density were designed and manufactured by Agilent (Agilent Technologies Inc.). Hi-C libraries were hybridized to probes as specified by the manufacturer. Enriched libraries were sequenced using Illumina NextSeq sequencer to generate paired-end 150-bp reads.
For the ChIP-seq libraries.For the chromatin immunoprecipitation (ChIP) of histone modifications, CTCF, and Rad21, both young and old primary Rag2-/- pro-B cells underwent crosslinking with 1% formaldehyde (Sigma) for 10 minutes at room temperature. The reaction was subsequently quenched with 125 mM glycine, and cell lysis was initiated in a buffer containing 1% SDS. Chromatin was then sheared using a Bioruptor (Diagenode) in cycles of 30 seconds on and 30 seconds off, totaling 15 minutes of shearing time. Immunoprecipitation was performed using specific antibodies, with 1×106 cells used for each assay, and antibody dilutions followed established protocols.
As for Brg1 and p300 ChIPs, we followed the protocol by Bossen et al., 2015, with some modifications. In this case,2×106 young and old primary Rag2-/- pro-B cells were first crosslinked with 1.5 mM EGS at room temperature with rotation for 15 minutes. Subsequently, the cells were fixed with 1% formaldehyde (Sigma) for 15 minutes at room temperature with rotation and quenched with 200 mM glycine. After two PBS washes, the cells were lysed in a buffer containing 1% SDS. Notably, we extended the sonication time to a total of 20 minutes of shearing time, while the subsequent steps of the protocol mirrored the previously mentioned procedure.
For the RNA-seq libraries.The RNA libraries for young and old Rag2-/- primary pro-B cells (four biological replicates for each group) were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit (PerkinElmer, Cat#NOVA-5138-07,) and sequenced 2×75 bp on an Illumina NovaSeq instrument at the Single Cell & Transcriptomics Core at Johns Hopkins University. RNA libraries for Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+, Rag2-/-Ebf1+/−Pax5+/− and D345-BFP and D345-Wapl-BFP pro-B cell lines (two replicates for each group) were prepared using SMARTer Stranded Total RNASeq Kit v2 (Takara, Cat# 634412) and sequenced 1×100 bp on an Illumina NovaSeq instrument at the Single Cell & Transcriptomics Core at Johns Hopkins University. RNA libraries for pro-B cells infected with Ebf1-GFP or GFP containing retrovirus were prepared using the SMART-Seq mRNA kit (Takara, Cat#634773) and sequenced 2×100 bp on an Illumina NovaSeq instrument at the Computational Biology and Genomics Core in NIA.
For the HiChIP libraries. The H3K27ac HiChIP procedure was executed employing the Arima Hi-C+ Kit (Arima Genetics Inc. Cat# A101020), strictly adhering to the manufacturer's guidelines outlined in the Arima-HiC+ documents A160168 v00 (HiChIP) and A160169 v00 (library preparation). In each sample, a total of 5×106 cells were utilized. These libraries were individually barcoded and then combined for sequencing on an Illumina NovaSeq instrument.
For the VDJ-Seq. It was performed following the HTGTS-Rep-Seq protocol by Hu et al., 2016. Briefly, 200 ng – 2 μg of genomic DNA isolated from primary pro-B cells sorted from young and old C57BL/6J mice was sonicated with Covaris using the setting of Durations 10s, Peak power 50, Duty Factor 20%, Cycles/ Burst 200. Sheared DNA was linearly amplified using a biotinylated JH1 primer and enriched with streptavidin C1 beads (Thermo Fisher Scientific). A bridge adaptor was ligated to enriched single stranded DNA to the 3’ end and then amplified by a nested primer set. Products were further amplified using P5-I5 and P7-I7 primers to be final libraries and sequenced by Illumina MiSeq sequencer to generate paired-end 250-bp reads.

treatment_protocol: Retrovirus was produced by transfection of Plat-E cells with retroviral plasmids containing Ebf1 cDNA and a selective GFP marker (pMYs-Ebf1-IRES-EGFP, as described in Treiber et al., 2010), or with GFP-only plasmids as the control (pMSCV-IRES-GFP, Addgene Cat# 20672). Supernatants were collected at both 48 and 72 hours post-transfection and subsequently concentrated using the Retro-X Concentrator (Takara, Cat#631456), following the manufacturer's instructions. Young and old Rag2-/- CD19+ cells were cultured with 2 ng/mL IL-7 for three days and then exposed to the resuspended virus with the supplement of 10 μg/ml polybrene. The cells were cultured for an additional 72 hours and subsequently sorted based on GFP expression before subsequent analysis. Lentivirus was produced by transfection of 293T cells with the pHIV-Wapl-IRES-BFP and pHIV-IRES-BFP plasmids. To make these plasmids, the BFP DNA fragment was amplified from plasmid pEJS614_pTetR-P2A-BFPnls/sgNS (Addgene, #108650), and then integrated into pHIV-IRES-Zsgreen (Addgene, #18121) using the NEBuilder® HiFi DNA Assembly Master Mix (New England Biolabs, #E2621S) as per the manufacturer's instructions, resulting in the generation of pHIV-IRES-BFP plasmids. Subsequently, Wapl cDNA was introduced into pHIV-IRES-BFP, creating the pHIV-Wapl-IRES-BFP. Supernatants were collected at both 48 and 72 hr post-transfection and subsequently concentrated using the Lenti-X Concentrator (Takara, Cat#631232). D345 cells were infected with the resuspended lentivirus with the addition of 8 μg/ml polybrene. After infection, the cells were cultured for 72 hr and sorted based on BFP expression. The sorted cells were then cultured for 2-3 additional days to obtain an increased number of BFP-positive cells for experimental purpose.

