title: CBB_31a

description: Library name: CBB_31a


title: CBB_30

status: Public on Nov 30 2025

type: SRA

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Library name: CBB_30

library_source: transcriptomic

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, v.20 101 214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: A. thaliana plants were grown for 5-6 weeks  in jiffy pellets, 21 oC, 10/14 light/dark

extract_protocol:
RNeasy Plant MiniKit (Qiagen)
performed by Eurofins Genomics

treatment_protocol: Rosettes were sprayed and left for 24 h with elicitor chitosan (0.001% with 0.005% Silwett), or with mock (0.005% Silwett).

tag: tissue

value: leaf tissue

tag: cell type

value: whole leaf tissues and cells

tag: genotype

tag: treatment

value: chitosan


title: Control 2

type: genomic

city: London

first: Samuel

last: Asfaha

address: 1151 Richmond St

country: Canada

institute: Univeristy of Western Ontario

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

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

data_processing: Preprocessing of IDAT files was done using the R package SeSaMe and included calculation of detection p values (probes with a detection p value of <0.05 were retained), background subtraction, strain interference, and dye bias correction.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: Colon

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from isolated colonic epithelial cells using the Invitrogen DNA isolation kit according to manufacturer's instructions.

treatment_protocol: C57Bl6/J mice were treated with one dose 5 mg/kg 5-AZA-2'-deoxycytidine or vehicle (saline) 2 days prior to 2.5% DSS treatment for 5 days. 5 and 10 days post the end of DSS mice recevied additional doses of 5mg/kg 5-AZA or vehicle. 14 days post the end of DSS, colonic epithelial cells were isolated for analysis.

value: Colon

tag: Sex

value: Male

value: Colonic epithelial cells

value: Saline+water


title: Ventricular fibroblasts, TGFB, rep2

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

country: USA

institute: Univeristy of Chicago

description: Library name: Sample 4

library_source: genomic

data_processing:
For each biological condition, paired-end reads (*_R1 and *_R2 fastqs) from all replicates were combined and run through HiC-Pro40 v2.10.0 with default parameters, using an in silico digested genome file provided by Arima genomics to align to the mm10 reference and ultimately generate a .validPairs file for further processing. Validpairs file were then converted to hic files using fithic tools and Juicebox tools.
Assembly: mm10
Supplementary files format and content: .hic files

source_name: Adult mouse ventricular fibroblasts

extract_protocol:
Following cell collection, genomic DNA was isolated, crosslinked, and digested with a proprietary restriction enzyme cocktail. Digested DNA overhangs were filled with biotin-14-dATP, and the resulting blunt ends were ligated to capture proximity interactions. The ligated DNA was then purified, sonicated, and size-selected, followed by streptavidin-based enrichment to capture biotinylated ligation junctions.
Final Hi-C libraries were constructed using distinct Illumina indexed adapters and subjected to paired-end sequencing

value: Adult mouse ventricular fibroblasts

value: TGFB


title: cdMSC22

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Processed data file 2.xlsx

data_processing:
Strand NGS software was used.
Assembly: Human hg38
Supplementary files format and content: Processsed excel file includes raw counts and normalized value of each samples

organism: Homo sapiens

source_name: human dermal fibroblasts

extract_protocol:
RNA was extracted using QIAqube and RNeasy kit with Dnase treatment.
RNA libraries for RNA-seq was prepared using the TruSeq Standed mRNA library prep kit.

value: human dermal fibroblasts


title: SNI-Mef2c-NAc, replicate5

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
Raw sequencing reads were mapped to the mm10 genome using the NGS-Data-Charmer pipeline.  In brief, reads were trimmed to remove adaptor and low-quality sequences, then the reads were aligned to the reference genome. Duplicate alignments were removed prior to gene counting and downstream analysis. Counts of mapped reads were obtained using featureCounts against the GENCODE m25 annotation.
Assembly: mm10
Supplementary files format and content: counts_matrix.txt: Tab-delimited text file containing the raw read counts for annotated genes, with individual samples present as columns. fpkm_matrix.txt: Tab-delimited text file containing the normalized read counts (in fragments per kilobase per million) for annotated genes, with individual samples present as columns.

source_name: Nucleus Accumbens

extract_protocol:
RNA was isolated using a TRIzol:chloroform phase separation protocol.
Stranded mRNA Prep Kit (Illumina)

treatment_protocol: Mice were euthanized by decapitation, and bilateral NAc tissue was rapidly dissected on ice from 1-mm thick coronal sections using a 14G punch and flash frozen on dry ice.

