title: I2A cells, SMARCB1-reexpression, day 10, rep1


title: day1BMsurvived_4

status: Public on Jun 29 2026

type: SRA

city: Tokyo

first: Riho

last: Saito

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

description:
Library name: Sample4
Survival group

library_source: transcriptomic

data_processing:
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads. Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
Mice anesthetized with 200 µl of combination anesthetic and cells were aspirated with a syringe 27G needle inserted directly from knee into the femur at 1 day after the infection. Total RNA was isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

tag: tissue

value: Blood

tag: strain

tag: cell type

value: CXCR2+ cells

tag: genotype

value: WT

tag: treatment

value: VSV (New Jersey) intranasal infection

tag: batch


title: I2A cells, DMSO-treated, rep3

type: genomic

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

hyb_protocol: please refer to GEO:GSE175892

scan_protocol: please refer to GEO:GSE175892

data_processing: RnBeads Bioconductor R package version 2.12.2 was used to process the data from IDAT files. All samples and all probes were kept after quality control. Probe intensities were normalized using the rnb.execute.normalization() function with the “swan” method. Probes outside CpG context, targeting single nucleotide polymorphisms or targeting X and Y chromosomes were all filtered out before subsequent analysis.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: I2A cells, DMSO-treated, control

label_protocol: please refer to GEO:GSE175892

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. In order to induce SMARCB1 expression, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline.

extract_protocol: please refer to GEO:GSE175892

treatment_protocol: I2A cells were treated with DMSO as a control for 21 days.

tag: cell line

value: Rhabdoid tumor cells

value: DMSO


title: Transcriptiome of 0 hour Marchantia spores, 1st biological replicate, lane 4

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description:
Library name: spores_0h_rep1_lane4
RNAseq derived from spores of six sporangia at their collection (time zero)

data_processing:
Raw reads were returned as fastq.gz files.Reads passing quality control (Phred +33 quality score >30 assessed with FastQC) were trimmed by removing the first and last 10 bases, and adapters were removed using Trimmomatic (v0.32). Paired-end reads were interleaved. Residual bacterial rRNA sequences were filtered with SortMeRNA (v2.1b). Reads were error-corrected using BayesHammer within SPAdes (v3.10.1) and aligned to the Marchantia polymorpha reference genome JGI (v3.1) and its association gene annotations, using Salmon. Differential gene expression analysis was performed with DESeq2.Gene annotations were obtained from the Marchantia polymorpha reference genome (v3.1) (functional annotation downloaded from https://marchantia.info/download/v31/). Pairwise comparisons were conducted, with an adjusted p-value (padj) <0.05 considered significant. Genes with log2FoldChange <0 were classified as downregulated, >0 as upregulated, and NA indicated no significant change.
Assembly: Marchantia polymorpha Takaragaike-1 (MpTak1_v3.1)
Supplementary files format and content: Dataset1_DESeq2_output_annotated_2021.xlsx; Excel sheet; Shows pairwise differential expression analysis, genome-wide, based on Marchantia polymorpha JGI 3.1 reference genome and its associated gene predictions (v3.1), including Log2FoldChanges and statsitical significance values for per-gene comparisons between samples and conditions.
Supplementary files format and content: Normalized_Read_Counts_2_transcriptome_shared_final.xlsx; Excel sheet; Contains genome-wide read counts across all samples and biological replicates, normalized by sampling depth.

organism: Marchantia polymorpha

source_name: spores

growth_protocol: Wild type Marchantia polymorpha sporangia, derived from a cross of Tak-1 and Tak-2, were collected and surface-sterilized with 1% NaDCC, followed by washing three times with sterile water. The spore suspension was plated and maintained under continuous white light (PFD 50-60 µmol m⁻² s⁻¹) for the indicated durations.

extract_protocol:
For collection of samples, the cellophane with adhered spores was peeled from the medium, flash-frozen in liquid nitrogen, and ground to a fine powder using a mixer mill (RETSCH MM 400) at 30 Hz for 4 minutes. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions, followed by Turbo DNase treatment to remove residual genomic DNA.
mRNA library preparation, RNA sequencing was performed at the Wellcome Trust Centre for Human Genetics, University of Oxford, using an Illumina HiSeq 4000 platform generating 75 bp paired-end reads. Each sample was sequenced in five technical replicates, with replicates distributed across five independent sequencing lanes.

treatment_protocol: Spores were grown under standard white light for 0, 15, or 30 hours after plating.

value: spores

value: spore

value: Takaragaike-1 (Tak-1, male) x Takaragaike-2 (Tak-2, female)

value: 0 hours


title: Pull-down at 12 hours with Control miRNA, Rep 1

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

country: USA

institute: Arizona State University

description: Library name: Pull-down_12h_Control_1

data_processing:
The libraries were paired-end sequenced (2 x 150bp) using an Illumina HiSeq.
Reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
The number of mapped reads per transcript were calculated using featureCounts from the Subread package v.1.5.2, and only unique reads that fell within the exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: Processed files are provided as counts files.

molecule: polyA RNA

growth_protocol: Grown as monolayers in 5% CO2 in RPMI 1640 supplemented with 10% FBS and 1 % PenStrep at 37 degrees C.

extract_protocol:
All steps involved in the biotin-miRNA streptavidin pulldown affinity purification were performed per established protocol 24. At both timepoints, purified miRNA-bound products were obtained from the experimental and control cells. In parallel, at both timepoints, transcripts altered (up- and down-regulated) by miRNA mimics were isolated (i.e. input). Cytoplasmic extract and Streptavidin-Dynabeads (M-280, Invitrogen) were prepared, then incubated for 4 hours. Biotin-miR-mRNA complexes were collected in a magnetic stand. (PMID = 25240884)
For high-throughput RNA-sequencing (RNA-seq), libraries were constructed with Poly(A) selection by GeneWiz© for both the 12h (pulldown and input) and 72h (pulldown and input) products. In the manuscript pulldown is referred to as bound targets, and input is treated as RNA-seq to find differentially expressed genes. (PMID = 25240884)

treatment_protocol: Lipofectamine RNAiMAX was used to Lipofectamine RNAiMAX was used to transfect a custom-made 3’-biotinylated miR-497-5p mimic (experimental) or 3’-biotinylated scrambled, non-targeting miRNA mimic (control) for 12 hours and 72 hours (20 nM, Dharmacon).

tag: cellosaurus accession

tag: time (hours)

value: Control

tag: replicate

tag: method

value: Pull-down

tag: captures

value: mRNA targets of miR-497-5p

tag: method long

value: Biotinylated miRNA target pull-down


title: day1BMsurvived_3

description:
Library name: Sample3
Survival group


title: Transcriptiome of 0 hour Marchantia spores, 1st biological replicate, lane 3

description:
Library name: spores_0h_rep1_lane3
RNAseq derived from spores of six sporangia at their collection (time zero)


title: I2A cells, DMSO-treated, rep2


title: RNA-seq at 12 hours with Control miRNA, Rep 1

description: Library name: RNA-seq_12h_Control_1

value: RNA-seq

value: mRNA expression


title: day1BMsurvived_2

description:
Library name: Sample2
Survival group


title: Transcriptiome of 0 hour Marchantia spores, 1st biological replicate, lane 2

description:
Library name: spores_0h_rep1_lane2
RNAseq derived from spores of six sporangia at their collection (time zero)


title: I2A cells, DMSO-treated, rep1


title: Transcriptiome of 0 hour Marchantia spores, 1st biological replicate, lane 1

description:
Library name: spores_0h_rep1_lane1
RNAseq derived from spores of six sporangia at their collection (time zero)


title: I2A cells, day 0, rep4

source_name: I2A cells, control


title: MCF7-ESR1-Y537S-24 siCCND1-2 CSS abemaciclib RNAseq replicate 3

status: Public on Jun 28 2026

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample 36
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-16_CSS_Abema_R3

data_processing:
Adapters and low quality reads were removed using BBMap bbduk.sh with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Trimmed reads were aligned to the human reference genome (hg38) using STAR.
Aligned reads were counted using featureCounts with GENCODE gene annotations (gencode.v35.annotation.gtf).
Assembly: hg38
Supplementary files format and content: CSV file includes raw, non-normalised gene counts for each sample.

growth_protocol: RPMI-1640 supplemented with 10% FBS, 1% GlutaMax, and 1% HEPES, incubated at 37C at 5% CO2.

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using a QuantSeq 3' mRNA sequencing workflow and sequenced as 101-cycle single-end reads on an Illumina NextSeq 2000.

treatment_protocol: Cells were transfected with non-targeting siRNA or one of two siRNA against CCND1. After 24 hours, cells were cultured in phenol-free RPMI-164 supplemented with 10% charcoal-stripped FBS, 1% GlutaMax, and 1% HEPES treated with DMSO control, abemaciclib 500 nM, and estradiol 1 nM for 3 days.

value: ESR1 Y537S mutant

tag: sirna

tag: hormone condition

value: Hormone-deprived

value: Abemaciclib


title: NC/ID

type: RNA

city: Niigata

first: Manabu

last: Yamazaki

state: Niigata

address: Gakkocho-dori 2-5274, Chuo-ku

department: Division of Oral Pathology

institute: Niigata University Graduate School of Medical and Dental Sciences

description: HSC-3 cells indirectly co-cultured with necrotic HSC-3 cells for 16 h

hyb_protocol: Hybridization was performed by a commercial service provider following standard Agilent microarray hybridization protocols.

scan_protocol: Microarray slides were scanned by a commercial service provider using an Agilent microarray scanner according to the manufacturer’s instructions.

data_processing: Raw signal intensities were extracted from scanned images using Agilent Feature Extraction software by a commercial service provider. Processed data were generated from Feature Extraction output files using quantile normalization procedures.

source_name: HSC-3 cells, indirectly co-cultured with necrotic HSC-3 cells, 16 h

label_protocol: Total RNA labeling was performed by a commercial service provider using standard Agilent labeling protocols.

