title: Brain single cell 675

description: Brain single cell 675


title: Brain single cell 696

status: Public on Sep 28 2023

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain single cell 696

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Fluorescent cells were sorted by FACS from Pdgfra-H2BGFP mice and Tagl-CREERT2;Ai14 mice as previously described (Vanlandewijck et al, 2018). Briefly, brain tissue from both males and females were mechanically and enzymatically digested and vascular fragments isolated using CD31 antibody coated Dynabeads and further digested into cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: brain

tag: age

value: adult mice


title: Brain single cell 680

description: Brain single cell 680


title: Brain single cell 678

description: Brain single cell 678


title: Brain single cell 671

description: Brain single cell 671


title: Brain single cell 674

description: Brain single cell 674


title: Brain single cell 676

description: Brain single cell 676


title: Brain single cell 670

description: Brain single cell 670


title: Brain single cell 669

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title: Brain single cell 668

description: Brain single cell 668


title: Brain single cell 667

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title: Brain single cell 673

description: Brain single cell 673


title: Brain single cell 666

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title: Brain single cell 664

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title: Brain single cell 663

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title: Brain single cell 659

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title: Brain single cell 657

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title: Brain single cell 652

description: Brain single cell 652


title: Brain single cell 658

description: Brain single cell 658


title: Brain single cell 655

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title: Brain single cell 653

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title: Brain single cell 650

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title: Brain single cell 672

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title: Brain single cell 643

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title: Brain single cell 649

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title: Brain single cell 644

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title: Brain single cell 648

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title: Brain single cell 645

description: Brain single cell 645


title: Brain single cell 646

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title: Brain single cell 640

description: Brain single cell 640


title: Brain single cell 642

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title: Brain single cell 641

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title: Brain single cell 639

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title: Brain single cell 638

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title: Brain single cell 636

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title: Brain single cell 647

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title: Brain single cell 626

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description: Brain single cell 618


title: Brain single cell 619

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title: Brain single cell 623

description: Brain single cell 623


title: Brain single cell 617

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title: Brain single cell 615

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title: Brain single cell 616

description: Brain single cell 616


title: Brain single cell 621

description: Brain single cell 621


title: Brain single cell 635

description: Brain single cell 635


title: Brain single cell 611

description: Brain single cell 611


title: Brain single cell 608

description: Brain single cell 608


title: Brain single cell 609

description: Brain single cell 609


title: Brain single cell 612

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title: Brain single cell 610

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title: Brain single cell 631

description: Brain single cell 631


title: Brain single cell 613

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description: Brain single cell 607


title: Brain single cell 602

description: Brain single cell 602


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title: Brain single cell 600

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title: Brain single cell 622

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title: Brain single cell 603

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title: Brain single cell 592

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title: Brain single cell 589

description: Brain single cell 589


title: Brain single cell 595

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title: Brain single cell 591

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description: Brain single cell 590


title: Brain single cell 593

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title: Brain single cell 604

description: Brain single cell 604


title: Brain single cell 588

description: Brain single cell 588


title: Brain single cell 587

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title: Brain single cell 585

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title: Brain single cell 584

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title: Brain single cell 583

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title: Brain single cell 581

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title: Brain single cell 573

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title: Brain single cell 553

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title: Brain single cell 559

description: Brain single cell 559


title: Brain single cell 578

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title: Brain single cell 551

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title: Brain single cell 545

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title: Brain single cell 523

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title: Brain single cell 518

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title: Brain single cell 516

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title: Brain single cell 538

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title: Brain single cell 510

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title: Brain single cell 509

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title: Brain single cell 512

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title: Brain single cell 507

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title: Brain single cell 502

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title: Brain single cell 504

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title: Brain single cell 521

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title: Brain single cell 488

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title: Brain single cell 490

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title: Brain single cell 489

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title: Brain single cell 492

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title: Brain single cell 475

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title: Brain single cell 473

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title: Brain single cell 467

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title: Brain single cell 470

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title: Brain single cell 505

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title: Brain single cell 464

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title: Brain single cell 465

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title: Brain single cell 463

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title: Brain single cell 456

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title: Brain single cell 460

description: Brain single cell 460


title: Brain single cell 458

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title: Brain single cell 461

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title: Brain single cell 459

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title: Brain single cell 454

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title: Brain single cell 457

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title: Brain single cell 455

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title: Brain single cell 452

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title: Brain single cell 448

description: Brain single cell 448


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title: Brain single cell 445

description: Brain single cell 445


title: Brain single cell 443

description: Brain single cell 443


title: Brain single cell 462

description: Brain single cell 462


title: Brain single cell 444

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title: Brain single cell 440

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title: Brain single cell 447

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title: Brain single cell 441

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title: Brain single cell 439

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description: Brain single cell 424


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title: Brain single cell 433

description: Brain single cell 433


title: Brain single cell 421

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title: Brain single cell 446

description: Brain single cell 446


title: Brain single cell 427

description: Brain single cell 427


title: Brain single cell 432

description: Brain single cell 432


title: Brain single cell 425

description: Brain single cell 425


title: Brain single cell 419

description: Brain single cell 419


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title: Brain single cell 417

description: Brain single cell 417


title: Brain single cell 426

description: Brain single cell 426


title: Brain single cell 409

description: Brain single cell 409


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description: Brain single cell 408


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description: Brain single cell 407


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description: Brain single cell 402


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description: Brain single cell 398


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description: Brain single cell 396


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description: Brain single cell 393


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description: Brain single cell 392


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description: Brain single cell 390


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title: Brain single cell 410

description: Brain single cell 410


title: Brain single cell 389

description: Brain single cell 389


title: Brain single cell 388

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title: Brain single cell 386

description: Brain single cell 386


title: Brain single cell 387

description: Brain single cell 387


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description: Brain single cell 385


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description: Brain single cell 384


title: Brain single cell 380

description: Brain single cell 380


title: Brain single cell 381

description: Brain single cell 381


title: Brain single cell 382

description: Brain single cell 382


title: Brain single cell 377

description: Brain single cell 377


title: Brain single cell 395

description: Brain single cell 395


title: Brain single cell 378

description: Brain single cell 378


title: Brain single cell 400

description: Brain single cell 400


title: Brain single cell 374

description: Brain single cell 374


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description: Brain single cell 376


title: Brain single cell 373

description: Brain single cell 373


title: Brain single cell 368

description: Brain single cell 368


title: Brain single cell 369

description: Brain single cell 369


title: Brain single cell 370

description: Brain single cell 370


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description: Brain single cell 371


title: Brain single cell 366

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title: Brain single cell 367

description: Brain single cell 367


title: Brain single cell 364

description: Brain single cell 364


title: Brain single cell 363

description: Brain single cell 363


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description: Brain single cell 362


title: Brain single cell 361

description: Brain single cell 361


title: Brain single cell 365

description: Brain single cell 365


title: Brain single cell 358

description: Brain single cell 358


title: Brain single cell 360

description: Brain single cell 360


title: Brain single cell 379

description: Brain single cell 379


title: Brain single cell 356

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title: Brain single cell 359

description: Brain single cell 359


title: Brain single cell 357

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title: Brain single cell 375

description: Brain single cell 375


title: Brain single cell 355

description: Brain single cell 355


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description: Brain single cell 352


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description: Brain single cell 354


title: Brain single cell 351

description: Brain single cell 351


title: Brain single cell 353

description: Brain single cell 353


title: Brain single cell 347

description: Brain single cell 347


title: Brain single cell 348

description: Brain single cell 348


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description: Brain single cell 350


title: Brain single cell 349

description: Brain single cell 349


title: Brain single cell 346

description: Brain single cell 346


title: Brain single cell 344

description: Brain single cell 344


title: RIBO_pH5.8_3

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

data_processing:
Basecalling
Adapter sequence "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" was trimmed using cutadapt 2.1 (HRIBO 1.6.0)
Mapping with segemehl 0.3.4 (HRIBO 1.6.0)
rRNA filtering with samtools 1.9 (HRIBO 1.6.0)
Coverage file creation with HRIBO 1.6.0
wig files were generated with full read or single nucleotide mapping
wig files were normalized using the Counts Per Million (CPM) method and converted to bigwig format
Assembly: ASM584v2
Supplementary files format and content: bigwig format files containing CPM normalized read coverage for each sample (global mapping)
Library strategy: Ribo-seq