value: progenitor B cells

value: Bone marrow

value: WT C57BL/6J

value: B220+CD43+IgM- sorted primary pro-B cells


title: p32.S055.day28


title: RNA-seq_GFP_Young_rep2

data_processing:
Hi-C, H3K27ac HiChIP,and capture Hi-C raw reads were processed to the mouse reference genome mm10 by HiCUP (v0.7.2) with the settings of Arima. High-quality and unique paired-end tags (PETs) from HiCUP were further processed to the HIC file through Juicer (v1.6.0) for visualization with Juicebox. These PETs were also processed with cLoops2 (v0.0.2) for quantifications. Chromosome X was excluded from the analysis.Replicates from H3K27ac HiChIP samples were combined and down-sampling equally to 39 million PETs for all following analysis.
ChIP-Seq raw reads were mapped to the mouse reference genome mm10 by Bowtie2 (v2.3.5) . Only non-redundant reads with MAPQ >=10 were saved as BED files for the following analysis. Bigwig tracks were generated by bamCoverage in deepTools (v3.3.0) with parameters of --ignoreDuplicates --minMappingQuality 10 --normalizeUsing CPM for visualization and quantification aggregation analysis.Visualization of ChIP-Seq tracks were performed by IGV or the cLoops2 plot module (v0.0.2) .ChIP-Seq peaks were identified using the cLoops2 callPeaks module. For transcription factor data, the key parameters -eps 150 -minPts 20,50 were employed. For H3K27ac data, the parameters -eps 150,300 -minPts 20,50 -sen were used. Peak identification was performed on each replicate individually, followed by the compilation of a union set encompassing both conditions (young and old) and overlapping replicates. Differential peaks were identified for young and old conditions using a Poisson test. The test utilized average counts from replicates for each peak and considered normalized total reads of 30 million. A p-value cutoff of <1e-5 and a fold change cutoff of >=2 were used to identify significant differential peaks. ChIP-seq peak or domain regions aggregation analyses, including heatmaps and average profile plots, were generated using the computeMatrix and plotHeatmap commands from the deepTools (v3.3.0) package.Quantification of ChIP-seq signals in Hi-C compartments was performed by the cLoops2 quant module. H3K27ac peak annotations were performed by the anoPeaks.py script in cLoops2 package. H3K27ac peaks within a 2 kb range upstream or downstream of the transcription start site (TSS) are annotated as promoters, while those outside this range are labeled as enhancers for the downstream analysis.
RNA-seq raw reads were mapped to mm10 by STAR (v2.7.3a) and quantified into RPKM with Cufflinks (v2.2.1).
VDJ-Seq analysis was performed using HTGTS-Rep.
Assembly: mm10
Supplementary files format and content: BEDPE files for capture Hi-C, Hi-C, HiChIP samples were provided for valid interactions.BED (BEDPE) files for single-end (paired-end) ChIP-seq samples were provided for processed high quality unqiue reads. TEXT files for processed VDJ-seq were provided. TEXT files for processed gene expression in FPKM from RNA-seq data were also provided.

value: Rag2-/- cultured in vitro

value: Primary pro-B cells by CD19+ selection, cultured with IL-7


title: RNA-seq_GFP_Old_rep3


title: p32.S053.day7


title: p32.S052.day1or2


title: RNA-seq_GFP_Old_rep2


title: p31.S048.day7


title: p31.S050.day28


title: p32.S051.day0


title: RNA-seq_GFP_Old_rep1


title: p31.S047.day1or2


title: RNA-seq_Ebf1OE_Young_rep1


title: RNA-seq_Ebf1OE_Old_rep3


title: p31.S046.day0


title: High coverage scRNA-Seq of MCF7 and HEK293-ZRT cells

city: New Orleans

first: Victoria

last: Belancio

state: LA

address: 1430 Tulane Avenue

department: Structural and Cellular Biology

institute: Tulane University School of Medicine

description: breast cancer derived MCF7 cells and kidney derived HEK293 cells

data_processing:
Raw sequencing files were demultiplexed using 10X Genomics bcl2fastq
Sequencing reads were aligned to the hg38 genome using 10X Genomics count
Genome_build: hg38
Supplementary_files_format_and_content: txt files with cell barcodes, expressed genes, and gene expression matrix

source_name: MCF7 and HEK293-ZRT

growth_protocol: MCF7 (ATCC HTB-22) and HEK293-ZRT cells were maintained in DMEM with high glucose (Gibco) supplemented with 10% fetal bovine serum (Gibco), sodium pyruvate, essential and nonessential amino acids, and L-glutamine.

extract_protocol:
Cells at 100% confluency were detached using accutase (Innovative Cell Technologies) and resuspended in DPBS. MCF7 and HEK293-ZRT cells were combined at a 9:1 ratio with 180 MCF7 and 20 HEK293 cells per uL.
Single-cell RNA sequencing was carried out on individual cells using the 10X Genomics Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 and 150 cycle kit. Sequencing was performed on an Illumina NextSeq 2000.

value: multiplexed sample:MCF7 and HEK293-ZRT


title: p29.S045.day28


title: p29.S043.day7


title: RNA-seq_Ebf1OE_Old_rep2


title: AB10122

description:
20200724_D6_T1_aPD1_Tim3+PD1+
MARSseq


title: p29.S042.day1or2


title: VDJ-seq_Old_rep1


title: p29.S041.day0


title: RNA-seq_Ebf1OE_Old_rep1


title: RNA-seq_Wapl+_rep1

value: Rag1 inactivated

value: In vitro cultured cell line


title: p28.S040.day28

value: blood

value: F


title: RNA-seq_Wapl+_rep2


title: RNA-seq_GFP_Young_rep1


title: p28.S038.day7

value: SLE

value: R


title: RNA-seq_D345Ctrl_rep1


title: RNA-seq_Ebf1OE_Young_rep2


title: RNA-seq_D345Ctrl_rep2


title: HiC_Wapl+_rep2


title: p21.S033.day7

value: NR


title: HiC_D345Ctrl_rep1


title: p21.S035.day28


title: HiC_D345Ctrl_rep2


title: HiChIP_H3K27ac_young_rep2

data_processing:
Hi-C, H3K27ac HiChIP,and capture Hi-C raw reads were processed to the mouse reference genome mm10 by HiCUP (v0.7.2) with the settings of Arima. High-quality and unique paired-end tags (PETs) from HiCUP were further processed to the HIC file through Juicer (v1.6.0) for visualization with Juicebox. These PETs were also processed with cLoops2 (v0.0.2) for quantifications. Chromosome X was excluded from the analysis.Replicates from H3K27ac HiChIP samples were combined and down-sampling equally to 39 million PETs for all following analysis.
ChIP-Seq raw reads were mapped to the mouse reference genome mm10 by Bowtie2 (v2.3.5) . Only non-redundant reads with MAPQ >=10 were saved as BED files for the following analysis. Bigwig tracks were generated by bamCoverage in deepTools (v3.3.0) with parameters of --ignoreDuplicates --minMappingQuality 10 --normalizeUsing CPM for visualization and quantification aggregation analysis.Visualization of ChIP-Seq tracks were performed by IGV or the cLoops2 plot module (v0.0.2) .ChIP-Seq peaks were identified using the cLoops2 callPeaks module. For transcription factor data, the key parameters -eps 150 -minPts 20,50 were employed. For H3K27ac data, the parameters -eps 150,300 -minPts 20,50 -sen were used. Peak identification was performed on each replicate individually, followed by the compilation of a union set encompassing both conditions (young and old) and overlapping replicates. Differential peaks were identified for young and old conditions using a Poisson test. The test utilized average counts from replicates for each peak and considered normalized total reads of 30 million. A p-value cutoff of <1e-5 and a fold change cutoff of >=2 were used to identify significant differential peaks. ChIP-seq peak or domain regions aggregation analyses, including heatmaps and average profile plots, were generated using the computeMatrix and plotHeatmap commands from the deepTools (v3.3.0) package.Quantification of ChIP-seq signals in Hi-C compartments was performed by the cLoops2 quant module. H3K27ac peak annotations were performed by the anoPeaks.py script in cLoops2 package. H3K27ac peaks within a 2 kb range upstream or downstream of the transcription start site (TSS) are annotated as promoters, while those outside this range are labeled as enhancers for the downstream analysis.
RNA-seq raw reads were mapped to mm10 by STAR (v2.7.3a) and quantified into RPKM with Cufflinks (v2.2.1).
VDJ-Seq analysis was performed using HTGTS-Rep.
Assembly: mm10
Supplementary files format and content: BEDPE files for capture Hi-C, Hi-C, HiChIP samples were provided for valid interactions.BED (BEDPE) files for single-end (paired-end) ChIP-seq samples were provided for processed high quality unqiue reads. TEXT files for processed VDJ-seq were provided. TEXT files for processed gene expression in FPKM from RNA-seq data were also provided.
Library strategy: HiChIP