growth_protocol: HSC-3 cells were maintained in Minimum essential medium (MEM, Thermo Fisher Scientific) containing 10% fetal bovine serum (FBS, HyClone)

extract_protocol: RNA was extracted using the NucleoSpin RNA kit (MACHEREY-NAGEL GmbH & Co.) following the manufacturer's instructions. RNA was quantified using a Nanodrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HSC-3 cells were subjected to indirect co-culture with necrotic HSC-3 cells using 1 µm pore inserts for 16 h or maintained as monoculture controls prior to RNA extraction.

value: Squamous cell carcinoma


title: MCF7-ESR1-Y537S-24 siCCND1-2 CSS abemaciclib RNAseq replicate 2

description:
Library name: Sample 35
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-16_CSS_Abema_R2


title: mono

description: HSC-3 cells mono-cultured for 16 h

source_name: HSC-3 cells, mono-culture, 16 h


title: MCF7-ESR1-Y537S-24 siCCND1-2 CSS abemaciclib RNAseq replicate 1

description:
Library name: Sample 34
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-16_CSS_Abema_R1


title: MCF7-ESR1-Y537S-24 siCCND1-2 CSS DMSO RNAseq replicate 3

description:
Library name: Sample 33
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-16_CSS_DMSO_R3


title: MCF7-ESR1-Y537S-24 siCCND1-2 CSS DMSO RNAseq replicate 2

description:
Library name: Sample 32
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-16_CSS_DMSO_R2


title: day1BMsurvived_1

description:
Library name: Sample1
Survival group

value: Blood

value: CXCR2+ cells

value: WT

value: VSV (New Jersey) intranasal infection


title: MCF7-ESR1-Y537S-24 siCCND1-2 CSS DMSO RNAseq replicate 1

description:
Library name: Sample 31
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-16_CSS_DMSO_R1

value: DMSO


title: MCF7-ESR1-Y537S-24 siCCND1-1 CSS abemaciclib RNAseq replicate 3

description:
Library name: Sample 30
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-15_CSS_Abema_R3


title: MCF7-ESR1-Y537S-24 siCCND1-1 CSS abemaciclib RNAseq replicate 2

description:
Library name: Sample 29
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-15_CSS_Abema_R2


title: MCF7-ESR1-Y537S-24 siCCND1-1 CSS DMSO RNAseq replicate 3

description:
Library name: Sample 27
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-15_CSS_DMSO_R3


title: MCF7-ESR1-Y537S-24 siCCND1-1 CSS abemaciclib RNAseq replicate 1

description:
Library name: Sample 28
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-15_CSS_Abema_R1


title: MCF7-ESR1-Y537S-24 siCCND1-1 CSS DMSO RNAseq replicate 2

description:
Library name: Sample 26
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-15_CSS_DMSO_R2


title: MCF7-ESR1-Y537S-24 siCCND1-1 CSS DMSO RNAseq replicate 1

description:
Library name: Sample 25
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCCND1-15_CSS_DMSO_R1


title: MCF7-ESR1-Y537S-24 siCTRL CSS abemaciclib RNAseq replicate 3

description:
Library name: Sample 24
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS_Abema_R3

value: Non-targeting siRNA


title: MCF7-ESR1-Y537S-24 siCTRL CSS abemaciclib RNAseq replicate 2

description:
Library name: Sample 23
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS_Abema_R2


title: MCF7-ESR1-Y537S-24 siCTRL CSS abemaciclib RNAseq replicate 1

description:
Library name: Sample 22
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS_Abema_R1


title: MCF7-ESR1-Y537S-24 siCTRL CSS DMSO RNAseq replicate 3

description:
Library name: Sample 21
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS_DMSO_R3


title: MCF7-ESR1-Y537S-24 siCTRL CSS DMSO RNAseq replicate 2

description:
Library name: Sample 20
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS_DMSO_R2


title: MCF7-ESR1-Y537S-24 siCTRL CSS-E2 abemaciclib RNAseq replicate 3

description:
Library name: Sample 18
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS-E2_Abema_R3

value: Estradiol


title: MCF7-ESR1-Y537S-24 siCTRL CSS DMSO RNAseq replicate 1

description:
Library name: Sample 19
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS_DMSO_R1


title: MCF7-ESR1-Y537S-24 siCTRL CSS-E2 abemaciclib RNAseq replicate 2

description:
Library name: Sample 17
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS-E2_Abema_R2


title: MCF7-ESR1-Y537S-24 siCTRL CSS-E2 abemaciclib RNAseq replicate 1

description:
Library name: Sample 16
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS-E2_Abema_R1


title: MCF7-ESR1-Y537S-24 siCTRL CSS-E2 DMSO RNAseq replicate 3

description:
Library name: Sample 15
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS-E2_DMSO_R3


title: MCF7-ESR1-Y537S-24 siCTRL CSS-E2 DMSO RNAseq replicate 2

description:
Library name: Sample 14
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS-E2_DMSO_R2


title: MCF7-ESR1-Y537S-24 siCTRL CSS-E2 DMSO RNAseq replicate 1

description:
Library name: Sample 13
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-Y537S-24_siCTRL_CSS-E2_DMSO_R1


title: MCF7-ESR1-WT siCTRL CSS abemaciclib RNAseq replicate 3

description:
Library name: Sample 12
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS_Abema_R3


title: MCF7-ESR1-WT siCTRL CSS abemaciclib RNAseq replicate 2

description:
Library name: Sample 11
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS_Abema_R2


title: MCF7-ESR1-WT siCTRL CSS abemaciclib RNAseq replicate 1

description:
Library name: Sample 10
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS_Abema_R1


title: MCF7-ESR1-WT siCTRL CSS DMSO RNAseq replicate 3

description:
Library name: Sample 9
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS_DMSO_R3


title: MCF7-ESR1-WT siCTRL CSS DMSO RNAseq replicate 2

description:
Library name: Sample 8
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS_DMSO_R2


title: MCF7-ESR1-WT siCTRL CSS DMSO RNAseq replicate 1

description:
Library name: Sample 7
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS_DMSO_R1


title: MCF7-ESR1-WT siCTRL CSS-E2 abemaciclib RNAseq replicate 3

description:
Library name: Sample 6
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS-E2_Abema_R3


title: MCF7-ESR1-WT siCTRL CSS-E2 abemaciclib RNAseq replicate 2

description:
Library name: Sample 5
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS-E2_Abema_R2


title: MCF7-ESR1-WT siCTRL CSS-E2 abemaciclib RNAseq replicate 1

description:
Library name: Sample 4
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS-E2_Abema_R1


title: MCF7-ESR1-WT siCTRL CSS-E2 DMSO RNAseq replicate 3

description:
Library name: Sample 3
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS-E2_DMSO_R3


title: MCF7-ESR1-WT siCTRL CSS-E2 DMSO RNAseq replicate 2

description:
Library name: Sample 2
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS-E2_DMSO_R2


title: MCF7-ESR1-WT siCTRL CSS-E2 DMSO RNAseq replicate 1

description:
Library name: Sample 1
Column name in RNAseq_MCF7_ESR1_Y537S_abema_siCCND1_rawcounts.csv: MCF7-ESR1-WT_siCTRL_CSS-E2_DMSO_R1


title: M453 abemaciclib and fulvestrant combination RNAseq replicate 3

description:
Library name: Sample 24
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Fulv-Abema_R3

data_processing:
Adapters and low quality reads were removed using BBMap bbduk.sh with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Trimmed reads were aligned to the human reference genome (hg38) using STAR.
Aligned reads were counted using featureCounts with GENCODE gene annotations (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: CSV file includes raw, non-normalised gene counts for each sample.

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640 supplemented with 10% FBS, 1% GlutaMax, and 1% HEPES. MDA-MB-453 cells were cultured in DMEM supplemented with 10% FBS. Both cell lines were incubated at 37C at 5% CO2.

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent).

treatment_protocol: Cells were treated with DMSO control, abemaciclib 500 nM, fulvestrant 5 nM, or a combination of abemaciclib and fulvestrant for 5 days.

value: Wild-type

value: AbemaFulv


title: M453 abemaciclib and fulvestrant combination RNAseq replicate 1

description:
Library name: Sample 22
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Fulv-Abema_R1


title: M453 Fulvestrant RNAseq replicate 3

description:
Library name: Sample 21
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Fulvestrant_R3

value: Fulvestrant


title: M453 abemaciclib and fulvestrant combination RNAseq replicate 2

description:
Library name: Sample 23
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Fulv-Abema_R2


title: M453 Fulvestrant RNAseq replicate 2

description:
Library name: Sample 20
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Fulvestrant_R2


title: M453 Fulvestrant RNAseq replicate 1

description:
Library name: Sample 19
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Fulvestrant_R1


title: M453 abemaciclib RNAseq replicate 3

description:
Library name: Sample 18
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Abema_R3

value: Abema


title: M453 abemaciclib RNAseq replicate 2

description:
Library name: Sample 17
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Abema_R2


title: M453 abemaciclib RNAseq replicate 1

description:
Library name: Sample 16
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_Abema_R1


title: M453 DMSO RNAseq replicate 3

description:
Library name: Sample 15
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_DMSO_R3


title: M453 DMSO RNAseq replicate 2

description:
Library name: Sample 14
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_DMSO_R2


title: M453 DMSO RNAseq replicate 1

description:
Library name: Sample 13
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M453_DMSO_R1


title: M231 abemaciclib and fulvestrant combination RNAseq replicate 3

description:
Library name: Sample 12
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Combination_R3


title: M231 abemaciclib and fulvestrant combination RNAseq replicate 2

description:
Library name: Sample 11
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Combination_R2


title: M231 abemaciclib and fulvestrant combination RNAseq replicate 1

description:
Library name: Sample 10
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Combination_R1


title: M231 Fulvestrant RNAseq replicate 3

description:
Library name: Sample 9
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Fulvestrant_R3


title: M231 Fulvestrant RNAseq replicate 2

description:
Library name: Sample 8
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Fulvestrant_R2


title: M231 Fulvestrant RNAseq replicate 1

description:
Library name: Sample 7
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Fulvestrant_R1


title: M231 abemaciclib RNAseq replicate 3

description:
Library name: Sample 6
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Abema_R3


title: M231 abemaciclib RNAseq replicate 1

description:
Library name: Sample 4
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Abema_R1


title: M231 abemaciclib RNAseq replicate 2

description:
Library name: Sample 5
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_Abema_R2


title: M231 DMSO RNAseq replicate 3

description:
Library name: Sample 3
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_DMSO_R3


title: M231 DMSO RNAseq replicate 2

description:
Library name: Sample 2
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_DMSO_R2


title: M231 DMSO RNAseq replicate 1

description:
Library name: Sample 1
Column name in RNAseq_M231_M453_abema_fulv_rawcounts.csv: M231_DMSO_R1


title: CAMA1 abemaciclib and fulvestrant combination RNAseq replicate 3

description:
Library name: Sample 12
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Comb_3

data_processing:
Adapters and low quality reads were removed using BBMap bbduk.sh with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Trimmed reads were aligned to the human reference genome (hg38) using STAR.
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: CSV file includes raw, non-normalised gene counts for each sample.

