title: Lung, TNS1 KO 6

city: Madison

first: Nathan

last: Sandbo

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin-Madison

description:
Library name: KO6
RosaTNS1-43-2 (KO6)

data_processing:
Sequencing reads were first demultiplexed.
Next, low-abundance genes with an average read count below a threshold of 1.0 in two or more samples were filtered and then reads were trimmed using the trimming software Skewer.
Alignment of adapter-trimmed (Skewer v0.1.123), 2x150 (paired-end, PE) base pair strand-specific Illumina reads to the Mus musculus GRCm38.p5 genome (assembly accession NCBI GCA 000001635.7) was achieved with the Spliced Transcripts Alignment to a Reference (STAR v2.5.3a) software, a splice-junction aware aligner, using annotation provided by Ensembl release 91.
Expression estimation was performed with RSEM v1.3.0 (RNASeq by Expectation Maximization).
To test for differential gene expression among individual group contrasts, expected read counts obtained from RSEM were used as input into edgeR (v3.16.5).
Inter-sample normalization was achieved with the trimmed mean of M-values (TMM) method.
Prior to statistical analysis with edgeR, independent filtering was applied and required genes to have a count-per-million (CPM) above k in n samples, where k is determined by minimum read count (10 reads) and by the sample library sizes where n is determined by the number of biological replicates in each group.
Assembly: Alignment of adapter-trimmed (Skewer v0.1.123), 2x150 (paired-end, PE) base pair strand-specific Illumina reads to the Mus musculus GRCm38.p5 genome (assembly accession NCBI GCA 000001635.7).
Supplementary files format and content: Processed data consist of gene-level expression matrices generated from bulk RNA-seq. Reads were aligned and quantified at the gene level using RSEM. Expression values are provided as expected counts with one column per mouse sample and one row per gene. Genes are identified by Ensembl gene IDs (ENSMUSG). Submitted as csv file.

molecule: polyA RNA

source_name: Whole lung lysate

growth_protocol: The mice were housed under controlled temperature (~ 74 °F), humidity (~30%), and illumination (12-hour light/12-hour dark cycle), and laboratory chow and water were provided ad libitum. Animals received daily care and health checks and weekly cage changes.

extract_protocol:
Whole mouse lungs were used for isolation of RNA. Lungs were flash frozen 14 days after the completion of tamoxifen treatment, and suspended in RNA STAT-60 (Amsbio, Abingdon, UK) and then bullet blended with RNase free 0.9-2.0mm stainless steel beads SSB14B-RNA (Next Advance, Troy, NY) until homogenized. Additional RNA STAT-60 followed by chloroform were added prior to centrifugation. RNA was precipitated from the resulting colorless upper aqueous phase. RNA pellets were washed with 75% ethanol and resuspended in nuclease free water. The Ambion (Austin, TX) AM1907 Turbo DNA-free kit was used to remove any remaining DNA.
RNA libraries for RNA sequencing were prepared with the Illumina TruSeq Stranded mRNA (polyA enrichment) Library.

treatment_protocol: All mice were treated with tamoxifen (100 mg/kg/day, IP) for seven days, followed by a one-time dose of intratracheal 50 µl 0.9% normal saline on day 8.

value: Whole lung lysate

tag: Sex

value: F

value: TNS1 KO

value: Tamoxifen 100 mg/kg/day (intraperitoneal) x7 days followed by 50 µl 0.9% normal saline (intratracheal) on day 8

value: Summer 2021


title: LbJ_98333

status: Public on Feb 14 2026

type: SRA

city: Kunming

first: Zhu

last: zhengna

state: YunNan

address: Kunming University of Science and Technology, Wujiaying Street, Chenggong District, Kunming city, Yunnan Province

country: China

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat (version 4.0.3) software package was used to analyze the filtered gene expression data of counts
Assembly: Mmul_10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: total RNA

organism: Macaca mulatta

source_name: Mesenteric lymph

extract_protocol:
Venous blood samples were derived from two age groups of rhesus monkeys using Ficoll-hypaque density solution, heparinized and then processed by standard density gradient centrifugation methods to isolate peripheral blood mononuclear cells (PBMCs).  Using standard operating procedures, cells from bone marrow aspirates.  Upon tissue harvest, the spleen was dissected and splenocytes isolated by using mechanical dissociation protocol.  The mesenteric lymph white adipose tissue was dissected, washed in PBS, minced to small pieces with scissors and digested during 30 min at 37℃in 1mg/mL collagenase II（Cat# V900892,Merck Millipore） and collagenase IV(Cat#17104019,Thermo Fisher Scientific).  All cells suspension was filtered through a 40μm strainer.
Single-cell RNA (scRNAseq) sequencing using Chromium Single Cell 3'Reagent Kit as per manufacturer’s instructions (10x Genomics).

tag: tissue

value: Mesenteric lymph

tag: age

value: 23 years


title: MOT3_aS95_aG76_aN60_aQ68_aF63_2

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: Library name: MOT3_aS95_aG76_aN60_aQ68_aF63_2

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: cell type

value: yeast cells

tag: genotype

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::MOT3(S95 G76 N60 Q68 F63) SV40 NLS Mnase::kanMX

tag: treatment

value: budding yeast culture at OD=4


title: MOT3_aS95_aG76_aN60_aQ68_aF63_1

description: Library name: MOT3_aS95_aG76_aN60_aQ68_aF63_1


description: Library name: MOT3_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_6

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::MOT3(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase::kanMX


title: Lung, WT 3

country: USA

description:
Library name: WT3
RosaTNS1-19-6 (WT3)

library_source: transcriptomic

organism: Mus musculus

value: WT

tag: batch


title: Lung, WT 4

description:
Library name: WT4
RosaTNS1-19-9 (WT4)


description: Library name: MOT3_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::MOT3(S74 T55 N110 Q61 D16 E14 L67) SV40 NLS Mnase::kanMX


title: Lung, WT 1

description:
Library name: WT1
RosaTNS1-19-10 (WT1)


title: Lung, WT 2

description:
Library name: WT2
RosaTNS1-19-4 (WT2)

value: M


description: Library name: MOT3_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::MOT3(S114 G89 N43 Q53 D14 E15 F63) SV40 NLS Mnase::kanMX


description: Library name: MOT3_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::MOT3(S74 T55 N110 Q61 D16 E14 L130) SV40 NLS Mnase::kanMX


title: GS_145269

institute: Kunming University of Science and Technology

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow

value: 7 years


description: Library name: MOT3_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_1


title: Lung, TNS1 KO 8

description:
Library name: KO8
RosaTNS1-44-2 (KO8)

value: Whole lung lysate


description: Library name: MOT3_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_1


title: Lung, TNS1 KO 7

description:
Library name: KO7
RosaTNS1-44-1 (KO7)

value: TNS1 KO


title: Gr4_86_Quad

city: Neuherberg

first: Robert

middle: Michael

last: Gutgesell

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Center Munich

description: Library name: 25L001226

data_processing:
Quality control for the raw transcriptomics sequencing reads was performed using FastQC.
Transcripts were aligned and quantified to the GRCm38 reference genome using STAR with default parameters.
Transcript counts were imported into Python using scanpy and decoupler.
Gene expression was normalized using the median ratio method implemented in pyDESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing raw integer counts. Rows are Genes, Columns are Samples.

source_name: Quadriceps

growth_protocol: Mice were double- or single-housed and fed ad libitum with either a regular chow (#1314, Altromin, Germany or #5L0D, LabDiet, USA) or a high-fat diet (58% fat, D12331, Research Diets, New Brunswick, USA). Animals were kept under constant ambient conditions of 22 ± 2°C with constant humidity (45–65%) and a 12h/12h light/dark cycle.

extract_protocol:
Total RNA was isolated using the RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
Sequencing libraries were generated from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit with poly-A enrichment, according to the manufacturer's instructions.

treatment_protocol: Mice were treated with either Vehicle, Lanifibranor, semaglutide, GLP-1:Lani, GLP-1:Tesa, GLP1:GIP, GLP-1:GIP:Tesa, GLP-1:GIP:Lani, or physical co-therapies of these combinations. Following treatment, specific tissues (e.g., Liver, WAT, etc.) were excised and processed for RNA extraction.

value: Quadriceps


title: MOT3_NQ_toG_2_341_1

description: Library name: MOT3_NQ_toG_2_341_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::SV40 NLS MOT3(NQ toG)Mnase::kanMX


title: Gr4_58_Quad

description: Library name: 25L001225


description: Library name: MOT3_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_7


title: Lung, WT 5

description:
Library name: WT5
RosaTNS1-43-1 (WT5)

value: F

value: Tamoxifen 100 mg/kg/day (intraperitoneal) x7 days followed by 50 µl 0.9% normal saline (intratracheal) on day 8

value: Summer 2021


title: Gr4_87-2_Quad

description: Library name: 25L001222


description: Library name: MOT3_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_6

value: yeast cells


description: Library name: MOT3_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_5

value: budding yeast culture at OD=4


title: MOT3_KR_toNQ_2_341_1

description: Library name: MOT3_KR_toNQ_2_341_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::SV40 NLS MOT3(KR toNQ)Mnase::kanMX


description: Library name: MOT3_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_3


title: MOT3_FWY_toL_2_341_2

description: Library name: MOT3_FWY_toL_2_341_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::SV40 NLS MOT3(FWY toL)Mnase::kanMX


title: Gr4_59_Quad

description: Library name: 25L001227

value: WT


title: MIG2_shift_LIVFWY_101_382_2

description: Library name: MIG2_shift_LIVFWY_101_382_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(shift LIVFWY) SV40 NLS Mnase::kanMX


title: Gr3_5_Quad

description: Library name: 25L001218


title: MOT3_NQ_toG_2_341_2

description: Library name: MOT3_NQ_toG_2_341_2


title: GS_146057

description: 10x Genomics


title: Gr4_60_Quad

description: Library name: 25L001224


title: MOT3_LIV_toF_2_341_2

description: Library name: MOT3_LIV_toF_2_341_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MOT3::SV40 NLS MOT3(LIV toF)Mnase::kanMX


title: MOT3_LIV_toF_2_341_1

description: Library name: MOT3_LIV_toF_2_341_1


title: MIG2_scramble_101_382_2

description: Library name: MIG2_scramble_101_382_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(scramble) SV40 NLS Mnase::kanMX


title: Gr3_32_Quad

description: Library name: 25L001216


title: MIG2_scramble_101_382_1

description: Library name: MIG2_scramble_101_382_1


title: Gr4_89_Quad

description: Library name: 25L001223


title: Gr3_31_Quad

description: Library name: 25L001214


title: MIG2_shift_LIVFWY_101_382_1

description: Library name: MIG2_shift_LIVFWY_101_382_1


title: MIG2_neg_toNQ_101_382_1

description: Library name: MIG2_neg_toNQ_101_382_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(neg toNQ) SV40 NLS Mnase::kanMX


title: Gr3_4_Quad

description: Library name: 25L001217


title: Gr3_30_Quad

description: Library name: 25L001215


title: MIG2_hyd_toNQ_101_382_2

description: Library name: MIG2_hyd_toNQ_101_382_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(hyd toNQ) SV40 NLS Mnase::kanMX


title: MIG2_neg_toNQ_101_382_2

description: Library name: MIG2_neg_toNQ_101_382_2


title: Gr4_87-1_Quad

description: Library name: 25L001220


title: Gr3_1_Quad

description: Library name: 25L001219


title: MOT3_FWY_toL_2_341_1

description: Library name: MOT3_FWY_toL_2_341_1


title: MOT3_KR_toNQ_2_341_2

description: Library name: MOT3_KR_toNQ_2_341_2


title: Gr4_88_Quad

description: Library name: 25L001221


title: Gr2_2_Quad

description: Library name: 25L001209


title: Gr3_6_Quad

description: Library name: 25L001212


title: Gr2_4_Quad

description: Library name: 25L001211


title: MIG2_d101_382_1

description: Library name: MIG2_d101_382_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(D101 382) SV40 NLS Mnase::kanMX