value: Nucleus Accumbens

tag: viral injection

value: SNI


title: Control 1


title: SNI-Mef2c-NAc, replicate6


title: SNI-Mef2c-NAc, replicate3


title: Ventricular fibroblasts, DMSO, rep2

description: Library name: Sample 2

value: DMSO


title: SNI-Mef2c-NAc, replicate4


title: CBB_29

description: Library name: CBB_29


title: CB2_27

description: Library name: CB2_27


title: HDF22

description: Processed data file 2.xlsx


title: CB2_28

description: Library name: CB2_28


title: Ventricular fibroblasts, TGFB, rep1

description: Library name: Sample 3


title: SNI-Mef2c-NAc, replicate2


title: Ventricular fibroblasts, DMSO, rep1

description: Library name: Sample 1


title: SNI-Mef2c-NAc, replicate1


title: Control 3


title: Single nuclei,Acute Day 1 post injection of saline,  biol rep 3 and 4

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

description:
Library name: 1FS2
Nuclei
1FS2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger Cell Ranger software v7.1.0 (10X v3.1 HT kit), or Space Ranger v1.3.1
Further processing was done with Seurat v4.1(cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using FindVariableFeatures from Seurat R package version 4.1
Assembly: Rnor-6.0-premrna
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: Cardiac

extract_protocol:
Nuclei from cardiac tissue was isolated as mentioned previously. In brief, flash frozen LV free wall samples were resuspended in nuclei lysis buffer (Millipore Sigma, Nuclei EZ prep, NUC101), 0.2 U/L RNase inhibitor (Enzymatic Y9240L) and finely chopped with scissors. Samples were homogenized with a 2 mL dounce grinder (KIMBLE) with the lysates filtered through a 100 µm, 50 µm, 20 µm strainers (CellTrics filters), respectively. The samples were centrifuged at 1000g for 5 min at 4C to pellet nuclei. The nuclear pellet was resuspended in a sucrose gradient buffer  and centrifuged at 1000g at 4ºC for 10 minutes. The pellet was then washed with a nuclei storage buffer containing 10 μg ml−1 4′,6-diamidino-2-phenylindole DAPI and centrifuged at 500 g and 4ºC for 5 minutes, with the pellet resuspending in 200 mL of 2% BSA in 1x PBS. Nuclei were then counted on a hemocytometer and volume adjusted to 1000 nuclei/µL for loading. snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics (Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 7.1.0 or Space Ranger v1.3.1 from 10X Genomics.
snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics (Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 or NovaSeq X Plus instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 7.1.0 pipeline or Space ranger v1.3.1 from 10X Genomics.

value: Cardiac

value: intracoronary infusion of saline


title: HDF18

description: Processed data file 2.xlsx


title: CB1_24a

description: Library name: CB1_24a


title: RNA-Seq, TAC, right atria, Day 9, Replicate 2

description: Library name: Sample 19

data_processing:
Dataset was processed  with the UCSC mm10 genome assembly through nf-core/rnaseq v3.13.2. The pipeline employed reproducible environments from the Bioconda and Biocontainers projects, using STAR v2.6.1d for read alignment, Samtools v1.10 for file processing, and Salmon v1.10.1 for transcript quantification. Pipeline execution was coordinated with Nextflow v23.10.0.
Assembly: mm10
Supplementary files format and content: Salmon quant files

molecule: polyA RNA

source_name: Heart, right atria

extract_protocol:
RNA was prepared with a TRIzol-based extraction protocol, and isolated using a Qiagen RNeasy Mini Column.
RNA libraries for RNA-seq were prepared using Lexogen CORALL PolyA selection module and Lexogen CORALL Total RNA Library Kit.