treatment_protocol: Cells were treated with DMSO control, abemaciclib 100 nM, fulvestrant 5 nM, or a combination of abemaciclib and fulvestrant.

value: Abemaciclib + Fulvestrant


title: CAMA1 abemaciclib and fulvestrant combination RNAseq replicate 2

description:
Library name: Sample 11
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Comb_2


title: CAMA1 abemaciclib and fulvestrant combination RNAseq replicate 1

description:
Library name: Sample 10
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Comb_1


title: CAMA1 fulvestrant RNAseq replicate 3

description:
Library name: Sample 9
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Fulv_3


title: CAMA1 fulvestrant RNAseq replicate 2

description:
Library name: Sample 8
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Fulv_2


title: CAMA1 fulvestrant RNAseq replicate 1

description:
Library name: Sample 7
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Fulv_1


title: CAMA1 abemaciclib RNAseq replicate 3

description:
Library name: Sample 6
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Abema_3


title: CAMA1 abemaciclib RNAseq replicate 2

description:
Library name: Sample 5
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Abema_2


title: CAMA1 abemaciclib RNAseq replicate 1

description:
Library name: Sample 4
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_Abema_1


title: CAMA1 DMSO RNAseq replicate 3

description:
Library name: Sample 3
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_DMSO_3


title: CAMA1 DMSO RNAseq replicate 2

description:
Library name: Sample 2
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_DMSO_2


title: CAMA1 DMSO RNAseq replicate 1

description:
Library name: Sample 1
Column name in RNAseq_CAMA1_abema_fulv_rawcounts.csv: CAMA-1_DMSO_1


title: HumanAlveolusChip-IIAM-scRNAseq

city: Boston

first: Yuncheng

last: Man

state: MA

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

description:
Library name: Sample 1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Genewiz Azenta and Pluto software
Assembly: GRCh37
Supplementary files format and content: Fastq files and excel file with cell summary analysis

source_name: Lung

extract_protocol:
Cells in the human Lung Chip were washed with PBS, enzymatically lifted with ACCUMAX, washed with cell culture medium and cryopreserved. Cells were shipped to Genewiz Azenta on dry ice for single-cell RNAseq analysis.
Genewiz Azenta

value: Lung


title: Kuramochi INX315 Rep2 RB

description: Library name: Kuramochi-INX315-Rep2-RB

library_source: genomic

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for treated samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 20, --smoothLength 60, --scaleFactor scalefactor, --extendReads, where the scalefactor generated by a background normalisation from DiffBind was used as a normalisation factor. Bigwig for the input sample was normalised with BPM.
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter, --format BAMPE -gsize hs. Peaks for the negative input (IgG2a) and positive control (H3K4me3) were called without a control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, narrowPeaks
Library strategy: Cut&Run

source_name: Kuramochi

growth_protocol: OVCAR-3 and Kuramochi cells were cultured in RPMI-1640, supplemented with 10% FBS and 1x Glutamax. All cells were maintained at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
CUT&RUN was performed using the Cell Signaling Technologies (CST) CUT&RUN Assay Kit (#86652) as per manufacturer's protocol.
CUT&RUN libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit for Illumina, following the CST DNA Library Prep Kit protocol for CUT&RUN.

treatment_protocol: Cells were treated with INX-315 300 nM or the equivalent volume of DMSO (control) for 2 days.

value: Kuramochi

tag: antibody


title: Kuramochi INX315 Rep1 RB

description: Library name: Kuramochi-INX315-Rep1-RB


title: Kuramochi DMSO Rep2 RB

description: Library name: Kuramochi-DMSO-Rep2-RB


title: Kuramochi DMSO Rep1 RB

description: Library name: Kuramochi-DMSO-Rep1-RB


title: Kuramochi DMSO IgG2a

description: Library name: Kuramochi-DMSO-IgG2a


title: D13 organoid from line A1/A2/B1/B2

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 285833
10X Geomics FLEX

data_processing:
Fastq files were analysed using the Cell Ranger pipeline (10xGenomics, version 8.0.0) with Gfp and tdTom sequence added to Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv to generate count matrices
Assembly: mm10
Supplementary files format and content: feature-barcode matrices HDF5

source_name: cerebral organoid

growth_protocol: Organoids: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures. Mice: All animal procedures were approved by the Austrian Federal Ministry of Women, Science and Research in accordance with the Austrian and European Union animal law. Experimental mice were bred and maintained according to regulations approved by institutional animal care and use committee, institutional ethics committee and the guidelines of the preclinical facility (PCF) at ISTA. Mice were bred and maintained in experimental rodent facilities (room temperature 21 ± 1°C [mean ± SEM]; relative humidity 40%–55%; photoperiod 12L:12D). Food (V1126, Ssniff Spezialitaten GmbH, Soest, Germany) and tap water were available ad libitum. Emx1-Cre (PMID: 12151506) and mTmG reporter (PMID: 17868096) mouse lines have been reported previously. All mouse lines were kept in a mixed C57/Bl6 and CD1 genetic background. Mice were used at an age range from 2 – 8 months for general breeding. All efforts were made to minimize the number of animals by following the 3R principles.

extract_protocol:
In order to collect 1-2 million fixed cells per replicate, appropriate numbers of organoids/embryos were pooled for dissociation per replicate. Embryos: A total 40, 30, 10, and 4 brains were pooled from 8, 4, 2, and 2 litters for E10, E13, E16 and P1 timepoints, respectively. Organoids D8: organoids generated from 4-5 Aggrewells, ~800 organoids; D13: ~300 organoids; D20: 80 organoids; D25: 60 organoids). Organoids/Embryos were dissociated following a previously published protocol with some modifications (PMID: 33377108). Organoids/Embryos were first incubated in Earle’s Balanced Salt Solution (EBSS, Thermo Fischer Scientific) containing Papain (Worthington) and DNaseI (Worthington) for a total of 20 (D8, D13) or 25 min at 37°C with gentle shaking at 150 rpm. Organoids/Embryos were gently pipetted 3x with a P1000 tip. After adding Ovomucoid I-Albumin (Worthington), tissue suspension was briefly dissociated mechanically with a pipette. After centrifugation at 1000 rpm for 10 mins at room temperature, the cell pellet was re-suspended and further mechanically dissociated until a homogeneous cell suspension was obtained (up to 20X with a P1000 tip). The cell suspension was passed through a 70 µm filter, and centrifuged again at 1500 rpm for 10 mins at room temperature. Samples were next processed to remove debris prior to fixation. Cell pellets were re-suspended and mixed with cold Debris Removal Solution (Miltenyi Biotec). The mixture was carefully overlaid with cold PBS before centrifugation at 3000 x g for 10 mins at 4°C. The top two layers containing PBS and debris were then aspirated and removed. The remaining cleaned cell suspension was collected by a last centrifugation step at 1000 x g for 10 mins at 4°C. Following manual cell counting with Trypan blue, 1-2 million cells were collected and pelleted. Cells were then fixed with the kit and protocol for Chromium Fixed RNA Profiling (10X Genomics, protocol CG000478, RevD). Pellets were re-suspended in a solution containing 4% formaldehyde and 1X Fix and Perm Buffer, and were stored at 4°C for 22h. Cells were then pelleted and re-suspended in a solution containing 1X Quenching Buffer. Cells were counted again, followed by addition of Enhancer solution and glycerol, after which samples were stored at -80°C until processed.
Library construction performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF-NGS), member of the Vienna BioCenter (VBC), Austria. Single cell libraries were prepared based on the 10X Genomics Flex workflow according to manufacturer’s instructions (CG000527). Four samples were barcoded (BC001 – BC004) and processed together. In order to detect Gfp and tdTom mRNA expression, custom probes were designed according to 10X Genomics Technical Note CG000621 and ordered from Integrated DNA Technologies (IDT) as 4 different oPools, one for each FLEX barcode sequence (BC001 - BC004, custom probe sequence are provided as supplementary file in tab separated text format). Custom probes were added to the mouse probes (PN-100496, 10X Genomics) following manufacturer instructions (CG000621).

value: cerebral organoid

tag: barcode

tag: age


title: OVCAR3 DMSO IgG2a

description: Library name: OVCAR3-DMSO-IgG2a


title: OVCAR3 INX315 Rep2 RB

description: Library name: OVCAR3-INX315-Rep2-RB


title: OVCAR3 INX315 Rep1 RB

description: Library name: OVCAR3-INX315-Rep1-RB


title: OVCAR3 DMSO Rep2 RB

description: Library name: OVCAR3-DMSO-Rep2-RB


title: OVCAR3 DMSO Rep1 RB

description: Library name: OVCAR3-DMSO-Rep1-RB


title: ZR751 Parent palbociclib RNAseq replicate 3

description: Library name: Sample 18

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38)
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

extract_protocol:
RNA was extracted using NucleoSpin RNA Plus kit (Macherey-Nagel).
Libraries were prepared using the QuantaSeq Lexogen 3’mRNA RW kit.

