title: M79 line with Dox-inducible PARK7 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C95
Donor age 79, Passage 13


title: M79 line with Dox-inducible NPM1 transgene, Dox_1000ng/mL, P13, Rep2

status: Public on Aug 15 2026

type: SRA

city: Boston

first: Alex

last: Plesa

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description:
Library name: C88
Donor age 79, Passage 13

library_source: transcriptomic

data_processing:
To minimize variability arising from differences in sequencing depth, FASTQ files for all libraries (except LIB058979, LIB092645, and LIB083102) were downsampled to 20 million reads using Seqtk-1.3.
Raw RNA-seq reads were aligned to the GRCh38/GRCm39 reference genome using STAR v2.5.2b and checked for quality control using FastQC v0.11.5
Alignment files were indexed using SAMtools v1.3.154 and gene-level counts were obtained using featureCounts from the Subread v2.0.1 package
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: NHDFs were maintained in low-glucose DMEM supplemented with 15% fetal bovine serum (FBS) and 1% Pen-strep (P/S) in humidified atmosphere with 5% CO2 and 5% O2, at 37C. iPSCs were maintained in mTESR+supplement in humidified atmosphre with 5% CO2 at 37C.

extract_protocol:
Cells were lysed using the Monarch DNA/RNA Protection Reagent (NEB T2011) and stored at -80°C until RNA extraction. Total RNA was extrqacted using the Monarch Total RNA Miniprep kit (NEB T2010). Mouse tissues were processed by Novogene.
Libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the polyA mRNA workflow according to manufacturer's instructions. LIB058979 was genereated using the Tecan MagicPrepRevelo mRNA-seq kit acoording to manufacturare's instructions. LIB083102 was generated by Novogene using a directional mRNA library preparation method.

treatment_protocol: Transgene was induced using doxycycline at the specified concentration for the specified amount of time. Similarly, rapamycin was added to the media at the 100nM for the specified amount of time.

tag: cell line

tag: cell type

value: Fibroblast

tag: genotype

tag: treatment

value: Dox_1000ng/mL, 3days

tag: batch


title: M79 line with Dox-inducible MCM7 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C80
Donor age 79, Passage 13


title: M79 line with Dox-inducible NFKB1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C84
Donor age 79, Passage 13


title: M79 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C82
Donor age 79, Passage 13


title: M79 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C81
Donor age 79, Passage 13


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C92
Donor age 79, Passage 13


title: M79 line with Dox-inducible MCM7 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C79
Donor age 79, Passage 13


title: M79 line with Dox-inducible MAPK7 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C77
Donor age 79, Passage 13


title: M79 line with Dox-inducible NPM1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C87
Donor age 79, Passage 13


title: M79 line with Dox-inducible MAPK14 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C75
Donor age 79, Passage 13


title: M79 line with Dox-inducible KAT7 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C69
Donor age 79, Passage 13


title: M79 line with Dox-inducible KDM6A transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C71
Donor age 79, Passage 13


title: M79 line with Dox-inducible ISG15 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C67
Donor age 79, Passage 13


title: M79 line with Dox-inducible MAPK14 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C76
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSPA8 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C63
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSPA5 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C61
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSPA8 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C64
Donor age 79, Passage 13


title: M79 line with Dox-inducible MAPK7 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C78
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSPA5 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C62
Donor age 79, Passage 13


title: M79 line with Dox-inducible KAT7 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C70
Donor age 79, Passage 13


title: M79 line with Dox-inducible LRRK2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C73
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSPD1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C65
Donor age 79, Passage 13


title: M79 line with Dox-inducible LRRK2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C74
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSP90AB1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C58
Donor age 79, Passage 13


title: M79 line with Dox-inducible KDM6A transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C72
Donor age 79, Passage 13


title: M79 line with Dox-inducible HES1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C54
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSP90B1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C60
Donor age 79, Passage 13


title: M79 line with Dox-inducible ISG15 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C68
Donor age 79, Passage 13


title: M79 line with Dox-inducible HNRNPA2B1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C56
Donor age 79, Passage 13


title: M79 line with Dox-inducible HSPD1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C66
Donor age 79, Passage 13


title: M79 line with Dox-inducible HES1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C53
Donor age 79, Passage 13


title: M79 line with Dox-inducible HDAC6 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C51
Donor age 79, Passage 13


title: M79 line with Dox-inducible HDAC6 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C52
Donor age 79, Passage 13


title: M79 line with Dox-inducible GSK3B transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C48
Donor age 79, Passage 13


title: M79 line with Dox-inducible HDAC1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C49
Donor age 79, Passage 13


title: M79 line with Dox-inducible GART transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C46
Donor age 79, Passage 13

value: GART


title: M79 line with Dox-inducible GART transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C45
Donor age 79, Passage 13


title: PRAD_ARi_NOTCHi_D8_Rep3

status: Public on Aug 16 2026

city: New York

first: Teng

last: Han

state: New York

address: 417 E 68th St

institute: MSKCC

description:
Library name: PRAD_ARi_NOTCHi_D8_Rep3
AD5CASDA-3_IGO_16181_18_S9_L004

data_processing:
Raw FASTQ files were quality checked, aligned to the mouse reference genome (mm10), and gene-level read counts were generated. Normalized expression matrices were generated for downstream analyses.
Assembly: mus musculus mm10
Supplementary files format and content: Raw count

organism: Mus musculus

source_name: prostate organoid

extract_protocol:
Organoids were dissociated to obtain total RNA for library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for bulk RNA-seq.

value: prostate organoid


title: PRAD_YAPi_D8_Rep3

description:
Library name: PRAD_YAPi_D8_Rep3
AD5IN3-3_IGO_16181_9_S63_L004


title: M79 line with Dox-inducible FAU transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C43
Donor age 79, Passage 13

value: FAU


title: M79 line with Dox-inducible FAU transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C44
Donor age 79, Passage 13


title: PRAD_ARi_YAPi_D8_Rep3

description:
Library name: PRAD_ARi_YAPi_D8_Rep3
AD5CASIN3-3_IGO_16181_15_S6_L004


title: M79 line with Dox-inducible EEF2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C40
Donor age 79, Passage 13


title: M79 line with Dox-inducible ESR1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C42
Donor age 79, Passage 13


title: M79 line with Dox-inducible DDX3X transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C36
Donor age 79, Passage 13


title: M79 line with Dox-inducible DDX3X transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C35
Donor age 79, Passage 13


title: M79 line with Dox-inducible EEF2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C39
Donor age 79, Passage 13


title: M79 line with Dox-inducible DICER1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C37
Donor age 79, Passage 13


title: PRAD_COMBO_D42_Rep3

description:
Library name: PRAD_COMBO_D42_Rep3
AD5COMBOD42-3_IGO_16181_30_S20_L004


title: M79 line with Dox-inducible DICER1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C38
Donor age 79, Passage 13


title: M79 line with Dox-inducible CYCS transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C34
Donor age 79, Passage 13

value: CYCS


title: M79 line with Dox-inducible CHEK2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C27
Donor age 79, Passage 13


title: M79 line with Dox-inducible CTNNB1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C30
Donor age 79, Passage 13


title: M79 line with Dox-inducible CHEK2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C28
Donor age 79, Passage 13


title: M79 line with Dox-inducible CXCR2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C32
Donor age 79, Passage 13


title: M79 line with Dox-inducible CYCS transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C33
Donor age 79, Passage 13


title: M79 line with Dox-inducible CXCR2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C31
Donor age 79, Passage 13


title: M79 line with Dox-inducible CHEK1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C26
Donor age 79, Passage 13


title: M79 line with Dox-inducible CTNNB1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C29
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDKN2A transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C24
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDK4 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C22
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDK4 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C21
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDK2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C19
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDC34 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C16
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDK1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C17
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDC20 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C14
Donor age 79, Passage 13


title: M79 line with Dox-inducible CDC20 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C13
Donor age 79, Passage 13


title: M79 line with Dox-inducible ATG5 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C7
Donor age 79, Passage 13


title: M79 line with Dox-inducible CCNB1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C11
Donor age 79, Passage 13


title: M79 line with Dox-inducible CCNB1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C12
Donor age 79, Passage 13


title: M79 line with Dox-inducible CCNA2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C9
Donor age 79, Passage 13


title: M79 line with Dox-inducible AKT1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C5
Donor age 79, Passage 13


title: M79 line with Dox-inducible ACTL6A transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C3
Donor age 79, Passage 13


title: M79 line with Dox-inducible ACTG1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C2
Donor age 79, Passage 13


title: M65 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P5, Rep2

description:
Library name: B110
Donor age 65, Passage 5

value: WT


title: M65 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B107
Donor age 65, Passage 10, High GC


title: M65 line with Dox-inducible YWHAQ transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B106
Donor age 65, Passage 10

value: YWHAQ


title: M65 line with Dox-inducible WDTC1 transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B102
Donor age 65, Passage 9


title: M65 line with Dox-inducible YWHAB transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B103
Donor age 65, Passage 10

value: YWHAB


title: M65 line with Dox-inducible YWHAQ transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B105
Donor age 65, Passage 10


title: M79 line with Dox-inducible HNRNPA2B1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C55
Donor age 79, Passage 13


title: M65 line with Dox-inducible UBB transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B96
Donor age 65, Passage 10

value: UBB


title: M65 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B94
Donor age 65, Passage 10, <10M reads


title: M65 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B93
Donor age 65, Passage 10


title: M65 line with Dox-inducible TP53 (DN) transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B90
Donor age 65, Passage 10

value: TP53 (DN)


title: M79 line with Dox-inducible CDC34 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C15
Donor age 79, Passage 13


title: M65 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B88
Donor age 65, Passage 10


title: M65 line with Dox-inducible SOD2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B87
Donor age 65, Passage 10


title: M65 line with Dox-inducible WDTC1 transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B101
Donor age 65, Passage 9