value: Primary pro-B cells by CD19+ selection


title: p21.S031.day0


title: p18.S028.day7


title: HiChIP_H3K27ac_young_rep1


title: HiChIP_H3K27ac_old_rep2


title: p18.S026.day0


title: p17.S025.day28


title: HiChIP_H3K27ac_old_rep1


title: p17.S024.day23


title: p17.S023.day7


title: ChIP-seq_Young_p300_rep1


title: ChIP-seq_Young_p300_rep2


title: ChIP-seq_Young_Brg1_rep2


title: p17.S022.day1or2


title: p28.S036.day0


title: ChIP-seq_Old_p300_rep2


title: p17.S021.day0


title: ChIP-seq_Young_Brg1_rep1


title: p14.S019.day23


title: HiC_Wapl+_rep1


title: p14.S020.day28


title: ChIP-seq_Old_p300_rep1


title: p18.S030.day28


title: ChIP-seq_Old_Brg1_rep2


title: p18.S027.day1or2


title: ChIP-seq_Old_Brg1_rep1


title: p14.S018.day7


title: p14.S017.day1or2


title: MIS-4

city: Chongqing

first: Huiling

last: Chen

address: Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

institute: Chongqing Medical University

data_processing:
The clean reads were mapped to the human genome (GRCh38) using HISAT2 . FPKM of each gene was calculated using Cufflinks , and the read counts of each gene were obtained by HTSeq- count . Differential expression analysis was performed using the DESeq (2012) R package . P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution.
After reads ressembled by StringTie , gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
Assembly: ASprofile  was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons.
Supplementary files format and content: SNPs and InDels were called using SAMtools and BCFtools, and the details were shown on SAMtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then SnpEff  annotates and predicts the effects of variants on genes (such as amino acid changes).

source_name: heart

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated. About xxxxx raw reads for each sample were generated. Raw data (raw reads) of fastq format were firstly processed using Trimmomatic  and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses.

value: heart

value: DAPA


title: p14.S016.day0


title: p12.S015.day28


title: MIS-2


title: MIS-3


title: p12.S014.day23


title: MIS-1


title: p12.S013.day7


title: p12.S011.day0


title: p8.S010.day28


title: MI-2

value: vehicle


title: p8.S009.day23


title: Pt6 pre-treatment

city: Salt Lake City

first: Gabor

last: Marth

state: Utah

department: Human Genetics

institute: University of Utah

description:
MAS-Seq
instrument model: Revio

data_processing:
The Iso-Seq single-cell workflow was used to trim, tag, and align reads using the default settings of the tools distributed by PacBio via Bioconda (https://github.com/PacificBiosciences/pbbioconda).
Lima v2.7.1 was used to remove primers from the segmented reads.
Isoseq v4.0.0 added tags for unique molecular identifiers (UMIs), and barcodes, followed by trimming of the PolyA and primer sequences. Isoseq was then used to correct cell barcodes and deduplicate reads.
pbmm2 v1.10.0 was used to align reads to the reference genome using the GRCh38 reference sequence.
Pigeon v1.2.0 then makes Seurat-compatible files for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were initially isolated from whole blood using ficoll density gradient centrifugation. PBMCs were then viably frozen. Prior to sequencing, samples were processed by sequentially using the EasySep™ Dead Cell Removal (Annexin V) Kit (cat # 17899) followed by buffer exchange and B-cell selection using the EasySep™ Human B Cell Enrichment Kit II Without CD43 Depletion (cat # 17963) from Stemcell Technologies (Vancouver, BC).
The 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) was used for cell barcoding and cDNA generation. The standard protocol was followed until the end of step 2, stopped before cDNA cleavage. The resulting cDNA was used as input for the MAS-Seq for 10x Single Cell 3’ kit by PacBio.

value: Blood

value: B-Cell

tag: disease state

value: chronic lymphocytic leukemia (CLL)


title: Pt5 pre-treatment

description:
MAS-Seq
instrument model: Revio


title: Pt5 post-treatment

description:
MAS-Seq
instrument model: Revio


title: Pt6 post-treatment

description:
MAS-Seq
instrument model: Revio


title: p8.S008.day7


title: Pt4 post-treatment

description: MAS-Seq


title: MI-1


title: week 6 aristolochic acid_FB

city: Birmingham

first: Kyle

middle: Hartley

last: Moore

state: Alabama

department: Division of Nephrology

institute: University of Alabama at Birmingham

description:
10X Genomics
W6_1 was B0301, W6_2 was B0302, W6_3 was B0303

data_processing:
Libraries were multiplex sequenced and processed following 10X Genomics protocol for CellRanger.
Assembly: mm10

source_name: kidney

extract_protocol: Cells were isolated, tagged with hashing antibodies, and combined (week 2 samples combined and week 6 samples combined separately) for multiplex sequencing, and sequenced per 10x genomics instruction.