treatment_protocol: Abemaciclib 500 nM, palbociclib 500 nM, or equal volume of DMSO (control) for 5 days.

value: Palbociclib


title: ZR751 Parent palbociclib RNAseq replicate 2

description: Library name: Sample 17


title: ZR751 Parent palbociclib RNAseq replicate 1

description: Library name: Sample 16


title: ZR751 Parent abemaciclib RNAseq replicate 3

description: Library name: Sample 15

value: Abemaciclib


title: ZR751 Parent abemaciclib RNAseq replicate 2

description: Library name: Sample 14


title: ZR751 Parent DMSO RNAseq replicate 3

description: Library name: Sample 12


title: ZR751 Parent abemaciclib RNAseq replicate 1

description: Library name: Sample 13


title: ZR751 Parent DMSO RNAseq replicate 2

description: Library name: Sample 11


title: ZR751 Parent DMSO RNAseq replicate 1

description: Library name: Sample 10


title: CAMA1 Parent palbociclib RNAseq replicate 3

description: Library name: Sample 9


title: CAMA1 Parent palbociclib RNAseq replicate 1

description: Library name: Sample 7


title: CAMA1 Parent abemaciclib RNAseq replicate 3

description: Library name: Sample 6


title: CAMA1 Parent palbociclib RNAseq replicate 2

description: Library name: Sample 8


title: CAMA1 Parent abemaciclib RNAseq replicate 2

description: Library name: Sample 5


title: CAMA1 Parent DMSO RNAseq replicate 3

description: Library name: Sample 3


title: CAMA1 Parent abemaciclib RNAseq replicate 1

description: Library name: Sample 4


title: CAMA1 Parent DMSO RNAseq replicate 1

description: Library name: Sample 1


title: CAMA1 Parent DMSO RNAseq replicate 2

description: Library name: Sample 2


title: ZR-75-1 parent palbociclib IgG2a C&R negative control

description: Library name: ZR751_parent_PB_IgG2a

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for treated samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 20, --smoothLength 60, --scaleFactor scalefactor, --extendReads, where the scalefactor generated by a background normalisation from DiffBind was used as a normalisation factor. Bigwig for the input sample was normalised with BPM.
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter, --format BAMPE -gsize hs. Peaks for the negative input (IgG2a) were called without a control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, narrowPeaks
Library strategy: Cut&Run

treatment_protocol: Palbociclib 500 nM or equal volume of DMSO (control) for 4 days.

value: Parent


title: ZR-75-1 RB1 KO palbociclib Rb C&R

description: Library name: ZR751_sgRB_PB_RB_Rep1

value: RB1 KO


title: scramble_cyto_rep2

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

description: Subcellular RNA-seq of cytoplasmic polyA+ RNA in control mouse keratinocytes infected with sh-scramble (ctrl), replicate 2

data_processing:
Following quality controls, sequencing reads were  aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Tab-delimited text file of raw read counts per gene/samples.

source_name: Keratinocytes

growth_protocol: Mouse keratinocytes were grownin low-calcium Dulbecco’s modified Eagle medium supplemented with 10% FBS, 100 U ml−1 penicillin–streptomycin, HCE cocktail consisting of hydrocortisone 0.5 μg ml−1, insulin 5 μg ml−1 (Thermo Fisher), cholera enterotoxin 10−10 M (Sigma-Aldrich) and EGF 10 ng ml−1 (PeproTech) and cultured at 37 °C in a humidifiedatmosphere, with 8% CO2.

extract_protocol:
Cell protrusions were isolated from mouse keratinocytes (expressing shRNAs for Cbx3, or a scramble shRNA) as described before (Mardakheh M. et al., 2020) with some modiﬁcations to also fractionate the cytoplasm and the nucleus. 2 million cells were seeded on the top of 5 mg/ml collagen-I coated 24.5 mm polycarbonate transwell ﬁlters with 3 μm pore size (Greiner Bio-one) in complete DMEM. Cells were allowed to adhere without the addition of media to the bottom chamber of the transwells. Subsequently, the media on the top of the transwell ﬁlter was replaced by FBS and epidermal growth factor free DMEM, and protrusions were induced by addition of complete DMEM to the bottom chamber. Transwells were then washed with cold PBS, and protrusions were collected by shaving the bottom of the ﬁlter using a glass coverslip dipped in lysis buffer containing RNAse inhibitor (50mM Tris 1M HCl pH7.5, 100mM NaCl, 1% NP40, 0.1%SDS, 0.5%DOC). The cell-body fraction was subsequently purified by direct addition of the hypotonic cytoplasmatic buffer containing RNAse inhibitors on ice for 20min (10mM HEPES pH7.9, 60mM KCl, 1mM DTT, 1mM EDTA, 0.075% NP40) to the top of the ﬁlter, followed by subsequent centrifugation (16,000 × g, for 5 min at 4 °C). The supernatant was retained as cytoplasmic fraction. The nuclei pellet was washed in a washing buffer (10mM HEPES pH7.9, 60mM KCl, 1mM DTT, 1mM EDTA), centrifuged (16,000 × g for 15 min at 4 °C) and then resuspended in a hypertonic nuclear buffer (20mM Tris pH 8.0, 1.5mM MgCl2, 420mM NaCl, 0.2mM  EDTA, 25% Glycerol and 1:100 Protease-inhibitor Mix M). Pellet was dispersed with a pipette and passed through a 27 G needle 5 times. After 10 min-incubation on ice, nuclei were centrifuged (16,000 × g for 15 min at 4 °C) to collect supernatant as nuclear fraction. RNA was extracted from protrusion, cytoplasm and nucleus fractions using the RNeasy Mini Kit (Qiagen).
For library preparation, the quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) selection, and libraries were prepared using the TruSeq stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 1000 System.

value: Keratinocytes

tag: condition

tag: compartment

value: cytoplasm

tag: shRNA

value: sh-Scramble

tag: shRNA type


title: ZR-75-1 parent palbociclib Rb C&R replicate 2

description: Library name: ZR751_parent_PB_RB_Rep2

tag: genotype

tag: treatment


title: ZR-75-1 RB1 KO DMSO Rb C&R

description: Library name: ZR751_sgRB_DMSO_RB_Rep1

tag: cell line

value: DMSO


title: ZR-75-1 parent palbociclib Rb C&R replicate 1

description: Library name: ZR751_parent_PB_RB_Rep1


title: ZR-75-1 parent DMSO Rb C&R replicate 2

description: Library name: ZR751_parent_DMSO_RB_Rep2


title: ZR-75-1 parent DMSO Rb C&R replicate 1

description: Library name: ZR751_parent_DMSO_RB_Rep1


title: ZR-75-1 Parent DMSO IgG2a C&R negative control

description: Library name: ZR751_Par_DMSO_IgG2a

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for treated samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 20, --smoothLength 60, --scaleFactor scalefactor, --extendReads, where the scalefactor generated by a background normalisation from DiffBind was used as a normalisation factor. Bigwig for the input sample was normalised with BPM.
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter, --format BAMPE -gsize hs. Peaks for the negative input (IgG2a) were called without a control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, narrowPeaks
Library strategy: CUT&Run

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 4 days.


title: ZR-75-1 Parent abemaciclib Rb C&R replicate 2

description: Library name: ZR751_Par_LY_RB_native_Rep2


title: ZR-75-1 Parent abemaciclib Rb C&R replicate 1

description: Library name: ZR751_Par_LY_RB_native_Rep1


title: ZR-75-1 Parent DMSO Rb C&R replicate 2

description: Library name: ZR751_Par_DMSO_RB_native_Rep2


title: ZR-75-1 Parent DMSO Rb C&R replicate 1

description: Library name: ZR751_Par_DMSO_RB_native_Rep1


title: MCF7 Parent abemaciclib H3K4me3 C&R replicate 2

description: Library name: MCF7_Par_LY_H3K4me3_native_Rep2

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 1 --normalizeUsing RPKM
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter,-f BAMPE -g hs --broad --broad-cutoff 0.1 -q 0.05. Peaks for the negative input (IgG) were called without a control parameter, -f BAMPE -g hs -q 0.05.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, broadPeaks, narrowPeaks
Library strategy: CUT&Run

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 5 days.


title: MCF7 Parent DMSO IgG C&R negative control

description: Library name: MCF7_Par_DMSO_IgG


title: MCF7 Parent abemaciclib H3K4me3 C&R replicate 1

description: Library name: MCF7_Par_LY_H3K4me3_native_Rep1


title: MCF7 Parent DMSO H3K4me3 C&R replicate 2

description: Library name: MCF7_Par_DMSO_H3K4me3_native_Rep2


title: MCF7 Parent DMSO H3K4me3 C&R replicate 1

description: Library name: MCF7_Par_DMSO_H3K4me3_native_Rep1


title: ZR751_AbemaFulv_rep3

description: Library name: Sample 24

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent). Reads were sequenced on NextSeq500 (Illumina) using 75-cycle High Output Reagent kits

treatment_protocol: Abemaciclib 500 nM, Fulvestrant 5nM, Abemaciclib + Fulvestrant or equal volume of DMSO (control) for 5 days.