title: Gr3_29_Quad

description: Library name: 25L001213


title: MIG2_hyd_toNQ_101_382_1

description: Library name: MIG2_hyd_toNQ_101_382_1


title: Gr2_3-1_Quad

description: Library name: 25L001208


title: Gr2_3-2_Quad

description: Library name: 25L001210


title: Gr2_58_Quad

description: Library name: 25L001207


title: MIG2_d101_382_2

description: Library name: MIG2_d101_382_2


title: Gr2_57_Quad

description: Library name: 25L001206


title: MIG2_NQ_toG_101_382_3

description: Library name: MIG2_NQ_toG_101_382_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(NQ toG) SV40 NLS Mnase::kanMX


title: MIG2_LIV_toF_101_382_1

description: Library name: MIG2_LIV_toF_101_382_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(LIV toF) SV40 NLS Mnase::kanMX


title: MIG2_KR_toNQ_101_382_2

description: Library name: MIG2_KR_toNQ_101_382_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(KR toNQ) SV40 NLS Mnase::kanMX


title: MIG2_LIV_toF_101_382_2

description: Library name: MIG2_LIV_toF_101_382_2


title: Vhcl_68_Quad

description: Library name: 25L001202

value: Quadriceps

value: Vhcl


title: MIG2_KR_toNQ_101_382_1

description: Library name: MIG2_KR_toNQ_101_382_1


title: Gr2_86_Quad

description: Library name: 25L001204


title: MIG2_NQ_toG_101_382_4

description: Library name: MIG2_NQ_toG_101_382_4


title: MIG2_FWY_toL_101_382_2

description: Library name: MIG2_FWY_toL_101_382_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG2::MIG2(FWY toL) SV40 NLS Mnase::kanMX


title: Vhcl_61_Quad

description: Library name: 25L001201


title: Vhcl_69_Quad

description: Library name: 25L001203


title: MIG2_FWY_toL_101_382_1

description: Library name: MIG2_FWY_toL_101_382_1

value: yeast cells


title: Gr2_88_Quad

description: Library name: 25L001205


title: MIG1_neg_toNQ_96_504_2

description: Library name: MIG1_neg_toNQ_96_504_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(neg toNQ 96 50) SV40 NLS Mnase::kanMX

value: budding yeast culture at OD=4


title: MIG1_hyd_toNQ_96_504_1

description: Library name: MIG1_hyd_toNQ_96_504_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(hyd toNQ 96 50) SV40 NLS Mnase::kanMX


title: MIG1_neg_toNQ_96_504_1

description: Library name: MIG1_neg_toNQ_96_504_1


title: Vhcl_66_Quad

description: Library name: 25L001197

value: WT


title: MIG1_hyd_toNQ_96_504_2

description: Library name: MIG1_hyd_toNQ_96_504_2


title: Vhcl_85_Quad

description: Library name: 25L001199


title: Vhcl_59_Quad

description: Library name: 25L001198


title: MIG1_aS95_aG76_aN60_aQ68_aF63_2

description: Library name: MIG1_aS95_aG76_aN60_aQ68_aF63_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(S95 G76 N60 Q68 F63) SV40 NLS Mnase::kanMX


title: Gr4_59_WAT

description: Library name: 25L001196

source_name: White adipose tissue

value: White adipose tissue


title: MIG1_aS95_aG76_aN60_aQ68_aF63_1

description: Library name: MIG1_aS95_aG76_aN60_aQ68_aF63_1


title: Vhcl_60_Quad

description: Library name: 25L001200


title: Gr4_86_WAT

description: Library name: 25L001195


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(S74 T55 N110 Q61 D16 E14 Y67) SV40 NLS Mnase::kanMX


title: Gr4_58_WAT

description: Library name: 25L001194


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(S74 T55 N110 Q61 D16 E14 L67) SV40 NLS Mnase::kanMX


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_1


title: Gr4_89_WAT

description: Library name: 25L001192


title: Gr4_60_WAT

description: Library name: 25L001193


title: Gr4_87-2_WAT

description: Library name: 25L001191


title: Gr4_88_WAT

description: Library name: 25L001190


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase::kanMX


title: Gr3_1_WAT

description: Library name: 25L001188


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_1


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(S74 T55 N110 Q61 D16 E14 L130) SV40 NLS Mnase::kanMX


title: Gr3_5_WAT

description: Library name: 25L001187


title: Gr3_4_WAT

description: Library name: 25L001186


description: Library name: MIG1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(S114 G89 N43 Q53 D14 E15 F63) SV40 NLS Mnase::kanMX


title: Gr3_32_WAT

description: Library name: 25L001185


title: Gr3_30_WAT

description: Library name: 25L001184


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_1


title: MIG1_NQ_toG_96_504_2

description: Library name: MIG1_NQ_toG_96_504_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(NQ toG 96 50) SV40 NLS Mnase::kanMX


description: Library name: MIG1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_1


title: MIG1_NQ_toG_96_504_1

description: Library name: MIG1_NQ_toG_96_504_1


title: MIG1_KR_toNQ_96_504_2

description: Library name: MIG1_KR_toNQ_96_504_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(KR toNQ 96 50) SV40 NLS Mnase::kanMX


title: Gr3_6_WAT

description: Library name: 25L001181


description: Library name: MIG1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_2


title: Gr3_31_WAT

description: Library name: 25L001183


title: Gr4_87-1_WAT

description: Library name: 25L001189


title: Gr2_4_WAT

description: Library name: 25L001180


title: MIG1_KR_toNQ_96_504_1

description: Library name: MIG1_KR_toNQ_96_504_1


title: MIG1_FWY_toL_96_504_2

description: Library name: MIG1_FWY_toL_96_504_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(FWY toL 96 50) SV40 NLS Mnase::kanMX


title: MIG1_LIV_toF_96_504_2

description: Library name: MIG1_LIV_toF_96_504_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MIG1::MIG1(LIV toF 96 50) SV40 NLS Mnase::kanMX


title: Gr2_2_WAT

description: Library name: 25L001178


title: MIG1_LIV_toF_96_504_1

description: Library name: MIG1_LIV_toF_96_504_1


title: Gr2_3-2_WAT

description: Library name: 25L001179


title: Gr2_3-1_WAT

description: Library name: 25L001177


title: MBP1_neg_toNQ_5

description: Library name: MBP1_neg_toNQ_5

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(neg toN) SV40 NLS Mnase


title: MBP1_neg_toNQ_6

description: Library name: MBP1_neg_toNQ_6

value: yeast cells


title: Gr3_29_WAT

description: Library name: 25L001182


title: MIG1_FWY_toL_96_504_1

description: Library name: MIG1_FWY_toL_96_504_1


title: MBP1_hyd_toNQ_6

description: Library name: MBP1_hyd_toNQ_6

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(hyd toN) SV40 NLS Mnase


title: Gr2_88_WAT

description: Library name: 25L001174


title: Gr2_58_WAT

description: Library name: 25L001176


title: Gr2_86_WAT

description: Library name: 25L001173


title: MBP1_aS95_aG76_aN60_aQ68_aF63_2

description: Library name: MBP1_aS95_aG76_aN60_aQ68_aF63_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(S95 G76 N60 Q68 F63) SV40 NLS Mnase

value: budding yeast culture at OD=4


title: Vhcl_69_WAT

description: Library name: 25L001172

value: WT

value: Vhcl


title: MBP1_aS95_aG76_aN60_aQ68_aF63_1

description: Library name: MBP1_aS95_aG76_aN60_aQ68_aF63_1


title: Vhcl_68_WAT

description: Library name: 25L001171

value: White adipose tissue


title: Gr2_57_WAT

description: Library name: 25L001175


description: Library name: MBP1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(S74 T55 N110 Q61 D16 E14 L130) SV40 NLS Mnase


description: Library name: MBP1_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(S74 T55 N110 Q61 D16 E14 Y67) SV40 NLS Mnase


title: Vhcl_85_WAT

description: Library name: 25L001168


title: Vhcl_60_WAT

description: Library name: 25L001169


description: Library name: MBP1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase


title: Vhcl_66_WAT

description: Library name: 25L001166


description: Library name: MBP1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_1


description: Library name: MBP1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_1


description: Library name: MBP1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_4

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(S114 G89 N43 Q53 D14 E15 F63) SV40 NLS Mnase


description: Library name: MBP1_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_2


title: MBP1_hyd_toNQ_5

description: Library name: MBP1_hyd_toNQ_5


title: Vhcl_67_WAT

description: Library name: 25L001165


title: Vhcl_61_WAT

description: Library name: 25L001170


title: Vhcl_59_WAT

description: Library name: 25L001167


title: Gr4_58_Liv

description: Library name: 25L001162

source_name: Liver

value: Liver


description: Library name: MBP1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_3


title: MBP1_NQ_toG_151_833_2

description: Library name: MBP1_NQ_toG_151_833_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(NQ toG) SV40 NLS Mnase


title: Gr4_86_Liv

description: Library name: 25L001163


title: MBP1_LIV_toF_151_833_2

description: Library name: MBP1_LIV_toF_151_833_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(LIV toF) SV40 NLS Mnase


title: Gr4_60_Liv

description: Library name: 25L001161


title: MBP1_LIV_toF_151_833_1

description: Library name: MBP1_LIV_toF_151_833_1


title: MBP1_KR_toNQ_151_833_4

description: Library name: MBP1_KR_toNQ_151_833_4

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(KR toNQ) SV40 NLS Mnase


title: Gr4_89_Liv

description: Library name: 25L001160


title: MBP1_NQ_toG_151_833_1

description: Library name: MBP1_NQ_toG_151_833_1


title: Gr4_88_Liv

description: Library name: 25L001158


title: Gr4_87-2_Liv

description: Library name: 25L001159


title: Gr4_59_Liv

description: Library name: 25L001164


title: MBP1_KR_toNQ_151_833_3

description: Library name: MBP1_KR_toNQ_151_833_3


title: MBP1_FWY_toL_151_833_4

description: Library name: MBP1_FWY_toL_151_833_4

value: MATa his3D0 leu2D0 met15D0 ura3D0 MBP1::MBP1(FWY toL) SV40 NLS Mnase


title: Gr3_1_Liv

description: Library name: 25L001156


title: MBP1_FWY_toL_151_833_2

description: Library name: MBP1_FWY_toL_151_833_2


title: Gr4_87-1_Liv

description: Library name: 25L001157


title: Gr3_5_Liv

description: Library name: 25L001155


title: Gr3_4_Liv

description: Library name: 25L001154


title: INO2_hyd_toNQ_2_200_6

description: Library name: INO2_hyd_toNQ_2_200_6

value: MATa his3D0 leu2D0 met15D0 ura3D0 INO2::SV40 NLS INO2(hyd toNQ)Mnase


title: Gr3_32_Liv

description: Library name: 25L001153


title: Gr3_30_Liv

description: Library name: 25L001152


title: INO2_hyd_toNQ_2_200_5

description: Library name: INO2_hyd_toNQ_2_200_5

value: yeast cells


title: Gr3_29_Liv

description: Library name: 25L001150


title: INO2_NQ_toG_2_200_3

description: Library name: INO2_NQ_toG_2_200_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 INO2::SV40 NLS INO2(NQ toG)Mnase