title: M65 line with Dox-inducible UBE2S transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B98
Donor age 65, Passage 10


title: M65 line with Dox-inducible SOD1 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B84
Donor age 65, Passage 10


title: M65 line with Dox-inducible SOD1 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B83
Donor age 65, Passage 10


title: M65 line with Dox-inducible YWHAB transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B104
Donor age 65, Passage 10


title: M65 line with Dox-inducible UBE2S transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B97
Donor age 65, Passage 10


title: M79 line with Dox-inducible HSP90B1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C59
Donor age 79, Passage 13


title: M65 line with Dox-inducible SLC2A13 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B81
Donor age 65, Passage 10


title: M65 line with Dox-inducible TXN transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B92
Donor age 65, Passage 10

value: TXN


title: M79 line with Dox-inducible ACTG1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C1
Donor age 79, Passage 13, <10M reads


title: M65 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B86
Donor age 65, Passage 10


title: M65 line with Dox-inducible UBQLN1 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B100
Donor age 65, Passage 10


title: M65 line with Dox-inducible SOD2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B85
Donor age 65, Passage 10


title: M79 line with Dox-inducible ESR1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C41
Donor age 79, Passage 13


title: M65 line with Dox-inducible SLC2A10 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B79
Donor age 65, Passage 10


title: M65 line with Dox-inducible SLC2A13 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B82
Donor age 65, Passage 10


title: M65 line with Dox-inducible UBB transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B95
Donor age 65, Passage 10


title: M65 line with Dox-inducible SIRT1 transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B78
Donor age 65, Passage 9


title: M65 line with Dox-inducible TP53 (DN) transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B89
Donor age 65, Passage 10


title: M79 line with Dox-inducible HSP90AB1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C57
Donor age 79, Passage 13


title: M65 line with Dox-inducible SIRT1 transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B77
Donor age 65, Passage 9


title: M65 line with Dox-inducible RPS27A transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B75
Donor age 65, Passage 10


title: M79 line with Dox-inducible GSK3B transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C47
Donor age 79, Passage 13


title: M65 line with Dox-inducible RPLP0 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B73
Donor age 65, Passage 10


title: M79 line with Dox-inducible HDAC1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C50
Donor age 79, Passage 13


title: M65 line with Dox-inducible RAD23B transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B72
Donor age 65, Passage 10


title: M65 line with Dox-inducible SLC2A10 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B80
Donor age 65, Passage 10


title: M65 line with Dox-inducible PTEN transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B69
Donor age 65, Passage 10

value: PTEN


title: M65 line with Dox-inducible PSMC6 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B67
Donor age 65, Passage 10


title: M79 line with Dox-inducible CDK1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C18
Donor age 79, Passage 13


title: M65 line with Dox-inducible RPS27A transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B76
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPP4C transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B66
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPP3CA transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B63
Donor age 65, Passage 9


title: M79 line with Dox-inducible CHEK1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C25
Donor age 79, Passage 13


title: M65 line with Dox-inducible PPP1CC transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B61
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPP1CB transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B60
Donor age 65, Passage 10


title: M79 line with Dox-inducible ACTL6A transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C4
Donor age 79, Passage 13


title: M65 line with Dox-inducible PPP1CB transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B59
Donor age 65, Passage 10


title: M65 line with Dox-inducible RAD23B transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B71
Donor age 65, Passage 10


title: M65 line with Dox-inducible RPLP0 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B74
Donor age 65, Passage 10


title: M65 line with Dox-inducible PTEN transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B70
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPP1CA transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B57
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPIA transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B55
Donor age 65, Passage 10

value: PPIA


title: M65 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B108
Donor age 65, Passage 10


title: M65 line with Dox-inducible PKM transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B53
Donor age 65, Passage 10

value: PKM


title: M65 line with Dox-inducible PIK3C3 transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B50
Donor age 65, Passage 9


title: M65 line with Dox-inducible PIK3CA transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B52
Donor age 65, Passage 9


title: M65 line with Dox-inducible PPP1CC transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B62
Donor age 65, Passage 10


title: M79 line with Dox-inducible CCNA2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C10
Donor age 79, Passage 13


title: M65 line with Dox-inducible PIK3C2A transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B48
Donor age 65, Passage 9


title: M65 line with Dox-inducible P4HB transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B43
Donor age 65, Passage 10


title: M65 line with Dox-inducible PIK3C2A transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B47
Donor age 65, Passage 9


title: M65 line with Dox-inducible PARK7 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B46
Donor age 65, Passage 10


title: M79 line with Dox-inducible AKT1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C6
Donor age 79, Passage 13


title: M65 line with Dox-inducible PPP1CA transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B58
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPIA transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B56
Donor age 65, Passage 10


title: M65 line with Dox-inducible UBQLN1 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B99
Donor age 65, Passage 10


title: M65 line with Dox-inducible PSMC6 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B68
Donor age 65, Passage 10


title: M65 line with Dox-inducible PIK3CA transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B51
Donor age 65, Passage 9


title: M79 line with Dox-inducible ATG5 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C8
Donor age 79, Passage 13


title: M65 line with Dox-inducible PPP4C transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B65
Donor age 65, Passage 10


title: M65 line with Dox-inducible PPP3CA transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B64
Donor age 65, Passage 9


title: M65 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B42
Donor age 65, Passage 9

value: OSKM


title: M65 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P5, Rep1

description:
Library name: B109
Donor age 65, Passage 5


title: M79 line with Dox-inducible CDK2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C20
Donor age 79, Passage 13


title: M65 line with Dox-inducible PKM transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B54
Donor age 65, Passage 10


title: M65 line with Dox-inducible PIK3C3 transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B49
Donor age 65, Passage 9


title: M65 line with Dox-inducible NFKB1 transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B37
Donor age 65, Passage 9


title: M65 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B36
Donor age 65, Passage 10


title: M65 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B35
Donor age 65, Passage 10


title: M65 line with Dox-inducible KAT7 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B30
Donor age 65, Passage 10


title: M65 line with Dox-inducible ISG15 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B28
Donor age 65, Passage 10


title: M65 line with Dox-inducible LRRK2 transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B31
Donor age 65, Passage 9


title: M79 line with Dox-inducible CDKN2A transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C23
Donor age 79, Passage 13


title: M65 line with Dox-inducible TXN transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B91
Donor age 65, Passage 10


title: M65 line with Dox-inducible P4HB transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B44
Donor age 65, Passage 10


title: M65 line with Dox-inducible ESR1 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B21
Donor age 65, Passage 10


title: M65 line with Dox-inducible PARK7 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B45
Donor age 65, Passage 10


title: M65 line with Dox-inducible ESR1 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B22
Donor age 65, Passage 10


title: M65 line with Dox-inducible OGT transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B40
Donor age 65, Passage 10, <10M reads

value: OGT


title: M65 line with Dox-inducible OGT transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B39
Donor age 65, Passage 10

value: Fibroblast


title: M65 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B41
Donor age 65, Passage 9

value: Dox_1000ng/mL, 3days


title: M65 line with Dox-inducible MAPK7 transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: B33
Donor age 65, Passage 9


title: M65 line with Dox-inducible CXCR2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B18
Donor age 65, Passage 10


title: M65 line with Dox-inducible ISG15 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B27
Donor age 65, Passage 10


title: M65 line with Dox-inducible EEF2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B19
Donor age 65, Passage 10


title: M65 line with Dox-inducible CHEK2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B16
Donor age 65, Passage 10


title: M65 line with Dox-inducible CDKN2A transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B13
Donor age 65, Passage 10


title: M65 line with Dox-inducible CDKN2A transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B14
Donor age 65, Passage 10


title: M65 line with Dox-inducible CHEK2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B15
Donor age 65, Passage 10


title: M65 line with Dox-inducible CDK1 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B12
Donor age 65, Passage 10


title: M65 line with Dox-inducible CDC20 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B10
Donor age 65, Passage 10


title: 4T1 tumor, simulated 3,500 m, IOX2, biological replicate 3

city: Lanzhou

first: Jianming

last: Tang

state: Gansu

address: No. 1 Donggang West Road, Chengguan District

department: Department of Radiation Oncology

country: China

institute: The First Clinical Medical College of Lanzhou University

description:
Library name: HI3
Tumor collected on study day 22 from one independent mouse; HI biological replicate 3.

data_processing:
Raw FASTQ reads were quality filtered and adapter trimmed using fastp v0.20.1 with --length_required 50 to obtain clean reads.
Clean reads were aligned to the Mus musculus GRCm39 reference genome (NCBI accession GCF_000001635.27) using HISAT2 v2.1.0 with --rna-strandness rf --fr.
Gene-level read counts were generated using HTSeq-count v0.11.2 with the parameter -s reverse, and FPKM values were calculated for each gene.
Differential expression analysis was performed using DESeq2 v1.22.2. Exploratory analyses used nominal P < 0.05 and absolute log2 fold change > 1; key differentially expressed genes were identified using false discovery rate < 0.05 and absolute log2 fold change > 1.
Principal component analysis and hierarchical clustering were performed in R v3.5.1, and Kyoto Encyclopedia of Genes and Genomes enrichment analysis was performed for pathway annotation.
Assembly: GRCm39 (NCBI GCF_000001635.27)
Supplementary files format and content: GEO_counts_all_samples.txt is a tab-delimited text matrix containing raw gene-level read counts for all 12 libraries; rows are genes and columns are library names MC1-MC3, MI1-MI3, HC1-HC3, and HI1-HI3.
Supplementary files format and content: GEO_FPKM_all_samples.txt is a tab-delimited text matrix containing gene-level FPKM values for all 12 libraries; rows are genes and columns are library names MC1-MC3, MI1-MI3, HC1-HC3, and HI1-HI3.