title: ZR751_AbemaFulv_rep1

description: Library name: Sample 22


title: ZR751_AbemaFulv_rep2

description: Library name: Sample 23


title: ZR751_Fulv_rep1

description: Library name: Sample 21

value: Fulv


title: ZR751_Fulv_rep3

description: Library name: Sample 20


title: ZR751_Fulv_rep2

description: Library name: Sample 19


title: ZR751_Abema_rep3

description: Library name: Sample 18


title: ZR751_DMSO_rep3

description: Library name: Sample 15


title: ZR751_Abema_rep2

description: Library name: Sample 17


title: ZR751_DMSO_rep2

description: Library name: Sample 14


title: ZR751_Abema_rep1

description: Library name: Sample 16


title: ZR751_DMSO_rep1

description: Library name: Sample 13


title: MCF7_AbemaFulv_rep3

description: Library name: Sample 12


title: MCF7_AbemaFulv_rep2

description: Library name: Sample 11


title: MCF7_AbemaFulv_rep1

description: Library name: Sample 10


title: MCF7_Fulv_rep3

description: Library name: Sample 9


title: MCF7_Fulv_rep2

description: Library name: Sample 8


title: MCF7_Fulv_rep1

description: Library name: Sample 7


title: MCF7_Abema_rep3

description: Library name: Sample 6


title: MCF7_Abema_rep2

description: Library name: Sample 5


title: MCF7_Abema_rep1

description: Library name: Sample 4


title: MCF7_DMSO_rep3

description: Library name: Sample 3


title: MCF7_DMSO_rep2

description: Library name: Sample 2


title: MCF7_DMSO_rep1

description: Library name: Sample 1


title: MCF7 Parent DMSO IgG2a C&R negative control

description: Library name: MCF7_Par_DMSO_IgG2a

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for treated samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 20, --smoothLength 60, --scaleFactor scalefactor, --extendReads, where the scalefactor generated by a background normalisation from DiffBind was used as a normalisation factor. Bigwig for the input sample was normalised with BPM.
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter, --format BAMPE -gsize hs. Peaks for the negative input (IgG2a) and positive control (H3K4me3) were called without a control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, narrowPeaks
Library strategy: CUT&Run

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 2 days.


title: MCF7 RB1 KO abemaciclib H3K4me3 C&R positive control

description: Library name: MCF7_sgRB_Abema_H3K4me3

value: RB1 knockout


title: MCF7 RB1 KO abemaciclib Rb C&R replicate 2

description: Library name: MCF7_sgRB_LY_RB_native_Rep2


title: MCF7 RB1 KO abemaciclib Rb C&R replicate 1

description: Library name: MCF7_sgRB_LY_RB_native_Rep1


title: MCF7 RB1 KO DMSO Rb C&R replicate 2

description: Library name: MCF7_sgRB_DMSO_RB_native_Rep2


title: MCF7 RB1 KO DMSO Rb C&R replicate 1

description: Library name: MCF7_sgRB_DMSO_RB_native_Rep1


title: MCF7 Parent abemaciclib Rb C&R replicate 2

description: Library name: MCF7_Par_LY_RB_native_Rep2


title: MCF7 Parent abemaciclib Rb C&R replicate 1

description: Library name: MCF7_Par_LY_RB_native_Rep1


title: MCF7 Parent DMSO Rb C&R replicate 1.

description: Library name: MCF7_Par_DMSO_RB_native_Rep1


title: MCF7 Parent DMSO Rb C&R replicate 2.

description: Library name: MCF7_Par_DMSO_RB_native_Rep2


title: MCF7 Parent palbociclib Rb C&R replicate 2

description: Library name: MCF7_parent_PB_RB_Rep2

treatment_protocol: Palbociclib 500 nM or equal volume of DMSO (control) for 2 days.


title: MCF7 Parent palbociclib Rb C&R replicate 1

description: Library name: MCF7_parent_PB_RB_Rep1


title: MCF7 Parent palbociclib IgG2a C&R negative control

description: Library name: MCF7_parent_Palb_IgG2a


title: MCF7 Parent DMSO Rb C&R replicate 2

description: Library name: MCF7_parent_DMSO_RB_Rep2


title: MCF7 Parent DMSO Rb C&R replicate 1

description: Library name: MCF7_parent_DMSO_RB_Rep1


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, HFD, biological replicate 5

city: Ariel

first: Tovit

last: Rosenzweig

address: 3 Kiryat HaMada St.

institute: Ariel University

description:
Library name: eWAT_DomHFD_rep5
Column name in featurecounts_eWAT.txt: eWAT_DomHFD_rep5

data_processing:
Raw reads underwent quality control using FastQC (v0.11.7). Adapter sequences and low-quality reads were removed using Trim Galore (v0.5.0).
High-quality reads were aligned to the mouse genome (GRCm38/mm10) using HISAT2 (v2.2.1).
Gene-level read counts were quantified using featureCounts (v1.6.3) with Mus_musculus.GRCm38.97.gtf annotation.
TMM normalization with edgeR; differential expression with voom/limma; BH correction for multiple testing. DEGs: FDR < 0.05 and |log2FC| > 1.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file with raw gene-level read counts from featureCounts. Rows = genes (Ensembl IDs), columns = samples.

source_name: epididymal white adipose tissue (eWAT)

growth_protocol: Male Submissive (Sub) and Dominant (Dom) mice were housed in groups of 5 per cage under standard conditions (12h light/dark, 22°C, ad libitum food and water). At 6 weeks of age, mice were randomly assigned to STD (18% calories from fat) or HFD (60% calories from fat; Research Diets Inc. D12492) for 8 weeks.

extract_protocol:
Adipose tissues (iWAT and eWAT) were dissected, snap-frozen in liquid nitrogen, and stored at -80°C. Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen). RNA quality was assessed using TapeStation 4200 (Agilent).
RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat. E7760). 250 ng total RNA was used. mRNA pull-down was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat. E7490). Library QC was performed using Qubit (Invitrogen) and TapeStation 4200 with High Sensitivity D1000 kit. Sequencing was performed on Illumina NextSeq2000 using P2 100 cycles (Read1-100; Index1-8; Index2-8) at the Technion Genomics Center, Haifa, Israel. Libraries were sequenced as single-end 100 bp reads.

treatment_protocol: No pharmacological treatment was applied to the RNA-seq cohort. Mice were sacrificed at 14 weeks of age.

tag: tissue

value: epididymal white adipose tissue (eWAT)

value: Dominant (Dom)

value: high-fat diet (HFD, 60% calories from fat)


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, HFD, biological replicate 4

description:
Library name: eWAT_DomHFD_rep4
Column name in featurecounts_eWAT.txt: eWAT_DomHFD_rep4


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, HFD, biological replicate 3

description:
Library name: eWAT_DomHFD_rep3
Column name in featurecounts_eWAT.txt: eWAT_DomHFD_rep3


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, HFD, biological replicate 2

description:
Library name: eWAT_DomHFD_rep2
Column name in featurecounts_eWAT.txt: eWAT_DomHFD_rep2


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, STD, biological replicate 5

description:
Library name: eWAT_DomSTD_rep5
Column name in featurecounts_eWAT.txt: eWAT_DomSTD_rep5

value: standard diet (STD, 18% calories from fat)


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, HFD, biological replicate 1

description:
Library name: eWAT_DomHFD_rep1
Column name in featurecounts_eWAT.txt: eWAT_DomHFD_rep1


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, STD, biological replicate 4

description:
Library name: eWAT_DomSTD_rep4
Column name in featurecounts_eWAT.txt: eWAT_DomSTD_rep4


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, STD, biological replicate 2

description:
Library name: eWAT_DomSTD_rep2
Column name in featurecounts_eWAT.txt: eWAT_DomSTD_rep2


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, STD, biological replicate 3

description:
Library name: eWAT_DomSTD_rep3
Column name in featurecounts_eWAT.txt: eWAT_DomSTD_rep3


title: Mus musculus, epididymal WAT, Dominant (Dom) mouse, STD, biological replicate 1

description:
Library name: eWAT_DomSTD_rep1
Column name in featurecounts_eWAT.txt: eWAT_DomSTD_rep1


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, HFD, biological replicate 5

description:
Library name: eWAT_SubHFD_rep5
Column name in featurecounts_eWAT.txt: eWAT_SubHFD_rep5

value: Submissive (Sub)


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, HFD, biological replicate 4

description:
Library name: eWAT_SubHFD_rep4
Column name in featurecounts_eWAT.txt: eWAT_SubHFD_rep4


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, HFD, biological replicate 3

description:
Library name: eWAT_SubHFD_rep3
Column name in featurecounts_eWAT.txt: eWAT_SubHFD_rep3


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, HFD, biological replicate 2

description:
Library name: eWAT_SubHFD_rep2
Column name in featurecounts_eWAT.txt: eWAT_SubHFD_rep2


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, STD, biological replicate 5

description:
Library name: eWAT_SubSTD_rep5
Column name in featurecounts_eWAT.txt: eWAT_SubSTD_rep5


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, HFD, biological replicate 1

description:
Library name: eWAT_SubHFD_rep1
Column name in featurecounts_eWAT.txt: eWAT_SubHFD_rep1


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, STD, biological replicate 4

description:
Library name: eWAT_SubSTD_rep4
Column name in featurecounts_eWAT.txt: eWAT_SubSTD_rep4


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, STD, biological replicate 3

description:
Library name: eWAT_SubSTD_rep3
Column name in featurecounts_eWAT.txt: eWAT_SubSTD_rep3


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, STD, biological replicate 2

description:
Library name: eWAT_SubSTD_rep2
Column name in featurecounts_eWAT.txt: eWAT_SubSTD_rep2


title: Mus musculus, epididymal WAT, Submissive (Sub) mouse, STD, biological replicate 1

description:
Library name: eWAT_SubSTD_rep1
Column name in featurecounts_eWAT.txt: eWAT_SubSTD_rep1


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, HFD, biological replicate 4

description:
Library name: iWAT_DomHFD_rep4
Column name in featurecounts_iWAT.txt: iWAT_DomHFD_rep4

source_name: inguinal white adipose tissue (iWAT)

value: inguinal white adipose tissue (iWAT)