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

source_name: bacterial cell

growth_protocol: Cells were inoculated to a starting OD600 of 0.05 from overnight cultures and aerobically grown to exponential phase in 200 ml of unbuffered LB media (pH 7.6) in 1 liter glas flasks. After reaching an OD600 of 0.5, cultures were either grown for 30 further min at pH 7.6 under non-stress conditions, 30 min at pH 5.8, or first 15 min at pH 5.8 and then shifted again for 15 min to pH 4.4

extract_protocol:
Cells were flash frozen in liquid nitrogen and lysed by cryogenic grinding in a SPEX SamplePrep 6875 Freezer/Mill. Polysome fractions were isolated using ultracentrifugation. Nuclease digestion was performed using MNase (NEB). Monosomes were recovered using MicroSpin S-400 HR columns (GE Healthcare) and RNA was isolated using the miRNeasy Mini Kit (QIAGEN) in combination with the RNase-Free DNase Set (QIAGEN). The isolated RNA was loaded on a 15% TBE Urea size selection gel and after staining with SYBR Gold (Invitrogen), ribosomal footprints between 15 and 45 nt were excised from the gel. Gel pieces were crushed and RNA was recovered by precipitation using Corning-Costar Spin-X Centrifuge Tube Filters. Isolation of RNA fragments corresponding to ribosomal footprints of 15 – 45 nt size was verified using the RNA 6000 Nano Kit (Agilent). 5´ phosphorylation of RNA fragments was achieved using T4 Polynucleotide Kinase (NEB) and Adenosine 5´-Triphosphate (ATP) (NEB). After RNA recovery using an RNA MinElute Cleanup Kit (QIAGEN), footprint fragments were again evaluated using the Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina (NEB) with modifications described in Latif et al. 2017 DOI: 10.2144/000114302. cDNA library quality was assessed by using a High Sensitivity DNA Kit (Agilent).

treatment_protocol: Once OD600 = 0.5 was reached, cells were grown further at pH 7.6, or 5M hydrochloric acid was directly added to growing cultutes to adjust pH values to either pH 5.8, or pH 4.4.

tag: cell type

value: bacterial cell

tag: genotype

value: WT

tag: treatment

tag: rna fraction

value: ribosome-protected mRNA fragments


title: Brain single cell 343

description: Brain single cell 343


title: RIBO_pH7.6_3


title: RIBO_pH4.4_2


title: Brain single cell 341

description: Brain single cell 341


title: RIBO_pH5.8_2


title: RIBO_pH7.6_2


title: Brain single cell 340

description: Brain single cell 340


title: Brain single cell 337

description: Brain single cell 337


title: RIBO_pH5.8_1


title: Brain single cell 338

description: Brain single cell 338


title: RIBO_pH4.4_1


title: Brain single cell 336

description: Brain single cell 336


title: Brain single cell 345

description: Brain single cell 345


title: RIBO_pH4.4_3


title: RIBO_pH7.6_1


title: Brain single cell 335

description: Brain single cell 335


title: RAS 4OHT / DMSO Day 3, Replicate 3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
RAS4OHTDMSOR3
RAS4OHTDMSOR3_S58
IMR90 ER:RAS 4OHT + DMSO
polyA

data_processing:
Primary analysis RTA 3.9.25 and Secondary analysis DRAGEN GenerateFastQ 3.7.4.
Sequencing was conducted on an Illumina NextSeq 2000 system with 71 base pair single-end reads.
Sequencing reads were mapped to hg38 genome using STAR aligner (version 2.7.8a).
Gene based counting was performed using the STAR aligner (version 2.7.8a).
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.32.0).
Assembly: hg38
Supplementary files format and content: Rawcounts.csv: Comma-delimited text file includes raw counts for each Sample generated by STAR aligner.

organism: Homo sapiens

source_name: IMR90 ER:RAS

growth_protocol: IMR90 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol: RNA was harvested by way of Trizol/ Chloroform extraction followed by RNeasy mini plus kit (Qiagen).

treatment_protocol: IMR90 ER:RAS cells were treated with 100nM 4-OHT (Sigma) or DMSO and then cultured for 7 days before addition of IMP1088 (300nM) or DDD86481 (1.5uM). Cells treated with drugs for 3 days after senescence induction were collected.

tag: cell line

value: IMR90 ER:RAS

value: Lung Fibroblast

value: 4OHT + DMSO

tag: timepoint

value: Day 10


title: RAS 4OHT / IMP1088 Day 3, Replicate 3

description:
RAS4OHTIMP1088R3
RAS4OHTIMP1088R3_S59
IMR90 ER:RAS 4OHT + IMP1088
polyA

value: 4OHT + IMP1088


title: RAS 4OHT / DDD86481 Day 3, Replicate 3

description:
RAS4OHTDDD86481R3
RAS4OHTPCLX001R3_S60
IMR90 ER:RAS 4OHT + DDD86481
polyA


title: Brain single cell 333

description: Brain single cell 333


title: Brain single cell 334

description: Brain single cell 334


title: RAS DMSO / IMP1088 Day 3, Replicate 3

description:
RASDMSOIMP1088R3
RASDMSOIMP1088R3_S56
IMR90 ER:RAS DMSO + IMP1088
polyA

value: DMSO + IMP1088


title: Brain single cell 332

description: Brain single cell 332


title: Brain single cell 342

description: Brain single cell 342


title: RAS DMSO / DMSO Day 3, Replicate 3

description:
RASDMSODMSOR3
RASDMSODMSOR3_S55
IMR90 ER:RAS DMSO + DMSO
polyA

value: DMSO + DMSO


title: Brain single cell 331

description: Brain single cell 331


title: RAS 4OHT / DDD86481 Day 3, Replicate 2

description:
RAS4OHTDDD864811R2
RAS4OHTPCLX001R2_S54
IMR90 ER:RAS 4OHT + DDD86481
polyA


title: Brain single cell 328

description: Brain single cell 328


title: Brain single cell 330

description: Brain single cell 330


title: Brain single cell 329

description: Brain single cell 329


title: Brain single cell 339

description: Brain single cell 339


title: RAS 4OHT / IMP1088 Day 3, Replicate 2

description:
RAS4OHTIMP1088R2
RAS4OHTIMP1088R2_S53
IMR90 ER:RAS 4OHT + IMP1088
polyA


title: RAS 4OHT / DMSO Day 3, Replicate 2

description:
RAS4OHTDMSOR2
RAS4OHTDMSOR2_S52
IMR90 ER:RAS 4OHT + DMSO
polyA


title: RAS DMSO / DDD86481 Day 3, Replicate 2

description:
RASDMSODDD864811R2
RASDMSOPCLX001R2_S51
IMR90 ER:RAS DMSO + DDD86481
polyA

value: DMSO + DDD86481


title: Brain single cell 327

description: Brain single cell 327


title: RAS DMSO / DDD86481 Day 3, Replicate 3

description:
RASDMSODDD864811R3
RASDMSOPCLX001R3_S57
IMR90 ER:RAS DMSO + DDD86481
polyA


title: Brain single cell 326

description: Brain single cell 326


title: RAS DMSO / IMP1088 Day 3, Replicate 2

description:
RASDMSOIMP1088R2
RASDMSOIMP1088R2_S50
IMR90 ER:RAS DMSO + IMP1088
polyA


title: RAS 4OHT / IMP1088 Day 3, Replicate 1

description:
RAS4OHTIMP1088R1
RAS4OHTIMP1088R1_S47
IMR90 ER:RAS 4OHT + IMP1088
polyA


title: Brain single cell 323

description: Brain single cell 323


title: RAS 4OHT / DDD86481 Day 3, Replicate 1

description:
RAS4OHTDDD86481R1
RAS4OHTPCLX001R1_S48
IMR90 ER:RAS 4OHT + DDD86481
polyA


title: Brain single cell 324

description: Brain single cell 324


title: Brain single cell 325

description: Brain single cell 325


title: Brain single cell 321

description: Brain single cell 321


title: RAS DMSO / IMP1088 Day 3, Replicate 1

description:
RASDMSOIMP1088R1
RASDMSOIMP1088R1_S44
IMR90 ER:RAS DMSO + IMP1088
polyA


title: RAS 4OHT / DMSO Day 3, Replicate 1

description:
RAS4OHTDMSOR1
RAS4OHTDMSOR1_S46
IMR90 ER:RAS 4OHT + DMSO
polyA


title: Brain single cell 322

description: Brain single cell 322


title: Brain single cell 319

description: Brain single cell 319


title: IMR90 COPB2 shRNA #2 / BLEO, Replicate 4

description:
I90BLEOshB2_2R4
I90BLEOshB2_2R4_S42
IMR90_Bleomycin
polyA

extract_protocol:
Cells with induced shRNAs were collected 72h after doxycycline addition. RNA was harvested by way of Trizol/ Chloroform extraction followed by RNeasy mini plus kit (Qiagen).
Libraries were made from 200ng of total RNA using the NEBNext UltraII RNA library preparation kit, following the manufacturer protocol.

treatment_protocol: IMR90 or IMR90 ER:RAS cells were treated with 100nM 4-OHT (Sigma), DMSO or 50µg/ml of Bleomycin (Bleomycin treatment for 24hr) and then cultured for 7 days before addition of 1µg/ml of Doxycycline to induce shRNAs.