molecule: total RNA

source_name: subcutaneous 4T1 tumor

growth_protocol: Twenty-four specific pathogen-free female BALB/c mice (6-8 weeks old, 18-22 g) were maintained in Lanzhou either under conventional ambient-altitude conditions (approximately 1,500 m) or in a hypobaric chamber simulating an altitude of 3,500 m. Mice were acclimatized for 3 days before tumor inoculation and were maintained under the same light/dark cycle with food and water provided ad libitum.

extract_protocol:
Total RNA was extracted from tumor tissue using TRIzol reagent according to the manufacturer's protocol. RNA purity and quantity were evaluated using a NanoDrop 2000 spectrophotometer, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

treatment_protocol: After 3 days of acclimatization, 1 x 10^6 4T1 cells suspended in 100 microliters of phosphate-buffered saline were injected subcutaneously into the dorsal region of each mouse. IOX2 treatment began 9 days after tumor inoculation and was administered intraperitoneally at 10 mg/kg once daily for 10 consecutive days; control mice received the corresponding vehicle. Tumors were collected at the predefined endpoint on study day 22.

tag: tissue

value: subcutaneous 4T1 tumor

tag: strain

value: BALB/c

tag: Sex

value: female

tag: age

value: 6-8 weeks

value: Hypobaric chamber simulating an altitude of 3,500 m; IOX2 administered intraperitoneally at 10 mg/kg once daily for 10 consecutive days beginning 9 days after tumor inoculation.


title: M65 line with Dox-inducible CDC20 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B9
Donor age 65, Passage 10


title: M65 line with Dox-inducible CCNB1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: B8
Donor age 65, Passage 13


title: M65 line with Dox-inducible CDK1 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B11
Donor age 65, Passage 10


title: M65 line with Dox-inducible CCNB1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: B7
Donor age 65, Passage 13


title: 4T1 tumor, simulated 3,500 m, IOX2, biological replicate 1

description:
Library name: HI1
Tumor collected on study day 22 from one independent mouse; HI biological replicate 1.


title: M65 line with Dox-inducible CCNA2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B6
Donor age 65, Passage 10


title: 4T1 tumor, simulated 3,500 m, IOX2, biological replicate 2

description:
Library name: HI2
Tumor collected on study day 22 from one independent mouse; HI biological replicate 2.


title: 4T1 tumor, simulated 3,500 m, vehicle, biological replicate 3

description:
Library name: HC3
Tumor collected on study day 22 from one independent mouse; HC biological replicate 3.

value: Hypobaric chamber simulating an altitude of 3,500 m; vehicle administered intraperitoneally once daily for 10 consecutive days beginning 9 days after tumor inoculation.


title: M65 line with Dox-inducible CCNA2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B5
Donor age 65, Passage 10


title: 4T1 tumor, simulated 3,500 m, vehicle, biological replicate 2

description:
Library name: HC2
Tumor collected on study day 22 from one independent mouse; HC biological replicate 2.


title: M65 line with Dox-inducible ATG5 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B4
Donor age 65, Passage 10


title: 4T1 tumor, simulated 3,500 m, vehicle, biological replicate 1

description:
Library name: HC1
Tumor collected on study day 22 from one independent mouse; HC biological replicate 1.


title: 4T1 tumor, ambient altitude, IOX2, biological replicate 3

description:
Library name: MI3
Tumor collected on study day 22 from one independent mouse; MI biological replicate 3.

value: Ambient-altitude conditions in Lanzhou (approximately 1,500 m); IOX2 administered intraperitoneally at 10 mg/kg once daily for 10 consecutive days beginning 9 days after tumor inoculation.


title: M65 line with Dox-inducible ATG5 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B3
Donor age 65, Passage 10


title: M65 line with Dox-inducible ACTL6A transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B2
Donor age 65, Passage 10


title: 4T1 tumor, ambient altitude, IOX2, biological replicate 2

description:
Library name: MI2
Tumor collected on study day 22 from one independent mouse; MI biological replicate 2.


title: 4T1 tumor, ambient altitude, IOX2, biological replicate 1

description:
Library name: MI1
Tumor collected on study day 22 from one independent mouse; MI biological replicate 1.


title: M55 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P9, Rep1

description:
Library name: A185
Donor age 55, Passage 9

value: WT


title: M55 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: A186
Donor age 55, Passage 9


title: 4T1 tumor, ambient altitude, vehicle, biological replicate 3

description:
Library name: MC3
Tumor collected on study day 22 from one independent mouse; MC biological replicate 3.

value: Ambient-altitude conditions in Lanzhou (approximately 1,500 m); vehicle administered intraperitoneally once daily for 10 consecutive days beginning 9 days after tumor inoculation.


title: M65 line with Dox-inducible ACTL6A transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B1
Donor age 65, Passage 10


title: 4T1 tumor, ambient altitude, vehicle, biological replicate 2

description:
Library name: MC2
Tumor collected on study day 22 from one independent mouse; MC biological replicate 2.


title: 4T1 tumor, ambient altitude, vehicle, biological replicate 1

description:
Library name: MC1
Tumor collected on study day 22 from one independent mouse; MC biological replicate 1.


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A183
Donor age 55, Passage 12


title: M55 line with Dox-inducible YWHAQ transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A182
Donor age 55, Passage 12

value: YWHAQ


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A184
Donor age 55, Passage 12


title: kidney, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 4

city: Wuhan

first: Zhenghong

last: Kang

state: Hubei

address: 461 Luoyu Road, Hongshan District, Wuhan City, Hubei Province

department: School of Sports Medicine

institute: Wuhan Sports University

description:
Library name: KHM4
FPKM_allTranscript_Kidney.txt

data_processing:
Base calling was performed using CASAVA software. Raw sequencing data in FASTQ format were assessed for quality using FastQC.
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.36) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
High-quality clean reads were aligned to the mouse reference genome (GRCm39) using STAR aligner (version 2.7.9a) with default parameters.
Gene-level read counts were generated using featureCounts (version 2.0.1) with default parameters against the mouse reference genome annotation (GENCODE).
Additionally, transcript assembly and expression quantification were performed using StringTie (version 2.1.4), and expression levels were normalized as FPKM and TPM values.
Assembly: GRCm39
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing gene-level count matrix for all samples. Rows represent genes (annotated with Ensembl gene IDs and gene symbols), and columns represent individual samples. Values are raw read counts generated by featureCounts.

source_name: kidney

growth_protocol: Eight-week-old male db/db mice were randomly assigned to four groups: sedentary control (CON), HIIT only, semaglutide only, and combined intervention (HIIT + semaglutide). HIIT was performed on a motorized treadmill, consisting of 10 bouts of 4-minute high-intensity running at 85-90% of maximal running speed interspersed with 2-minute active recovery at 50-60% of maximal speed, 5 days per week for 8 weeks. Semaglutide was administered via subcutaneous injection at a dose of 30 nmol/kg once daily for 8 weeks. The combined group received both interventions simultaneously.

extract_protocol:
Immediately after euthanasia, heart, kidney, hippocampus, liver, and soleus muscle were rapidly harvested, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted from each tissue sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's standard protocol. RNA quality and integrity were assessed using a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.
Stranded mRNA-seq libraries were constructed using poly(A) mRNA enrichment with oligo(dT) magnetic beads. Library preparation was performed following the standard protocol of the NEB Next Ultra RNA Library Prep Kit for Illumina. The constructed libraries were sequenced on the Illumina NovaSeq 6000 platform in paired-end 150 bp (PE150) mode. Library construction and sequencing services were provided by Qingke Biotechnology Co., Ltd.

value: kidney

value: C57BL/KsJ db/db mice

value: HIIT Exercise AND Semaglutide injection


title: M55 line with Dox-inducible YWHAQ transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A181
Donor age 55, Passage 12


title: kidney, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 3

description:
Library name: KHM3
FPKM_allTranscript_Kidney.txt


title: kidney, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 2

description:
Library name: KHM2
FPKM_allTranscript_Kidney.txt


title: kidney, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 1

description:
Library name: KHM1
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible YWHAB transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A179
Donor age 55, Passage 12

value: YWHAB


title: kidney, semaglutide,0.05 mg/kg, rep4

description:
Library name: KSEM4
FPKM_allTranscript_Kidney.txt

value: Semaglutide injection


title: M55 line with Dox-inducible XPO1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A178
Donor age 55, Passage 12

value: Fibroblast


title: kidney, semaglutide,0.05 mg/kg, rep3

description:
Library name: KSEM3
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible XPO1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A177
Donor age 55, Passage 12

value: Dox_1000ng/mL, 3days


title: kidney, semaglutide,0.05 mg/kg, rep2

description:
Library name: KSEM2
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible WDTC1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A176
Donor age 55, Passage 12


title: kidney, semaglutide,0.05 mg/kg, rep1

description:
Library name: KSEM1
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible VCP transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: A174
Donor age 55, Passage 13

value: VCP


title: kidney, exercised,60min, rep4

description:
Library name: KHITT4
FPKM_allTranscript_Kidney.txt

value: HIIT Exercise


title: M55 line with Dox-inducible YWHAB transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A180
Donor age 55, Passage 12


title: M65 line with Dox-inducible EEF2 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B20
Donor age 65, Passage 10


title: M55 line with Dox-inducible WDTC1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A175
Donor age 55, Passage 12


title: M55 line with Dox-inducible VCP transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: A173
Donor age 55, Passage 13


title: kidney, exercised,60min, rep3

description:
Library name: KHITT3
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible UBXN7 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: A172
Donor age 55, Passage 13


title: kidney, exercised,60min, rep2

description:
Library name: KHITT2
FPKM_allTranscript_Kidney.txt


title: kidney, exercised,60min, rep1

description:
Library name: KHITT1
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible UBXN7 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: A171
Donor age 55, Passage 13