title: Gr3_6_Liv

description: Library name: 25L001149


title: Gr3_31_Liv

description: Library name: 25L001151


title: Gr2_4_Liv

description: Library name: 25L001148


title: INO2_LIV_toF_2_200_2

description: Library name: INO2_LIV_toF_2_200_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 INO2::SV40 NLS INO2(LIV toF)Mnase


title: INO2_LIV_toF_2_200_1

description: Library name: INO2_LIV_toF_2_200_1

value: budding yeast culture at OD=4


title: Gr2_3-2_Liv

description: Library name: 25L001147

value: WT


title: INO2_neg_toNQ_2_200_8

description: Library name: INO2_neg_toNQ_2_200_8

value: MATa his3D0 leu2D0 met15D0 ura3D0 INO2::SV40 NLS INO2(neg toNQ)Mnase


title: Gr2_3-1_Liv

description: Library name: 25L001145


title: Gr2_2_Liv

description: Library name: 25L001146


title: Vhcl_69_Liv

description: Library name: 25L001140

value: Vhcl


title: INO2_neg_toNQ_2_200_7

description: Library name: INO2_neg_toNQ_2_200_7


title: Gr2_57_Liv

description: Library name: 25L001143


title: Gr2_88_Liv

description: Library name: 25L001142


title: INO2_KR_toNQ_2_200_7

description: Library name: INO2_KR_toNQ_2_200_7

value: MATa his3D0 leu2D0 met15D0 ura3D0 INO2::SV40 NLS INO2(KR toNQ)Mnase


title: HOT1_neg_toNQ_2_500_3

description: Library name: HOT1_neg_toNQ_2_500_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 HOT1::SV40 NLS HOT1(neg toNQ)Mnase::kanMX


title: INO2_FWY_toL_2_200_1

description: Library name: INO2_FWY_toL_2_200_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 INO2::SV40 NLS INO2(FWY toL)Mnase


title: INO2_KR_toNQ_2_200_8

description: Library name: INO2_KR_toNQ_2_200_8


title: Gr2_86_Liv

description: Library name: 25L001141


title: INO2_FWY_toL_2_200_2

description: Library name: INO2_FWY_toL_2_200_2


title: INO2_NQ_toG_2_200_4

description: Library name: INO2_NQ_toG_2_200_4


title: HOT1_neg_toNQ_2_500_4

description: Library name: HOT1_neg_toNQ_2_500_4


title: Gr2_58_Liv

description: Library name: 25L001144


title: HOT1_hyd_toNQ_2_500_1

description: Library name: HOT1_hyd_toNQ_2_500_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HOT1::SV40 NLS HOT1(hyd toNQ)Mnase::kanMX


title: HOT1_hyd_toNQ_2_500_2

description: Library name: HOT1_hyd_toNQ_2_500_2


title: Vhcl_68_Liv

description: Library name: 25L001139

value: Liver


title: Vhcl_60_Liv

description: Library name: 25L001137


title: HOT1_KR_toNQ_2_500_2

description: Library name: HOT1_KR_toNQ_2_500_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 HOT1::SV40 NLS HOT1(KR toNQ)Mnase::kanMX


title: Vhcl_61_Liv

description: Library name: 25L001138


title: HOT1_LIV_toF_2_500_1

description: Library name: HOT1_LIV_toF_2_500_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HOT1::SV40 NLS HOT1(LIV toF)Mnase::kanMX


title: Vhcl_85_Liv

description: Library name: 25L001136


title: Vhcl_66_Liv

description: Library name: 25L001134


title: HOT1_LIV_toF_2_500_2

description: Library name: HOT1_LIV_toF_2_500_2


title: Vhcl_59_Liv

description: Library name: 25L001135


title: HOT1_KR_toNQ_2_500_1

description: Library name: HOT1_KR_toNQ_2_500_1


title: HOT1_FWY_toL_2_500_1

description: Library name: HOT1_FWY_toL_2_500_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HOT1::SV40 NLS HOT1(FWY toL)Mnase::kanMX


title: HCM1_neg_toNQ_251_564_4

description: Library name: HCM1_neg_toNQ_251_564_4

value: MATa his3D0 leu2D0 met15D0 ura3D0 HCM1::HCM1(neg toNQ) SV40 NLS Mnase


title: HOT1_FWY_toL_2_500_2

description: Library name: HOT1_FWY_toL_2_500_2


title: HCM1_hyd_toNQ_251_564_2

description: Library name: HCM1_hyd_toNQ_251_564_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 HCM1::HCM1(hyd toNQ) SV40 NLS Mnase


title: Gr4_59_BS

description: Library name: 25L001132

source_name: Brain stem

value: Brain stem


title: Gr4_86_BS

description: Library name: 25L001131


title: MDA-MB-231-control-3

city: Nanjing

first: Jianjiang

last: Shen

state: Jiangsu

address: HanZhong load 155#

institute: Jiangsu Province Hospital of Chinese Medicine

description: Library name: C3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

organism: Homo sapiens

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: cell line

value: control


title: HCM1_hyd_toNQ_251_564_1

description: Library name: HCM1_hyd_toNQ_251_564_1

value: yeast cells


title: HCM1_NQ_toG_251_564_1

description: Library name: HCM1_NQ_toG_251_564_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HCM1::HCM1(NQ toG) SV40 NLS Mnase

value: budding yeast culture at OD=4


title: HCM1_neg_toNQ_251_564_3

description: Library name: HCM1_neg_toNQ_251_564_3


title: MDA-MB-231-control-1

description: Library name: C1


title: Gr4_58_BS

description: Library name: 25L001130

value: WT


title: MDA-MB-231-control-2

description: Library name: C2


title: HCM1_LIV_toF_251_564_1

description: Library name: HCM1_LIV_toF_251_564_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HCM1::HCM1(LIV toF) SV40 NLS Mnase


title: HCM1_LIV_toF_251_564_2

description: Library name: HCM1_LIV_toF_251_564_2


title: MDA-MB-231 -overexpressing-3

description: Library name: P3

value: tsRNA‑Gly‑5‑0006 overexpressing


title: HCM1_NQ_toG_251_564_2

description: Library name: HCM1_NQ_toG_251_564_2


title: Vhcl_67_Liv

description: Library name: 25L001133

value: Vhcl


title: HCM1_KR_toNQ_251_564_1

description: Library name: HCM1_KR_toNQ_251_564_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HCM1::HCM1(KR toNQ) SV40 NLS Mnase


title: HCM1_KR_toNQ_251_564_2

description: Library name: HCM1_KR_toNQ_251_564_2


title: Gr4_60_BS

description: Library name: 25L001129


title: MDA-MB-231 -overexpressing-1

description: Library name: P1


title: Gr4_89_BS

description: Library name: 25L001128


title: MDA-MB-231 -overexpressing-2

description: Library name: P2


title: HCM1_FWY_toL_251_564_1

description: Library name: HCM1_FWY_toL_251_564_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 HCM1::HCM1(FWY toL) SV40 NLS Mnase


title: GIS1_neg_toNQ_311_700_2

description: Library name: GIS1_neg_toNQ_311_700_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 GIS1::SV40 NLS GIS1(D02 310)(neg toNQ)Mnase


title: LNCaP-resistance cells-H3K27me3-R2

city: guagnzhou

first: Chenwei

last: Wu

address: 南方医科大学高层学生公寓1635

institute: 南方医科大学

description: Library name: sample8

data_processing:
The CUT&Tag reads were mapped to the hg38 human genome using bowtie2 (v2.2.5) with parameters “-X 2000 --very-sensitive-local -no-discordant”. PCR duplicated reads were removed by sambamba (v0.6.6). SAM files were converted to BAM files using samtools (v1.6). MACS2 (v2.2.6) was used to call peaks with -q 0.05. Deeptools (v3.5.2) was used to convert BAM files to Bigwig files and generate the profile plot and heatmap. Homer (v4.11) was used to perform motif analysis. CUT&Tag signal tracks were visualized by IGV (v2.16.2). R package EdgeR (3.22.5) was used to perform differential peaks analysis.
Assembly: hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: CUT&Tag

source_name: prostate

growth_protocol: LNCaP, LNCaP-resistance cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
CUT&Tag was performed using the Hieff NGS® In-Situ DNA Binding Profiling Library Prep Kit for Illumina (Yeasen, 12597ES) according to the manufacturer’s instructions. Briefly, 1x105 of cells were used for the CUT&Tag experiment, cells were collected, washed, incubated with concanavalin A-coated magnetic beads, incubated with primary antibodies, secondary antibodies and cutted by pA-Tn5 transposase to generate DNA fragments.
CUT&Taglibrary amplification, puried DNA was mixed with 2×HiFi Amplification Mix and uniquely barcoded i5 and i7 primers provided by Hieff NGS® Tagment Index Kit for Illumina® (Yeasen, 12416)following PCR program and purified by DNA Selection Beads.

value: prostate

value: LNCaP-resistance

value: prostate cancer cell line

value: resistance cells

value: treat with enzalutamide-H3K27me3


title: GIS1_neg_toNQ_311_700_1

description: Library name: GIS1_neg_toNQ_311_700_1


title: Gr4_87-2_BS

description: Library name: 25L001127

value: Brain stem


title: LNCaP-resistance cells-H3K27me3-R1

address: 南方医科大学高层学生公寓1635

description: Library name: sample7


title: HCM1_FWY_toL_251_564_2

description: Library name: HCM1_FWY_toL_251_564_2


title: GIS1_hyd_toNQ_311_700_2

description: Library name: GIS1_hyd_toNQ_311_700_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 GIS1::SV40 NLS GIS1(D02 310)(hyd toNQ)Mnase


title: Gr4_88_BS

description: Library name: 25L001126


title: LNCaP cells-H3K27me3-R2

address: 南方医科大学高层学生公寓1635

description: Library name: sample6

value: LNCaP


title: GIS1_NQ_toG_311_700_2

description: Library name: GIS1_NQ_toG_311_700_2

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 GIS1::SV40 NLS GIS1(D02 310)(NQ toG)Mnase


title: GIS1_hyd_toNQ_311_700_1

description: Library name: GIS1_hyd_toNQ_311_700_1

value: budding yeast culture at OD=4


title: Gr4_87-1_BS

description: Library name: 25L001125

value: WT


title: LNCaP cells-H3K27me3-R1

address: 南方医科大学高层学生公寓1635

description: Library name: sample5


title: Gr3_rep_6_BS

description: Library name: 25L001123


title: Gr3_4_BS

description: Library name: 25L001122


title: GIS1_NQ_toG_311_700_1

description: Library name: GIS1_NQ_toG_311_700_1


title: LNCaP-resistance cells-H3K27ac-R1

address: 南方医科大学高层学生公寓1635

description: Library name: sample3

value: treat with enzalutamide-H3K27ac


title: GIS1_LIV_toF_311_700_2

description: Library name: GIS1_LIV_toF_311_700_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 GIS1::SV40 NLS GIS1(D02 310)(LIV toF)Mnase


title: GIS1_KR_toNQ_311_700_1

description: Library name: GIS1_KR_toNQ_311_700_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 GIS1::SV40 NLS GIS1(D02 310)(KR toNQ)Mnase


title: LNCaP-resistance cells-H3K27ac-R2

address: 南方医科大学高层学生公寓1635

description: Library name: sample4


title: GIS1_FWY_toL_311_700_2

description: Library name: GIS1_FWY_toL_311_700_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 GIS1::SV40 NLS GIS1(D02 310)(FWY toL)Mnase