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, HFD, biological replicate 3

description:
Library name: iWAT_DomHFD_rep3
Column name in featurecounts_iWAT.txt: iWAT_DomHFD_rep3


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, HFD, biological replicate 2

description:
Library name: iWAT_DomHFD_rep2
Column name in featurecounts_iWAT.txt: iWAT_DomHFD_rep2


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, HFD, biological replicate 1

description:
Library name: iWAT_DomHFD_rep1
Column name in featurecounts_iWAT.txt: iWAT_DomHFD_rep1


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, STD, biological replicate 4

description:
Library name: iWAT_DomSTD_rep4
Column name in featurecounts_iWAT.txt: iWAT_DomSTD_rep4


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, STD, biological replicate 3

description:
Library name: iWAT_DomSTD_rep3
Column name in featurecounts_iWAT.txt: iWAT_DomSTD_rep3


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, STD, biological replicate 2

description:
Library name: iWAT_DomSTD_rep2
Column name in featurecounts_iWAT.txt: iWAT_DomSTD_rep2


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, HFD, biological replicate 4

description:
Library name: iWAT_SubHFD_rep4
Column name in featurecounts_iWAT.txt: iWAT_SubHFD_rep4


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, HFD, biological replicate 3

description:
Library name: iWAT_SubHFD_rep3
Column name in featurecounts_iWAT.txt: iWAT_SubHFD_rep3


title: Mus musculus, inguinal WAT, Dominant (Dom) mouse, STD, biological replicate 1

description:
Library name: iWAT_DomSTD_rep1
Column name in featurecounts_iWAT.txt: iWAT_DomSTD_rep1


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, HFD, biological replicate 2

description:
Library name: iWAT_SubHFD_rep2
Column name in featurecounts_iWAT.txt: iWAT_SubHFD_rep2


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, HFD, biological replicate 1

description:
Library name: iWAT_SubHFD_rep1
Column name in featurecounts_iWAT.txt: iWAT_SubHFD_rep1


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, STD, biological replicate 4

description:
Library name: iWAT_SubSTD_rep4
Column name in featurecounts_iWAT.txt: iWAT_SubSTD_rep4


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, STD, biological replicate 3

description:
Library name: iWAT_SubSTD_rep3
Column name in featurecounts_iWAT.txt: iWAT_SubSTD_rep3


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, STD, biological replicate 2

description:
Library name: iWAT_SubSTD_rep2
Column name in featurecounts_iWAT.txt: iWAT_SubSTD_rep2


title: Mus musculus, inguinal WAT, Submissive (Sub) mouse, STD, biological replicate 1

description:
Library name: iWAT_SubSTD_rep1
Column name in featurecounts_iWAT.txt: iWAT_SubSTD_rep1


title: HBV HCMS, Tg-HBV-Mouse Liver, Vehicle, 6

first: Jennifer

last: Marlowe

state: Massachusetts

address: 201 Brookline Avenue

institute: nChroma Bio

description: Library name: NGSHC2164

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to a genotype specific HBV reference genome (dependant on sample) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: Genotype D (GenBank Accession: U95551.1) or Genotype A (GenBank Accession: AF305422.1)
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark cytosine report file
Library strategy: EM-seq

source_name: Liver

growth_protocol: HepG2.2.15 cells were cultured in DMEM (Gibco, 11965092) with 10% fetal bovine serum (FBS) (Gibco, A5670501) and 1% Pen-Strep (Gibco, 15140122). One day prior to treatment, 20,000 cells/well were seeded in collagen type I-coated 96-well plates. Plates were maintained and subcultured (cell trypsinization every 3-4 days).  HepG2-NTCP cells were plated at 20,000 cells/well in collagen coated 96-well plates and infected 24 hours later with HBV Genotype D at 2,000 multiplicity of genome equivalents (MGE) using DMEM media supplemented with 4% PEG8000 and 2.5% DMSO. At 16 hours post-infection, media was removed, cells were washed with PBS and were maintained in DMEM media supplemented with 2.5% DMSO.  C57BL/6-HBV transgenic mice (Tg-HBV), 5-6 weeks old, carrying two copies per diploid host genome of the 1.28× Genotype A HBV genome were obtained from Beijing Vitalstar Biotechnology Co., Ltd.

extract_protocol:
HepG2.2.15, cell samples were collected at a timepoint 14 days after treatment. Nucleic acids were extracted using simultaneous RNA and DNA extraction protocols (Beckman Coulter) for methylation assessments.  cccDNA was extracted from HepG2-NTCP using a modified Hirt protocol, using the MasterPure Complete DNA and RNA Purification Kit (LucigenEpicentre) without the proteinase K digestion. Total DNA was digested using 10 U of T5 exonuclease per 1 ug of DNA for 30 mins at 37°C, followed by heat inactivation at 80°C for 20 minutes. One third of the extracted total DNA was not digested and used as a control. After digestion, all samples were concentrated using a standard sodium acetate DNA precipitation protocol.  Tg-HBV mice were euthanized, and liver samples were collected for methylation assessment.
Genomic or cccDNA was sheared to a target size of 350bp using a Covaris 96 AFA-Tube TPX plate. Sequencing libraries were then constructed from the sheared genomic DNA using the NEBNext Enzymatic Methyl-seq (EM-seq) kit plus NEBNext Multiplex Oligos for Enzymatic Methyl-seq. After methylation conversion, a custom panel targeting the appropriate HBV genome (genotype A for Tg-HBV mouse and genotype D for HepG2.2.15 cells and cccDNA) was used to enrich for regions of interest, following the recommended Twist protocol for 8-plex pools. Libraries were then amplified and sequenced using an Illumina NextSeq2000 running NextSeq1000/2000 Control software version 1.7.0.45751 with 2 x 150 bp reads to a sequencing depth of > 5 million read pairs per sample.

treatment_protocol: HepG2.2.15 cells were treated with 100 µL of fresh media supplemented with LNP-formulated epigenetic silencers at a dose of 0.5 µg/mL (or 1.0 µg/mL for CRMA-1001) and/or 1 µg/mL of rhApoE3. Untreated controls were also included for one study.  Infected HepG2-NTCP cells were treated with 1 µg/mL of CRMA-1001 or vehicle. Cells were washed with PBS and snap frozen on Day 7.  All Tg-HBV mice were acclimated for 10 days before receiving a single IV bolus administration of vehicle, or HBV-EE4000 (0.2, 0.5, 1 and 3 mg/kg).

value: Liver

value: HBV Genotype A


title: HBV HCMS, Tg-HBV-Mouse Liver, Vehicle, 5

description: Library name: NGSHC2163


title: HBV HCMS, Tg-HBV-Mouse Liver, Vehicle, 4

description: Library name: NGSHC2162


title: HBV HCMS, Tg-HBV-Mouse Liver, Vehicle, 3

description: Library name: NGSHC2161


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 3.0  mg/kg, 4

description: Library name: NGSHC2168


title: HBV HCMS, Tg-HBV-Mouse Liver, Vehicle, 2

description: Library name: NGSHC2160


title: HBV HCMS, Tg-HBV-Mouse Liver, Vehicle, 1

description: Library name: NGSHC2159


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 3.0  mg/kg, 2

description: Library name: NGSHC2166


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 3.0  mg/kg, 1

description: Library name: NGSHC2165


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 3.0  mg/kg, 3

description: Library name: NGSHC2167


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 1.0  mg/kg, 6

description: Library name: NGSHC2174


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 1.0  mg/kg, 5

description: Library name: NGSHC2173


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 1.0  mg/kg, 4

description: Library name: NGSHC2172


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 1.0  mg/kg, 3

description: Library name: NGSHC2171


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 1.0  mg/kg, 2

description: Library name: NGSHC2170


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.5  mg/kg, 5

description: Library name: NGSHC2179


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.5  mg/kg, 4

description: Library name: NGSHC2178


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 1.0  mg/kg, 1

description: Library name: NGSHC2169


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.5  mg/kg, 3

description: Library name: NGSHC2177


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.5  mg/kg, 1

description: Library name: NGSHC2175


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.5  mg/kg, 2

description: Library name: NGSHC2176


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.2  mg/kg, 4

description: Library name: NGSHC2183


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.2  mg/kg, 2

description: Library name: NGSHC2181


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.2  mg/kg, 1

description: Library name: NGSHC2180


title: HBV HCMS, Tg-HBV-Mouse Liver, HBV-EE4000 0.2  mg/kg, 3

description: Library name: NGSHC2182


title: LRRK2-WT brain, biological replicate 3

city: Incheon

first: jeehoon

last: Lee

country: South Korea

institute: Inha University

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
Raw data were summarized and normalized via the Signal Space Transformation-Robust Multichip Analysis (SST-RMA) method within the Affymetrix Power Tools (APT) suite

label: Biotin

source_name: HFD-fed LRRK2-WT mouse brain

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: LRRK2-WT and LRRK2-GS mice (FVB background) were housed in a specific pathogen-free animal facility under strictly controlled environmental conditions. The facility was maintained at a constant temperature of 22 ± 2°C and a relative humidity of 50 ± 10%, with a standard 12-hour light/dark cycle. Prior to the experimental dietary assignments, all mice were provided ad libitum access to a standard laboratory chow diet and sterile water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: To induce systemic metabolic stress, mice were randomly assigned to one of two dietary cohorts: a standard control diet (CD; 12% w/w) or a high-fat diet (HFD; 45% w/w). The respective dietary regimens were maintained continuously for a duration of 12 weeks. Throughout the 12-week dietary intervention period, body weights and food consumption were routinely monitored to validate the onset and progression of the diet-induced metabolic phenotype.