value: Lung fibroblast

value: COPI Knockdown

value: Bleomycin


title: Brain single cell 320

description: Brain single cell 320


title: RAS DMSO / DMSO Day 3, Replicate 1

description:
RASDMSODMSOR1
RASDMSODMSOR1_S43
IMR90 ER:RAS DMSO + DMSO
polyA


title: IMR90 COPB2 shRNA #1 / BLEO, Replicate 4

description:
I90BLEOshB2_1R4
I90BLEOshB2_1R4_S41
IMR90_Bleomycin
polyA


title: IMR90 shRNA control / BLEO, Replicate 4

description:
I90BLEOshEVR4
I90BLEOshEVR4_S40
IMR90_Bleomycin
polyA


title: Brain single cell 314

description: Brain single cell 314


title: Brain single cell 316

description: Brain single cell 316


title: Brain single cell 315

description: Brain single cell 315


title: IMR90 COPB2 shRNA #2 / DMSO, Replicate 4

description:
I90DMSOshB2_2R4
I90DMSOshB2_2R4_S39
IMR90 + DMSO
polyA

value: DMSO


title: Brain single cell 313

description: Brain single cell 313

value: brain


title: Brain single cell 436

description: Brain single cell 436

value: adult mice


title: RAS DMSO / DMSO Day 3, Replicate 2

description:
RASDMSODMSOR2
RASDMSODMSOR2_S49
IMR90 ER:RAS DMSO + DMSO
polyA


title: Brain single cell 312

description: Brain single cell 312


title: IMR90 COPB2 shRNA #1 / DMSO, Replicate 4

description:
I90DMSOshB2_1R4
I90DMSOshB2_1R4_S38
IMR90 + DMSO
polyA


title: IMR90 COPB2 shRNA #2 / BLEO, Replicate 3

description:
I90BLEOshB2_2R3
I90BLEOshB2_2R3_S36
IMR90_Bleomycin
polyA


title: RAS DMSO / DDD86481 Day 3, Replicate 1

description:
RASDMSODDD86481R1
RASDMSOPCLX001R1_S45
IMR90 ER:RAS DMSO + DDD86481
polyA