title: Gr3_rep_30_BS

description: Library name: 25L001124


title: GIS1_LIV_toF_311_700_1

description: Library name: GIS1_LIV_toF_311_700_1


title: GIS1_KR_toNQ_311_700_2

description: Library name: GIS1_KR_toNQ_311_700_2


title: FKH2_neg_toNQ_451_862_2

description: Library name: FKH2_neg_toNQ_451_862_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(neg toNQ 451 86) SV40 NLS Mnase::kanMX


title: GIS1_FWY_toL_311_700_1

description: Library name: GIS1_FWY_toL_311_700_1


title: LNCaP cells-H3K27ac-R2

address: 南方医科大学高层学生公寓1635

description: Library name: sample2

value: prostate


title: Gr3_32_BS

description: Library name: 25L001121


title: LNCaP cells-H3K27ac-R1

address: 南方医科大学高层学生公寓1635

description: Library name: sample1


title: FKH2_hyd_toNQ_451_862_2

description: Library name: FKH2_hyd_toNQ_451_862_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(hyd toNQ 451 86) SV40 NLS Mnase::kanMX


title: FKH2_hyd_toNQ_451_862_1

description: Library name: FKH2_hyd_toNQ_451_862_1


title: Gr3_31_BS

description: Library name: 25L001119


title: FKH2_aS95_aG76_aN60_aQ68_aF63_1

description: Library name: FKH2_aS95_aG76_aN60_aQ68_aF63_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(S95 G76 N60 Q68 F63) SV40 NLS Mnase::kanMX


title: FKH2_aS95_aG76_aN60_aQ68_aF63_2

description: Library name: FKH2_aS95_aG76_aN60_aQ68_aF63_2


title: FKH2_neg_toNQ_451_862_1

description: Library name: FKH2_neg_toNQ_451_862_1


title: K206R3

city: Guangzhou

first: Weihao

last: Li

address: 651 Dongfeng Road east

institute: Sun yat-sen university cancer center

description:
Library name: K206R3
Column name in RNA-Seq_Diff_information.xlsx: K206R2

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data.
HISAT2 was used to align the clean reads to the human reference genome hg19 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DE sequencing read counts as input. The Benjamini-Hochberg multiple test correction method was enabled.
Differentially expressed genes were chosen according to the criteria of p-value < 0.05.
Assembly: hg19
Supplementary files format and content: xlsx file includes raw counts and FPKM values for each Sample

growth_protocol: HCT116 colon cancer cells were cultured in complete DMEM, supplemented with 100 μg/mL streptomycin, 100 IU/mL penicillin, and 10% fetal bovine serum at 37 ℃ in 5% CO2

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). The RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0.
Library was generated using the PrimeScript RT reagent kit (TaKaRa Bio, RR037A) according to the manufacturer’s instructions. The cDNA was used for qPCR using SYBR Green PCR master mix (Life Technologies) on a CFX96 real-time PCR detection system (Bio-Rad).

value: Human colon cancer cells

value: PKM2 K206R mutant


title: Gr3_29_BS

description: Library name: 25L001118

value: Brain stem


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(S74 T55 N110 Q61 D16 E14 Y67) SV40 NLS Mnase::kanMX


title: K206R2

description:
Library name: K206R2
Column name in RNA-Seq_Diff_information.xlsx: K206R2


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(S74 T55 N110 Q61 D16 E14 L67) SV40 NLS Mnase::kanMX


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_1

value: yeast cells


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_2


title: K206R1

description:
Library name: K206R1
Column name in RNA-Seq_Diff_information.xlsx: K206R1


title: WT3

description:
Library name: WT3
Column name in RNA-Seq_Diff_information.xlsx: WT3

value: wildtype


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_1

value: budding yeast culture at OD=4


title: Gr3_6_BS

description: Library name: 25L001117

value: WT


title: Gr3_30_BS

description: Library name: 25L001120


title: Gr2_4_BS

description: Library name: 25L001116


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(S74 T55 N110 Q61 D16 E14 L130) SV40 NLS Mnase::kanMX


title: WT2

description:
Library name: WT2
Column name in RNA-Seq_Diff_information.xlsx: WT2


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_1


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_2


title: WT1

description:
Library name: WT1
Column name in RNA-Seq_Diff_information.xlsx: WT1


title: Gr2_3-2_BS

description: Library name: 25L001115


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase::kanMX


title: Anti-PKM2

description: Library name: Anti-PKM2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Nocaseq output. CUT&Tag reads were trimmed from 3' end until the final base had quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20bp.
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie v1.1.2, Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS V2.1.0 with the significance cut-off q-value <=0.01. bigWig files were generated using the genomicRanges R package, Score represents the nomalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS V2 with default settings.
Assembly: hg38
Supplementary files format and content: peaks.annotation.xlsx
Library strategy: CUT&Tag

extract_protocol:
Cells were washed twice gently with wash buffer. 10 μL Concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at RT for 10 min.
Remove unbound supernatant and resuspended bead-bound cells with dig wash buffer and a 1:50 dilution of primary antibody or IgG control antibody incubated on a rotating platform overnight at 4°C. The primary antibody was removed using a magnet stand. The secondary antibody was diluted 1:100 in dig wash buffer and cells were incubated for 60 min. Cells were washed using the magnet stand 2-3 times in dig wash buffer. A 1:100 dilution of pA-Tn5 adapter complex was prepared in dig-med buffer (0.01% Digitonin; 20 mm HEPES pH 7.5; 300 mm NaCl; 0.5 mm Spermidine; 1 × Protease inhibitor cocktail) and incubated with cells for 1 h. Cells were washed 2-3 × for 5 min in 1 mL Dig-med buffer. Then cells were resuspended in a tagmentation buffer (10 mm MgCl2 in Dig-med Buffer) and incubated at 37°C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. Purified DNA fragments were constructed and added to libraries, amplified, and sequenced.


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_2


title: Gr2_2_BS

description: Library name: 25L001114


title: Anti-FOSL1

description: Library name: Anti-FOSL1


description: Library name: FKH2_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_1


description: Library name: FKH2_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(S114 G89 N43 Q53 D14 E15 F63) SV40 NLS Mnase::kanMX


title: Gr2_58_BS

description: Library name: 25L001112


title: FKH2_NQ_toG_451_862_2

description: Library name: FKH2_NQ_toG_451_862_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(NQ toG 451 86) SV40 NLS Mnase::kanMX


title: Gr2_57_BS

description: Library name: 25L001111


title: Anti-H3K27Ac_PKM2 K206R

description: Library name: Anti-H3K27Ac_PKM2 K206R


title: FKH2_NQ_toG_451_862_1

description: Library name: FKH2_NQ_toG_451_862_1


title: K206R_S3_L001

description: Library name: K206R

data_processing:
Amplified ATAC-seq libraries were then size selected with AMPure XP Reagent (Beckman Coulter) and sequenced on HiSeqX.
All cell line based ATAC-seq experiments were performed with at least two biological replicates.
Differential analysis between ATAC-seq peaks was performed using DiffBind and the heatmaps were plotted using deepTools.
TF Footprinting and differential TF binding analysis was performed using TOBIAS114 where volcano plots were generated using R.
Assembly: hg38
Supplementary files format and content: peaks.annotation.xlsx

extract_protocol:
Cells were lysed in ATAC Resuspension buffer containing NP40, TWEEN-20 and Digitonin. While clinical samples were disrupted and homogenised with TissueRuptor II (Qiagen) and nuclei were isolated through Iodixanol density gradient centrifugation.
Lysed cells or nuclei were transposed in a transposition mix containing digitonin and Tn5 transposase for 30 min at 37℃ while shaking at 1000 rpm. The transposition reaction was then cleaned up with DNA Clean and Concentrator kit (Zymo), followed by amplification through PCR with Nextera DNA CD Indexes (Illumina) and NEBNext Ultra II Q5 Master mix (NEB).


title: Gr2_88_BS

description: Library name: 25L001110


description: Library name: FKH2_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_1


title: FKH2_KR_toNQ_451_862_2

description: Library name: FKH2_KR_toNQ_451_862_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(KR toNQ 451 86) SV40 NLS Mnase::kanMX


title: FKH2_LIV_toF_451_862_1

description: Library name: FKH2_LIV_toF_451_862_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(LIV toF 451 86) SV40 NLS Mnase::kanMX


title: FKH2_KR_toNQ_451_862_1

description: Library name: FKH2_KR_toNQ_451_862_1


title: FKH2_LIV_toF_451_862_2

description: Library name: FKH2_LIV_toF_451_862_2


title: Gr2_86_BS

description: Library name: 25L001109


title: FKH2_FWY_toL_451_862_1

description: Library name: FKH2_FWY_toL_451_862_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 FKH2::FKH2(FWY toL 451 86) SV40 NLS Mnase::kanMX


title: Gr2_3-1_BS

description: Library name: 25L001113


title: WT_S4_L001

description: Library name: WT


title: DOT6_neg_toNQ_121_670_6

description: Library name: DOT6_neg_toNQ_121_670_6

value: MATa his3D0 leu2D0 met15D0 ura3D0 DOT6::DOT6(neg toNQ) SV40 NLS Mnase


title: Anti-H3K27Ac_PKM2 WT

description: Library name: Anti-H3K27Ac_PKM2 WT

value: Human colon cancer cells


title: Vhcl_69_BS

description: Library name: 25L001108

value: Vhcl


title: Vhcl_68_BS

description: Library name: 25L001107

value: Brain stem


title: FKH2_FWY_toL_451_862_2

description: Library name: FKH2_FWY_toL_451_862_2


title: DOT6_neg_toNQ_121_670_5

description: Library name: DOT6_neg_toNQ_121_670_5


title: DOT6_NQ_toG_121_670_2

description: Library name: DOT6_NQ_toG_121_670_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 DOT6::DOT6(NQ toG) SV40 NLS Mnase


title: DOT6_NQ_toG_121_670_1

description: Library name: DOT6_NQ_toG_121_670_1


title: CM TKI + Yoda 7 Day 2

city: Palo Alto

first: Nazish

last: Sayed

state: CA

address: 240 Pasteur Drive, 3500 BMI

institute: Stanford University

description: Library name: Sample 12

data_processing:
RNAseq reads are trimmed using trimmomatic and HISAT2 tool is used for alignment
RPKM values are calculated using excel and read counts using featureCounts
differential analysis is perfomed using deseq2
Assembly: hg38
Supplementary files format and content: raw counts

source_name: iPSC

growth_protocol: Cultured iPSC-ECs were exposed to VEGFR-TKIs (Apatinib, Axitinib, Cabozantinib, Lenvatinib, Pazopanib, Ponatinib, Regorafenib, Sorafenib, Sunitinib, Vandetanib) at 0 to 100 μM for 24 h to assess cell viability using CellTiter-Glo Viability Assay (Promega). For gene expression assays, iPSC-ECs were exposed to Sorafenib, Ponatinib, and Sunitinib at 0, 0.1, 0.3, and 1 μM for 1d, 3d, and 7d.

extract_protocol:
Total RNA was extracted from COs using RNeasy plus mini-Kit (Qiagen) as per manufacturer’s instructions
Dyna Oligo(dT) beads (Life technologies) were used to purify mRNA and then fragmentated to 200-300 bp fragments to prepare index-tagged paired-end cDNA libraries as previously descibed7. Illumina sequencing adapters were ligated to cDNA fragments through PCR and sequencing was performed on Novaseq 6000. Obtained fastq (paired end) sequencing reads were mapped to human reference genome (hg38) using STAR (2.5.4b), and quantified raw counts and RPKM values were annotated using Homer (analyzeRepeats.pl). Heatmaps were generated through normalized DESEQ2 counts. Gene ontology analysis was conducted using R package.