title: kidney, db/db control group, rep3

description:
Library name: KCON3
FPKM_allTranscript_Kidney.txt

value: Normal rearing


title: M55 line with Dox-inducible UBQLN1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A170
Donor age 55, Passage 12


title: M55 line with Dox-inducible UBQLN1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A169
Donor age 55, Passage 12


title: kidney, db/db control group, rep4

description:
Library name: KCON4
FPKM_allTranscript_Kidney.txt


title: kidney, db/db control group, rep1

description:
Library name: KCON1
FPKM_allTranscript_Kidney.txt


title: M55 line with Dox-inducible UBE2S transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A167
Donor age 55, Passage 12


title: M55 line with Dox-inducible UBE2N transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A166
Donor age 55, Passage 12


title: kidney, db/db control group, rep2

description:
Library name: KCON2
FPKM_allTranscript_Kidney.txt


title: primary astrocytes,control5

city: suzhou

first: wenjun

last: zou

address: No. 1055, Sanxiang Road, Gu Suzhou District, Suzhou City, Jiangsu Province

institute: The Second Affiliated Hospital of Soochow University

description: Library name: Sample 15

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork(parameter.Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwok(parameters-mismath cost 2insertion cost3 deletion cost:3length fraction:0.8 sim
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) 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 VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: mouse brain

value: primary astrocytes

value: control


title: M55 line with Dox-inducible UBE2N transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A165
Donor age 55, Passage 12


title: primary astrocytes,control3

description: Library name: Sample 13


title: M55 line with Dox-inducible UBE2S transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A168
Donor age 55, Passage 12


title: primary astrocytes,control4

description: Library name: Sample 14


title: primary astrocytes,control2

description: Library name: Sample 12


title: M55 line with Dox-inducible UBE2I transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A163
Donor age 55, Passage 12


title: M55 line with Dox-inducible UBE2I transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A164
Donor age 55, Passage 12


title: primary astrocytes,control1

description: Library name: Sample 11


title: M55 line with Dox-inducible UBE2A transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A162
Donor age 55, Passage 12


title: primary astrocytes,SCI5

description: Library name: Sample 10

value: SCI


title: M55 line with Dox-inducible UBE2A transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A161
Donor age 55, Passage 12


title: primary astrocytes,SCI4

description: Library name: Sample 9


title: M55 line with Dox-inducible UBB transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A159
Donor age 55, Passage 12

value: UBB


title: primary astrocytes,SCI3

description: Library name: Sample 8


title: primary astrocytes,SCI1

description: Library name: Sample 6


title: M55 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A157
Donor age 55, Passage 12


title: M55 line with Dox-inducible UBB transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A160
Donor age 55, Passage 12


title: primary astrocytes,SCI2

description: Library name: Sample 7


title: primary astrocytes,Rg15

description: Library name: Sample 5


title: primary astrocytes,Rg13

description: Library name: Sample 3


title: primary astrocytes,Rg14

description: Library name: Sample 4


title: M55 line with Dox-inducible TXN transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A156
Donor age 55, Passage 12

value: TXN


title: M55 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A158
Donor age 55, Passage 12


title: M55 line with Dox-inducible TXN transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A155
Donor age 55, Passage 12


title: primary astrocytes,Rg12

description: Library name: Sample 2


title: M55 line with Dox-inducible TP53 (DN) transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A154
Donor age 55, Passage 12

value: TP53 (DN)


title: M55 line with Dox-inducible TP53 (DN) transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A153
Donor age 55, Passage 12


title: primary astrocytes,Rg11

description: Library name: Sample 1


title: M55 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A152
Donor age 55, Passage 12


title: Neuro-2a cells, miRbmxl1, biol rep 4

city: Illkirch

first: Juliette

last: GODIN

address: 1 rue LAurent Fries

country: France

institute: IGBMC

description: Library name: JTGD16

data_processing:
Final pooled library samples were sequenced on ILLUMINA Novaseq6000 with S1-200 cartridge (2x1600Millions 100 bases reads), corresponding to 2x100Millions reads per sample after demultiplexing.
Reads were preprocessed to remove adapter, polyA and low-quality sequences (Phred quality score below 20) using cutadapt v.1.1037 and then, reads shorter than 40 bases were discarded for further analysis.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR v.2.5.3a.
Quantification of gene expression was performed from uniquely aligned reads using HTSeq-count v.0.6.1p1, with union mode and annotations coming from Ensembl version 102
Comparisons of interest have been performed using R v.3.3.2 with DESeq2 v.1.16.1. More precisely, read counts were normalized from the estimated size factors using the median-of-ratios method and a Wald test was used to estimate the P-values. P-values were adjusted for multiple testing using the Benjamini and Hochberg method.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. Each row corresponds to a gene (Ensembl ID), columns represent individual samples. Values are FPKM.

growth_protocol: Mouse neuroblastoma N2A (ATCC) cells were cultured in DMEM (Gibco) supplemented with 5% Fetal calf serum (FCS) and gentamicin 40 μg/ml in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Total RNA were extracted using the AllPrep DNA/RNA Kits from Qiagen.
mRNA libraries were prepared using the ILLUMINA Stranded Total RNA Prep, Ligation with Ribo-Zero Plus reagents, following manufacturer’s recommendations.

treatment_protocol: Transfections were performed at 50-60% confluency using Lipofectamine 2000 (ThermoFisher Scientific), according to the manufacturer’s protocol. N2A cells were co-transfected in one well of a 6-well plate per condition with 1 μg of pCAGGs-linkB-IRES-GFP and either 3 μg of pCAG-miR30-scramble or a pool of pCAG-miR30-miRNAs targeting mouse Rbmx (Rbmx #1 + #2 + #3) or Rbmxl1 (Rbmxl1 #1 + #2) (1μg each). A total of 3 μg of miRNA constructs was used per condition. 48 hours post-transfection, N2A cells were washed with 1 ml of PBS 1X, treated with 1 ml of diluted trypsin for 1-2 min, and dissociated by pipetting. Trypsin was neutralized by adding 1 ml of DMEM (1 g/l glucose) supplemented with 5% FCS and 40 μg/ml gentamicin. N2A cells were centrifuged (5 min, 1200 rpm), and resuspended in cold FACS buffer (PBS 1X, 0.5% BSA, 2 mM EDTA). N2A cells were then passed through a 100 μm cell strainer and kept on ice until sorting of GFP-positives cells. N2A cells were sorted using FACS ARIA II (BD) with a 100 µm nozzle, in cold FACS buffer. After sorting, N2A cells were centrifuged (5 min, 1000 rpm, 4 °C), the supernatant was removed, and cell pellets were snap-frozen in liquid nitrogen before storage at -80 °C until RNA extraction

value: mouse neuroblastoma cell line

value: Rbmxl1 knockdown


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A150
Donor age 55, Passage 12


title: Neuro-2a cells, miRbmxl1, biol rep 2

description: Library name: JTGD14


title: Neuro-2a cells, miRbmxl1, biol rep 1

description: Library name: JTGD13


title: Neuro-2a cells, miRbmxl1, biol rep 3

description: Library name: JTGD15


title: M55 line with Dox-inducible SOD2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A148
Donor age 55, Passage 12


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A149
Donor age 55, Passage 12


title: M55 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A151
Donor age 55, Passage 12


title: M55 line with Dox-inducible SOD1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A146
Donor age 55, Passage 12


title: M55 line with Dox-inducible SOD2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A147
Donor age 55, Passage 12


title: Neuro-2a cells, miRbmx, biol rep 3

description: Library name: JTGD11

value: Rbmx knockdown


title: Neuro-2a cells, miRbmx, biol rep 2

description: Library name: JTGD10


title: Neuro-2a cells, miRbmx, biol rep 4

description: Library name: JTGD12


title: M55 line with Dox-inducible SOD1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A145
Donor age 55, Passage 12


title: Neuro-2a cells, miRbmx, biol rep 1

description: Library name: JTGD9


title: M55 line with Dox-inducible SMARCA4 transgene, Dox_1000ng/mL, P11, Rep2

description:
Library name: A144
Donor age 55, Passage 11


title: M55 line with Dox-inducible SMARCA4 transgene, Dox_1000ng/mL, P11, Rep1

description:
Library name: A143
Donor age 55, Passage 11


title: Neuro-2a cells, miScramble, biol rep 4

description: Library name: JTGD4

value: Scramble knockdown


title: Neuro-2a cells, miScramble, biol rep 3

description: Library name: JTGD3


title: M55 line with Dox-inducible SLC2A13 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A142
Donor age 55, Passage 12


title: M55 line with Dox-inducible SLC2A10 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A140
Donor age 55, Passage 12


title: M55 line with Dox-inducible SLC2A13 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A141
Donor age 55, Passage 12


title: M55 line with Dox-inducible SLC2A10 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A139
Donor age 55, Passage 12


title: chip-KLF11-4_R2_001.fastq.gz

city: Shanghai

first: Lijun

last: Wang

address: 333 Nan Chen Road

institute: Shanghai University

description: Library name: Sample1

library_source: genomic

data_processing:
Basecalls were performed usina bcl2fasta y2.17 for Novaseq output.
ChIP -seq reads were trimmed from 3' end until the final base had a quality score > 30 using skewer-0.2.2, discarding reads left with< 50 bp.
ChlP -seq reads were aligned to the mouse mm10 genome using Bowtie version 2-2.2.3. Only uniquely mapping reads with at most two mismatches were retained.
To create ChlP-seq coverage plots, the locations of the mapped ChlP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads permillion, rm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the sianifcance cutoff p-value <=1e-3.
Assembly: Mouse mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: heart

extract_protocol:
Cells were fixed with 1% fommaldehyde for 10 minutes. After quenching and cell lysis. chromatin was sonicated using a ultrasonicator (SCIENTZ08-III).
ChlP-seq libraries were prepared using the KAPAHTP Library Preparation Kitcomplemented with NEXTflex DNA Barcodes from Bio Scientifc. 10 ng of DNA wasused as starting material for input and ip samples. Libraries were amplifed using 13cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Couter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: heart

value: adult mouse cardiac myocytes


title: TetO-OSKM-HSPC_Klf4_24h_rep2

city: Tianjin

first: Kuangyu

last: Yen

address: Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Reads were aligned to mm10 mouse genome assembly by BWA
Data were filtered using Samtools
Peaks were called using macs2
Assembly: mm10
Supplementary files format and content: bigwig

source_name: bone marrow

extract_protocol:
2~5*10^6 cells were incubated in 1% formaldehyde for 10 mins. After being quenched with 125 mM final concentration of glycine for 5 min, cells were harvested and washed.
In the ChIP-seq method, chromatin pellets were directly sonicated using a Bioruptor sonicator. The supernatant in ChIP-seq was subjected to the chromatin immunoprecipitation step and completed library construction in the standard protocol. All libraries were sequenced in the Illumina Novaseq 6000 platform in the PE150 strategy.