title: IMR90 COPB2 shRNA #1 / BLEO, Replicate 3

description:
I90BLEOshB2_1R3
I90BLEOshB2_1R3_S35
IMR90_Bleomycin
polyA


title: IMR90 shRNA control / DMSO, Replicate 4

description:
I90DMSOshEVR4
I90DMSOshEVR4_S37
IMR90 + DMSO
polyA


title: Brain single cell 310

description: Brain single cell 310


title: IMR90 shRNA control / BLEO, Replicate 3

description:
I90BLEOshEVR3
I90BLEOshEVR3_S34
IMR90_Bleomycin
polyA


title: IMR90 COPB2 shRNA #2 / DMSO, Replicate 3

description:
I90DMSOshB2_2R3
I90DMSOshB2_2R3_S33
IMR90 + DMSO
polyA


title: Brain single cell 311

description: Brain single cell 311


title: Brain single cell 309

description: Brain single cell 309


title: Brain single cell 307

description: Brain single cell 307


title: Brain single cell 318

description: Brain single cell 318


title: Brain single cell 308

description: Brain single cell 308


title: IMR90 COPB2 shRNA #1 / DMSO, Replicate 3

description:
I90DMSOshB2_1R3
I90DMSOshB2_1R3_S32
IMR90 + DMSO
polyA


title: RAS COPB2 shRNA #2 / 4OHT, Replicate 3

description:
RAS4OHTshB2_2R3
RAS4OHTshB2_2R3_S30
IMR90 ER:RAS + 4OHT
polyA


title: Brain single cell 306

description: Brain single cell 306


title: Brain single cell 317

description: Brain single cell 317


title: Brain single cell 305

description: Brain single cell 305


title: RAS shRNA control / 4OHT, Replicate 3

description:
RAS4OHTshEVR3
RAS4OHTshEVR3_S28
IMR90 ER:RAS + 4OHT
polyA


title: RAS COPB2 shRNA #2 / DMSO, Replicate 3

description:
RASDMSOshB2_2R3
RASDMSOshB2_2R3_S27
IMR90 ER:RAS + DMSO
polyA


title: RAS COPB2 shRNA #1 / 4OHT, Replicate 3

description:
RAS4OHTshB2_1R3
RAS4OHTshB2_1R3_S29
IMR90 ER:RAS + 4OHT
polyA


title: Brain single cell 304

description: Brain single cell 304


title: RAS shRNA control / DMSO, Replicate 3

description:
RASDMSOshEVR3
RASDMSOshEVR3_S25
IMR90 ER:RAS + DMSO
polyA


title: Brain single cell 302

description: Brain single cell 302


title: IMR90 COPB2 shRNA #2 / BLEO, Replicate 2

description:
I90BLEOshB2_2R2
I90BLEOshB2_2R2_S24
IMR90_Bleomycin
polyA


title: IMR90 shRNA control / DMSO, Replicate 3

description:
I90DMSOshEVR3
I90DMSOshEVR3_S31
IMR90 + DMSO
polyA


title: Brain single cell 301

description: Brain single cell 301


title: Brain single cell 303

description: Brain single cell 303


title: IMR90 COPB2 shRNA #2 / DMSO, Replicate 2

description:
I90DMSOshB2_2R2
I90DMSOshB2_2R2_S21
IMR90 + DMSO
polyA


title: RAS COPB2 shRNA #1 / DMSO, Replicate 3

description:
RASDMSOshB2_1R3
RASDMSOshB2_1R3_S26
IMR90 ER:RAS + DMSO
polyA


title: Brain single cell 300

description: Brain single cell 300


title: Brain single cell 298

description: Brain single cell 298


title: IMR90 shRNA control / BLEO , Replicate 2

description:
I90BLEOshEVR2
I90BLEOshEVR2_S22
IMR90_Bleomycin
polyA


title: IMR90 COPB2 shRNA #1 / BLEO, Replicate 2

description:
I90BLEOshB2_1R2
I90BLEOshB2_1R2_S23
IMR90_Bleomycin
polyA


title: Brain single cell 297

description: Brain single cell 297


title: Brain single cell 296

description: Brain single cell 296


title: Brain single cell 299

description: Brain single cell 299


title: Brain single cell 294

description: Brain single cell 294


title: IMR90 shRNA control / DMSO, Replicate 2

description:
I90DMSOshEVR2
I90DMSOshEVR2_S19
IMR90 + DMSO
polyA


title: RAS COPB2 shRNA #2 / 4OHT, Replicate 2

description:
RAS4OHTshB2_2R2
RAS4OHTshB2_2R2_S18
IMR90 ER:RAS + 4OHT
polyA


title: Brain single cell 293

description: Brain single cell 293


title: RAS COPB2 shRNA #1 / 4OHT, Replicate 2

description:
RAS4OHTshB2_1R2
RAS4OHTshB2_1R2_S17
IMR90 ER:RAS + 4OHT
polyA


title: Brain single cell 292

description: Brain single cell 292


title: RAS shRNA control / 4OHT, Replicate 2

description:
RAS4OHTshEVR2
RAS4OHTshEVR2_S16
IMR90 ER:RAS + 4OHT
polyA


title: RAS COPB2 shRNA #2 / DMSO, Replicate 2

description:
RASDMSOshB2_2R2
RASDMSOshB2_2R2_S15
IMR90 ER:RAS + DMSO
polyA


title: Brain single cell 291

description: Brain single cell 291


title: Brain single cell 290

description: Brain single cell 290


title: Brain single cell 289

description: Brain single cell 289


title: RAS shRNA control / DMSO, Replicate 2

description:
RASDMSOshEVR2
RASDMSOshEVR2_S13
IMR90 ER:RAS + DMSO
polyA


title: Brain single cell 288

description: Brain single cell 288


title: IMR90 COPB2 shRNA #2 / BLEO, Replicate 1

description:
I90BLEOshB2_2R1
I90BLEOshB2_2R1_S12
IMR90_Bleomycin
polyA


title: IMR90 COPB2 shRNA #1 / BLEO, Replicate 1

description:
I90BLEOshB2_1R1
I90BLEOshB2_1R1_S11
IMR90_Bleomycin
polyA


title: Brain single cell 295

description: Brain single cell 295


title: Brain single cell 285

description: Brain single cell 285


title: IMR90 COPB2 shRNA #1 / DMSO, Replicate 2

description:
I90DMSOshB2_1R2
I90DMSOshB2_1R2_S20
IMR90 + DMSO
polyA


title: IMR90 COPB2 shRNA #1 / DMSO, Replicate 1

description:
I90DMSOshB2_1R1
I90DMSOshB2_1R1_S8
IMR90 + DMSO
polyA


title: Brain single cell 287

description: Brain single cell 287


title: Brain single cell 284

description: Brain single cell 284


title: Brain single cell 286

description: Brain single cell 286


title: IMR90 shRNA control / BLEO, Replicate 1

description:
I90BLEOshEVR1
I90BLEOshEVR1_S10
IMR90_Bleomycin
polyA


title: Brain single cell 283

description: Brain single cell 283


title: RAS COPB2 shRNA #2 / 4OHT, Replicate 1

description:
RAS4OHTshB2_2R1
RAS4OHTshB2_2R1_S6
IMR90 ER:RAS + 4OHT
polyA


title: RAS COPB2 shRNA #1 / 4OHT, Replicate 1

description:
RAS4OHTshB2_1R1
RAS4OHTshB2_1R1_S5
IMR90 ER:RAS + 4OHT
polyA


title: IMR90 shRNA control / DMSO, Replicate 1

description:
I90DMSOshEVR1
I90DMSOshEVR1_S7
IMR90 + DMSO
polyA


title: Brain single cell 281

description: Brain single cell 281


title: Brain single cell 282

description: Brain single cell 282


title: Brain single cell 280

description: Brain single cell 280


title: RAS shRNA control / 4OHT, Replicate 1

description:
RAS 4OHTshEVR1
RAS4OHTshEVR1_S4
IMR90 ER:RAS + 4OHT
polyA


title: RAS COPB2 shRNA #1 / DMSO, Replicate 2

description:
RASDMSOshB2_1R2
RASDMSOshB2_1R2_S14
IMR90 ER:RAS + DMSO
polyA


title: RAS COPB2 shRNA #2 / DMSO, Replicate 1

description:
RASDMSOshB2_2R1
RASDMSOshB2_2R1_S3
IMR90 ER:RAS + DMSO
polyA


title: Brain single cell 279

description: Brain single cell 279


title: Brain single cell 278

description: Brain single cell 278


title: RAS COPB2 shRNA #1 / DMSO, Replicate 1

description:
RASDMSOshB2_1R1
RASDMSOshB2_1R1_S2
IMR90 ER:RAS + DMSO
polyA


title: RAS shRNA control / DMSO, Replicate 1

description:
RASDMSOshEVR1
RASDMSOshEVR1_S1
IMR90 ER:RAS + DMSO
polyA


title: OMPtTAtetOP2(nc), control HiC, r2

city: New York

first: Ariel

last: Pourmorady

state: NY

address: 3227 Broadway

department: Neurobiology and Behavior

country: USA

institute: Columbia University

description: Control Hi-C libraries performed on an individual biological replicate of GFP+ OSNs sorted from adult mice

library_source: genomic

data_processing:
Reads were aligned to the mm10 genome using the distiller pipeline (https://github.com/mirnylab/distiller-nf), uniquely mapped reads (mapq > 30) were retained and duplicate reads discarded. Contacts were then binned into matrices using cooler 45. Analysis was performed on data pooled from two (HiChIP, Hi-C) or three biological replicates (Liquid Hi-C), after confirming that the results of analysis of individual replicates were similar.
genome build/assembly: mm10
processed data files format and content: HiC matrix

molecule: genomic DNA

source_name: Olfactory Sensory Neurons

extract_protocol: MOE were dissociated using the Worthington Papain Dissociation kit, and cells were fixed in 1% formaldehyde in 1x PBS, and quenched with 1/10th vol. 1.25M Glycine, and washed with 1x PBS either immediately before or after cell sorting. Nuclei were processed for HiC exactly as described in "LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice" (Horta et al. 2019). Briefly nuclei were lysed, permeabilized, quenched, and then digested over night in DpnII . The next day we performed biotin-fill in with biotinylated dUTP, ligation with T4, and shearing. Cross-links were reversed overnight and DNA was purified with a 2x AMPure bead purification. Library prep was performed on MyOne Streptavidin beads to purify biotinylated contacts. Libraries were prepared using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit.

value: OMPtTA > tetO-P2(nc)

tag: sample type

value: HiC

value: Olfactory Sensory Neurons


title: Brain single cell 276

description: Brain single cell 276


title: IMR90 COPB2 shRNA #2 / DMSO, Replicate 1

description:
I90DMSOshB2_2R1
I90DMSOshB2_2R1_S9
IMR90 + DMSO
polyA


title: Brain single cell 274

description: Brain single cell 274


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, HiC, rep3

description: Hi-C libraries performed on an individual biological replicate of OSNs sorted from adult mice

data_processing:
Reads were aligned to the mm10 genome using the distiller pipeline (https://github.com/mirnylab/distiller-nf), uniquely mapped reads (mapq > 30) were retained and duplicate reads discarded. Contacts were then binned into matrices using cooler 45. Analysis was performed on data pooled from two (HiChIP, Hi-C) or three biological replicates (Liquid Hi-C), after confirming that the results of analysis of individual replicates were similar.
mm10

source_name: main olfactory epithelium

value: main olfactory epithelium

value: mor28iCre, tdTom, OMPtTA, tetOP26

value: 4 weeks old


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, HiC, rep3

value: mor28iCre, tdTom, OMPtTA, tetOP27


title: Brain single cell 273

description: Brain single cell 273


title: Brain single cell 272

description: Brain single cell 272


title: Brain single cell 271

description: Brain single cell 271


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, HiC, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP25

value: 7 weeks old


title: Brain single cell 270

description: Brain single cell 270


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, HiC, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP22

value: 5.5 weeks old


title: Brain single cell 268

description: Brain single cell 268


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, HiC, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP23


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, HiC, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP20


title: Brain single cell 265

description: Brain single cell 265


title: Brain single cell 277

description: Brain single cell 277


title: Brain single cell 267

description: Brain single cell 267


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, RNA-seq, rep3

description: RNA-seq performed on FAC sorted cells from the main olfactory epithelium of adult mice using the following kit: SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2.

data_processing:
Data processing and analysis was performed as described in "Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons" (Monahan et al. 2017). Briefly Adapter sequences were removed from raw sequencing data with CutAdapt. RNA-seq reads were aligned to the mouse genome (mm10) using STAR. Samtools was used to select uniquely aligning reads by remove reads with alignment quality alignments below 30 (-q 30). RNA-seq data analysis was performed in R with the DESeq2 package.
mm10

extract_protocol: All RNA-seq experiments were performed under RNA clean conditions. For RNA-seq, live cells were sorted into RNase free 1x PBS, pelleted at 600-g, for 5-min, at 4 ̊C, then resuspended in 500-uL Trizol, flash frozen in liquid nitrogen and stored O/N at -80 ̊C. RNA extraction was performed the next day. Trizol suspensions were thawed on ice, 1/5V of 1-bromo-3-chloropropane was added, and tubes were shook vigorously to combine phases. Phases were allowed to separate for 2-min at room temperature and then tubes were centrifuged at 10,500 rpm, for 15-min at 4  ̊C in an Eppendorf centrifuge C5424R. We collected the upper aqueous phase which was transferred to a new tube. 1/2V of Isopropanol and 1-uL of linear polyacrylamide (Sigma Aldrich 56575) were added, tube was inverted to mix, and RNA was allowed to precipitate for 10-min at RT. Tubes were centrifuged for 10-min at 10,500 rpm and 4- ̊C. The supernatant was removed and 1V of 75% EtOH was added to the pellet, which was dislodged by flicking the tube. Tubes were centrifuged for another 5-min, at 10,500-rpm, and 4  ̊C. EtOH was removed and tubes were allowed to air dry for 5-min until the pellet turned clear. Next we added 26- uL of RNase free water, 3-uL of Ambion DNase I 10x buffer and 1-uL of DNase I (AM2222) to remove all DNA, and incubated tubes at 37  ̊C for 30-min. RNA was purified doing a 1.5x AMPure bead cleanup, measured on a nanodrop, and used as the input for library preparation with SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2 (Takara Bio USA). OMP-tTA>tetO-GFP and gg8-tTA>tetO-GFP libraries were prepared with the TruSeq kit. However, mature OSN samples were compared to both OMP-tTA>tetO-GFP (TruSeq prep) and OMP-IRES-GFP (Takara Bio USA), which label the same neurons, and produced the same results. Libraries were sequenced on either a NextSeq550 or a NextSeq2000 and were sequenced to a targeted coverage of ~25M reads. All RNA-seq experiments were performed with 2-3 biological replicates.

value: mor28iCre, tdTom, OMPtTA, tetOP19

value: 5 weeks old


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, HiC, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP21


title: Brain single cell 264

description: Brain single cell 264

value: brain

value: adult mice


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, RNA-seq, rep3

value: mor28iCre, tdTom, OMPtTA, tetOP17


title: Brain single cell 266

description: Brain single cell 266


title: Brain single cell 263

description: Brain single cell 263


title: OMPtTAtetOP2(nc), control HiC, r1

value: OMPtTA > tetO-P2(nc)

value: HiC

value: Olfactory Sensory Neurons


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, RNA-seq, rep2

value: main olfactory epithelium

value: mor28iCre, tdTom, OMPtTA, tetOP16

value: 8 weeks old


title: Brain single cell 262

description: Brain single cell 262


title: Brain single cell 275

description: Brain single cell 275


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, HiC, rep3

value: mor28iCre, tdTom, OMPtTA, tetOP28

value: 4 weeks old


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, RNA-seq, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP15


title: Brain single cell 261

description: Brain single cell 261


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, RNA-seq, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP14


title: Brain single cell 269

description: Brain single cell 269


title: Brain single cell 260

description: Brain single cell 260


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, HiC, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP24

value: 7 weeks old


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, RNA-seq, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP13


title: Brain single cell 259

description: Brain single cell 259


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, ATAC, rep3

description: ATAC-seq generated from individual biological replicate of OSNs FACsorted from adult mice