value: iPSC

value: iPSC-CM, iPSC-EC

value: control

value: TKI


title: Vhcl_61_BS

description: Library name: 25L001106

value: WT


title: Vhcl_60_BS

description: Library name: 25L001105


title: CM TKI 7 Day 2

description: Library name: Sample 10


title: DOT6_FWY_toL_121_670_1

description: Library name: DOT6_FWY_toL_121_670_1

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 DOT6::DOT6(FWY toL) SV40 NLS Mnase

value: budding yeast culture at OD=4


title: CRZ1_neg_toNQ_2_500_1

description: Library name: CRZ1_neg_toNQ_2_500_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::SV40 NLS CRZ1(neg toNQ)Mnase


title: CM TKI 7 Day 1

description: Library name: Sample 9


title: DOT6_FWY_toL_121_670_2

description: Library name: DOT6_FWY_toL_121_670_2


title: CRZ1_neg_toNQ_2_500_2

description: Library name: CRZ1_neg_toNQ_2_500_2


title: CM TKI + Yoda 7 Day 1

description: Library name: Sample 11


title: CMEC TKI + Yoda 7 Day 2

description: Library name: Sample 8

value: Mock


title: CMEC TKI + Yoda 7 Day 1

description: Library name: Sample 7


title: Vhcl_59_BS

description: Library name: 25L001103


title: CRZ1_aS95_aG76_aN60_aQ68_aF63_3

description: Library name: CRZ1_aS95_aG76_aN60_aQ68_aF63_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::CRZ1(S95 G76 N60 Q68 F63) SV40 NLS Mnase


title: Vhcl_66_BS

description: Library name: 25L001102


title: CMEC TKI 7 Day 2

description: Library name: Sample 6


title: CRZ1_hyd_toNQ_2_500_1

description: Library name: CRZ1_hyd_toNQ_2_500_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::SV40 NLS CRZ1(hyd toNQ)Mnase


title: CRZ1_aS95_aG76_aN60_aQ68_aF63_2

description: Library name: CRZ1_aS95_aG76_aN60_aQ68_aF63_2


title: Vhcl_67_BS

description: Library name: 25L001101


title: CRZ1_hyd_toNQ_2_500_2

description: Library name: CRZ1_hyd_toNQ_2_500_2


title: CMEC TKI 7 Day 1

description: Library name: Sample 5


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::CRZ1(S74 T55 N110 Q61 D16 E14 Y67) SV40 NLS Mnase


title: Vhcl_85_BS

description: Library name: 25L001104


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::CRZ1(S74 T55 N110 Q61 D16 E14 L67) SV40 NLS Mnase


title: Pretreatment whole blood RNA-seq, Sample51

city: tsukuba

first: Satoka

last: Kinase

address: tenoudai 1-1-1

country: Japan

institute: University of tsukuba

description: Library name: Sample51

data_processing:
Raw sequencing reads were processed using standard RNA-seq analysis pipelines. Reads were quality-controlled, aligned to the human reference genome, and gene-level counts were generated.
Assembly: Human reference genome GRCh38 (hg38)
Supplementary files format and content: GEO_raw_counts_SampleID.csv (Processed gene expression count matrices containing raw read counts for all samples.)

source_name: Whole blood

growth_protocol: Peripheral blood was collected from patients prior to treatment.

extract_protocol:
Total RNA from whole-blood samples was isolated using a PAXgene Blood RNA kit (PreAnalytix) according to the manufacturer’s instructions. Globin RNA was removed from total RNA using a GLOBINclear-Human Kit (Thermo Fisher Scientific). For RNA sequencing, 500 ng total RNA were rRNA depleted using an NEBNext rRNA Depletion Kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s instructions. Library preparation was performed using an NEBNext Ultra-Directional RNA Library Prep Kit (New England Biolabs). Libraries were validated via Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to determine size distribution and concentration. Validated libraries were then sequenced at Tsukuba i-Laboratory LLP (Tsukuba, Japan) on a NextSeq500 (Illumina, San Diego, CA, USA) with the paired-end, 36-base read option.
RNA-seq libraries were prepared using a poly(A)-selected library preparation kit and sequenced on an Illumina platform.

treatment_protocol: No treatment was applied prior to sample collection.

value: Whole blood

tag: disease state

value: metastatic renal cell carcinoma

value: nivolumab plus ipilimumab

tag: timepoint

value: pretreatment

tag: irae status

value: Yes


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_3


title: CMEC Control 2

description: Library name: Sample 4

value: iPSC

value: iPSC-CM

value: control


title: Gr4_59_Hy

description: Library name: 25L001100

source_name: Hypothalamus

value: Hypothalamus

value: WT


title: Pretreatment whole blood RNA-seq, Sample49

description: Library name: Sample49

value: No


title: CMEC Control 1

description: Library name: Sample 3


title: Gr4_86_Hy

description: Library name: 25L001099


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_2

value: yeast cells

value: budding yeast culture at OD=4


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_1


title: Pretreatment whole blood RNA-seq, Sample48

description: Library name: Sample48


title: CM Control 2

description: Library name: Sample 2

value: Mock


title: Gr4_58_Hy

description: Library name: 25L001098


title: Gr4_89_Hy

description: Library name: 25L001096


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::CRZ1(S74 T55 N110 Q61 D16 E14 L130) SV40 NLS Mnase


title: Gr4_60_Hy

description: Library name: 25L001097


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_2


title: Pretreatment whole blood RNA-seq, Sample47

description: Library name: Sample47


title: Pretreatment whole blood RNA-seq, Sample45

description: Library name: Sample45


title: A. suci FSLR14 0023 D3 Rep 3

city: ITHACA

first: Katerina

last: Roth

state: New York

address: 411 Tower rd

institute: Cornell University

description:
Library name: KR43c_0023_C_D3
0023 D3 Rep 3

data_processing:
Adapter and low-quality bases were trimmed with fastp v.0.23.4. Using bowtie2 v.2.5.1 with relaxed criteria, trimmed reads were aligned to the reference genome of A. acidoterrestris ATCC 3922. HTSeq-counts v2.0.9 was used to generate read counts per gene
Assembly: CP080467.1
Supplementary files format and content: tab delimiited text file contains raw counts for each sample

organism: Alicyclobacillus suci

source_name: Bacteria

extract_protocol:
After three days of incubation, 2 mL of the inoculated juice of each strain replicate was placed into a microcentrifuge tube and spun down. The supernatant was discarded and the remaining pellet was washed three times with PBS. RNA extraction was performed using the ZYMO Quick-DNA/DNA Miniprep Plus kit (Zymo Research; Irvine, CA) as directed, with the described DNASE I step included.
UDI-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with the HS DNA Qubit assay (Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Agilent) prior to pooling.

value: Bacteria


title: Pretreatment whole blood RNA-seq, Sample50

description: Library name: Sample50


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_1


title: CM Control 1

description: Library name: Sample 1


title: A. suci FSLR140023 D3 Rep 2

description:
Library name: KR31c_0023_B_D3
0023 D3 Rep 2


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::CRZ1(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase


description: Library name: CRZ1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_1


title: Pretreatment whole blood RNA-seq, Sample46

description: Library name: Sample46

value: Whole blood


title: A. suci FSLR140023 D3 Rep 1

description:
Library name: KR11c_0023_P_D3
0023 D3 Rep 1


title: Gr4_88_Hy

description: Library name: 25L001094


title: Gr4_87-1_Hy

description: Library name: 25L001093


title: Gr4_87-2_Hy

description: Library name: 25L001095


description: Library name: CRZ1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::CRZ1(S114 G89 N43 Q53 D14 E15 F63) SV40 NLS Mnase


title: Pretreatment whole blood RNA-seq, Sample43

description: Library name: Sample43

value: metastatic renal cell carcinoma

value: nivolumab plus ipilimumab


title: Pretreatment whole blood RNA-seq, Sample42

description: Library name: Sample42

value: pretreatment


title: A. suci FSLR140049 D3 Rep 2

description:
Library name: KR20c_0049_A_D3
0049 D3 Rep 2


title: Pretreatment whole blood RNA-seq, Sample44

description: Library name: Sample44


title: Gr3_rep_30_Hy

description: Library name: 25L001092


title: Gr3_rep_31_Hy

description: Library name: 25L001091


description: Library name: CRZ1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_2


title: A. suci FSLR140049 D3 Rep 3

description:
Library name: KR30c_0049_B_D3
0049 D3 Rep 3


title: Pretreatment whole blood RNA-seq, Sample40

description: Library name: Sample40


title: Gr3_32_Hy

description: Library name: 25L001089


title: Pretreatment whole blood RNA-seq, Sample41

description: Library name: Sample41


title: Gr3_4_Hy

description: Library name: 25L001090


title: Pretreatment whole blood RNA-seq, Sample39

description: Library name: Sample39

value: Yes


title: A. suci FSLR140049 D3 Rep 1

description:
Library name: KR10c_0049_P_D3
0049 D3 Rep 1


title: CRZ1_NQ_toG_2_500_2

description: Library name: CRZ1_NQ_toG_2_500_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::SV40 NLS CRZ1(NQ toG)Mnase


description: Library name: CRZ1_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_1


title: CRZ1_NQ_toG_2_500_1

description: Library name: CRZ1_NQ_toG_2_500_1


title: A. suci FSLR140051 D3 Rep 2

description:
Library name: KR19c_0051_A_D3
0051 D3 Rep 2


title: Gr3_30_Hy

description: Library name: 25L001088


title: A. suci FSLR140051 D3 Rep 1

description:
Library name: KR9c_0051_P_D3
0051 D3 Rep 1


title: Pretreatment whole blood RNA-seq, Sample38

description: Library name: Sample38


title: CRZ1_LIV_toF_2_500_4

description: Library name: CRZ1_LIV_toF_2_500_4

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::SV40 NLS CRZ1(LIV toF)Mnase


title: Pretreatment whole blood RNA-seq, Sample36

description: Library name: Sample36


title: A. suci FSLR140051 D3 Rep 3

description:
Library name: KR41c_0051_C_D3
0051 D3 Rep 3


title: CRZ1_KR_toNQ_2_500_2

description: Library name: CRZ1_KR_toNQ_2_500_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::SV40 NLS CRZ1(KR toNQ)Mnase


title: Pretreatment whole blood RNA-seq, Sample35

description: Library name: Sample35


title: Gr3_31_Hy

description: Library name: 25L001087

value: Hypothalamus

value: WT


title: Gr3_6_Hy

description: Library name: 25L001085


title: Pretreatment whole blood RNA-seq, Sample37

description: Library name: Sample37


title: Gr3_29_Hy

description: Library name: 25L001086


title: CRZ1_FWY_toL_2_500_4

description: Library name: CRZ1_FWY_toL_2_500_4

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 CRZ1::SV40 NLS CRZ1(FWY toL)Mnase


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 early_Day 7 _Rep-3

type: RNA

city: Houston

first: Sebastian

last: Wurster

state: Texas

address: 6565 MD Anderson Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing: Expression of immune-related genes was assessed using the 785-plex nCounter Immune Exhaustion panel (NanoString Technologies) according to the manufacturer’s instructions. Data was analyzed using the nSolver Analysis Software (NanoString Technologies), with background thresholding to the median of negative controls and normalization to the panel’s 12 housekeeping genes (geometric mean).

source_name: Lung tissue

growth_protocol: Eight-week-old female BALB/c mice were immunosuppressed with cyclophosphamide (Long Grove Pharmaceuticals; 250 mg/kg on day -4, 150 mg/kg on day -1, and 100 mg/kg twice weekly thereafter). On day 0, mice were infected intranasally with 50,000 spores of Rhizopus arrhizus (clinical isolate Ra-749), 50,000 conidia of Aspergillus fumigatus (reference strain Af-293), or 150,000 spores of Fusarium solani (clinical isolate Fs-001).