value: Heart, right atria

value: TAC


title: ATMSC 3

description: Processed data file 1.xlsx

value: ATMSC


title: SNI-Gfp-NAc, replicate6

value: Egfp


title: CB1_22

description: Library name: CB1_22

value: leaf tissue

value: whole leaf tissues and cells

value: chitosan


title: cdMSC18

description: Processed data file 2.xlsx


title: RNA-Seq, Sham, right atria, Day 9, Replicate 3

description: Library name: Sample 17

value: Sham


title: ATMSC 2

description: Processed data file 1.xlsx


title: ATMSC 1

description: Processed data file 1.xlsx


title: RNA-Seq, Sham, right atria, Day 9, Replicate 2

description: Library name: Sample 16


title: SNI-Gfp-NAc, replicate4


title: RNA-Seq, Sham, right atria, Day 9, Replicate 1

description: Library name: Sample 15


title: BB_14

description: Library name: BB_14

value: mock


title: CB2_26

description: Library name: CB2_26


title: BB_15

description: Library name: BB_15


title: cdMSC45 3

description: Processed data file 1.xlsx


title: cdMSC45 2

description: Processed data file 1.xlsx


title: BB_13

description: Library name: BB_13


title: SNI-Gfp-NAc, replicate3


title: Single nuclei, Acute Day 1 post injection of iECM,  biol rep 3 and 4

description:
Library name: 1Fi2
Nuclei
1Fi2

value: intracoronary infusion of iECM


title: SNI-Gfp-NAc, replicate2


title: cdMSC45 1

description: Processed data file 1.xlsx


title: SNI-Gfp-NAc, replicate1


title: RNA-Seq, TAC, left ventricle, Day 9, Replicate 2

description: Library name: Sample 13

source_name: Heart, left ventricle

value: Heart, left ventricle


title: Sham-Mef2c-NAc, replicate6


title: RNA-Seq, TAC, right atria, Day 9, Replicate 1

description: Library name: Sample 18


title: B2_9

description: Library name: B2_9


title: RNA-Seq, TAC, left ventricle, Day 9, Replicate 1

description: Library name: Sample 12


title: B2_11

description: Library name: B2_11


title: HDF45 2

description: Processed data file 1.xlsx

value: human dermal fibroblasts


title: SNI-Gfp-NAc, replicate5

value: Nucleus Accumbens


title: Sham-Mef2c-NAc, replicate5


title: RNA-Seq, Sham, left ventricle, Day 9, Replicate 4

description: Library name: Sample 11


title: HDF45 1

description: Processed data file 1.xlsx


title: RNA-Seq, Sham, left ventricle, Day 9, Replicate 3

description: Library name: Sample 10


title: RNA-Seq, TAC, left ventricle, Day 9, Replicate 3

description: Library name: Sample 14


title: B2_10

description: Library name: B2_10


title: B1_rep

description: Library name: B1_rep


title: Sham-Mef2c-NAc, replicate3


title: B1_7

description: Library name: B1_7


title: Sham-Mef2c-NAc, replicate2


title: RNA-Seq, Sham, left ventricle, Day 9, Replicate 1

description: Library name: Sample 8


title: B1_6a

description: Library name: B1_6a


title: Sham-Mef2c-NAc, replicate1


title: Sham-Gfp-NAc, replicate6


title: RNA-Seq, TAC, Left atria, Day 9, Replicate 3

description: Library name: Sample 7

source_name: Heart, left atria

value: Heart, left atria


title: RNA-Seq, TAC, Left atria, Day 9, Replicate 2

description: Library name: Sample 6


title: Sham-Gfp-NAc, replicate5


title: Sham-Gfp-NAc, replicate4


title: RNA-Seq, TAC, Left atria, Day 9, Replicate 1

description: Library name: Sample 5


title: CTRL #3

city: Yangsan-si

first: Hyerin

last: Lee

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan National University

data_processing:
Raw sequencing data quality and basic statistics were assessed using FastQC to ensure the integrity of the data before analysis. Reads with low quality (e.g., those with more than 10% N bases or a quality score below 20) were removed.
High-quality reads were aligned to the Danio rerio genome (GRCz11) using STAR (v2.7.11b). The genome and annotation files (Danio_rerio.GRCz11.104.gtf) were sourced from the Ensembl database. The alignment was conducted under default parameters to obtain a high alignment rate, and unmapped reads were excluded from further analysis.
Gene-level expression was quantified using Salmon, which provided normalized counts. These counts were then imported into R (v4.2.2) using the tximport package (v1.26.1) for downstream analysis.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Danio rerio

source_name: whole body

extract_protocol:
TRIzol reagent protocol
The libraries were prepared for 150bp paired-end sequencing using TruSeq Stranded mRNA Sample Prep Kit. Namely, mRNA molecules were purified and fragmented from 0.1-1μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×150bp) using Illumina Novaseq 6000 (Illumina, CA, USA).

value: whole body

value: WT

value: Vehicle


title: RNA-Seq, Sham, Left atria, Day 9, Replicate 3

description: Library name: Sample 3


title: Sham-Mef2c-NAc, replicate4


title: CTRL #2


title: HDF45 3

description: Processed data file 1.xlsx


title: Sham-Gfp-NAc, replicate2


title: siCBLL1 #3

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Assembly: GRCh38.83
Supplementary files format and content: Tab delimited text file contain gene expression in counts

source_name: Cell line

growth_protocol: MDA-MB-231 cells were maintained in in RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate and 10% fetal bovine serum (FBS).  siRNA-mediated functional depletion of CBLL1 (Smartpool, GE Dharmacon) was performed in MDA-MB-231 breast cancer cells grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% FBS. ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.The effect on global gene expression and alternative splicing was determined by RNA sequencing.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit with oncolumn DNase treatment
Illumina

treatment_protocol: A SmartPool siRNAs targeting CBLL1 (GE Dharmacon) were used to deplete CBLL1 in MDA-MB-231 breast cancer cells and the effects on gene expression determined.