value: kidney

value: Cd45+ FACS immune cells

tag: gender

value: male

value: Chronic kidney disease/ transition of acute kidney injury-to-chronic kidney disease


title: Pt4 pre-treatment

description: MAS-Seq


title: week 6 aristolochic acid_GEX


title: Pt3 post-treatment

description: MAS-Seq


title: p8.S006.day0


title: Pt2 post-treatment

description:
MAS-Seq
instrument model: Revio


title: week 2 aristolochic acid_FB

description:
10X Genomics
W2_1 was B0301, W2_2 was B0302, W2_3 was B0303


title: Pt3 pre-treatment

description: MAS-Seq


title: Pt2 pre-treatment

description:
MAS-Seq
instrument model: Revio


title: p1.S005.day28


title: week 2 aristolochic acid_GEX


title: p1.S003.day7


title: MI-4


title: Pt1 pre-treatment

description:
MAS-Seq
instrument model: Revio


title: MI-3


title: 499liver

city: Guangzhou

first: Liu

last: Yasong

address: Tianhe District Tianhe Road, No. 600

institute: Third Affiliated Hospital Of Sun Yat-Sen University

data_processing:
Illumina Casava 2.19 software was used for basecalling.
Clean reads were obtained by removing adapter, and excluded reads containing ploy-N and low-quality from raw data.
Reads were aligned to the mouse genome with Hisat2
For quantification of gene expression, only the reads aligned to exons, and with the mapping quality score larger than 10 were counted using the featureCounts v2.0.1
Assembly: GRCm38
Supplementary files format and content: text files include readcount values for each sample

source_name: liver

extract_protocol:
Mice were monitored in the calorimetry chambers with recordings at 4-min intervals. After 30 min, ambient temperature of the chambers was lowered from 22°C to 4°C, and remained 4°C for 6 h. The mice were then quickly perfused with saline solution. Epididymal WAT, BAT, thigh skeletal muscle, and liver samples were collected and snap frozen in liquid nitrogen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pre-diabetic obese mice with i.p. injected with KPT-330 (Selleck, 5 mg/kg) 30 min prior to acute cold stimulation; for vehicle control, mice were i.p. injected with equal amount of DMSO (1 ml/kg).

value: liver

value: WT

value: DMSO


title: p1.S002.day1or2

value: blood

value: F

value: SLE


title: Ab22liver


title: p8.S007.day1or2

value: R


title: MAO-TGFb_rep3

type: RNA

city: Kyoto

first: Masahiro

last: Inoue

address: Shimoadachi-cho 46, Sakyou-ku

country: Japan

institute: Kyoto University, Graduate School of Medicine

description: Gene expression in MAOs treated with TGF-β1 (started at day 3) after 7 days of culture

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Mouse airway epithelial organoids (MAOs)

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: 2D-MAO was plated in 6-well plates and cultured for 7 days in MAO medium (Sachs N et al., Long-term expanding human airway organoids for disease modeling., EMBO J., 2019)

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen, 74106) plus on-column DNAse I digestion (Qiagen, 79254) according to the manufacturer's instructions.

treatment_protocol: 2D-MAO was treated with or without TGF-β1 in medium without noggin and A83-01 on day 3. The cells were collected at day 7

value: Mouse lung airway epithelial cells


title: cp2_5H3

city: Groningen

first: Hermie

last: Harmsen

state: Groningen

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description: column cp2_5H3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (parameter- Quality limit: Q < 20 and length < 25 )
Trimmed sequence reads were filtered rRNA
Filtered sequence reads were mapped to F. prausnitzii A2-165 GCA_002734145.1 using STAR aligner
Read count extraction and normalization were performed using DESeq2
Assembly: GenBank assembly accession: GCA_002734145.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Faecalibacterium prausnitzii

growth_protocol: F. prausnitzii A2-165 was cultured in YCFAG medium

extract_protocol:
RNA was isolated by acid phenol and chloroform/isoamyl alcohol extraction. The RNA cleanup was performed using a QIAgen kit according to the manufacturer’s recommendation (QIAGEN, German).
Then depletion of rRNA was performed using the Ribo-off kit for bacteria (Epicentre, Madison, WI, USA), followed by library construction for whole-transcriptome sequencing using BGI library prep kits.

treatment_protocol: The growth broth were supplied with/witout 0.01 mg/mL calcium palmitate

value: without  calcium palmitate (CP2)/16h


title: Smyd5_rep3_Total

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the human reference genome (build hg38) using HISAT2 (v.2.0.4) (parameters: -no-mixed and -no-discordant). The aligned reads were summarized using the "featureCounts" function of the RSubread (v.2.6.4) R/Bioconductor package and the reads were assigned using the hg38 GTF annotation from the UCSC database {Karolchik, 2004 #1425}(parameters:ignoreDup=FALSE, useMetaFeatures=TRUE, countMultiMappingReads=FALSE).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: KKLS

extract_protocol:
Total RNA was extracted from control or SMYD5-depleted KKLS cells using Trizol reagent. Polysomal RNA was extracted from pooled fractions indicated as heavy polysomes. Both total RNA and polysomal RNA were subjected to polyA selection for RNA library construction. The RNA-seq libraries were sequenced by the BGI Genomics using DNBseq platform (pair-end 100 bp analysis).
cDNA
RNA-seq of polysomal and total RNA samples

value: KKLS

value: Smyd5 depleted

tag: group

value: total mRNA


title: T781liver

tag: tissue

value: CTRL


title: 4liver


title: MAO-TGFb_rep2


title: Smyd5_rep2_Total

tag: cell type


title: 2liver


title: cp2_5H2

description: column cp2_5H2


title: Pt1 post-treatment

description:
MAS-Seq
instrument model: Revio

value: Blood

value: B-Cell

value: chronic lymphocytic leukemia (CLL)


title: cp0_5H2

description: column cp0_5H2

value: without calcium palmitate (CP0)/5h


title: cp0_5H3

description: column cp0_5H3


title: cp0_5H1

description: column cp0_5H1


title: cp2_5H1

description: column cp2_5H1


title: 500liver

value: liver


title: cp2_16H2

description: column cp2_16H2

value: WT

value: with 0.01 mg/mL calcium palmitate (CP2)/16h


title: 494liver


title: cp2_16H3

description: column cp2_16H3


title: Smyd5_rep3_Poly

value: polysome associated mRNA


title: Smyd5_rep2_Poly


title: MAO-ctrl_rep3

description: Gene expression in MAOs after 7 days of culture


title: MAO-TGFb_rep1


title: Aa121liver

value: DMSO


title: cp2_16H1

description: column cp2_16H1


title: MAO-ctrl_rep2


title: p1.S001.day0

value: blood

value: F

value: SLE


title: cp0_16H3

description: column cp0_16H3

value: without calcium palmitate (CP0)/16h


title: Smyd5_rep1_Poly

value: KKLS


title: MAO-ctrl_rep1

value: Mouse lung airway epithelial cells


title: Smyd5_rep1_Total

value: Smyd5 depleted

value: total mRNA


title: cp0_16H2

description: column cp0_16H2


title: Control_rep3_Total

value: Control


title: B652liver

value: CTRL


title: 405liver


title: cp0_16H1

description: column cp0_16H1


title: Control_rep2_Total


title: Sample 16: 1110 GS cells, hypoxia, RRBS

city: Davis

first: Ryan

last: Toedebusch

state: CA

address: 1 Shields Avenue

institute: University of California

data_processing:
Sequence reads from bisulfite-treated Classic RRBS libraries were identified using standard Illumina base calling software and then raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore 0.6.4. FastQC 0.11.9 was used to assess the effect of trimming and overall quality distributions of the data.
Alignment to the Canis lupus familiaries reference genome was performed using Bismark 0.22.3
Methylated and unmethylated read totals for each CpG site were called using MethylDackel 0.5.0. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Assembly: canFam3
Supplementary files format and content: bedgraph files contain methylated regions

organism: Canis lupus

extract_protocol:
DNA was isolated using Zymo Research Quick DNA Mini-prep Plus kit.
40 ng of starting input genomic DNA was digested with 30 units of MspI (NEB). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™-5 (Cat#: D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Cat#: D5030). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™-5 (Cat#: D4003) for sequencing on an Illumina NovaSeq 6000 platform (150 bp PE reads).