extract_protocol: Lungs were weighed and flash-frozen in 1 mL RNAprotect Tissue Reagent (Qiagen). For RNA isolation, lungs were thawed and homogenized in 1 mL RLT Buffer (Qiagen) using a Mini Bead-Beater (Biospec Products) and 3-mm glass beads (Sigma-Aldrich). Total RNA was isolated from 30 mg of homogenized tissue using the RNeasy Tissue Kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. RNA concentration, purity, and integrity were analyzed using a NanoDrop OneC spectrophotometer (Thermo Fisher Scientific), Qubit 3.0 fluorometer (Thermo Fisher Scientific), and TapeStation 4200 (Agilent Technologies).

treatment_protocol: For therapeutic studies in the IPM model, treatment with ISAV was initiated on day 3 post-infection (64 mg/kg by oral gavage twice daily for 5 days), when the mice had developed significant infection-induced distress. Additionally, mice received 0.25 mg/kg α-PD-L1 (Leinco Technologies, #P371) or the corresponding IgG2b isotype antibody (Leinco Technologies, #I-1034) intraperitoneally either on days 3+5 (early) or days 6+8 (late).

tag: infection

value: Rhizopus arrhizus

tag: therapy

value: Isavuconazole + anti-PD-L1 early

tag: time

value: Day 7


title: CRZ1_LIV_toF_2_500_3

description: Library name: CRZ1_LIV_toF_2_500_3

value: budding yeast culture at OD=4


title: Pretreatment whole blood RNA-seq, Sample34

description: Library name: Sample34

value: Whole blood

value: No


title: CRZ1_FWY_toL_2_500_3

description: Library name: CRZ1_FWY_toL_2_500_3


title: Gr2_3-2_Hy

description: Library name: 25L001083


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 early_Day 7 _Rep-1


title: Pretreatment whole blood RNA-seq, Sample32

description: Library name: Sample32

value: metastatic renal cell carcinoma


title: Gr2_3-1_Hy

description: Library name: 25L001081


title: Pretreatment whole blood RNA-seq, Sample31

description: Library name: Sample31

value: nivolumab plus ipilimumab


title: Gr2_4_Hy

description: Library name: 25L001084


title: Gr2_2_Hy

description: Library name: 25L001082


title: Rhizopus arrhizus_Isavuconazole + isotype _Day 7 _Rep-3

value: Isavuconazole + isotype


title: BAS1_scramble_251_811_5

description: Library name: BAS1_scramble_251_811_5

value: MATa his3D0 leu2D0 met15D0 ura3D0 BAS1::BAS1(scramble) SV40 NLS Mnase


title: Pretreatment whole blood RNA-seq, Sample33

description: Library name: Sample33

value: pretreatment


title: CRZ1_KR_toNQ_2_500_1

description: Library name: CRZ1_KR_toNQ_2_500_1


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 early_Day 7 _Rep-2


title: BAS1_scramble_251_811_4

description: Library name: BAS1_scramble_251_811_4


title: Rhizopus arrhizus_Isavuconazole + isotype _Day 7 _Rep-1


title: Gr2_58_Hy

description: Library name: 25L001080


title: Gr2_57_Hy

description: Library name: 25L001079


title: Rhizopus arrhizus_Isavuconazole + isotype _Day 7 _Rep-2


title: Pretreatment whole blood RNA-seq, Sample29

description: Library name: Sample29


title: Fusarium solani_None_Day 4_Rep-3

value: Fusarium solani

value: Day 4


title: Fusarium solani_None_Day 4_Rep-2


title: Gr2_88_Hy

description: Library name: 25L001078

value: Hypothalamus


title: BAS1_neg_toNQ_251_811_1

description: Library name: BAS1_neg_toNQ_251_811_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 BAS1::BAS1(neg toNQ) SV40 NLS Mnase


title: Pretreatment whole blood RNA-seq, Sample28

description: Library name: Sample28


title: Pretreatment whole blood RNA-seq, Sample30

description: Library name: Sample30


title: BAS1_hyd_toNQ_251_811_2

description: Library name: BAS1_hyd_toNQ_251_811_2

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 BAS1::BAS1(hyd toNQ) SV40 NLS Mnase


title: BAS1_neg_toNQ_251_811_2

description: Library name: BAS1_neg_toNQ_251_811_2


title: BAS1_hyd_toNQ_251_811_1

description: Library name: BAS1_hyd_toNQ_251_811_1


title: Fusarium solani_None_Day 4_Rep-1


title: Gr2_86_Hy

description: Library name: 25L001077

value: WT


title: Vhcl_68_Hy

description: Library name: 25L001075

value: Vhcl


title: Aspergillus fumigatus_None_Day 4_Rep-4

value: Aspergillus fumigatus


title: Aspergillus fumigatus_None_Day 4_Rep-2


title: BAS1_LIV_toF_251_811_2

description: Library name: BAS1_LIV_toF_251_811_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 BAS1::BAS1(LIV toF) SV40 NLS Mnase

value: budding yeast culture at OD=4


title: Aspergillus fumigatus_None_Day 4_Rep-3


title: Pretreatment whole blood RNA-seq, Sample27

description: Library name: Sample27

value: Whole blood

value: No


title: Vhcl_69_Hy

description: Library name: 25L001076


title: BAS1_LIV_toF_251_811_1

description: Library name: BAS1_LIV_toF_251_811_1


title: Pretreatment whole blood RNA-seq, Sample24

description: Library name: Sample24

value: metastatic renal cell carcinoma

value: nivolumab plus ipilimumab

value: Yes


title: Pretreatment whole blood RNA-seq, Sample26

description: Library name: Sample26

value: pretreatment


title: Vhcl_61_Hy

description: Library name: 25L001074


title: Pretreatment whole blood RNA-seq, Sample23

description: Library name: Sample23


title: Vhcl_60_Hy

description: Library name: 25L001073


title: Aspergillus fumigatus_None_Day 4_Rep-1


title: BAS1_KR_toNQ_251_811_2

description: Library name: BAS1_KR_toNQ_251_811_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 BAS1::BAS1(KR toNQ) SV40 NLS Mnase


title: Uninfected_None_Day 4_Rep-3b

value: Uninfected

value: Day 4


title: Pretreatment whole blood RNA-seq, Sample22

description: Library name: Sample22


title: Pretreatment whole blood RNA-seq, Sample21

description: Library name: Sample21


title: BAS1_KR_toNQ_251_811_1

description: Library name: BAS1_KR_toNQ_251_811_1


title: Vhcl_59_Hy

description: Library name: 25L001071

value: Hypothalamus


title: BAS1_FWY_toL_251_811_1

description: Library name: BAS1_FWY_toL_251_811_1

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 BAS1::BAS1(FWY toL) SV40 NLS Mnase


title: Vhcl_85_Hy

description: Library name: 25L001072

value: WT


title: Uninfected_None_Day 4_Rep-1b


title: Uninfected_None_Day 4_Rep-2b


title: Pretreatment whole blood RNA-seq, Sample19

description: Library name: Sample19


title: Rhizopus arrhizus_Isavuconazole + isotype _Day 10_Rep-3

value: Rhizopus arrhizus

value: Isavuconazole + isotype

value: Day 10


title: Pretreatment whole blood RNA-seq, Sample18

description: Library name: Sample18


title: ASH1_NQ_toG_2_400_2

description: Library name: ASH1_NQ_toG_2_400_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 ASH1::SV40 NLS SH1(NQ toG)Mnase

value: budding yeast culture at OD=4


title: ASH1_NQ_toG_2_400_1

description: Library name: ASH1_NQ_toG_2_400_1


title: scRNAseq-Ovary-H6

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

description:
Library name: SAMPLES3
10XGenomics

data_processing:
Subsequently, quality control and read counting of Ensembl genes were conducted using the cellranger software with default parameters (v2.1.0). Normalization, dimensionality reduction, and clustering of single cells were also accomplished using cellranger. To reduce dimensionality, the top ten principal components were utilized, and t-Distributed Stochastic Neighbor Embedding (tSNE) was employed. Cell clustering was achieved through a graph-based clustering algorithm, involving the construction of a sparse nearest-neighbor graph followed by Louvain Modularity Optimization. Differential expression analysis between cell groups was performed using the Seurat-Bimod statistical test with significance set at FDR <= 0.05 and |log2 Fold Change| >= 1.5.
Assembly: Mouse mm10
Supplementary files format and content: cell expression values

source_name: Ovary

extract_protocol:
Ovaries were collected at 0 (H0), 1 (H1), and 6 hours (H6) post-hCG injection for single-cell RNA-seq.
Mouse ovaries were collected at H0, H1 and H6 for single-cell RNA-seq, which was conducted by Yingzi Gene (Wuhan, China). Initially, the cell number and viability were assessed, followed by loading cells onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl. The protocol included the generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification, and library construction per the manufacturer's instructions. Library quantification was performed using Qubit before pooling, and the final library pool was sequenced on the Illumina Nova6000 platform using 150-base-pair paired-end reads.

value: Ovary


title: BAS1_FWY_toL_251_811_2

description: Library name: BAS1_FWY_toL_251_811_2


title: Pretreatment whole blood RNA-seq, Sample20

description: Library name: Sample20

value: Whole blood

value: metastatic renal cell carcinoma


title: Pretreatment whole blood RNA-seq, Sample17

description: Library name: Sample17

value: nivolumab plus ipilimumab

value: Yes


title: Vhcl_67_Hy

description: Library name: 25L001069

value: Vhcl


title: ACE2_shift_LIVFWY_2_550_2

description: Library name: ACE2_shift_LIVFWY_2_550_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(shift LIVFWY)Mnase::kanMX


title: Rhizopus arrhizus_Isavuconazole + isotype _Day 10_Rep-2


title: Rhizopus arrhizus_Isavuconazole + isotype _Day 10_Rep-1


title: scRNAseq-Ovary-H1

description:
Library name: SAMPLES2
10XGenomics


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 late_Day 10_Rep-2

value: Isavuconazole + anti-PD-L1 late


title: Pretreatment whole blood RNA-seq, Sample16

description: Library name: Sample16

value: pretreatment


title: ACE2_shift_LIVFWY_2_550_1

description: Library name: ACE2_shift_LIVFWY_2_550_1

value: yeast cells


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 late_Day 10_Rep-3


title: ACE2_neg_toNQ_2_550_6

description: Library name: ACE2_neg_toNQ_2_550_6

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(neg toNQ)Mnase::kanMX


title: Pretreatment whole blood RNA-seq, Sample15

description: Library name: Sample15


title: scRNAseq-Ovary-H0

description:
Library name: SAMPLES1
10XGenomics


title: Liver-PENaF8-10 months

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

description: Library name: Foie-PENaF8

data_processing:
Illumina fastq files was download from Novogene server
Check sum and fastQC was use on each sample
Alignement on reference genome by Hisat2
Count SAM file by HTSeq-count
Assembly: mm10
Supplementary files format and content: Tabulated Separated Value text file, with Ensembl_ID, Gene_name and one sample by column with the raw count.

source_name: liver

growth_protocol: Mice were housed in specific pathogen-free conditions, in nest-enriched polysulfone cages, maintained at 22°C / 50% humidity and under a 12:12 h light-dark cycle, fed a standard diet (A03–10; Safe-diets), adhering to the ARRIVE guidelines. The drinking water was obtained from tap water treated by the Avoidy Science system (Edstrom, Waterford, USA) through a sequential treatment of 2 filtrations (1 micron sediment filter and activated carbon filter) and a reverse osmosis pump passage.