value: bone marrow

value: HSPC

tag: chip antibody


title: Neuro-2a cells, miScramble, biol rep 1

description: Library name: JTGD1


title: M55 line with Dox-inducible SIRT1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A137
Donor age 55, Passage 12

value: Fibroblast

value: Dox_1000ng/mL, 3days


title: M55 line with Dox-inducible SIRT1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A138
Donor age 55, Passage 12


title: TetO-OSKM-HSPC_Klf4_24h_rep1


title: M55 line with Dox-inducible RUVBL2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A136
Donor age 55, Passage 12


title: TetO-OSKM-HSPC_Klf4_12h_rep2


title: input-4_R1R2_001.fastq.gz

description: Library name: Sample2


title: M55 line with Dox-inducible RRM1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A134
Donor age 55, Passage 12


title: M55 line with Dox-inducible RUVBL2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A135
Donor age 55, Passage 12


title: TetO-OSKM-HSPC_Klf4_12h_rep1


title: TetO-OSKM-HSPC_Klf4_6h_rep2


title: M55 line with Dox-inducible RRM1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A133
Donor age 55, Passage 12


title: Neuro-2a cells, miScramble, biol rep 2

description: Library name: JTGD2


title: M55 line with Dox-inducible RPS27A transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A132
Donor age 55, Passage 12


title: TetO-OSKM-HSPC_Klf4_0h_rep2


title: M55 line with Dox-inducible RPS27A transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A131
Donor age 55, Passage 12


title: TetO-Klf4-AML_Klf4_6h_rep2

value: leukemia cells


title: M55 line with Dox-inducible RPLP0 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A130
Donor age 55, Passage 12


title: TetO-OSKM-HSPC_Klf4_0h_rep1


title: M55 line with Dox-inducible RPLP0 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A129
Donor age 55, Passage 12


title: M55 line with Dox-inducible RNASEL transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A128
Donor age 55, Passage 12

value: RNASEL


title: M55 line with Dox-inducible RNASEL transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A127
Donor age 55, Passage 12


title: TetO-Klf4-AML_Klf4_6h_rep1


title: TetO-Klf4-AML_Klf4_0h_rep2


title: TetO-OSKM-AML_Klf4_24h_rep2


title: M55 line with Dox-inducible RAD23B transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A126
Donor age 55, Passage 12


title: TetO-Klf4-AML_Klf4_0h_rep1


title: M55 line with Dox-inducible RAD51 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A125
Donor age 55, Passage 12


title: M55 line with Dox-inducible RAD51 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A124
Donor age 55, Passage 12


title: TetO-OSKM-AML_Klf4_12h_rep2


title: M55 line with Dox-inducible RAD23B transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A123
Donor age 55, Passage 12


title: TetO-OSKM-AML_Klf4_24h_rep1


title: TetO-OSKM-AML_Klf4_12h_rep1


title: M55 line with Dox-inducible PTEN transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A122
Donor age 55, Passage 12

value: PTEN


title: M55 line with Dox-inducible PTEN transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A121
Donor age 55, Passage 12


title: TetO-OSKM-AML_Klf4_6h_rep1


title: M55 line with Dox-inducible PSMD4 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: A120
Donor age 55, Passage 10


title: M55 line with Dox-inducible PSMD4 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: A119
Donor age 55, Passage 10


title: TetO-OSKM-AML_Klf4_0h_rep1


title: TetO-OSKM-AML_Klf4_0h_rep2


title: ATAC TetO-Klf4-AML 24h_rep2

library_source: other

data_processing:
Reads were aligned to mm10 mouse genome assembly by BWA
Data were filtered using Samtools
Peaks were called using macs2
Assembly: mm10
Supplementary files format and content: narrowPeak

molecule: other

extract_protocol: Briefly, 50,000 cells were lysed in lysis buffer (10mM Tirs-HCl, PH7.4, 10mM NaCl, 3mM MgCl2, 0.1%(v/v) IGPAL CA-630) for 10min on ice before centrifuged at 500g for 5min. The nuclei were added with 50ul transposition reaction buffer (5μL TruePrep Tagment Enzyme,10μL TruePrep Tagment Buffer L and 35μL ddH2O from Vazyme TD501-01) and followed with incubation at 37oC for 30min. After tagmentation, VAHTS DNA Clean Beads were used to stop the reaction and DNA was purified for final library construction (TruePrepTM DNA Library Prep Kit V2 for Illumina) before paired-end sequencing.


title: M55 line with Dox-inducible PSMC6 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A117
Donor age 55, Passage 12


title: M55 line with Dox-inducible PSMC6 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A118
Donor age 55, Passage 12


title: ATAC TetO-Klf4-AML 12h_rep2


title: M55 line with Dox-inducible PPP4C transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A115
Donor age 55, Passage 12


title: ATAC TetO-Klf4-AML 12h_rep1


title: ATAC TetO-Klf4-AML 24h_rep1


title: TetO-OSKM-HSPC_Klf4_6h_rep1


title: ATAC TetO-Klf4-AML 6h_rep2


title: M55 line with Dox-inducible PPP4C transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A116
Donor age 55, Passage 12


title: ATAC TetO-Klf4-AML 6h_rep1


title: M55 line with Dox-inducible PPP2CA transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A111
Donor age 55, Passage 12


title: ATAC TetO-Klf4-AML 0h_rep2


title: M55 line with Dox-inducible PPP2CA transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A112
Donor age 55, Passage 12


title: ATAC TetO-Klf4-AML 0h_rep1


title: M55 line with Dox-inducible PPP1CC transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A110
Donor age 55, Passage 12


title: M55 line with Dox-inducible PPP1CC transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A109
Donor age 55, Passage 12


title: M55 line with Dox-inducible PPP1CB transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A108
Donor age 55, Passage 12


title: TetO-Klf4-AML 12h_rep2

data_processing:
Reads were aligned to mm10 mouse genome assembly by STAR Viersion 2.7.5c with ENCODE recommended parameters.
Data were filtered using Samtools Version 1.3
Counts number were called using HTSeq Version 2.0.3
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene raw count number for each Sample

extract_protocol:
Total RNA from cells were extracted using the RNeasy purification kit (Qiagen).
Libraries were prepared using the Illumina RNA library preparation TruSeq PE kit

tag: time point


title: TetO-Klf4-AML 12h_rep1


title: M55 line with Dox-inducible PPP1CB transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A107
Donor age 55, Passage 12


title: M55 line with Dox-inducible PPP1CA transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A106
Donor age 55, Passage 12


title: TetO-Klf4-AML 6h_rep2


title: TetO-Klf4-AML 6h_rep1


title: M55 line with Dox-inducible PPIA transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A104
Donor age 55, Passage 12

value: PPIA


title: M55 line with Dox-inducible PPP1CA transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A105
Donor age 55, Passage 12


title: TetO-Klf4-AML 0h_rep2


title: M55 line with Dox-inducible PPIA transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A103
Donor age 55, Passage 12


title: TetO-Klf4-AML 0h_rep1


title: M55 line with Dox-inducible PLK1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A102
Donor age 55, Passage 12


title: myocardial tissue, AMI mice with RE, rep 3 [AMI-YD-3_miRNA]

city: Jining

first: xueying

last: Chen

state: Shandong

address: No.89 Guhuai Road

department: Department of Cardiology

institute: Affiliated Hospital of Jining Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Fastp to get clean reads.
Clean reads were mapped  to GrCM38/mm10 using HISAT2.
Read count extraction were performed using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: myocardial

extract_protocol:
The acquired mouse heart tissue is rinsed with PBS, ground with liquid nitrogen, and then total RNA was extracted with Trizol reagent.
For samll RNA sequencing, the library is constructed using the Small RNA Sample Pre Kit, using total RNA as the starting sample, directly adding a linker to both ends of the Small RNA, and then reverse transcription to synthesize cDNA. Subsequently, after PCR amplification, PAGE electrophoresis separates the target DNA fragment, and the cDNA library is recovered from the cut glue. For other RNA, the Ribo-Zero™ kit is generally used to remove rRNA from the total RNA sample. A fragmentation buffer is added to the enriched RNA to break the RNA into small fragments. Then, using fragmented RNA as a template, 6 bp random primers were added to reverse transcribe the first strand of cDNA, and then buffer, dNTPs (dTTP in dNTP was replaced by dUTP), DNA polymerase I and RNase H were added to synthesize the second strand of cDNA. After purification, end repair, addition of A, ligation sequencing linker, the synthesized double-stranded cDNA was processed by USER enzyme to degrade the second strand of cDNA containing U and PCR enrichment, and finally the PCR product was purified with AMPure XP beads to obtain the final strand-specific library.