treatment_protocol: 1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: glioma stem-like cell

value: hypoxia


title: Sample 18: 1110 GS cells, hypoxia, RRBS


title: Aa127liver

value: liver


title: Sample 17: 1110 GS cells, hypoxia, RRBS


title: Sample 15: 0514 GS cells, hypoxia, RRBS


title: Control_rep1_Total


title: AB45liver

value: WT


title: Sample 14: 0514 GS cells, hypoxia, RRBS


title: THP-1-CBX7-3

city: nanjing

first: Wu

last: Zhichong

state: china

institute: Nanjing university

data_processing:
Data alignment against the human hg19 genome and expression quantification, measured in FPKM values, were performed using HISAT2 and StringTie software. Differential expression analysis set criteria at a fold change >2 (either direction) and P-value <0.05.
Assembly: H19
Supplementary files format and content: mRNA_Expression_Summary.xlsx

growth_protocol: Stardard

extract_protocol: Total RNA was isolated from human cell lines transfected with lentivirus shCBX7 (n=3 for each cell lines) or shCtrl (n=3 for each cell lines). RNA-seq was performed by Genesky Bio-Tech Co., Ltd, Shanghai, China. Quality checks of total RNA were performed using the NanoDrop and Agilent 2100 Bioanalyzer. The QC-qualified mRNA was purified and fragmented, followed by cDNA synthesis. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit and sequenced on the Illumina HiSeq 2500 to generate paired-end reads.

value: CBX7 knock-down


title: Sample 13: 0514 GS cells, hypoxia, RRBS


title: 498liver


title: Control_rep2_Poly

value: polysome associated mRNA


title: Control_rep3_Poly


title: B679liver

value: DMSO


title: Sample 11: G06 cells, hypoxia, RRBS

value: glioma cell


title: THP-1-CBX7-2


title: 3liver


title: THP-1-CBX7-1


title: Sample 12: G06 cells, hypoxia, RRBS


title: 497liver


title: Sample 10: G06 cells, hypoxia, RRBS


title: K562-CBX7-2


title: TUDCA2

city: Braga

first: Sara

last: Duarte-silva

address: Campus de Gualtar

department: School of Medicine, ICVS

country: Portugal

institute: University of Minho

data_processing:
The quality of assembled libraries was assessed using the Agilent Bioanalyzer High Sensitivity chip
Library amplification was performed by emulsion PCR in an Ion Chef Instrument
cDNA quality was assessed with the Agilent TapeStation High Sensitivity tape
Sequencing was performed in the Ion S5TM XL sequencer
reads were aligned to the AmpliSeq Mouse Transcriptome v1, obtaining a total of 23,930 transcripts
Assembly: Ampliseq_Mouse_Transcriptome: MouseTxome_20170706
Supplementary files format and content: PDF file Auto_user_S5XL-Ipatimup-1574-SaraSilva_TMGE_15-06-2021_ChipB_3264 contains a run report
Supplementary files format and content: Excel file Auto_SaraSilva_TMGE_15-06-2021_ChipB_torrent-server_4361.bc_summary contains the number of reads per sample
Supplementary files format and content: Excel file RNASeq samples containing sample information
Supplementary files format and content: Excel file RNASeq TUDCA - All Genes containing all genes analysed
Supplementary files format and content: Excel file RNASeq TUDCA - Differentially Expressed Genes
Supplementary files format and content: Zip folders for each sample (accodingly to genotype) containing the fastq files - raw data

source_name: brainstem

growth_protocol: Animals were grown in a conventional animal facility, using sentinels to control their health status, accordingly to the guidelines

extract_protocol:
Brainstem was harvested on day 7 and total RNA was extracted using the AllPrep® DNA/RNA/miRNA kit (Qiagen)
Library preparation was carried out by targeted amplicon amplification for AmpliSeq, accordingly to the manufacture instructions (Thermo Fisher, https://assets.thermofisher.com/TFS-Assets/CSD/Flyers/COL05444-Mouse-Transcriptome.pdf)

treatment_protocol: WT and transgenic mice were treated for 7 days (i.p. injections) with saline; transgenic mice only were treated with TUDCA (50 mg/Kg, sigma)

value: brainstem

value: transgenic

value: TUDCA


title: TUDCA3


title: Sample 9: 1110 GS cells, normoxia, RRBS

value: normoxia


title: 496liver


title: Sample 7: 1110 GS cells, normoxia, RRBS


title: TUDCA1


title: Sample 8: 1110 GS cells, normoxia, RRBS


title: K562-CBX7-1


title: 499WAT

source_name: WAT

value: WAT


title: H1299-CBX7-3


title: Tg1

value: saline


title: T781WAT


title: Ab22WAT


title: Control_rep1_Poly

value: KKLS


title: wt5

value: wt


title: H1299-CBX7-2


title: K562-CBX7-3


title: 4WAT


title: H1299-CBX7-1


title: Sample 5: 0514 GS cells, normoxia, RRBS


title: wt2


title: Sample 4: 0514 GS cells, normoxia, RRBS


title: Sample 3: G06 cells, normoxia, RRBS


title: wt1


title: A549-CBX7-3


title: 2WAT


title: Sample 2: G06 cells, normoxia, RRBS


title: Aa121WAT


title: A549-CBX7-1


title: A549-CBX7-2


title: Tg6


title: Sample 6: 0514 GS cells, normoxia, RRBS


title: 500WAT

value: CTRL


title: Sample 1: G06 cells, normoxia, RRBS


title: B652WAT


title: 494WAT


title: Tg2


title: THP-1-CBX73

value: Control


title: Coral, col_J, temp_ELE, sym_WT10, rep_2

city: Parkville

first: Hugo

last: Scharfenstein

state: VIC

address: Grattan Street

country: Australia

institute: The University of Melbourne

description: Each sample was run on two NovaSeq 600 S4 lanes (L001 and L002)