extract_protocol:
Total RNA was isolated from livers using a silica membrane following manufacturer’s instructions (RNeasy Mini Kit, Qiagen). One microgram of total RNA quantiﬁed using a Qubit ﬂuorometers (Thermo Fisher Scientiﬁc).
RNA purity was assessed using the NanodropTM spectrophotometer. mRNA sequencing has been performed by iGenSeq core facility (ICM, Paris, France).

treatment_protocol: A total of four groups of mice were set up: control group (no exposure to the substances, exposure limited to 0.01% dimethyl sulfoxide, DMSO, used as a solvent), ED group (exposure to a mixture of 15 EDs; Table 1) with doses below the TDIs for most substances), 1 mM NaF group (20 ppm), and the ED mix + 1 mM NaF group (named ED NaF). All the animals were orally exposed via drinking water 15 days before the mating, females were exposed during the gestation and lactation (sacrificed after weaning of pups), and pups were exposed until the sacrifice at 30 days and 10 months after birth.

value: liver

value: WT

value: NaF + Mix of 15 endocrines disruptor

value: 10 months


title: Liver-PENaF6-10 months

description: Library name: Foie-PENaF6


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 late_Day 10_Rep-1

value: Rhizopus arrhizus

value: Day 10


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 early_Day 10_Rep-3

value: Isavuconazole + anti-PD-L1 early


title: ACE2_hyd_toNQ_2_550_1

description: Library name: ACE2_hyd_toNQ_2_550_1

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(hyd toNQ)Mnase::kanMX

value: budding yeast culture at OD=4


title: Pretreatment whole blood RNA-seq, Sample13

description: Library name: Sample13

value: Whole blood

value: metastatic renal cell carcinoma

value: nivolumab plus ipilimumab


title: ACE2_hyd_toNQ_2_550_2

description: Library name: ACE2_hyd_toNQ_2_550_2


title: Liver-PENaF5-10 months

description: Library name: Foie-PENaF5


title: ACE2_neg_toNQ_2_550_5

description: Library name: ACE2_neg_toNQ_2_550_5


title: Pretreatment whole blood RNA-seq, Sample12

description: Library name: Sample12

value: Yes


title: ACE2_aS95_aG76_aN60_aQ68_aF63_3

description: Library name: ACE2_aS95_aG76_aN60_aQ68_aF63_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::ACE2(S95 G76 N60 Q68 F63) SV40 NLS Mnase::kanMX


title: Liver-PENaF4-10 months

description: Library name: Foie-PENaF4


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 early_Day 10_Rep-2


title: Liver-PENaF1-10 months

description: Library name: Foie-PENaF1


title: Liver-PENaF2-10 months

description: Library name: Foie-PENaF2


title: Rhizopus arrhizus_Isavuconazole + anti-PD-L1 early_Day 10_Rep-1


title: Pretreatment whole blood RNA-seq, Sample10

description: Library name: Sample10

value: pretreatment


title: ACE2_aS95_aG76_aN60_aQ68_aF63_2

description: Library name: ACE2_aS95_aG76_aN60_aQ68_aF63_2

value: yeast cells


title: Pretreatment whole blood RNA-seq, Sample14

description: Library name: Sample14


title: Uninfected_None_Day 10_Rep-3

value: Uninfected


title: Uninfected_None_Day 10_Rep-2


title: Pretreatment whole blood RNA-seq, Sample09

description: Library name: Sample09


title: ACE2_aS95_aG76_aN60_aQ68_aF63_1

description: Library name: ACE2_aS95_aG76_aN60_aQ68_aF63_1


title: Pretreatment whole blood RNA-seq, Sample08

description: Library name: Sample08


title: Liver-PE5-10 months

description: Library name: FoiePE5

value: liver

value: Mix of 15 endocrines disruptor


title: Pretreatment whole blood RNA-seq, Sample11

description: Library name: Sample11


title: Rhizopus arrhizus_None_Day 4_Rep-3

value: Day 4


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::ACE2(S74 T55 N110 Q61 D16 E14 Y67) SV40 NLS Mnase::kanMX


title: Uninfected_None_Day 10_Rep-1


title: Liver-PE4-10 months

description: Library name: FoiePE4

value: WT

value: 10 months


title: Pretreatment whole blood RNA-seq, Sample07

description: Library name: Sample07


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aY67_1


title: Rhizopus arrhizus_None_Day 4_Rep-2

value: Rhizopus arrhizus


title: Liver-PE7-10 months

description: Library name: FoiePE7


title: Liver-PE3-10 months

description: Library name: FoiePE3


title: Rhizopus arrhizus_None_Day 4_Rep-1


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::ACE2(S74 T55 N110 Q61 D16 E14 L130) SV40 NLS Mnase::kanMX


title: Pretreatment whole blood RNA-seq, Sample05

description: Library name: Sample05


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aL67_3

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::ACE2(S74 T55 N110 Q61 D16 E14 L67) SV40 NLS Mnase::kanMX

value: budding yeast culture at OD=4


title: Pretreatment whole blood RNA-seq, Sample06

description: Library name: Sample06

value: Whole blood

value: metastatic renal cell carcinoma


title: Liver-PE2-10 months

description: Library name: FoiePE2


title: Pretreatment whole blood RNA-seq, Sample04

description: Library name: Sample04

value: nivolumab plus ipilimumab

value: Yes


title: Liver-PE1-10 months

description: Library name: FoiePE1


title: Uninfected_None_Day 4_Rep-3


title: Uninfected_None_Day 4_Rep-2


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_1


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aL130_2


title: Liver-NaF6-10 months

description: Library name: FoieNaF6

value: NaF


title: Pretreatment whole blood RNA-seq, Sample03

description: Library name: Sample03

value: pretreatment


title: Uninfected_None_Day 4_Rep-1

value: Uninfected


title: Pretreatment whole blood RNA-seq, Sample02

description: Library name: Sample02


title: Liver-NaF5-10 months

description: Library name: FoieNaF5

value: liver


title: Pretreatment whole blood RNA-seq, Sample01

description: Library name: Sample01


title: Liver-NaF4-10 months

description: Library name: FoieNaF4


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_1

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::ACE2(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase::kanMX


title: Fusarium solani_None_Day 7_Rep-3

value: Fusarium solani

value: Day 7


description: Library name: ACE2_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_2


title: Liver-NaF3-10 months

description: Library name: FoieNaF3

value: WT

value: 10 months


description: Library name: ACE2_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_4

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::ACE2(S114 G89 N43 Q53 D14 E15 F63) SV40 NLS Mnase::kanMX


title: Fusarium solani_None_Day 7_Rep-2


description: Library name: ACE2_aS114_aG89_aN43_aQ53_aD14_aE15_aF63_5


title: 7days_post_treatment_2

city: Boston

first: Bernardo

last: Lemos

state: MA

address: 665 Huntington Avenue

institute: Harvard Chan School of Public Health

description: replicate 2

data_processing:
Reads were trimmed using Trimgalore under default quality parameters (-q 30 --phred33)
Trimmed reads were mapped against the reference genome (annotation 6.07) using bowtie2 under --sensitive option
Samtools was used to convert between SAM and BAM files and to sort BAM files.
We used GFold function count to extract read counts for annotated genes from sorted BAM files according to the GTF file (annotation 6.07).
Read counts were used to calculate differential expression using DESeq2 (version 1.8.1), R software (version 3.2.3), and RStudio (version 0.99.467).
Genome_build: GRCh37 Primary Assembly (hg19)
Supplementary_files_format_and_content: Text files (*.txt) contain read counts. Supplementary files (*.csv) are expression data calculated by DESeq2, and combined files by the Fisher's method.

source_name: lymphoblastoid cell line

growth_protocol: Cells (LCLs) grown in standard RPMI medium

extract_protocol:
Total RNA was isolated with Trizol. In order to check the quality of the RNA extracts, samples were run in an 1% TAE-Agarose gel and integrity of the mRNA was estimated based on the sharpness of the ribosomal RNA bands. Samples that did not meet this quality control were re-extracted. Concentration of all samples was accessed with Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For mRNA-Seq, total RNA was subjected to mRNA isolation with magnetic beads linked to poly-T tails (Dynabeads® mRNA DIRECT™ Purification Kit) for two cycles. The quality of mRNA preparations was accessed with Agilent 2100 Bioanalyzer system (Agilent Technologies).
Samples with intact mRNA and less than 15% of rRNA contamination were subjected to library synthesis using the automated Apollo 324™ NGS Library Prep system with PrepX RNA-Seq kit (Wafergen). Final product of each library was subjected to 15 cycles of PCR enrichment in reactions containing one barcode for each sample. Final libraries were purified with magnetic beads to an average size of 350 bp and checked with Agilent 2200 TapeStation (Agilent Technologies). Samples were normalized with Qubit 3.0 Fluorometer, and twelve libraries were combined in a single mix. Multiplexed mix was submitted to 150 cycles of paired-end sequencing (2x150bp) using HiSeq 2500 (Illumina). Two biological replicates were sequenced for each sample.

treatment_protocol: Treatment consists of treatment with hexavaent Chromium (5 uM) for 24 hours

tag: cell  line

value: lymphoblastoid cell line

value: 7days post Cr6 treatment


title: Liver-NaF2-10 months

description: Library name: FoieNaF2


title: Fusarium solani_None_Day 7_Rep-1


title: 7days_post_treatment_1

description: replicate 1


title: Liver-NaF1-10 months

description: Library name: FoieNaF1


title: Rhizopus arrhizus_None_Day 7_Rep-3

value: Rhizopus arrhizus


title: 3days_post_treatment_2

description: replicate 2

value: 3days post Cr6 treatment


title: Rhizopus arrhizus_None_Day 7_Rep-1


title: 3days_post_treatment_1

description: replicate 1


title: ACE2_NQ_toG_2_550_2

description: Library name: ACE2_NQ_toG_2_550_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(NQ toG)Mnase::kanMX

value: budding yeast culture at OD=4


title: ACE2_NQ_toG_2_550_1

description: Library name: ACE2_NQ_toG_2_550_1


title: Liver-Control7-10 months

description: Library name: FoieC7

value: Control


title: Rhizopus arrhizus_None_Day 7_Rep-2


title: ACE2_LIV_toF_2_550_2

description: Library name: ACE2_LIV_toF_2_550_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(LIV toF)Mnase::kanMX


title: ACE2_LIV_toF_2_550_1

description: Library name: ACE2_LIV_toF_2_550_1


title: Liver-Control5-10 months

description: Library name: FoieC5


title: Liver-Control4-10 months

description: Library name: FoieC4


title: 24h_Cr6_treatment_2

description: replicate 2

value: 24h Cr6


title: ACE2_KR_toNQ_2_550_2

description: Library name: ACE2_KR_toNQ_2_550_2

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(KR toNQ)Mnase::kanMX


title: Liver-Control3-10 months

description: Library name: FoieC3

value: liver


title: 24h_Cr6_treatment_1

description: replicate 1


title: Aspergillus fumigatus_None_Day 7_Rep-3

value: Aspergillus fumigatus


title: control_2

description: replicate 2

value: control


title: Uninfected_None_Day 7_Rep-3

value: Uninfected

value: Day 7


title: ACE2_FWY_toL_2_550_2

description: Library name: ACE2_FWY_toL_2_550_2

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 ACE2::SV40 NLS CE2(FWY toL)Mnase::kanMX


title: Aspergillus fumigatus_None_Day 7_Rep-2


title: control_1

description: replicate 1

value: lymphoblastoid cell line


title: ACE2_KR_toNQ_2_550_1

description: Library name: ACE2_KR_toNQ_2_550_1


title: Aspergillus fumigatus_None_Day 7_Rep-1


title: Liver-Control1-10 months

description: Library name: FoieC1

value: WT

value: 10 months


title: Liver-Control2-10 months

description: Library name: FoieC2


title: Uninfected_None_Day 7_Rep-2


title: ACE2_FWY_toL_2_550_1

description: Library name: ACE2_FWY_toL_2_550_1


title: nicotine_withdrawal2

status: Public on Feb 13 2026

first: Yi-Xuan

last: Zhang

state: Jiangsu Sheng

address: Longmian avenue 101

department: Shool of pharmacy

institute: Nanjing Medical University

description: Library name: Nic2

data_processing:
Pass filter data of fastq format were processed by Cutadapt (V1.9.1, parameters: phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to remove technical sequences (adapters, PCR primers, or fragments thereof) and low-quality bases (quality < 20).
Clean data were aligned to the mm39 via Hisat2 (v2.2.1)
HTSeq (v0.6.1) estimated gene expression levels from the pair-end clean data.
Assembly: mm39
Supplementary files format and content: csv file include raw counts and FPKM values for each sample

source_name: cholinergic neurons isolated by FACS from medial habenula brain tissue

extract_protocol:
RNA was isolated with TRIzol reagent (Invitrogen), 1 μg total RNA was used for library preparation
RNA libraries for RNA-seg were prepared using VAHTS Universal V8 RNA-seg Library Prep Kit following manufacturer's protocols.