data_processing:
Adapter sequences were removed from raw sequencing data with CutAdapt. ATAC-seq reads were aligned to the mouse genome (mm10) using Bowtie2 (Langmead and Salzberg, 2012). Default settings were used, except a maximum insert size of 1000 (-X 1000) was allowed for ATAC-seq data since these data sets contained some large fragments. PCR duplicate reads were identified with Picard and removed with Samtools (Li et al., 2009). Samtools was used to select uniquely aligning reads by removing reads with alignment quality alignments below 30 (-q 30). Regions of open chromatin were identified by running HOMER peak calling in ‘region’ mode, with a fragment size of 150 bp and a peak size of 300 bp. For ATAC-seq signal tracks, replicate experiments were merged, and HOMER was used to generate 1 bp resolution signal tracks normalized to a library size of 10,000,000 reads. Reads were shifted 4 bp upstream in order to more accurately map the Tn5 insertion site. Reads were extended to the full fragment length, as determined by paired-end sequencing.
mm10

extract_protocol: ATAC-seq libraries were prepared from live sorted cells using the protocol developed by Buenrostro et al., 2015. Cells were pelleted (500 rcf, 5 min, 4°C) and then resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were immediately pelleted (1000 rcf, 10 min, 4°C). Pelleted nuclei were resuspended in transposition reaction mix prepared from Illumina Nextera reagents (for 50 uL: 22.5 uL water, 25 uL 2xTD buffer, 2.5 uL Tn5 Transposase). The volume of the Tn5 transposition reaction was scaled to the number of cells collected: 1 uL mix per 1000 cells. If fewer than 10,000 cells were collected by FACS, 10 uL scale reactions were performed. Transposed DNA was column purified using a Zymo DNA Clean & Concentrator-5 (Zymo). The transposed DNA was then amplified using barcoded primers and NEBNext High Fidelity 2x PCR Master Mix (NEB). Amplified libraries were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1.6 ul of beads per 1 uL of library and eluted in 30 uL of elution buffer (10 mM Tris-HCl pH 8, 0.1 mM EDTA).

value: mor28iCre, tdTom, OMPtTA, tetOP10


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, RNA-seq, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP12


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, RNA-seq, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP11


title: Brain single cell 258

description: Brain single cell 258

value: brain

value: adult mice


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, RNA-seq, rep3

value: mor28iCre, tdTom, OMPtTA, tetOP18

value: 5 weeks old


title: Brain single cell 257

description: Brain single cell 257


title: Brain single cell 256

description: Brain single cell 256


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, ATAC, rep3

value: main olfactory epithelium

value: mor28iCre, tdTom, OMPtTA, tetOP8


title: Brain single cell 254

description: Brain single cell 254


title: Brain single cell 253

description: Brain single cell 253


title: Brain single cell 255

description: Brain single cell 255


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, ATAC, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP6


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, ATAC, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP7


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, ATAC, rep3

value: mor28iCre, tdTom, OMPtTA, tetOP9


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, ATAC, rep2

value: mor28iCre, tdTom, OMPtTA, tetOP5


title: Brain single cell 252

description: Brain single cell 252


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+, ATAC, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP4


title: Brain single cell 251

description: Brain single cell 251


title: mor28iCre-tdTom OMPtTA-tetOP2, GFP+/tdTom+, ATAC, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP3


title: mor28iCre-tdTom OMPtTA-tetOP2, tdTom+, ATAC, rep1

value: mor28iCre, tdTom, OMPtTA, tetOP2

value: 7 weeks old


title: Brain single cell 248

description: Brain single cell 248


title: Brain single cell 247

description: Brain single cell 247


title: Brain single cell 249

description: Brain single cell 249


title: Brain single cell 246

description: Brain single cell 246


title: Brain single cell 245

description: Brain single cell 245


title: OMPtTAtetOM71(nc)tg, control HiC, r2

value: OMPtTA > tetO-M71(nc)tg

value: HiC

value: Olfactory Sensory Neurons


title: gg8tTAtetOP2(nc), RNA-seq, r4

value: gg8tTA > tetO-P2(nc)

value: RNA-seq


title: gg8tTAtetOP2(nc), control HiC, r1


title: gg8tTAtetOP2(nc), control HiC, r2


title: gg8tTAtetOP2, H3K27ac HiChIP, r2

description: H3K27ac HiChIP performed on GFP+ OSNs sorted from adult mice

data_processing:
Reads were aligned to the mm10 genome using the distiller pipeline (https://github.com/mirnylab/distiller-nf), uniquely mapped reads (mapq > 30) were retained and duplicate reads discarded. Contacts were then binned into matrices using cooler 45. Analysis was performed on data pooled from two (HiChIP, Hi-C) or three biological replicates (Liquid Hi-C), after confirming that the results of analysis of individual replicates were similar.
Assembly: mm10
Supplementary files format and content: Genomic Contacts binned at 50-kb resolution
Library strategy: Hi-C/Liquid Hi-C/HiChIP

extract_protocol:
MOE were dissociated using the Worthington Papain Dissociation kit, and cells were fixed in 1% formaldehyde in 1x PBS either before or after sorting for GFP+ cells. For Liquid Hi-C, nuclei were digested with Dpn-II for various lengths of time, on a thermomixer shaking at 900 rpm at 37˚C, placed on ice for 10-minutes, then fixed in 1% formaldehyde in 1x PBS. After cross-linking, nuclei were processed for HiC exactly as described in "LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice" (Horta et al. 2019). Briefly nuclei were lysed, permeabilized, quenched, and then digested over night in DpnII . The next day we performed biotin-fill in with biotinylated dUTP, ligation with T4, and shearing. Cross-links were reversed overnight and DNA was purified with a 2x AMPure bead purification. Library prep was performed on MyOne Streptavidin beads to purify biotinylated contacts.
The HiChIP protocol was kindly given by the Chang Lab and integrated into our Hi-C protocol to perform H3K27ac HiChIP on olfactory sensory neurons. MOE from 5-7 gg8-tTA>tetO-P2 mice were dissociated to obtain 4M GFP+ cells per replicate, for a total of 2 replicates. Cells were processed according to the in situ Hi-C protocol with the following exceptions, nuclei were digested for only 2 hours instead of overnight; complete nuclei digestion was verified by running reverse cross-linked digested nuclei on a DNA Agarose gel. After ligation, nuclei were pelleted at 2500-g, for 5-min, at 4-˚C and stored overnight at -20 ˚C. The next day, nuclei were resuspended in 130-uL of HiChIP nuclear lysis buffer (50 mM Tris pH 7.5, 10 mM EDTA, 1% SDS, 1X Protease Inhibitor in water), and sheared on a Covaris S220 with the following parameters: duty cycle – 2%, PIP – 140, cycles/burst – 200, time – 4 minutes. After shearing, samples were precleared and immunoprecipitation was performed with H3K27ac antibody (Abcam GR323193701),
Libraries were prepared using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit for HiC and Liquid HiC. For HiChIP, libraries were prepared using on-bead based tagmentation with Tn5 as described in "HiChIP: Efficient and sensitive analysis of protein-directed genome architecture" (Mumbach et al. 2016).

value: gg8-tTA >tetO-P2


title: Brain single cell 244

description: Brain single cell 244

value: brain

value: adult mice


title: Brain single cell 243

description: Brain single cell 243


title: Brain single cell 242

description: Brain single cell 242


title: OMPtTAtetOM71(nc)tg, control HiC, r1


title: gg8tTAtetOP2, H3K27ac HiChIP, r1


title: Brain single cell 250

description: Brain single cell 250


title: High Fat Diet + DDD86481, F114

description:
HFDddd114
S44
polyA

data_processing:
Primary analysis RTA 3.9.25 and Secondary analysis DRAGEN GenerateFastQ 3.7.4.
Sequencing was conducted on an Illumina NextSeq 2000 system with 71 base pair single-end reads.
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a).
Gene based counting was performed using the STAR aligner (version 2.7.1a).
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.28.1).
Assembly: mm10
Supplementary files format and content: Rawcounts.csv: Comma-delimited text file includes raw counts for each Sample generated by STAR aligner.

source_name: Liver

extract_protocol:
Frozen Bulk liver tissue was homogenized using Qiagen Tissue lyzer and tungsten carbide beads. RNA was harvested from homogenate by way of Trizol/ Chloroform extraction followed by RNeasy mini plus kit (Qiagen).
Libraries were made from 200ng of total RNA using the NEBNext UltraII RNA library preparation kit, following the manufacturer protocol.

value: Liver

value: WT

value: High Fat Diet + DDD86481

value: 19 weeks


title: High Fat Diet + DDD86481, F115

description:
HFDddd115
S45
polyA


title: Brain single cell 237

description: Brain single cell 237


title: High Fat Diet + DDD86481, F113

description:
HFDddd113
S43
polyA


title: Brain single cell 238

description: Brain single cell 238


title: Mouse leptomeninges sample R2

description: mouse leptomeninges cells

library_source: transcriptomic single cell

data_processing:
The raw sequence reads were analyzed by Cell Ranger with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text files with read counts for each sample

extract_protocol:
Mouse leptomeninges was manually carefully peeled off from cerebral hemispheres of 3 months old Pdgfra-H2BGFP males and females, digested into single-cell suspensions.
The cells were counted on a LUNA-FL Dual Fluorescence Cell Counter (LogosBio) and loaded on a Chromium controller, aiming for a maximal recovery of 5000 cells per sample.