value: myocardial

value: AMI+RE


title: myocardial tissue, AMI mice with RE, rep 2 [AMI-YD-2_miRNA]


title: M55 line with Dox-inducible PLK1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A101
Donor age 55, Passage 12


title: M55 line with Dox-inducible PKM transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A100
Donor age 55, Passage 12

value: PKM


title: M55 line with Dox-inducible PKM transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A99
Donor age 55, Passage 12


title: M55 line with Dox-inducible PIK3CA transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A98
Donor age 55, Passage 12


title: myocardial tissue, AMI mice without RE, rep 3 [AMI-NC-3_miRNA]

value: AMI


title: myocardial tissue, AMI mice with RE, rep 1 [AMI-YD-1_miRNA]


title: M55 line with Dox-inducible PIK3CA transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A97
Donor age 55, Passage 12


title: M65 line with Dox-inducible LRRK2 transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B32
Donor age 65, Passage 9


title: myocardial tissue, AMI mice without RE, rep 1 [AMI-NC-1_miRNA]


title: myocardial tissue, AMI mice with RE, rep 3 [AMI-YD-3]

description:
circ_rawcounts_matrix.txt
lnc_rawcounts_matrix.txt
mRNA_rawcounts_matrix.txt


title: M65 line with Dox-inducible HES1 transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: B26
Donor age 65, Passage 10


title: M55 line with Dox-inducible PIK3C2A transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A95
Donor age 55, Passage 12


title: myocardial tissue, AMI mice with RE, rep 2 [AMI-YD-2]


title: myocardial tissue, AMI mice with RE, rep 1 [AMI-YD-1]


title: M55 line with Dox-inducible PARK7 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A93
Donor age 55, Passage 12


title: M55 line with Dox-inducible PARK7 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A94
Donor age 55, Passage 12


title: M55 line with Dox-inducible P4HB transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A92
Donor age 55, Passage 12


title: myocardial tissue, AMI mice without RE, rep 3 [AMI-NC-3]


title: myocardial tissue, AMI mice without RE, rep 2 [AMI-NC-2]


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A90
Donor age 55, Passage 12

value: OSKM


title: myocardial tissue, AMI mice without RE, rep 1 [AMI-NC-1]


title: M55 line with Dox-inducible P4HB transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A91
Donor age 55, Passage 12


title: mESCs, E14TG2a, A-HIC, rep 4

city: Edinburgh

first: Sari

last: Pennings

state: Scotland

address: 47 Little France Crescent

department: Institute for Neuroscience and Cardiovascular Research

country: United Kingdom

institute: University of Edinburgh

description: Library name: A-HIC-derived-HLC_rep4

data_processing:
Paired-end reads were aligned to the mouse reference genome (GRCm39/mm39) using the STAR RNA-seq aligner. Reads with a mapping quality score <60 were excluded, and gene-level read counts were quantified using featureCounts.
Assembly: GRCm39/mm39
Supplementary files format and content: TXT files consist of raw gene read counts for four biological replicates of A-HIC-derived HLC samples.

source_name: mouse embryonic stem cells

extract_protocol:
Total RNA was extracted from independently generated A-HIC-derived hepatocyte-like cell samples using the RNeasy Kit (QIAGEN), according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following RNA fragmentation, first-strand cDNA was synthesised using random hexamer primers, followed by second-strand cDNA synthesis using dTTP to generate non-strand-specific libraries. Libraries were then subjected to end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The final libraries were sequenced on the Illumina NovaSeq X Plus platform using 150-bp paired-end sequencing, generating approximately 20 million paired-end reads per sample.

value: mouse embryonic stem cells

value: hepatocyte-like cells


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A89
Donor age 55, Passage 12


title: mESCs, E14TG2a, A-HIC, rep 3

description: Library name: A-HIC-derived-HLC_rep3


title: mESCs, E14TG2a, A-HIC, rep 2

description: Library name: A-HIC-derived-HLC_rep2


title: TetO-OSKM-AML_Klf4_6h_rep2


title: M55 line with Dox-inducible OGT transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: A87
Donor age 55, Passage 13

value: OGT


title: Spleen from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#19

description:
Library name: S462
Age at death 818 days, RIN-7.7

source_name: Spleen

value: Spleen

value: Dox_200mg/kg, 1wk-ON/1wk-OFF


title: mESCs, E14TG2a, A-HIC, rep 1

description: Library name: A-HIC-derived-HLC_rep1


title: M55 line with Dox-inducible OGT transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: A88
Donor age 55, Passage 13


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#19

description:
Library name: S461
Age at death 818 days, RIN-7.8

source_name: Liver

value: Liver


title: M55 line with Dox-inducible NPM1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A86
Donor age 55, Passage 12

value: Fibroblast


title: M55 line with Dox-inducible NOTCH1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A84
Donor age 55, Passage 12

value: Dox_1000ng/mL, 3days


title: M55 line with Dox-inducible NPM1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A85
Donor age 55, Passage 12


title: Heart from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#19

description:
Library name: S460
Age at death 818 days, RIN-6.1

source_name: Heart

value: Heart


title: M55 line with Dox-inducible NOTCH1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A83
Donor age 55, Passage 12


title: M65 line with Dox-inducible NFKB1 transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B38
Donor age 65, Passage 9


title: Brain from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#19

description:
Library name: S459
Age at death 818 days, RIN-7.2

source_name: Brain

value: Brain


title: M55 line with Dox-inducible NFKB1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A82
Donor age 55, Passage 12


title: Spleen from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#15

description:
Library name: S458
Age at death 872 days, RIN-8


title: M55 line with Dox-inducible PPP3CA transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A114
Donor age 55, Passage 12


title: M55 line with Dox-inducible NFKB1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A81
Donor age 55, Passage 12


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#15

description:
Library name: S457
Age at death 872 days, RIN-7.7


title: M55 line with Dox-inducible PPP3CA transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A113
Donor age 55, Passage 12


title: M55 line with Dox-inducible MTOR transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A80
Donor age 55, Passage 12

value: MTOR


title: Brain from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#15

description:
Library name: S455
Age at death 872 days, RIN-7.6


title: M55 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A78
Donor age 55, Passage 12


title: M55 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A77
Donor age 55, Passage 12


title: M55 line with Dox-inducible MTOR transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A79
Donor age 55, Passage 12


title: Spleen from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#10

description:
Library name: S454
Age at death 872 days, RIN-8.4


title: Heart from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#15

description:
Library name: S456
Age at death 872 days, RIN-6.9


title: M65 line with Dox-inducible GSK3B transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: B23
Donor age 65, Passage 12


title: TetO-Klf4-AML 24h_rep2

value: bone marrow

value: leukemia cells


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#10

description:
Library name: S453
Age at death 872 days, RIN-8.5


title: M55 line with Dox-inducible MCM7 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A76
Donor age 55, Passage 12


title: TetO-Klf4-AML 24h_rep1


title: Heart from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#10

description:
Library name: S452
Age at death 872 days, RIN-5.5


title: M55 line with Dox-inducible MCM7 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A75
Donor age 55, Passage 12


title: Brain from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#10

description:
Library name: S451
Age at death 872 days, RIN-7.4


title: Spleen from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#1

description:
Library name: S446
Age at death 901 days, RIN-5.8


title: Heart from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#1

description:
Library name: S444
Age at death 901 days, RIN-6


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#1

description:
Library name: S445
Age at death 901 days, RIN-4.4


title: M55 line with Dox-inducible MAPK7 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A74
Donor age 55, Passage 12


title: M55 line with Dox-inducible MAPK7 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A73
Donor age 55, Passage 12


title: M55 line with Dox-inducible KDM6A transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A70
Donor age 55, Passage 12


title: Spleen from systemic AAV8-GFP, Dox_200mg/kg, Mouse#9

description:
Library name: S441
Age at death 806 days, RIN-3.7

value: GFP


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#9

description:
Library name: S440
Age at death 806 days, RIN-7.4


title: Brain from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#1

description:
Library name: S443
Age at death 901 days, RIN-7.3


title: M55 line with Dox-inducible MAPK14 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A71
Donor age 55, Passage 12


title: M55 line with Dox-inducible KDM6A transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A69
Donor age 55, Passage 12


title: M55 line with Dox-inducible MAPK14 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A72
Donor age 55, Passage 12


title: M55 line with Dox-inducible KAT7 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A68
Donor age 55, Passage 12


title: Heart from systemic AAV8-GFP, Dox_200mg/kg, Mouse#9

description:
Library name: S439
Age at death 806 days, RIN-5.5


title: M55 line with Dox-inducible KAT7 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A67
Donor age 55, Passage 12


title: Brain from systemic AAV8-GFP, Dox_200mg/kg, Mouse#9

description:
Library name: S438
Age at death 806 days, RIN-6.8


title: M55 line with Dox-inducible ISG15 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A66
Donor age 55, Passage 12


title: Spleen from systemic AAV8-GFP, Dox_200mg/kg, Mouse#8

description:
Library name: S437
Age at death 865 days, RIN-4.1


title: M55 line with Dox-inducible HSPD1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A64
Donor age 55, Passage 12


title: myocardial tissue, AMI mice without RE, rep 2 [AMI-NC-2_miRNA]

value: myocardial


title: M55 line with Dox-inducible HSPD1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A63
Donor age 55, Passage 12


title: M55 line with Dox-inducible HSPA8 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A62
Donor age 55, Passage 12


title: Heart from systemic AAV8-GFP, Dox_200mg/kg, Mouse#8

description:
Library name: S435
Age at death 865 days, RIN-6.2


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#8

description:
Library name: S436
Age at death 865 days, RIN-8.1


title: Heart from systemic AAV8-GFP, Dox_200mg/kg, Mouse#7

description:
Library name: S431
Age at death 778 days, RIN-5.7


title: M65 line with Dox-inducible GSK3B transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: B24
Donor age 65, Passage 12


title: M55 line with Dox-inducible ISG15 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A65
Donor age 55, Passage 12


title: M55 line with Dox-inducible PIK3C2A transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A96
Donor age 55, Passage 12


title: M55 line with Dox-inducible HSPA5 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A59
Donor age 55, Passage 12


title: Brain from systemic AAV8-GFP, Dox_200mg/kg, Mouse#8

description:
Library name: S434
Age at death 865 days, RIN-6.7


title: M65 line with Dox-inducible MAPK7 transgene, Dox_1000ng/mL, P9, Rep2

description:
Library name: B34
Donor age 65, Passage 9


title: Spleen from systemic AAV8-GFP, Dox_200mg/kg, Mouse#5

description:
Library name: S429
Age at death 785 days, RIN-7.2


title: M65 line with Dox-inducible CXCR2 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B17
Donor age 65, Passage 10