value: Brain


title: LRRK2-WT brain, biological replicate 1


title: LRRK2-GS brain, biological replicate 3

source_name: HFD-fed LRRK2-GS mouse brain


title: LRRK2-GS brain, biological replicate 2


title: LRRK2-GS brain, biological replicate 1


title: colon_DKO_rep3

city: shijiazhuang

first: Hong

last: LIU

address: East side of South Taihang Street

country: China

institute: Hebei Public Security Police Vocational College

description: Gene expression data from healthy mouse colon at 12-16 weeks of age

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on microarray chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were washed and scanned using a GeneChip Scanner 3000 7G.

data_processing: Raw data were saved as CEL files and analyzed with Transcriptome Analysis Console (TAC) software, version 4.0.2.

label: biotin

source_name: healthy colonic tissues from DKO at 12-16 weeks of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male mice were housed at 22 ± 2°C under a 14-h light cycle with free access to food and water.

extract_protocol: Total RNA was extracted from colonic tissues using ISOGEN II (Nippon Gene Co., Ltd., Tokyo, Japan).

treatment_protocol: four healthy male mice (12-16 weeks of age) were randomly selected from each genotype group, and their colons and cecal contents were collected and stored at -80 ℃

value: colonic tissues

value: double knockout


title: colon_DKO_rep2


title: LRRK2-WT brain, biological replicate 2


title: colon_IL4i1 KO_rep2

source_name: healthy colonic tissues from IL4i1 KO at 12-16 weeks of age

value: IL4i1 knockout


title: colon_IL4i1 KO_rep3


title: colon_DKO_rep1


title: colon_LAO1 KO_rep3

source_name: healthy colonic tissues from LAO1 KO at 12-16 weeks of age

value: LAO1 knockout


title: colon_LAO1 KO_rep2


title: colon_IL4i1 KO_rep1


title: Human Methylome HCMS, HAdCC Donor 1, Untreated, 1

description: Library name: NGSHC3158

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to the human reference genome (GRCh38) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: GRCh38
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark methylation coverage file
Library strategy: EM-seq

source_name: Adrenal

growth_protocol: Primary human hepatocytes (PHH) isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium (dHCGM media [PhoenixBio], 10% FBS). Primary human splenic endothelial cells (HSECs) (Innoprot and Accegen) were cultured in media (endothelial cell medium (ScienCell) with 5% FBS, 1% Pen-Strep, and 1% endothelial cell growth supplement [ScienCell]) and incubated at 37˚C and in 5% CO2. Primary human adrenal cortical cells (HAdCCs) (Accegen) were cultured in media (Mesenchymal Stem Cell Medium (Innoprot) with 5% FBS, 1% Pen-Strep and 1% Mesenchymal Stem Cell Growth Serum (Innoprot) and incubated at 37˚C and in 5% CO2.

extract_protocol:
From each PHH donor, 4 x 105 µL aliquots of lysate were processed for DNA extraction. From each HAdCC and HSEC donor, 4 x 63 µL aliquots of lysate were mixed with 42 µL of additional LBE buffer per aliquot and processed for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter patented SPRI paramagnetic beads to bind total DNA from the cell lysate. DNA-bound beads were then pelleted with a plate magnet, and the supernatants were removed and discarded before DNA-bound beads were treated with RNase in Beckman Coulter WBA buffer, pelleted with a plate magnet, and the supernatants removed. The retained DNA-bound beads were then washed twice with 70% ethanol. gDNA was eluted from the paramagnetic beads in 10 mM Tris pH 8.0, all twelve technical replicate wells combined and transferred to a clean storage plate.
The first step of the Hybrid Capture Methylation Sequencing (HCMS) workflow was the preparation of EM-seq libraries using Twist NGS Methylation Detection System. Samples were normalized in 10 mM Tris pH 8.0 to generate aliquots containing 200 ng of gDNA in 50 µL. Samples were then mechanically sheared on a Covaris R230 Focused Ultrasonicator to a size range of 350 – 450 bp and at least 5% of the samples were evaluated on a D1000 HS ScreenTape to ensure target size range was reached. The second step of the HCMS workflow was enrichment of DNA fragments for sequencing. Target-enrichment for subsequent methylation sequencing was accomplished through a hybridization reaction in which biotinylated DNA probes were used to capture regions of interest from the whole genome EM-seq library. The biotinylated DNA probe panel and capture reagents were supplied by Twist Biosciences and the workflow was performed following the manufacturer’s recommendations. Briefly, the hybridization reaction was carried out by first drying down 8-plex library pools in a mix of the custom biotinylated DNA probe panel, reaction buffer, and universal blocking oligos, which prevent library fragments from annealing to each other at their adapter sequences. The dried reactions were then resuspended in prewarmed hybridization buffer (65˚C) and incubated on a thermocycler for a hybridization time of 16 hours. Following hybridization, biotinylated DNA probes bound to target gDNA sequences were enriched using streptavidin beads. Streptavidin beads bound to the probe-library complex were pelleted on a magnet and unbound (i.e., off panel) fragments removed through a series of heated washes. The final bead slurry was resuspended in water before performing a PCR amplification to enrich the captured library fragments. Following amplification, libraries were purified with Twist Total Purification beads. Final library concentrations were determined by using the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader. Library fragment size was assessed on a High Sensitivity DNA 1000 ScreenTape on the Agilent 4200 Tapestation instrument. Libraries were pooled in an equimolar manner and, to ensure proper quantitation of sequenceable library molecules, qPCR was also performed using the NEBNext Library Quant Kit for Illumina.  Enriched EM-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and a targeted sequencing depth of >200 M read-pairs per library.

treatment_protocol: For PHH, on the day of treatment cells were treated with 500 µL culture media supplemented with 1 µg/mL of rhApoE3 and 0.5 or 1 µg/mL CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HSEC, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of human fibronectin and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of fresh media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HAdCCs, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of Poly-L-Lysine (Sigma-Aldrich) and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). Plates were maintained, cells sub-cultured (cell trypsinization every 3-4 days, followed by transfer of ~10,000 cells to a new 96-well culture plate with fresh media). All cells were collected for extraction 14 days after treatment.

value: Adrenal

value: HAdCC cells

tag: cell type

value: Human Adrenal Cortical Cells


title: Human Methylome HCMS, HAdCC Donor 1, Untreated, 2

description: Library name: NGSHC3166


title: Human Methylome HCMS, HAdCC Donor 1, Untreated, 3

description: Library name: NGSHC3168


title: colon_wt_rep3

source_name: healthy colonic tissues from wt at 12-16 weeks of age

value: wild type


title: Human Methylome HCMS, HAdCC Donor 1, PCSK9-EE7000, 3

description: Library name: NGSHC3163


title: colon_wt_rep1


title: colon_LAO1 KO_rep1


title: colon_wt_rep2


title: Human Methylome HCMS, HAdCC Donor 1, PCSK9-EE7000, 2

description: Library name: NGSHC3160


title: Human Methylome HCMS, HAdCC Donor 1, PCSK9-EE7000, 1

description: Library name: NGSHC3155


title: Human Methylome HCMS, HAdCC Donor 1, Mock-treatment, 3

description: Library name: NGSHC3167


title: Human Methylome HCMS, HAdCC Donor 1, Mock-treatment, 1

description: Library name: NGSHC3157


title: Human Methylome HCMS, HAdCC Donor 1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3162


title: Human Methylome HCMS, HAdCC Donor 1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3154


title: Human Methylome HCMS, HAdCC Donor 1, Mock-treatment, 2

description: Library name: NGSHC3165


title: Human Methylome HCMS, HAdCC Donor 1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3161


title: Human Methylome HCMS, HAdCC Donor 1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3159


title: Human Methylome HCMS, HAdCC Donor 1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3164


title: Human Methylome HCMS, HAdCC Donor 1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3156


title: Custom Panel2 HCMS, HAdCC Donor3, Untreated, 3

description: Library name: NGSHC3640


title: Custom Panel2 HCMS, HAdCC Donor3, Untreated, 4

description: Library name: NGSHC3641


title: Custom Panel2 HCMS, HAdCC Donor3, Untreated, 2

description: Library name: NGSHC3639


title: Custom Panel2 HCMS, HAdCC Donor3, Untreated, 1

description: Library name: NGSHC3638


title: Custom Panel2 HCMS, HAdCC Donor3, PCSK9-EE7000, 4

description: Library name: NGSHC3629


title: Custom Panel2 HCMS, HAdCC Donor3, PCSK9-EE7000, 2

description: Library name: NGSHC3627


title: Custom Panel2 HCMS, HAdCC Donor3, PCSK9-EE7000, 3

description: Library name: NGSHC3628


title: Custom Panel2 HCMS, HAdCC Donor3, PCSK9-EE7000, 1

description: Library name: NGSHC3626


title: Custom Panel2 HCMS, HAdCC Donor3, Mock-treatment, 3

description: Library name: NGSHC3636


title: Custom Panel2 HCMS, HAdCC Donor3, Mock-treatment, 4

description: Library name: NGSHC3637


title: Custom Panel2 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSHC3625


title: Custom Panel2 HCMS, HAdCC Donor3, Mock-treatment, 1

description: Library name: NGSHC3634


title: Custom Panel2 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSHC3624


title: Custom Panel2 HCMS, HAdCC Donor3, Mock-treatment, 2

description: Library name: NGSHC3635


title: Custom Panel2 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSHC3623


title: Custom Panel2 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSHC3622