title: T1D_pancreas

city: Vienna

first: Manuel

last: Salzmann

address: Lazarettgasse 14

department: Department of Medicine II, Division of Cardiology

country: Austria

institute: Medical University of Vienna

description: Library name: MS1801

data_processing:
Sequencing data were demultiplexed and aligned using Cell Ranger software version 8.0.1 (10x Genomics), with the Mus musculus mm10 (Ensembl 98). Cell Ranger Loupe Browser output files were imported into R (version 4.4.1) for downstream processing. Nuclei with >45% mitochondrial transcript content, nFeature_RNA ≤ 500, or nCount_RNA ≥ 500 were excluded from analysis. Filtered data were normalized, log-transformed, and the resulting matrix was used for all downstream analyses.
Data integration was performed using RPCA-based batch correction implemented in Seurat v5 (https://satijalab.org/seurat/articles/seurat5_integration). Principal component analysis was conducted using the first 20 components, and clustering was performed with a resolution of 0.1. The final annotated dataset was exported as a cloupe file and reloaded into the Loupe Browser (10x Genomics) for visualization and manual inspection of clusters.
Pseudo-bulk differential expression analysis was performed using the DElegate package (https://github.com/cancerbits/DElegate).
Assembly: Mus musculus mm10 (Ensembl 98)
Supplementary files format and content: tab separated values files and matrix files
Supplementary files format and content: DEseq clusters vs all.xlsx, comparison of gene expression of one cluster, to gene expression of all other clusters

source_name: Pancreas

extract_protocol:
Pancreatic heads were dissected, snap-frozen, and stored in liquid nitrogen until processing. Tissue dissociation and fixation were performed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (PN-1000414, 10x Genomics, Pleasanton, CA, USA). Nuclei and single cells were isolated following the protocol “Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling” (CG000553). Samples from each group (control and TMZ-treated) were pooled and assigned one barcode per group for multiplexed analysis.
Library preparation was performed using the “Chromium Fixed RNA Profiling for Multiplexed Samples” protocol (CG000527, protocol version F), with the Chromium Fixed RNA Profiling Kit - Mouse Transcriptome (4 reactions × 4 barcodes, PN-1000496), Hybridization & Library Kit (PN-1000415), and the Chromium Next GEM Chip Q Single Cell Kit (16 reactions, PN-1000422), all from 10x Genomics. Sequencing was performed on an Illumina NextSeq 2000 instrument using a NextSeq 2000 P4 flow cell (100 cycles, PN-20100994, Lot #20879630, Illumina, San Diego, CA, USA).

treatment_protocol: Mice were enrolled when fasting glucose reached 150-180 mg/dL and received 62.5 mg/L Trimetazidine dihydrochloride (MedChemExpress, NJ, USA) in drinking water (approx. 15 mg/kg/day, in adaption to the human maximum dose of 70 mg/day.

value: Pancreas

value: whole pancreatic tissue

value: NOD/ShiLtJ (001976)

value: 1 week 15mg/kg/day trimetazidine


title: control4

description: Library name: con4

value: cholinergic neurons isolated by FACS from medial habenula brain tissue


title: Uninfected_None_Day 7_Rep-1


title: nicotine_withdrawal6

description: Library name: Nic6


title: nicotine_withdrawal4

description: Library name: Nic4


title: nicotine_withdrawal3

description: Library name: Nic3


title: nicotine_withdrawal1

description: Library name: Nic1


title: nicotine_withdrawal5

description: Library name: Nic5


title: control1

description: Library name: con1


title: Ctrl3

city: Bad Nauheim

first: Pieterjan

last: Dierickx

state: Hessen

address: Parkstrasse 1

department: Circadian Regulation of Cardiometabolism

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Ctrl3

data_processing:
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons.
The abundance of transcripts reflects gene expression level directly. In RNA-seq experiments, gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon(Goldstein et al., 2016). Read counts is proportional to gene expression level, gene length and sequencing depth(Liao et al., 2014). FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)(Trapnell, Cole, et al., 2010) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al., 2008).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: Heart

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.
RNA sequencing via Illumina platforms, based on the mechanism of SBS (sequencing by synthesis), offers a wide range of benefits on high throughput and high accuracy out of low sample requirements. This technical method can be a powerful tool for researching RNA transcriptional activity.

value: Heart

value: Cardiomyocyte


title: Ctrl2

description: Library name: Ctrl2


title: control3

description: Library name: con3


title: FK_NR_Ex3

description: Library name: FK_NR_Ex3


title: Ctrl1

description: Library name: Ctrl1


title: FK_NR2

description: Library name: FK_NR2


title: FK_NR1

description: Library name: FK_NR1


title: FK_NR3

description: Library name: FK_NR3


title: FK_NR_Ex1

description: Library name: FK_NR_Ex1


title: control2

description: Library name: con2


title: FK_NR_Ex2

description: Library name: FK_NR_Ex2


title: FK2

description: Library name: FK2


title: FK1

description: Library name: FK1


title: P16_MetLN_scRNA

city: shanghai

first: KUN

last: LIU

address: dong an Road

institute: Fudan university

description:
Library name: P16_MetLN
10x Genomics

data_processing:
Raw sequencing reads (FASTQ files) were aligned to the human reference genome (GRCh38) using CellRanger (v7.1.0, 10x Genomics) with default parameters, which included barcode/UMI demultiplexing, STAR-based alignment, and UMI counting. The CellRanger output was imported into Seurat (v4.4.0)72 via the CreateSeuratObject function. Initial quality control was performed by filtering cells with fewer than 200 or more than 5,000 detected genes to exclude low-quality cells and potential doublets. Cells exhibiting mitochondrial gene content exceeding 20% were further removed to eliminate apoptotic or stressed cells. To address batch effects across three independent biological samples, transcriptional profiles were integrated using Harmony (v1.2)73 with theta = 2 and lambda = 0.5 over 50 iterations. Post-integration principal component analysis (PCA) confirmed the removal of batch-specific clustering. Gene expression matrices were log-normalized (scale factor = 10,000) and scaled to regress out mitochondrial gene content. Highly variable genes were selected using the variance-stabilizing transformation method (top 2,000 genes) for downstream dimensionality reduction and clustering.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MetLN

extract_protocol:
Human peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by density gradient centrifugation using Ficoll-Paque (Cytiva). Tumor and lymph node tissues were minced thoroughly with surgical scissors and transferred to GentleMACs C Tubes containing 3 mg/ml Collagenase IV (Sigma-Aldrich) and 0.1 mg/ml DNase I (Sigma-Aldrich) in RPMI 1640 medium per 0.3g tissue. The tubes were then placed on the GentleMACs Octo Dissociator (Miltenyi Biotec) and incubated at 37°C for 20 min for lymph node samples or 25 min for tumor samples, according to the manufacturer's instructions. After incubation, the samples were quenched by adding 15 ml of RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). The cell suspensions were filtered through 70-μm cell strainers (Corning) to remove debris and centrifuged at 300×g for 5 min at 4°C to pellet the cells. When necessary, red blood cell lysis was performed using Red Blood Cell Lysis Solution (Miltenyi Biotec) according to the manufacturer's protocol.
Single-cell suspensions with viable cell rates greater than 80% were used for sequencing. The cell suspension was used for 10x Chromium Single cell 5’ (5’ Kit v2, 1000263) and human TCR/BCR library (TCR 1000252; BCR 1000253) construction as per the manufacturer's instructions. Purified libraries were subsequently sequenced using an Illumina NovaSeq 6000 sequencer with 150-base pair (bp) paired-end reads.

value: MetLN

value: All cells


title: PC9/cDDPr rep2

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

description:
Library name: Sample 12
PC9_DDPR2
PC9_counts.xlsx

data_processing:
Raw transcriptome sequencing data were first subjected to quality control using FastQC and summarized with MultiQC. Low-quality bases and residual adapter sequences were then removed using TrimGalore (https://github.com/FelixKrueger/TrimGalore). The cleaned reads were aligned to the human reference genome (GRCh38, Ensembl release) using Hisat2. Gene-level read counts were quantified with FeatureCounts. Differential expression analysis was performed using DESeq2. Genes with an absolute log2 fold change (|log2FC|) > 1 and a p-value < 0.05 were considered significantly differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Excel (.xlsx) files containing processed gene expression count matrices. Each file includes genes in rows and samples in columns. Values represent raw counts per gene.

source_name: lung

growth_protocol: All cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. To maintain the resistant phenotype, H226/cDDPr, H460/cDDPr and PC9/cDDPr cells were routinely cultured with 1 µM, 0.83 µM and 6.6 µM cisplatin, respectively. Cells were switched to drug free medium for one week prior to experiments. All cultures were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cells at 70–80% confluence using TRIzol reagent according to the manufacturer’s instructions.
Libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform.

value: lung

value: Non-Small Cell Lung Cancer

value: cisplatin-resistant


title: T5

city: Zhengzhou City

first: Yang

last: Bai

state: Henan Province

address: 1 Jianshe Dong Road, Erqi District, Zhengzhou City, Henan Pr

institute: Zhengzhou University

description:
Library name: I/R5
T5

data_processing:
Data quality control of raw data with fastp software; Removal of primers and adapter sequences (Adaptor)
Remove sequences with fragment length < 50 bp;
Remove N bases to a certain percentage of reads (default is set to 5 bp)
Removal of low-quality bases with mass values less than 20;
Calculate the base average mass value with a 4 base window, and excise it if the base average mass value is less than 20
Assembly: mm10

source_name: kidney

growth_protocol: After detissue, store in liquid nitrogen

extract_protocol:
Trizol (Invitrogen) method was used to extract total RNA from tissues
Trizol (Invitrogen) method was used to extract total RNA from tissues

treatment_protocol: We randomly assigned C57BL/6N mice to sham-operated (Sham, n=6) or I/R (n=6) groups. The I/R group received pentobarbital sodium anesthesia followed by renal pedicle occlusion. After 60 minutes of ischemia, we restored blood flow for 6h reperfusion before euthanasia and sample collection

value: kidney

value: I/R


title: PC9/Nor rep2

description:
Library name: Sample 10
PC9_NR2
PC9_counts.xlsx


title: T3

description:
Library name: I/R3
T3