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#5

description:
Library name: S428
Age at death 785 days, RIN-8.1


title: M55 line with Dox-inducible HSPA8 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A61
Donor age 55, Passage 12


title: M65 line with Dox-inducible HES1 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B25
Donor age 65, Passage 10


title: M55 line with Dox-inducible HSPA5 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A60
Donor age 55, Passage 12


title: Heart from systemic AAV8-GFP, Dox_200mg/kg, Mouse#5

description:
Library name: S427
Age at death 785 days, RIN-7.3


title: M55 line with Dox-inducible HSP90B1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A57
Donor age 55, Passage 12


title: M55 line with Dox-inducible HSP90B1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A58
Donor age 55, Passage 12


title: Brain from systemic AAV8-GFP, Dox_200mg/kg, Mouse#7

description:
Library name: S430
Age at death 778 days, RIN-6.8


title: M55 line with Dox-inducible HNRNPA2B1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A54
Donor age 55, Passage 12


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#7

description:
Library name: S432
Age at death 778 days, RIN-5.8


title: M55 line with Dox-inducible HSP90AB1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A55
Donor age 55, Passage 12


title: Brain from systemic AAV8-GFP, Dox_200mg/kg, Mouse#5

description:
Library name: S426
Age at death 785 days, RIN-7


title: M65 line with Dox-inducible KAT7 transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: B29
Donor age 65, Passage 10


title: M55 line with Dox-inducible HSP90AB1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A56
Donor age 55, Passage 12


title: M55 line with Dox-inducible HNRNPA2B1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A53
Donor age 55, Passage 12


title: M55 line with Dox-inducible HES1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A52
Donor age 55, Passage 12


title: OC_CTR

first: Xin

last: Liu

address: Luojia Hill, Wuchang District

institute: Wuhan University

description: Library name: Sample 2

data_processing:
Raw reads were filtered to remove adapter sequences, low-quality reads and reads with excessive ambiguous bases. The resulting clean reads were aligned to the mouse reference genome.
Assembly: Gene expression levels were quantified as FPKM values, and raw read counts were used for differential expression analysis with DESeq2.
Supplementary files format and content: Genes in Mdm2cKO compared with control mice with fold changes >2 and q < 0.05 were selected as significantly differentially expressed genes.

source_name: Primary osteocytes

extract_protocol:
Osteocytes were isolated from femurs and tibias as previously described and processed for bulk RNA-seq. Briefly, after removal of muscles and tendon tissues, bones were gently cut into small pieces and digested with 2.4 mg/ml Collagenase I (Biosharp) and 5 mM. Total RNAs were extracted from osteocytes using Trizol reagent (Takara). EDTA to obtain osteocytes.
Library construction and sequencing were carried out by Anoroad in Wuhan.

value: Primary osteocytes


title: M55 line with Dox-inducible HES1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A51
Donor age 55, Passage 12


title: WT_BCN1_D

type: RNA

city: Barcelona

first: Lluís

last: Hernández

state: Barcelona

address: Rossello 153

department: Area 5

country: Spain

institute: IDIBAPS

description: Sample from Barcelona

hyb_protocol: The ss-cDNA was fragmented and labeled and hybridized onto the  Affymetrix Human Clariom D, for 16hr at 45ºC and 60rpm, using Affymetrix Hybridization 645 oven. Afterwards, arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 System

data_processing: The data was analyzed with Transcriptome Expression Console Software (TAC v4.0.2) using (log2)  SST-RMA algorithm normalization.

label: biotin

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition D

label_protocol: Starting from 10ng of purified total RNA , a reverse transcription reaction was initiated at the Poly-A tail as well as throughout the entire length of RNA to capture both coding and multiple forms of non-coding RNA. Complementary RNA (cRNA) amplification was achieved using low-cycle PCR followed by linear amplification using T7 in vitro transcription (IVT) technology. The cRNA was then converted to biotinylated sense-strand DNA hybridization targets for unbiased coverage of the transcriptomeand scanned using the Affymetrix GeneChip Scanner 3000 System.

growth_protocol: RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin+IL-2 (1.54 ng/ml)+CpG-ODN2006 (0.38 ug/ml)

extract_protocol: miRNAeasy kit (Qiagen)

treatment_protocol: see samples/summary for the different protocols

value: Primary CLL cells

value: Condition D


title: M55 line with Dox-inducible HDAC6 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A49
Donor age 55, Passage 12


title: WT_BCN2_A

description: Sample from Barcelona

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition A

value: Condition A


title: M55 line with Dox-inducible HDAC1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A48
Donor age 55, Passage 12


title: WT_BCN2_B

description: Sample from Barcelona

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition B

value: Condition B


title: MCM-input-5_210930N_S54_L002_R1R2_001.fastq.gz

description: Library name: Sample3

data_processing:
Basecalls were performed usina bcl2fasta y2.17 for Novaseq output.
RIP-seq reads were trimmed from 3' end until the final base had a quality score > 30using skewer-0.2.2, discarding reads left with< 50 bp.
RIP-seq reads were aligned to the mouse mm10 genome using Bowtie version 2-2.2.3. Only uniquely mapping reads with at most two mismatches were retained.
To create RIP-seq coverage plots, the locations of the mapped RIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads permillion, rm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the sianifcance cutoff p-value <=1e-3.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was extracted with miRNeasy Mini Kit (Qiagen) and send for sequencing.
RIP-seq

value: heart

value: adult mouse cardiac myocytes


title: M55 line with Dox-inducible HDAC1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A47
Donor age 55, Passage 12


title: MCM-input-3_210930N_S53_L002_R1R2_001.fastq.gz

description: Library name: Sample2


title: MCM-input-1_210930N_S52_L002_R1R2_001.fastq.gz

description: Library name: Sample1


title: M55 line with Dox-inducible GSK3B transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A46
Donor age 55, Passage 12


title: WT_BCN1_A

description: Sample from Barcelona


title: M55 line with Dox-inducible GSK3B transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A45
Donor age 55, Passage 12


title: M65 line with Dox-inducible MDM2 transgene, Dox_1000ng/mL, P10, Rep1, redo

description:
Library name: S72
Donor age 65, Passage 9


title: M65 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P10, Rep1, redo

description:
Library name: S65
Donor age 65, Passage 10


title: M65 line with Dox-inducible UBE2I transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: S60
Donor age 65, Passage 10


title: M65 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P10, Rep2, redo

description:
Library name: S73
Donor age 65, Passage 9


title: MEC-1 cell line- RP11-161H23.5 Gapmer 2 treatment - rep2

source_name: MEC-1 cell line after RP11-161H23.5 Gapmer 2 treatment by 4 days

growth_protocol: RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin

treatment_protocol: 1uM of each Gapmer along 4 days

value: RP11-161H23.5 silencing Gapmer 2


title: WT_BCN1_B

description: Sample from Barcelona


title: MEC-1 cell line- RP11-161H23.5 Gapmer 2 treatment - rep1


title: M65 line with Dox-inducible CYCS transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: S58
Donor age 65, Passage 10

value: Fibroblast

value: CYCS


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: S56
Donor age 79, Passage 12

value: Dox_1000ng/mL, 3days


title: M65 line with Dox-inducible CYCS transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: S57
Donor age 65, Passage 10


title: M55 line with Dox-inducible GART transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: A43
Donor age 55, Passage 13

value: GART


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: S55
Donor age 79, Passage 12


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, Rep2

description:
Library name: S54
Donor age 55, Passage 11


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, Rep1

description:
Library name: S53
Donor age 55, Passage 11


title: M55 line with Dox-inducible FAU transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A41
Donor age 55, Passage 12

value: FAU


title: M65 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, Rep2

description:
Library name: S44
Donor age 65, Passage 11


title: MEC-1 cell line- RP11-161H23.5 Gapmer 1 treatment - rep2

source_name: MEC-1 cell line after RP11-161H23.5 Gapmer 1 treatment by 4 days

value: RP11-161H23.5 silencing Gapmer 1


title: MEC-1 cell line- RP11-161H23.5 Gapmer 1+2 treatment - rep3

source_name: MEC-1 cell line after RP11-161H23.5 Gapmer 1+2 treatment by 4 days

value: RP11-161H23.5 silencing Gapmer 1+2


title: MEC-1 cell line- RP11-161H23.5 Gapmer 1+2 treatment - rep2


title: MEC-1 cell line- RP11-161H23.5 Gapmer 1 treatment - rep1


title: M55 line with Dox-inducible ESR1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A40
Donor age 55, Passage 12


title: M65 line with Dox-inducible SUMO1 transgene, Rep2

description:
Library name: S42
Donor age 65, Passage 11

value: NT


title: M65 line with Dox-inducible SUMO1 transgene, Rep1

description:
Library name: S41
Donor age 65, Passage 11


title: M66 WT iPSC line (isogenic with S39)

description:
Library name: S40
Donor age 66, Passage 2

value: iPSC

value: WT


title: M55 line with Dox-inducible ESR1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A39
Donor age 55, Passage 12


title: M66 WT line (isogenic with S40)

description:
Library name: S39
Donor age 66, Passage 4


title: M55 line with Dox-inducible EEF2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A38
Donor age 55, Passage 12


title: M79 WT line (isogenic with S37)

description:
Library name: S38
Donor age 79, Passage 7


title: MEC-1 cell line- RP11-161H23.5 Gapmer 1 treatment - rep3


title: MEC-1 cell line- RP11-161H23.5 Gapmer 1+2 treatment - rep1


title: M55 line with Dox-inducible EEF2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A37
Donor age 55, Passage 12


title: M68 WT line (isogenic with S35)

description:
Library name: S36
Donor age 68, Passage 9


title: M60 WT line (isogenic with S38)

description:
Library name: S37
Donor age 60, Passage 3


title: M55 line with Dox-inducible DDX3X transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A36
Donor age 55, Passage 12