data_processing:
Quality of the raw sequences was verified using FastQC (version 0.12.0)
End-trimming of  sequences was carried out using fastp (version 0.23.2)
Concatanation of reads from lanes 1 and 2 for each sample and read direction
Trimmed sequences were first mapped to a P. daedalea reference genome using STAR (version 2.7.10b). This provided the gene count matrix for the coral host reads (processed file: "gene_counts_matrix_pdae.txt")
Unassigned sequences were then mapped to a C. proliferum reference genome using STAR (version 2.7.10b). This provided the gene count matrix for the photosymbiont reads (processed file: "gene_counts_matrix_cpol.txt")
Assembly: P. daedalea reference genome retrieved from: http://pdae.reefgenomics.org/. C. proliferum reference genome retrived from: https://espace.library.uq.edu.au/view/UQ:fba3259
Supplementary files format and content: Tab-delimited raw exon counts. Each column corresponds to a sample. One file for coral host reads, the second for photosymbiont reads.

organism: Alveopora daedalea

source_name: P. daedalea colonies

extract_protocol:
Total RNA was isolated using a RNEasy Plant Mini Kit (Qiagen). The purified total RNA was normalised to a concentration of 50 ng/µl.
Messenger RNA libraries were constructed using Illumina Stranded mRNA Prep kit with 500 ng of starting input.

value: P. daedalea colonies

tag: temperature treatment

value: Elevated

tag: coral genotype

value: Colony J

tag: inoculation treatment


title: THP-1-CBX72


title: AB45WAT

value: WT

tag: treatment


title: K562-CBX71

tag: cell line


title: Coral, col_L, temp_ELE, sym_WT10, rep_2

value: Colony L


title: THP-1-CBX71

tag: genotype


title: Coral, col_I, temp_ELE, sym_WT10, rep_1

value: Colony I


title: Coral, col_L, temp_ELE, sym_SS8, rep_1


title: 405WAT


title: Coral, col_L, temp_ELE, sym_WT10, rep_1


title: 3WAT


title: K562-CBX73


title: Aa127WAT


title: 497WAT


title: K562-CBX72


title: 498WAT


title: H1299-CBX73


title: 496WAT


title: Coral, col_L, temp_ELE, sym_SS1, rep_2


title: 499BAT

source_name: BAT

value: BAT

value: DMSO


title: H1299-CBX72


title: Coral, col_J, temp_ELE, sym_SS8, rep_1


title: Coral, col_J, temp_ELE, sym_WT10, rep_1


title: H1299-CBX71


title: Coral, col_I, temp_ELE, sym_SS8, rep_2


title: A549-CBX73


title: Ab22BAT


title: Coral, col_J, temp_ELE, sym_SS1, rep_2


title: Coral, col_I, temp_ELE, sym_SS8, rep_1


title: X8125

type: genomic

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC array using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Raw intensity data from IDAT files were read and processed in R (v. 4.2.1) via the ChAMP package (v 2.21.1) according to the default settings without the 'arratype' setting. Data pre-processing consisted of masking probes with poor design, control probes, X-/Y chromosome probes and non-cg and non-ch probes. For quality control,  β-value densities were calculated using the quality control function in ChAMP (v 2.21.1). The difference in signal intensity between the two-colour channels (dye bias correction) was corrected for using the beta mixture interquartile matrix (BMIQ) method.

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from fresh cell pellets using Qiagen DNeasy Kit according to standard instructions

value: MASH

value: female

value: liver


title: A549-CBX72


title: H1 ESCs, XMD , 24h.2

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

data_processing:
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Differential expression genes (DEGs) were identified with the criteria of p adjusted value < 0.05 and the absolute value of log2(Fold Change) > 1 after profile normalized using DESeq2 version 1.26.0
DEGs analysis were performed the GO and KEGG enrichment analysis through the R package ClusterProfiler 4.0
Assembly: hg38

growth_protocol: H1 ESCs  was maintained in E8 medium supplemented with  antibiotics  with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.

extract_protocol:
Cells was harvested in RNAiso Plus reagent (Takara). The poly(A) mRNA isolation was performed using Oligo(dT) beads according to manufacturer’s instructions
1 μg total RNA was used for following library preparation. The RNA Library were sequenced for paired end reads on Illumina NextSeq 500 (Illumina).

treatment_protocol: XMD892 1uM was treated with E8 medium for 12/24/48hr in H1 ESCs.

value: Human embryonic stem cells

value: XMD892 1 uM treatment for 24h


title: A549-CBX71


title: 2BAT


title: Coral, col_L, temp_ELE, sym_RIC, rep_2

value: RIC


title: H1 ESCs, XMD , 12h.1

value: XMD892 1 uM treatment for 12h


title: X7425

value: male


title: X7993


title: H1 ESCs, XMD , 48h.2

value: XMD892 1 uM treatment for 48h


title: 494BAT

value: CTRL


title: H1 ESCs, E8 , 48h.2

value: E8 for 48h


title: 4BAT


title: H1 ESCs, XMD , 48h.1


title: Coral, col_J, temp_ELE, sym_SS1, rep_1

value: P. daedalea colonies

value: Elevated

value: Colony J


title: Coral, col_J, temp_ELE, sym_RIC, rep_1


title: Coral, col_L, temp_ELE, sym_SS1, rep_1

value: Colony L


title: T781BAT

value: BAT

value: WT


title: X6493

value: MASH


title: Coral, col_I, temp_ELE, sym_RIC, rep_2

value: Colony I


title: X7487

value: Healthy

value: female

value: liver


title: X7416


title: 500BAT


title: 405BAT


title: Coral, col_I, temp_ELE, sym_SS1, rep_1


title: H1 ESCs, XMD, 12h.1

treatment_protocol: XMD892 1uM was treated with E8 medium for 12hr in H1 ESCs.

value: Human embryonic stem cells


title: X6545


title: H1 ESCs, E8, 12h.2

value: E8 for 12h


title: B679WAT

value: WAT

value: DMSO


title: Coral, col_L, temp_ELE, sym_RIC, rep_1

value: RIC


title: As-500D-02

city: Ottawa

first: Santokh

last: Gill

state: Ontario

address: 251 SIR FREDERICK BANTING

department: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

description: DifferentialExpression_MicroPlastics_Astrocytes_Gill_500.tsv

data_processing:
Quality filtering and trimming Bbduk (38.84) maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment STAR (2.7.1a) OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting FeatureCounts (2.0.0) -p -Q=12 -C -t exon -g gene_id
Differential Expression calling DESeq2 (1.26.0) alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2

organism: Rattus norvegicus

source_name: Rat fetal neural stem cell-derived Astrocyte

growth_protocol: Rat fetal neural stem cells (NSCs) were cultured in KnockOut DMEM/F12 supplemented with StemPro NSC SFM (2%), b-FGF and EGF (20ng/mL) (Peprotech, NJ, USA), GlutaMAX-1 (2mM) and 1% penicillin/streptomycin. These cells were culture on poly-L-ornithine (MilliporeSigma, ON, Canada) or Geltrex (ThermoFisher, ON, Canada) coated culture dishes. NSCs were differentiated into astrocytes with differentiation media consisting of D-MEM Medium with N-2 supplement (1%), 2mM GlutaMAX-1 supplement and 1% FBS, while plated on Geltrex coated plates.