value: Brain

value: adult


title: Mouse leptomeninges sample R1

description: mouse leptomeninges cells


title: High Fat Diet + DDD86481, F111

description:
HFDddd111
S42
polyA


title: High Fat Diet + DDD86481, F105

description:
HFDddd105
S41
polyA


title: Brain single cell 240

description: Brain single cell 240


title: Brain single cell 234

description: Brain single cell 234


title: Brain single cell 235

description: Brain single cell 235


title: Brain single cell 236

description: Brain single cell 236


title: Brain single cell 241

description: Brain single cell 241


title: Brain single cell 239

description: Brain single cell 239


title: High Fat Diet + DDD86481, F102

description:
HFDddd102
S40
polyA


title: Brain single cell 233

description: Brain single cell 233


title: High Fat Diet + DDD86481, F95

description:
HFDddd95
S39
polyA


title: Brain single cell 232

description: Brain single cell 232


title: High Fat Diet + DDD86481, F94

description:
HFDddd94
S38
polyA


title: Brain single cell 230

description: Brain single cell 230


title: High Fat Diet + DDD86481, F93

description:
HFDddd93
S37
polyA


title: Brain single cell 231

description: Brain single cell 231


title: Brain single cell 229

description: Brain single cell 229


title: High Fat Diet + DDD86481, F92

description:
HFDddd92
S36
polyA


title: Brain single cell 228

description: Brain single cell 228


title: Brain single cell 227

description: Brain single cell 227


title: High Fat Diet + Vehicle, F84

description:
HFDveh84
S33
polyA

value: High Fat Diet + Vehicle


title: Brain single cell 226

description: Brain single cell 226


title: High Fat Diet + Vehicle, F83

description:
HFDveh83
S32
polyA


title: Brain single cell 225

description: Brain single cell 225


title: Brain single cell 224

description: Brain single cell 224


title: Brain single cell 223

description: Brain single cell 223


title: Brain single cell 221

description: Brain single cell 221


title: Brain single cell 222

description: Brain single cell 222


title: High Fat Diet + DDD86481, F65

description:
HFDddd65
S23
polyA


title: Chow Diet + Vehicle, F74

description:
ChowVEH74
S27
polyA

value: Chow Diet + Vehicle


title: High Fat Diet + Vehicle, F82

description:
HFDveh82
S31
polyA


title: High Fat Diet + Vehicle, F81

description:
HFDveh81
S30
polyA


title: Chow Diet + Vehicle, F71

description:
ChowVEH71
S24
polyA


title: Chow Diet + Vehicle, F75

description:
ChowVEH75
S28
polyA


title: High Fat Diet + DDD86481, F64

description:
HFDddd64
S22
polyA


title: High Fat Diet + DDD86481, F91

description:
HFDddd91
S35
polyA


title: High Fat Diet + Vehicle, F85

description:
HFDveh85
S34
polyA


title: High Fat Diet + DDD86481, F63

description:
HFDddd63
S21
polyA


title: Chow Diet + Vehicle, F55

description:
ChowVEH55
S19
polyA


title: High Fat Diet + DDD86481, F62

description:
HFDddd62
S20
polyA


title: Chow Diet + Vehicle, F72

description:
ChowVEH72
S25
polyA


title: Chow Diet + Vehicle, F73

description:
ChowVEH73
S26
polyA


title: Chow Diet + Vehicle, F54

description:
ChowVEH54
S18
polyA


title: Chow Diet + Vehicle, F52

description:
ChowVEH52
S16
polyA


title: Chow Diet + Vehicle, F51

description:
ChowVEH51
S15
polyA


title: High Fat Diet + Vehicle, F45

description:
HFDveh45
S14
polyA


title: High Fat Diet + Vehicle, F44

description:
HFDveh44
S13
polyA


title: High Fat Diet + Vehicle, F43

description:
HFDVeh43
S12
polyA


title: High Fat Diet + Vehicle, F33

description:
HFDveh33
S10
polyA


title: High Fat Diet + Vehicle, F32

description:
HFDveh32
S9
polyA


title: Chow Diet + Vehicle, F53

description:
ChowVEH53
S17
polyA


title: Chow Diet + Vehicle, F25

description:
ChowVEH25
S8
polyA


title: Chow Diet + Vehicle, F24

description:
ChowVEH24
S7
polyA


title: Chow Diet + Vehicle, F23

description:
ChowVEH23
S6
polyA


title: Chow Diet + Vehicle, F22

description:
ChowVEH22
S5
polyA


title: High Fat Diet + Vehicle, F34

description:
HFDveh34
S11
polyA


title: Chow Diet + Vehicle, F21

description:
ChowVEH21
S4
polyA


title: High Fat Diet + Vehicle, F15

description:
HFDveh15
S3
polyA


title: High Fat Diet + Vehicle, F14

description:
HFDveh14
S2
polyA


title: Drosophila melanogaster embryo total RNA-seq r2

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in H.vulgare cells; Experiment SD616
D.melanogaster-embryo-10.tss.txt
D.melanogaster_total_RNA-seq.bed.gz

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: embryo


title: Brain single cell 194

description: Brain single cell 194


title: Brain single cell 198

description: Brain single cell 198


title: Brain single cell 195

description: Brain single cell 195


title: Brain single cell 200

description: Brain single cell 200


title: Brain single cell 216

description: Brain single cell 216


title: Brain single cell 212

description: Brain single cell 212


title: Brain single cell 205

description: Brain single cell 205


title: Brain single cell 202

description: Brain single cell 202


title: Brain single cell 201

description: Brain single cell 201


title: Brain single cell 208

description: Brain single cell 208


title: Brain single cell 204

description: Brain single cell 204


title: Brain single cell 219

description: Brain single cell 219


title: Brain single cell 214

description: Brain single cell 214


title: Brain single cell 210

description: Brain single cell 210


title: Brain single cell 209

description: Brain single cell 209


title: Brain single cell 197

description: Brain single cell 197


title: Brain single cell 199

description: Brain single cell 199


title: Brain single cell 207

description: Brain single cell 207


title: Brain single cell 215

description: Brain single cell 215


title: Brain single cell 196

description: Brain single cell 196


title: Brain single cell 211

description: Brain single cell 211


title: Brain single cell 218

description: Brain single cell 218


title: Brain single cell 203

description: Brain single cell 203


title: Brain single cell 213

description: Brain single cell 213


title: Brain single cell 206

description: Brain single cell 206


title: Brain single cell 217

description: Brain single cell 217


title: Brain single cell 220

description: Brain single cell 220


title: Drosophila melanogaster embryo total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in H.vulgare cells; Experiment SD539
D.melanogaster-embryo-10.tss.txt
D.melanogaster_total_RNA-seq.bed.gz


title: High Fat Diet + Vehicle, F11

description:
HFDveh11
S1
polyA


title: Brain single cell 193

description: Brain single cell 193


title: Zea mays shoot7d total RNA-seq r2

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in Z.mays leaf; Experiment MS081
Z.mays-shoot7d-10.tss.txt

organism: Zea mays

source_name: shoot 7d old

value: shoot 7d old


title: Brain single cell 191

description: Brain single cell 191


title: Brain single cell 192

description: Brain single cell 192


title: Brain single cell 189

description: Brain single cell 189


title: Brain single cell 182

description: Brain single cell 182


title: Brain single cell 188

description: Brain single cell 188


title: Zea mays root7d total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in Z.mays leaf; Experiment MS082
Z.mays-root7d-10.tss.txt

source_name: root 7d old

value: root 7d old


title: Lung immune cell, scRNAseq

city: Beijing

first: Yanxiao

last: Wang

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Seurat package (v2.3.4) was used to perform dimensionality reduction, clustering, and visualization for the scRNA-seq data presented using UMAP plots. To filter valid cell barcodes, cells with more than 6000 transcripts profiled or more than 20% of the transcriptome of mitochondrial origin were then removed from each object.
To limit the bias in gating of FACS, the four Seurat objects were then combined into a merged dataset. The batch effects between different sequencing batches were corrected using the Cell Ranger ‘aggr’ script. According to the general markers EPCAM+ (epithelial cells), CDH5+ (endothelial cells), PTPRC+ (immune cells), DCN+ (stromal cells), the cells of the paraquat-injured lung were separated into four supergroups.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Freshly collected lung specimens of the paraquat poisoning patient were obtained from the lung removed at the time of lung transplantation. For primary cell isolation, the lung specimens without mesothelial layer were minced mechanically into small pieces (<1 mm3) and digested in modified DMEM medium with an enzyme cocktail containing 10 U/mL neutral protease, 400 U/mL collagenase type I, 8 U/mL elastase, and 0.66 U/mL DNase I for 50 mins at 37°C. To stop the enzymatic reaction, the digested tissues were added 10% FBS and incubated for 10 mins at RT. Digested tissue was filtered using 100 m- and 40 m-cell strainer. The filtrated suspension was centrifuged at 400 g at 4°C for 8 mins to collect the dissociated cells. The cell pellet was resuspended in RBC lysis buffer and incubated for 2 mins at RT to lyse the red blood cells. After centrifugation, the cell pellet was resuspended in freezing DMEM+5% FBS to stain with PE anti-human EPCAM, FITC anti-human CD45, APC anti-human CD31 at 4 °C for 30 mins. The cell pellet was resuspended with DMEM+2% FBS and filtered through a 40 m cell strainer again before the sorting process. DAPI was used to label dead cells. Sorting was performed on a BD FACS Aria III appliance.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung

value: Immune cells

value: 18 years old

value: 34 days post paraquat-poisoning


title: Zea mays leaves7d csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in Z.mays cells; Experiment MS072
Z.mays-leaves7d-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: csRNA-Seq

source_name: leaves 7d old

value: leaves 7d old


title: Zea mays leaves7d csRNA-seq r2

description:
csRNA-seq; nascent TSS mapping in Z.mays cells; Experiment MS074
Z.mays-leaves7d-10.tss.txt


title: Brain single cell 184

description: Brain single cell 184

value: brain

value: adult mice


title: Brain single cell 190

description: Brain single cell 190


title: Zea mays leaf total RNA-seq r1

description:
Total RNA-seq (Ribo0), steady state transcriptome profiling in Z.mays leaf; Experiment SD923
Z.mays-leaf-10.tss.txt

source_name: adult leaf

value: adult leaf


title: Brain single cell 185

description: Brain single cell 185


title: Brain single cell 180

description: Brain single cell 180


title: Brain single cell 183

description: Brain single cell 183


title: Brain single cell 186

description: Brain single cell 186


title: Brain single cell 187

description: Brain single cell 187


title: Zea mays leaves7d total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in Z.mays leaf; Experiment MS079
Z.mays-leaves7d-10.tss.txt


title: Zea mays leaves7d sRNA-seq r1

description:
sRNA-seq; small RNA mapping in Z.mays cells; Experiment MS075
Z.mays-leaves7d-10.tss.txt


title: Zea mays root7d sRNA seq- r1

description:
sRNA-seq; small RNA mapping in Z.mays cells; Experiment SD953
Z.mays-root7d-10.tss.txt


title: Zea mays root7d csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in Z.mays cells; Experiment SD933
Z.mays-root7d-10.tss.txt


title: Zea mays leaves7d sRNA-seq r2

description:
sRNA-seq; small RNA mapping in Z.mays cells; Experiment MS073
Z.mays-leaves7d-10.tss.txt


title: Zea mays shoot7d csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in Z.mays cells; Experiment SD932
Z.mays-shoot7d-10.tss.txt


title: Zea mays leaves7d total RNA-seq r2

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in Z.mays leaf; Experiment MS080
Z.mays-leaves7d-10.tss.txt


title: Brain single cell 179

description: Brain single cell 179


title: Lung endothelial cell, scRNAseq

description: 10x Genomics

value: Endothelial cells


title: Zea mays shoot7d sRNA-seq r1

description:
sRNA-seq; small RNA mapping in Z.mays cells; Experiment SD952
Z.mays-shoot7d-10.tss.txt


title: Brain single cell 181

description: Brain single cell 181


title: Brain single cell 178

description: Brain single cell 178


title: Brain single cell 177

description: Brain single cell 177


title: Lung stromal cell, scRNAseq

description: 10x Genomics

value: Stromal cells


title: Lung epithelail cell, scRNAseq

description: 10x Genomics

value: Epithelial cells


title: Brain single cell 173

description: Brain single cell 173


title: Brain single cell 176

description: Brain single cell 176


title: Brain single cell 171

description: Brain single cell 171


title: Brain single cell 169

description: Brain single cell 169


title: Brain single cell 166

description: Brain single cell 166


title: Brain single cell 172

description: Brain single cell 172


title: Brain single cell 163

description: Brain single cell 163


title: Brain single cell 167

description: Brain single cell 167


title: Brain single cell 164

description: Brain single cell 164


title: Brain single cell 161

description: Brain single cell 161


title: Brain single cell 160

description: Brain single cell 160


title: CRC-PKU-39-N

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.3a_modified) was used to map clean reads to the hg38 genome index built with the GENCODE v27 annotation
Duplicates in the aligned reads were removed using Picard Tools MarkDuplicates (version 2.20.0)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v27 annotation, transcripts with uncertain coding potential annotation extracted from mitranscriptome, circular RNA annotation from circBase, Promoter, enhancer and repeat regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Normal adjacent tumor tissue

extract_protocol:
RNA was extracted from patients' paired tumor and tumor adjacent normal tissue sample using Trizol.
RNA library is prepared using NEB®Ultra™ II RNA Library Prep Kit.

tag: gender

value: female

tag: Stage


title: Brain single cell 168

description: Brain single cell 168


title: CRC-PKU-40-N

value: male


title: Brain single cell 165

description: Brain single cell 165


title: Brain single cell 159

description: Brain single cell 159


title: CRC-PKU-38-N


title: Brain single cell 157

description: Brain single cell 157


title: Brain single cell 158

description: Brain single cell 158


title: CRC-PKU-37-N


title: CRC-PKU-36-N


title: Brain single cell 175

description: Brain single cell 175


title: Brain single cell 156

description: Brain single cell 156


title: Brain single cell 174

description: Brain single cell 174


title: CRC-PKU-35-N


title: Brain single cell 162

description: Brain single cell 162


title: Brain single cell 170

description: Brain single cell 170


title: Brain single cell 155

description: Brain single cell 155


title: CRC-PKU-34-N


title: CRC-PKU-41-N


title: CRC-PKU-30-N


title: Brain single cell 152

description: Brain single cell 152


title: CRC-PKU-29-N


title: Brain single cell 151

description: Brain single cell 151


title: CRC-PKU-32-N


title: Brain single cell 149

description: Brain single cell 149


title: CRC-PKU-28-N


title: CRC-PKU-27-N


title: CRC-2399129-N


title: Brain single cell 148

description: Brain single cell 148


title: CRC-2384058-N


title: CRC-PKU-40-T

source_name: Tumor


title: Brain single cell 146

description: Brain single cell 146


title: Brain single cell 150

description: Brain single cell 150


title: CRC-PKU-41-T


title: CRC-PKU-38-T


title: CRC-PKU-39-T


title: Brain single cell 143

description: Brain single cell 143


title: CRC-PKU-36-T


title: Brain single cell 153

description: Brain single cell 153


title: CRC-PKU-37-T


title: Brain single cell 141

description: Brain single cell 141


title: CRC-PKU-35-T


title: Brain single cell 147

description: Brain single cell 147


title: Brain single cell 144

description: Brain single cell 144


title: CRC-PKU-34-T


title: Brain single cell 142

description: Brain single cell 142


title: Brain single cell 139

description: Brain single cell 139


title: Brain single cell 138

description: Brain single cell 138


title: Brain single cell 140

description: Brain single cell 140


title: Brain single cell 137

description: Brain single cell 137


title: Arabidopsis thaliana col-0 mature leaf total RNA-seq r3

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in A.thaliana leaf;
A.thaliana-leaf-10.tss.txt

organism: Arabidopsis thaliana

source_name: mature leaves

value: mature leaves


title: CRC-PKU-32-T


title: Arabidopsis thaliana col-0 mature leaf total RNA-seq r1


title: Brain single cell 134

description: Brain single cell 134


title: CRC-PKU-28-T


title: Brain single cell 132

description: Brain single cell 132


title: Brain single cell 131

description: Brain single cell 131


title: CRC-PKU-27-T


title: Arabidopsis thaliana col-0 cells total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in A.thaliana cells;
A.thaliana-cells-10.tss.txt

source_name: cells

value: cells

tag: ecotype


title: Brain single cell 133

description: Brain single cell 133


title: Brain single cell 128

description: Brain single cell 128


title: Brain single cell 130

description: Brain single cell 130


title: Brain single cell 145

description: Brain single cell 145


title: CRC-2399129-T


title: Brain single cell 129

description: Brain single cell 129


title: Brain single cell 154

description: Brain single cell 154


title: Brain single cell 127

description: Brain single cell 127


title: Brain single cell 136

description: Brain single cell 136


title: Brain single cell 135

description: Brain single cell 135


title: CRC-PKU-29-T


title: CRC-2384058-T


title: CRC-PKU-30-T


title: RNA_NRVM-BUT_rep3

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

institute: University of Oxford

data_processing:
RNA-seq reads were aligned to the rn6 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using DESeq2
Assembly: rn6

molecule: polyA RNA

organism: Rattus norvegicus

source_name: polyA RNA-seq in control NRVMs treated with 6mM butyrate for 48h

growth_protocol: Primary neonatal rat ventricular myocytes were isolated from P1/P2 hearts of 1-2 day old Sprague-Dawley rats by enzymatic digestion, and a ‘pre-plating’ step was introduced to reduce fibroblasts in the myocyte-containing supernatant. Cells were plated onto fibronectin-coated TC culture dishes and cultured in M2 medium (80% DMEM medium containing 24 mM NaHCO3 and 20% M199 medium with 26mM NaHCO3) and incubated in a 5% CO2 atmosphere.  Initially, medium was supplemented with 10% horse serum, 5% newborn calf serum and penicillin/streptomycin mixture. Next day, cells were serum-starved, followed, where appropriate, by treatment with sodium propionate or sodium butyrate, with NaCl added to balance osmolality between treatment media.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions and eluted into nuclease-free water.
PolyA RNA was purified using the NEBNext Poly(A) mRNA magnetic isolation module (E7490) and DNA libraries were prepared using the NEBNext Ultra II Directional RNA library preparation kit for Illumina (E7765).