title: Custom Panel2 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3633


title: Custom Panel2 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3632


title: Custom Panel2 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3631


title: Custom Panel2 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3630


title: Custom Panel2 HCMS, HAdCC Donor2, Untreated, 4

description: Library name: NGSHC3621


title: Custom Panel2 HCMS, HAdCC Donor2, Untreated, 3

description: Library name: NGSHC3620


title: Custom Panel2 HCMS, HAdCC Donor2, Untreated, 2

description: Library name: NGSHC3619


title: Custom Panel2 HCMS, HAdCC Donor2, Untreated, 1

description: Library name: NGSHC3618


title: Custom Panel2 HCMS, HAdCC Donor2, PCSK9-EE7000, 4

description: Library name: NGSHC3597


title: Custom Panel2 HCMS, HAdCC Donor2, PCSK9-EE7000, 3

description: Library name: NGSHC3596


title: Custom Panel2 HCMS, HAdCC Donor2, PCSK9-EE7000, 2

description: Library name: NGSHC3595


title: Custom Panel2 HCMS, HAdCC Donor2, PCSK9-EE7000, 1

description: Library name: NGSHC3594


title: Custom Panel2 HCMS, HAdCC Donor2, Mock-treatment, 4

description: Library name: NGSHC3613


title: Custom Panel2 HCMS, HAdCC Donor2, Mock-treatment, 2

description: Library name: NGSHC3611


title: Custom Panel2 HCMS, HAdCC Donor2, Mock-treatment, 3

description: Library name: NGSHC3612


title: Custom Panel2 HCMS, HAdCC Donor2, Mock-treatment, 1

description: Library name: NGSHC3610


title: Custom Panel2 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSHC3589


title: Custom Panel2 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSHC3588


title: Custom Panel2 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSHC3587


title: Custom Panel2 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSHC3586


title: Custom Panel2 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3605


title: Custom Panel2 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3602


title: Custom Panel2 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3603


title: Custom Panel2 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3604


title: Custom Panel2 HCMS, HAdCC Donor1, Untreated, 4

description: Library name: NGSHC3617


title: Custom Panel2 HCMS, HAdCC Donor1, Untreated, 2

description: Library name: NGSHC3615


title: Custom Panel2 HCMS, HAdCC Donor1, Untreated, 1

description: Library name: NGSHC3614


title: Custom Panel2 HCMS, HAdCC Donor1, PCSK9-EE7000, 4

description: Library name: NGSHC3593


title: Custom Panel2 HCMS, HAdCC Donor1, Untreated, 3

description: Library name: NGSHC3616


title: Custom Panel2 HCMS, HAdCC Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3592


title: Custom Panel2 HCMS, HAdCC Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3591


title: Custom Panel2 HCMS, HAdCC Donor1, Mock-treatment, 4

description: Library name: NGSHC3609


title: Custom Panel2 HCMS, HAdCC Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3590


title: Custom Panel2 HCMS, HAdCC Donor1, Mock-treatment, 2

description: Library name: NGSHC3607


title: Custom Panel2 HCMS, HAdCC Donor1, Mock-treatment, 3

description: Library name: NGSHC3608


title: Custom Panel2 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSHC3585


title: Custom Panel2 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3583


title: Custom Panel2 HCMS, HAdCC Donor1, Mock-treatment, 1

description: Library name: NGSHC3606


title: Custom Panel2 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3582


title: Custom Panel2 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3584


title: Custom Panel2 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3601


title: Custom Panel2 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3600


title: Custom Panel2 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3599


title: Custom Panel2 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3598


title: Human Methylome HCMS, HSEC Donor1, Untreated, 2

description: Library name: NGSHC3182

source_name: Spleen

value: Spleen

value: HSEC cells

value: Human Splenic Endothelial Cells


title: Human Methylome HCMS, HSEC Donor1, Untreated, 3

description: Library name: NGSHC3184


title: Human Methylome HCMS, HSEC Donor1, Untreated, 1

description: Library name: NGSHC3174


title: Human Methylome HCMS, HSEC Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3171


title: Human Methylome HCMS, HSEC Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3179


title: Human Methylome HCMS, HSEC Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3176


title: Human Methylome HCMS, HSEC Donor1, Mock-treatment, 2

description: Library name: NGSHC3181


title: Human Methylome HCMS, HSEC Donor1, Mock-treatment, 3

description: Library name: NGSHC3183


title: Human Methylome HCMS, HSEC Donor1, Mock-treatment, 1

description: Library name: NGSHC3173


title: Human Methylome HCMS, HSEC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3178


title: Human Methylome HCMS, HSEC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3175


title: Human Methylome HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3180


title: Human Methylome HCMS, HSEC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3170


title: Human Methylome HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3177


title: Custom Panel2 HCMS, HSEC Donor3, Untreated, 3

description: Library name: NGSHC3576


title: Custom Panel2 HCMS, HSEC Donor3, Untreated, 4

description: Library name: NGSHC3577


title: Human Methylome HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3172


title: Custom Panel2 HCMS, HSEC Donor3, Untreated, 2

description: Library name: NGSHC3575


title: Custom Panel2 HCMS, HSEC Donor3, Untreated, 1

description: Library name: NGSHC3574


title: Custom Panel2 HCMS, HSEC Donor3, PCSK9-EE7000, 4

description: Library name: NGSHC3565


title: Custom Panel2 HCMS, HSEC Donor3, PCSK9-EE7000, 3

description: Library name: NGSHC3564


title: Custom Panel2 HCMS, HSEC Donor3, PCSK9-EE7000, 2

description: Library name: NGSHC3563


title: Custom Panel2 HCMS, HSEC Donor3, PCSK9-EE7000, 1

description: Library name: NGSHC3562


title: Custom Panel2 HCMS, HSEC Donor3, Mock-treatment, 4

description: Library name: NGSHC3573


title: Custom Panel2 HCMS, HSEC Donor3, Mock-treatment, 3

description: Library name: NGSHC3572


title: Custom Panel2 HCMS, HSEC Donor3, Mock-treatment, 2

description: Library name: NGSHC3571


title: Custom Panel2 HCMS, HSEC Donor3, Mock-treatment, 1

description: Library name: NGSHC3570


title: Custom Panel2 HCMS, HSEC Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSHC3561


title: Custom Panel2 HCMS, HSEC Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSHC3560


title: Custom Panel2 HCMS, HSEC Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSHC3559


title: Custom Panel2 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3569


title: Custom Panel2 HCMS, HSEC Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSHC3558


title: Custom Panel2 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3567


title: Custom Panel2 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3568


title: Custom Panel2 HCMS, HSEC Donor2, Untreated, 4

description: Library name: NGSHC3557


title: Custom Panel2 HCMS, HSEC Donor2, Untreated, 3

description: Library name: NGSHC3556


title: Custom Panel2 HCMS, HSEC Donor2, Untreated, 2

description: Library name: NGSHC3555


title: Custom Panel2 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3566


title: Custom Panel2 HCMS, HSEC Donor2, Untreated, 1

description: Library name: NGSHC3554


title: Custom Panel2 HCMS, HSEC Donor2, PCSK9-EE7000, 4

description: Library name: NGSHC3545


title: Custom Panel2 HCMS, HSEC Donor2, PCSK9-EE7000, 3

description: Library name: NGSHC3544


title: Custom Panel2 HCMS, HSEC Donor2, PCSK9-EE7000, 1

description: Library name: NGSHC3542


title: Custom Panel2 HCMS, HSEC Donor2, PCSK9-EE7000, 2

description: Library name: NGSHC3543


title: Custom Panel2 HCMS, HSEC Donor2, Mock-treatment, 4

description: Library name: NGSHC3553


title: Custom Panel2 HCMS, HSEC Donor2, Mock-treatment, 3

description: Library name: NGSHC3552


title: Custom Panel2 HCMS, HSEC Donor2, Mock-treatment, 2

description: Library name: NGSHC3551


title: Custom Panel2 HCMS, HSEC Donor2, Mock-treatment, 1

description: Library name: NGSHC3550


title: Custom Panel2 HCMS, HSEC Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSHC3540


title: Custom Panel2 HCMS, HSEC Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSHC3541


title: Custom Panel2 HCMS, HSEC Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSHC3539


title: Custom Panel2 HCMS, HSEC Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSHC3538


title: day1died_21

description: Library name: Sample57

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

source_name: Blood

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: Blood

value: CXCR2+ cells

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

tag: batch

tag: group

value: Lethal group


title: Custom Panel2 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3549


title: Custom Panel2 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3548


title: Custom Panel2 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3546


title: Custom Panel2 HCMS, HSEC Donor1, Untreated, 4

description: Library name: NGSHC3537


title: Custom Panel2 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3547


title: Custom Panel2 HCMS, HSEC Donor1, Untreated, 2

description: Library name: NGSHC3535


title: Custom Panel2 HCMS, HSEC Donor1, Untreated, 1

description: Library name: NGSHC3534


title: Custom Panel2 HCMS, HSEC Donor1, PCSK9-EE7000, 4

description: Library name: NGSHC3525


title: Custom Panel2 HCMS, HSEC Donor1, Untreated, 3

description: Library name: NGSHC3536


title: Custom Panel2 HCMS, HSEC Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3524


title: Custom Panel2 HCMS, HSEC Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3523


title: Custom Panel2 HCMS, HSEC Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3522


title: Custom Panel2 HCMS, HSEC Donor1, Mock-treatment, 4

description: Library name: NGSHC3533


title: Custom Panel2 HCMS, HSEC Donor1, Mock-treatment, 3

description: Library name: NGSHC3532


title: Custom Panel2 HCMS, HSEC Donor1, Mock-treatment, 2

description: Library name: NGSHC3531


title: Custom Panel2 HCMS, HSEC Donor1, Mock-treatment, 1

description: Library name: NGSHC3530


title: Custom Panel2 HCMS, HSEC Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSHC3521


title: Custom Panel2 HCMS, HSEC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3519


title: Custom Panel2 HCMS, HSEC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3520


title: Custom Panel2 HCMS, HSEC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3518


title: Custom Panel2 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3529


title: Custom Panel2 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3528


title: Custom Panel2 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3527


title: Custom Panel2 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3526


title: Human Methylome HCMS, PHH Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3141

value: Liver

value: PXB cells

value: Primary Human Hepatocyte


title: Human Methylome HCMS, PHH Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3149


title: Human Methylome HCMS, PHH Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3133


title: Human Methylome HCMS, PHH Donor1, Mock-treatment, 3

description: Library name: NGSHC3147


title: Human Methylome HCMS, PHH Donor1, Mock-treatment, 2

description: Library name: NGSHC3139