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp RP11-161H23.5) - rep2

source_name: MEC-1 cell line after Scrambled Gapmer treatment by 4 days

value: Control RP11-161H23.5 silencing


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp RP11-161H23.5) - rep1


title: M92 WT line, Rapa_100ng/mL, 72h

description:
Library name: S32
Donor age 92, Passage 5


title: M92 WT line, Rapa_100ng/mL, 48h

description:
Library name: S31
Donor age 92, Passage 5


title: M55 line with Dox-inducible CYCS transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A34
Donor age 55, Passage 12


title: M92 WT line, Rapa_100ng/mL, 24h

description:
Library name: S30
Donor age 92, Passage 5


title: MEC-1 cell line- LINC00158 Gapmer 2 treatment - rep2

source_name: MEC-1 cell line after LINC00158 Gapmer 2 treatment by 4 days

value: LINC00158 silencing Gapmer 2


title: M92 WT line, No Rapa

description:
Library name: S29
Donor age 92, Passage 5


title: M55 line with Dox-inducible CYCS transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A33
Donor age 55, Passage 12


title: MEC-1 cell line- LINC00158 Gapmer 2 treatment - rep1


title: M73 WT line, Rapa_100ng/mL, 72h

description:
Library name: S28
Donor age 73, Passage 16


title: M73 WT line, Rapa_100ng/mL, 48h

description:
Library name: S27
Donor age 73, Passage 16


title: MEC-1 cell line- LINC00158 Gapmer 1 treatment - rep3

source_name: MEC-1 cell line after LINC00158 Gapmer 1 treatment by 4 days

value: LINC00158 silencing Gapmer 1


title: M55 WT line, Rapa_100ng/mL, 72h

description:
Library name: S24
Donor age 55, Passage 5


title: M73 WT line, No Rapa

description:
Library name: S25
Donor age 73, Passage 16


title: M55 WT line, Rapa_100ng/mL, 48h

description:
Library name: S23
Donor age 55, Passage 5


title: MEC-1 cell line- LINC00158 Gapmer 2 treatment - rep3


title: MEC-1 cell line- LINC00158 Gapmer 1 treatment - rep2


title: MEC-1 cell line- LINC00158 Gapmer 1 treatment - rep1


title: M55 line with Dox-inducible CTNNB1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A30
Donor age 55, Passage 12


title: M55 WT line (isogenic with S33)

description:
Library name: S34
Donor age 55, Passage 6


title: M55 line with Dox-inducible CTNNB1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A29
Donor age 55, Passage 12


title: M52 WT line (isogenic with S36)

description:
Library name: S35
Donor age 52, Passage 4


title: M55 WT line, No Rapa

description:
Library name: S21
Donor age 55, Passage 5


title: M55 WT line, Rapa_100ng/mL, 24h

description:
Library name: S22
Donor age 55, Passage 5


title: MEC-1 cell line- LINC00158 Gapmer 1+2 treatment - rep3

source_name: MEC-1 cell line after LINC00158 Gapmer 1+2 treatment by 4 days

value: LINC00158 silencing Gapmer 1+2


title: MEC-1 cell line- LINC00158 Gapmer 1+2 treatment - rep2


title: M36 WT line, Rapa_100ng/mL, 48h

description:
Library name: S19
Donor age 36, Passage 5


title: M36 WT line, Rapa_100ng/mL, 72h

description:
Library name: S20
Donor age 36, Passage 5


title: M55 line with Dox-inducible CHEK2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A28
Donor age 55, Passage 12


title: M36 WT line, Rapa_100ng/mL, 24h

description:
Library name: S18
Donor age 36, Passage 5


title: M36 WT line, No Rapa

description:
Library name: S17
Donor age 36, Passage 5


title: M94 WT line, 100ng/mL Rapa, 3 days

description:
Library name: S16
Donor age 94, Passage 4

value: Rapa_100ng/mL, 3days


title: M55 line with Dox-inducible CHEK2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A27
Donor age 55, Passage 12


title: MEC-1 cell line- LINC00158 Gapmer 1+2 treatment - rep1


title: M94 WT line, No Rapa

description:
Library name: S15
Donor age 94, Passage 4


title: M29 WT line, Rapa_100, 3 days

description:
Library name: S14
Donor age 29, Passage 4


title: M55 line with Dox-inducible CHEK1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A26
Donor age 55, Passage 12


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp LINC00158) - rep3

value: Control LINC00158 silencing


title: M29 WT line, No Rapa

description:
Library name: S13
Donor age 29, Passage 4


title: M55 line with Dox-inducible CHEK1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A25
Donor age 55, Passage 12


title: F3 line with Dox-inducible ZGLP1 transgene, Dox_2000ng/mL

description:
Library name: S12
Donor age 31

value: Dox_2000ng/mL, 3days


title: M73 WT line, Rapa_100ng/mL, 24h

description:
Library name: S26
Donor age 73, Passage 16

value: Fibroblast


title: B6 line, P+10

description:
Library name: S11
Donor age 36


title: B6 line, P+2

description:
Library name: S10
Donor age 36


title: M55 line with Dox-inducible CDKN2A transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A24
Donor age 55, Passage 12


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp LINC00158) - rep1


title: M55 line with Dox-inducible CXCR2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A31
Donor age 55, Passage 12


title: MEC-1 cell line- CYTOR Gapmer 2 treatment - rep3

source_name: MEC-1 cell line after CYTOR Gapmer 2 treatment by 4 days

value: LINC00152 silencing Gapmer 2


title: M55 line with Dox-inducible CDKN2A transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A23
Donor age 55, Passage 12

value: Dox_1000ng/mL, 3days


title: B6 line, P0

description:
Library name: S9
Donor age 36


title: F3 line with Dox-inducible ZGLP1 transgene

description:
Library name: S8
Donor age 31


title: F3 line with Dox-inducible OTX2 transgene

description:
Library name: S7
Donor age 31


title: M55 line with Dox-inducible CDK4 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A22
Donor age 55, Passage 12


title: F3 line with Dox-inducible GFP transgene, Dox_2000ng/mL

description:
Library name: S6
Donor age 31

value: GFP


title: MEC-1 cell line- CYTOR Gapmer 2 treatment - rep2


title: F3 line with Dox-inducible GFP transgene, Dox_250ng/mL

description:
Library name: S5
Donor age 31

value: Dox_250ng/mL, 3days


title: M86 WT line

description:
Library name: S3
Donor age 86, Passage 12


title: MEC-1 cell line- CYTOR Gapmer 2 treatment - rep1


title: M55 line with Dox-inducible CDK2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: A20
Donor age 55, Passage 13


title: M55 line with Dox-inducible CDK4 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A21
Donor age 55, Passage 12


title: M94 WT line

description:
Library name: S4
Donor age 94, Passage 3


title: Spleen from systemic AAV8-GFP, Dox_200mg/kg, Mouse#7

description:
Library name: S433
Age at death 778 days, RIN-5.8

value: Spleen

value: Dox_200mg/kg, 1wk-ON/1wk-OFF


title: M55 line with Dox-inducible CDK2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: A19
Donor age 55, Passage 13


title: MEC-1 cell line- CYTOR Gapmer 1 treatment - rep3

source_name: MEC-1 cell line after CYTOR Gapmer 1 treatment by 4 days

value: LINC00152 silencing Gapmer 1


title: OC_cKO

description: Library name: Sample 1

value: Primary osteocytes

value: Dmp1-Cre; Mdm2flox/flox


title: Blastocysts, MT-treated, rep1

city: Beijing

first: Kui

middle: Wen

last: Ma

address: No.2 Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

description:
Library name: M1
column name in RNA-Seq_TPM.csv : M1

data_processing:
Fastp 0.20.1 and FastQC 0.11.9 were used for data quality control.
Reads were aligned to the bovine reference genome (Bos_taurus.ARS-UCD1.3) with the corresponding genome annotation (Bos_taurus.ARS-UCD1.2.108) using STAR 2.7.9a.
Gene counting was performed with featureCounts (Subread 1.6.3) .
DESeq2 [35] was used to identify differentially expressed genes.
Assembly: Bos_taurus.ARS-UCD1.3
Supplementary files format and content: csv files include TPM values for each sample

organism: Bos taurus

source_name: embryo

growth_protocol: Blastocysts from the MT-treated (n = 3) and control (n = 3) groups were frozen in liquid nitrogen and stored at -80 ℃

extract_protocol:
total RNA was extracted from the embryos using TRIzol reagent (Ambion, USA) and treated with DNase I (Takara, China) to eliminate genomic DNA
RNA-seq libraries were constructed using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA). Double-stranded cDNA was synthesized (SuperScript Kit, Invitrogen, USA), amplified via PCR, and size-fractionated (200–300 bp) using magnetic beads. Libraries were quantified via a TBS380 fluorometer prior to paired-end sequencing (PE150) on an Illumina NovaSeq 6000 platform.

value: embryo

value: MT-treated


title: M29 WT line

description:
Library name: S1
Donor age 29, Passage 3

value: WT

value: NT


title: M69 WT line

description:
Library name: S2
Donor age 69, Passage 8


title: YF1-IP-1_210930N_S49_L002_R1R2_001.fastq.gz

description: Library name: Sample4

source_name: heart

value: heart

value: adult mouse cardiac myocytes