treatment_protocol: Serum-starved cells were incubated in 6mM sodium propionate or sodium butyrate for 48h as indicated

value: Neonatal rat ventricular myocytes (NRVMs)

value: Serum-starved cells were incubated in 6mM sodium butyrate for 48 h


title: RNA_NRVM-BUT_rep2


title: Arabidopsis thaliana col-0 cells totalRNA-seq r3

description:
Total RNA-seq (Ribo0), steady state transcriptome profiling in A.thaliana cells; Experiment SD728
A.thaliana-cells-10.tss.txt


title: STAD-PKU-33-qia

description: small RNA-seq of  homo sapiens: stomcah cancer patient's plasma; Provided by Peking University First Affiliated Hospital.

data_processing:
UMIs were extracted by umi_tools (version: 1.1.0) using regex: ^.+(?P<discard_1>AACTGTAGGCACCATCAAT)(?P<umi_1>.{{12}})(?P<discard_2>.+)
Adapters were removed by trim_galore (version 0.6.6) with parameters: --quality 30 --length 15 --trim-n --phred33
Reads were aligned  to reference by bowtie2 (version 2.3.5.1) with parameters: --norc --sensitive. Reads are aligned in the following sequnce: spikein_small, univec,  rRNA, miRNA, lncRNA, mRNA, piRNA, snoRNA, snRNA, srpRNA, tRNA, tucpRNA, Y_RNA, genome and circRNA. All reads unmapped in previous steps were mapped to the next reference.
Aligned reads were sorted by samtools (version 1.10)
Aligned reads were dedupliecated by umi_tools (version: 1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: plasma

extract_protocol:
RNA was extracted from 0.2mL of plasma using miRNeasy Serum/Plasma Kit.
cell-free small RNA library was prepared using QIAseq miRNA Library Kit.


title: RNA_NRVM-BUT_rep1


title: Brain single cell 126

description: Brain single cell 126

source_name: Brain


title: STAD-PKU-25-qia


title: Brain single cell 125

description: Brain single cell 125


title: RNA_NRVM-PRO_rep3

source_name: polyA RNA-seq in control NRVMs treated with 6mM propionate for 48h

value: Serum-starved cells were incubated in 6mM sodium propionate for 48 h


title: Brain single cell 124

description: Brain single cell 124


title: Brain single cell 123

description: Brain single cell 123


title: STAD-PKU-23-qia


title: Brain single cell 121

description: Brain single cell 121


title: Brain single cell 120

description: Brain single cell 120


title: STAD-PKU-22-qia


title: RNA_NRVM-PRO_rep2


title: RNA_NRVM-PRO_rep1


title: Brain single cell 118

description: Brain single cell 118


title: STAD-PKU-19-qia


title: STAD-PKU-21-qia


title: Brain single cell 116

description: Brain single cell 116


title: RNA_NRVM-CON_rep3

source_name: polyA RNA-seq in control NRVMs

value: Serum-starved cells were incubated for 48 h


title: RNA_NRVM-CON_rep2


title: Brain single cell 114

description: Brain single cell 114


title: RNA_NRVM-CON_rep1


title: Brain single cell 112

description: Brain single cell 112


title: Brain single cell 113

description: Brain single cell 113


title: STAD-PKU-17-qia


title: Brain single cell 117

description: Brain single cell 117


title: Brain single cell 115

description: Brain single cell 115


title: Brain single cell 110

description: Brain single cell 110


title: Brain single cell 109

description: Brain single cell 109


title: STAD-PKU-15-qia


title: STAD-PKU-13-qia


title: Brain single cell 122

description: Brain single cell 122


title: Brain single cell 111

description: Brain single cell 111


title: STAD-PKU-36-qia


title: Brain single cell 119

description: Brain single cell 119


title: Brain single cell 108

description: Brain single cell 108


title: Brain single cell 107

description: Brain single cell 107


title: STAD-PKU-35-qia


title: Brain single cell 106

description: Brain single cell 106


title: Brain single cell 105

description: Brain single cell 105


title: hVCF-IL-1B-282-cd4-

city: Providence

first: Sharon

last: Rounds

state: RI

address: 830 Chalkstone Avenue,, Building 35, Room 216

institute: Brown University

description:
Human ventricular cardiac fibroblasts (hVCF)_IL1B_rep2
hVCF-IL-1B-282-cd4-_R2

data_processing:
The raw data was obtained in FASTQ format and sequence reads were trimmed to remove possible adapter sequences and poor quality nucleotides using Trimmomatic v.0.36. The trimmed reads were mapped to Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The unique gene hit counts were calculated using feature counts from Subread package v.1.5.2. And the gene hit counts were used for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene hit counts

source_name: Human ventricular cardiac fibroblasts (hVCF) , IL1B

growth_protocol: Primary hVCFs from 3 human donors (males and female) were cultured in FGMTM-3 Fibroblast Growth Medium-3 BulletKitTM (Cat# CC-4526), 0.1% gentamicin/ amphotericin-B (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) for 96h with or without IL-1B at a concentration of 10ng/mL before replacing the media with ImmunoCultTM –XF T-cell expansion media (Cat # 10981) supplemented with IL-1B or no treatment. ImmunoCultTM Human CD3/CD28 T-Cell Activator was added after 72h of culture in ImmunoCultTM –XF T-cell expansion media.

extract_protocol:
Total RNA was extracted from cardiac fibroblast cells using Qiagen RNeasy Mini Kit (Cat# 74134) isolation kit
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303) by Genewiz company. Initial sample QC analysis was performed followed by RNA library preparation with polyA selection and sequenced on illumina Hi Seq in 2 x 150 bp paired end configuration.

treatment_protocol: Cells were cultured in T-cell expansion media with T Cell Activator in the presence or absence of IL-1B (10ng/mL) for 14 days

value: human ventricular cardiac fibroblast cells (hVCFs)

tag: donor info

value: hVCF (Lonza; Cat# CC-2904; Lot# 534282)

value: hVCF derived from explant during human heart transplant

tag: Sex

value: Female

tag: cells population

value: treated with IL-1B (10ng/mL) for 10 days

tag: site

value: Human Ventricle


title: hVCF-IL-1B-202-cd4+

description:
Human ventricular cardiac fibroblasts (hVCF)_IL1B_rep3
hVCF-IL-1B-202-cd4_R3

value: Male


title: hVCF-IL-1B-202-cd4-

description:
Human ventricular cardiac fibroblasts (hVCF)_IL1B_rep3
hVCF-IL-1B-202-cd4-_R3


title: hVCF-IL-1B-282-cd4+

description:
Human ventricular cardiac fibroblasts (hVCF)_IL1B_rep2
hVCF-IL-1B-282-cd4_R2


title: Brain single cell 104

description: Brain single cell 104

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

tag: strain

value: brain

value: adult mice


title: hVCF-IL-1B-557-cd4-

description:
Human ventricular cardiac fibroblasts (hVCF)_IL1B_rep1
hVCF-IL-1B-557-cd4-_R1
Missing R2 raw file, no longer retrievable from the service provider.

value: hVCF (Lonza; Cat# CC-2904; Lot# 67771)

tag: tissue


title: Brain single cell 103

description: Brain single cell 103

tag: age


title: STAD-PKU-18-qia

value: male


title: STAD-PKU-16-qia

value: female


title: Brain single cell 98

description: Brain single cell 98


title: Brain single cell 101

description: Brain single cell 101


title: Brain single cell 99

description: Brain single cell 99


title: NC-PKU-mix30-qia

description: small RNA-seq of  homo sapiens: healthy donor's plasma; Provided by Peking University First Affiliated Hospital.

value: No stage (healthy donor)


title: hVCF-veh-202-cd4-

description:
Human ventricular cardiac fibroblasts (hVCF)_Veh_rep3
hVCF-veh-202-cd4-_R3
Missing R1 and R2 raw files, no longer retrievable from the service provider.

source_name: Human ventricular cardiac fibroblasts (hVCF) , Veh

tag: cell type

value: untreated


title: Brain single cell 100

description: Brain single cell 100


title: Brain single cell 102

description: Brain single cell 102


title: hVCF-IL-1B-557-cd4+

description:
Human ventricular cardiac fibroblasts (hVCF)_IL1B_rep1
hVCF-IL-1B-557-cd4_R1
Missing R2 raw file, no longer retrievable from the service provider.

value: hVCF (Lonza; Cat# CC-2904; Lot#67771)


title: NC-PKU-mix28-qia


title: NC-PKU-mix29-qia


title: Brain single cell 97

description: Brain single cell 97


title: hVCF-veh-202-cd4+

description:
Human ventricular cardiac fibroblasts (hVCF)_Veh_rep3
hVCF-veh-202-cd4_R3


title: Brain single cell 94

description: Brain single cell 94


title: hVCF-veh-282-cd4-

description:
Human ventricular cardiac fibroblasts (hVCF)_Veh_rep2
hVCF-veh-282-cd4-_R2


title: NC-PKU-mix27-qia