extract_protocol:
Total RNA was extracted from cell culture samples using Qiagen miRNeasy kits. Subsequent steps were followed as per manufacture's instructions.
Polystyrene microsphere-treated astrocyte cDNA libraries were constructed using Illumina TruSeq Stranded mRNA protocol.

treatment_protocol: NSC-derived astrocytes were treated with non-fluorescent microspheres (Polybead®) 0-100 ug/ml for 7 days, with new microbeads in fresh media every 2-3 days.

value: 100 µg/ml 500nm polystyrene microspheres


title: Coral, col_L, temp_ELE, sym_C, rep_1

value: P. daedalea colonies

value: C


title: H1 ESCs, E8 , 48h.1

value: E8 for 48h


title: X6850


title: Aa121BAT


title: H1 ESCs, XMD, 12h.2

value: XMD892 1 uM treatment for 12h


title: High-risk serrated polyps cfDNA pool  A8

city: Vigo

first: María

last: Gallardo-Gómez

address: Campus As Lagoas Marcosende

country: Spain

institute: Universidad de Vigo

description: High-risk serrated polyps cfDNA pool  A8

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Matrix_signal_intensities_serrated.txt file contains: Unmethylated and methylated signal intensities, Detection P-value

label: Cy3, Cy5

source_name: serum

label_protocol: Standard Illumina labelling protocol

extract_protocol: Circulating cell-free DNA was isolated from serum samples by a phenol-chloroform protocol

value: serum

tag: pathology

value: HR-SP

tag: molecule subtype

value: circulating cell-free DNA


title: As-500D-04

value: Rat fetal neural stem cell-derived Astrocyte


title: H1 ESCs, XMD , 24h.1

value: WT

value: XMD892 1 uM treatment for 24h


title: H1 ESCs, MEK5DD.1

data_processing:
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Differential expression genes (DEGs) were identified with the criteria of p adjusted value < 0.05 and the absolute value of log2(Fold Change) > 1 after profile normalized using DESeq2 version 1.26.0
DEGs analysis were performed the GO and KEGG enrichment analysis through the R package ClusterProfiler 4.0

treatment_protocol: MAP2K5DD (MEK5DD) mutation (changed Ser311 to Asp, Ser315 to Asp) sequence was was subcloned into EZ-Lv195.1 cloning vector. MEK5DD-OE H1 ESC cell line was established after Lentiviral MAP2K5DD transduced in H1 ESCs and selected by puromycin.

value: MEK5DD overexpression

value: E8 medium


title: Coral, col_I, temp_ELE, sym_RIC, rep_1

value: Elevated

value: Colony I


title: As-500C-03

value: 10 µg/ml 500nm polystyrene microspheres


title: B652BAT

value: BAT

value: CTRL


title: B679BAT

value: DMSO


title: Coral, col_L, temp_ELE, sym_C, rep_2

value: P. daedalea colonies

value: Colony L

value: C


title: Aa127BAT


title: As-500D-03

value: 100 µg/ml 500nm polystyrene microspheres


title: As-500C-02


title: H1 ESCs, E8, 12h.1

value: Human embryonic stem cells

value: E8 for 12h


title: No colorectal findings cfDNA pool  C2

description: No colorectal findings cfDNA pool  C2

value: serum

value: NCF

value: circulating cell-free DNA


title: As-500D-01

value: Rat fetal neural stem cell-derived Astrocyte


title: Coral, col_J, temp_ELE, sym_C, rep_1

value: Colony J


title: As-500C-01


title: H1 ESCs, WT.1

value: WT

value: E8 medium


title: 498BAT


title: Coral, col_J, temp_AMB, sym_WT10, rep_2

value: Ambient


title: H1 ESCs, MEK5DD.2

value: MEK5DD overexpression


title: 496BAT

value: BAT


title: Coral, col_L, temp_AMB, sym_WT10, rep_1


title: D16h_CHIR4_M

city: West Lafayette

first: Vidhya

last: Munnamalai

address: 915 W State St

department: Biological Sciences

institute: Purdue

description:
Mouse cochlear culture E12.5 D1+6h CHIR99021 4
75bp fragments

data_processing:
HISAT2 aligner
Sequence reads were not trimmed
Sequence reads were mapped to Mus_musculus.GRCm38.91 using HISAT2 aligner
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: read counts for gene exp in each sample

source_name: E14.0 Cochlea cultures

growth_protocol: E12.5 cochleas were cultured for 24 hours on 'day 1'.

extract_protocol:
total RNA was phenol-chloroform extracted and the purified using Qiagen mini Rnease kit
Library was prepared using NEBNext Ultra Directional RNA library prep kit for Illumina, following manufacturer's protocols
Illumina HiSeq4000 low-input polyA-enriched RNAseq, strand-specific

treatment_protocol: Cochleas were treated with 10 uM CHIR99021 for 6 hours

value: E14.0 Cochlea cultures

value: Wildtype, Swiss Webster


title: 3BAT

value: CTRL


title: Coral, col_L, temp_AMB, sym_WT10, rep_2

value: P. daedalea colonies

value: Colony L


title: As-500B-04

value: 1 µg/ml 500nm polystyrene microspheres


title: Coral, col_J, temp_AMB, sym_WT10, rep_1


title: D16h_CHIR3_F

description:
Mouse cochlear culture E12.5 D1+6h CHIR99021 3
75bp fragments


title: H1 ESCs, WT.2

value: Human embryonic stem cells


title: As-500B-03


title: AB45BAT

value: DMSO


title: 497BAT


title: Ab22MUS

source_name: MUS

value: MUS


title: No colorectal findings cfDNA pool  C3

description: No colorectal findings cfDNA pool  C3

value: serum

value: NCF

value: circulating cell-free DNA


title: As-500B-02

value: Rat fetal neural stem cell-derived Astrocyte


title: 4MUS

value: WT


title: Low-risk serrated lesions cfDNA pool  B8

description: Low-risk serrated lesions cfDNA pool  B8

value: LR-SL


title: Coral, col_L, temp_AMB, sym_SS8, rep_2

value: Ambient


title: 499MUS


title: As-500B-01


title: High-risk hyperplastic polyps cfDNA pool  C5

value: HR-HP


title: Coral, col_I, temp_AMB, sym_WT10, rep_1

value: Colony I


title: Coral, col_L, temp_AMB, sym_SS8, rep_1


title: T781MUS


title: D16h_CHIR2_M

description:
Mouse cochlear culture E12.5 D1+6h CHIR99021 2
75bp fragments

value: E14.0 Cochlea cultures

value: Wildtype, Swiss Webster


title: D16h_CHIR1_F

description:
Mouse cochlear culture E12.5 D1+6h CHIR99021 1
75bp fragments


title: D16h_CTL4_M

description:
Mouse cochlear culture E12.5 D1+6h Control 4
75bp fragments

value: Control


title: As-500A-04


title: High-risk hyperplastic polyps cfDNA pool  C6


title: Low-risk serrated lesions cfDNA pool  C1

description: Low-risk serrated lesions cfDNA pool  C1


title: 2MUS


title: High-risk serrated polyps cfDNA pool  A7

description: High-risk serrated polyps cfDNA pool  A7

value: HR-SP


title: Coral, col_J, temp_AMB, sym_SS8, rep_1

value: P. daedalea colonies

value: Colony J


title: D16h_CTL3_F

description:
Mouse cochlear culture E12.5 D1+6h Control 3
75bp fragments


title: As-500A-03


title: Coral, col_I, temp_ELE, sym_C, rep_1

value: Elevated

value: C


title: 500MUS

value: MUS

value: CTRL


title: D16h_CTL2_M

description:
Mouse cochlear culture E12.5 D1+6h Control 2
75bp fragments


title: 494MUS


title: As-500A-02


title: Aa121MUS

value: DMSO


title: Coral, col_L, temp_AMB, sym_SS1, rep_2

value: Colony L


title: D16h_CTL1_F

description:
Mouse cochlear culture E12.5 D1+6h Control 1
75bp fragments


title: Coral, col_L, temp_AMB, sym_SS1, rep_1


title: Coral, col_I, temp_AMB, sym_SS8, rep_1


title: scRNA lungs, PRDM3/16KO, Rep2

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: 10X Genomics

data_processing:
Sequences from each sample were preprocessed, aligned, and quantified using the CellRanger pipeline (6.1.2, 10x Genomics) with mm10 reference genome (refdata-gex-mm10-2020-A, 10x Genomics)
EmptyDrops was used to identify quality cells (> 100 UMI, FDR < 0.01).
Scrublet was used to predict and remove doublet cells.
SoupX was used to remove ambient RNA contamination.
Seurat (4.1.0) was used for downstream analysis including normalization, batch correction, cell cluster identification and differential expression analysis
Assembly: mm10
Supplementary files format and content: filtered and raw matrix.h5 files

source_name: whole fetal lung

growth_protocol: Prdm3/16 double knockout mice were generated by crossing Prdm16 flox/flox ( Jackson Labs strain 024992) with Prdm3 flox/flox mice from the Mineo Kurokawa lab at the University of Tokyo and breeding in the ShhCre allele (Jackson laboratory strain  005622).  The cre allele was transmitted through the male germline from Prdm3fl/flPrdm16fl/wtShhCre+ animals bred to Prdm3fl/flPrdm16fl/fl females.

extract_protocol:
Fetal lung tissue was stored on ice in HypoThermosol FRS preservative solution (StemCell Technologies). Two lungs of the same genotype were minced with a razor blade for 2min. 25mg of tissue was digested on ice for 4min in 1mL of Collagenase/Elastase/Dispase enzyme mix (6mg/mL Collagenase A (Sigma, 10103578001), 4.3 units/mL Elastase (Worthington, LS002292), 9 units/mL Dispase (Worthington, LS02100) 5mM CaCl2, 125 units/mL DNase (Applichem, A3778), in DPBS (ThermoFisher, 14190144). Tissue was placed in a sterile petri dish for a further 2min of mincing. The cell suspension was pipetted into an Eppendorf tube on ice and the petri dish was rinshed with an additional 500mL of enzyme mix. The mixutre was triturated and shaken for 2min. Large tissue chunks were allowed to settle and the top 1200uL of supernatnat passed through a 30um filter (Miltenyi 130-098-458) on a 15mL conical tube. The filter was rinsed with 5mL ice cold PBS with 0.04% BSA. Remaining tissue was further digested with 1mL enzyme mix containing 10mg/mL Bacillus Licheniformis (Sigma, P5380) and 0.5mM EDTA in DPBS with periodic trituration for an additonal 10min. Resulting cell suspension was passed through 30um filter with 7mL PBS/BSA for rinsing the filter. Cells were pelleted at 300xg for 5min at 4C and supernatate was aspirated. Cells were resuspended in 900uL Red Blood Cell Lysis Bufer (Sigma, R7757) and incubated on ice for 2min. 12mL PBS/BSA was added, then cells pelleted at 200xg for 5min at 4C. Supernatant was asipirated and cells resuspended in 1mL PBS/BSA. Cells were counted using a hemacytometer with trypan blue and concentration adjusted to 1000cell/mL prior to seperation using the Chromium 10X Platform.
Cell separation and cDNA synthesis performed by Cincinnati Children's Hospital Single Cell Genomics Facility
Libraries generated and sequenced by Cincinnati Children's Hosptial Genomics Sequencing Facility

value: whole fetal lung

value: PRDM3/16 KO

tag: time


title: As-50D-04

description: DifferentialExpression_MicroPlastics_Astrocytes_Gill_50.tsv

value: Rat fetal neural stem cell-derived Astrocyte

value: 100 µg/ml 50nm polystyrene microspheres


title: As-500A-01


title: B652MUS

value: WT


title: No colorectal findings cfDNA pool  C4

description: No colorectal findings cfDNA pool  C4

value: serum

value: NCF

value: circulating cell-free DNA


title: scRNA lungs, PRDM3/16KO, Rep1

description: 10X Genomics


title: 405MUS


title: As-50D-03


title: As-50D-02


title: Coral, col_I, temp_AMB, sym_SS1, rep_1

value: Ambient

value: Colony I


title: scRNA lungs, Control, rep2

description: 10X Genomics

value: Control


title: High-risk serrated polyps cfDNA pool  B7

description: High-risk serrated polyps cfDNA pool  B7

value: HR-SP


title: As-50D-01


title: Aa127MUS


title: scRNA lungs, Control, rep1

description: 10X Genomics


title: Coral, col_L, temp_AMB, sym_RIC, rep_2

value: P. daedalea colonies

value: RIC


title: AB45MUS

value: MUS