value: Cell line

tag: cell line

value: Breast cancer

value: CBLL1 knockdown


title: CB1_21

description: Library name: CB1_21


title: PE 2um #3

value: polyethylene


title: Bo_Bacill_3610_2

city: Malaga

first: Alicia

last: Pérez Lorente

address: Av Louis Pasteur 49. IHSM

country: Spain

institute: University of Malaga

description:
Library name: Bo_Bacill_3610_2
COND_coculture_vs_COND_control_all_3610.xlsx

data_processing:
The raw reads were pre-processed with SeqTrimNext using the specific NGS technology configuration parameters (Falgueras et al., 2010). This pre-processing removes low quality, ambiguous and low complexity stretches, linkers, adapters, vector fragments, and contaminated sequences while keeping the longest informative parts of the reads. SeqTrimNext also discarded sequences below 25 bp. Subsequently, clean reads were aligned and annotated using the Cucumis melo genome as the reference with Bowtie2 (Langmead and Salzberg, 2012) in BAM files, which were then sorted and indexed using SAMtools v1.484110 (Li et al., 2009).
Uniquely localized reads were used to calculate the read number value for each gene via Sam2counts (https://github.com/vsbuffalo/sam2counts). Differentially expressed genes (DEGs) between treatments were analyzed via DEgenes Hunter, which provides a combined p value calculated (based on Fisher’s method) using the nominal p values provided by from edgeR113 (Robinson et al., 2010) and DEseq2114 (Anders and Huber, 2010).
Assembly: ASM34474v1 (B. subtilis) and ASM14353v4 (Botrytis cinerea)
Supplementary files format and content: tab-delimited Excel files include Log2FC of the comparison between treated and non-treated Botrytis with purified compounds or with Bacillus (or Bacillus in coculture with Botrytis), with p-value, gene names and descriptions

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: Liquid culture of PDB

extract_protocol:
Liquid growth cultures of B. subtilis and B. cinerea were grown 6h inPDB medium at 28°C. Overnight cultures were diluted and, after 3-4 hours (exponential phase), B. subtilis cells were treated with Tse1 or with control buffer. Cultures were grown for 3 h.  Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with Nucleo-Spin RNA Plant (Macherey–Nagel) kit. The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bacteria


title: PE 2um #2


title: RNA-Seq, Sham, left ventricle, Day 9, Replicate 2

description: Library name: Sample 9


title: Undetermined_mmu_SCRBSeq

city: Planegg-Martinsried

first: Vigo

last: Heissmeyer

state: Bavaria

address: Großhadernerstr. 9

department: Institute for Immunology, Biomedical Center Munich

country: Germany

institute: LMU Munich

description:
3-prime RNAseq
The files associated with this sample were not included in the analysis. These files contain sequencing errors in the barcodes which did not pass our filtering process and could not be assigned to a specific samples in our system. The files can be used with less stringent filtering and a txt file with barcode/sample information is provided.

data_processing:
RNA sequencing raw data processing and differential gene expression analysis was conducted using DESeq2.e6 (Macosko et al., 2015)
Reference genome (GRCm38) was used for alignment.
Transcript and gene definitions were used according to the GENCODE M25.
Assembly: GRCm38
Supplementary files format and content: tab-delimeted text file includes raw counts for each sample

source_name: primary tumor cell lines

growth_protocol: Bone marrow cells were isolated from femurs and tibias of WT or DKOT mice and immediately used for injection. Male and female congenically marked recipient mice (age 10-12w) were lethally irradiated with 2x5.5Gy using the XSTrahl 225 X-ray device (irradiation conditions: 0.5mm Cu filter, 195kV, 15mA). 5×106 bone marrow cells were injected i.v. into recipient mice. Mice were treated for two weeks with water supplemented with antibiotics in the drinking water (0,04% baytril).

extract_protocol:
Total RNA was from primary tumor cell lines or tumor tissue using the RNeasy RNA Isolation kit (Qiagen) with on column gDNA (genomic DNA) removal according to manufacturers’ instructions.
Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, RNA was isolated using Agencourt AMPure XP magnetic beads. Barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 5'-Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition.

treatment_protocol: Primary tumor cell lines: ~3mm3 pieces were excised from tumors and digested in DMEM supplemented with 20%FCS, 100U/ml Penicillin-Streptomycin and 200U/ml Collagenase II for 18h at 37°C, 800rpm. Digested tumors were cultivated in tumor medium (10% FCS, 100U/ml Penicillin-Streptomycin in DMEM) at 37°C, 5% CO2 and passaged when 90-100% confluency was reached. Cells were passaged as long as stromal cells could be detected. Successful removal of contaminating stromal cells were confirmed by PCR.

value: primary tumor cell lines

tag: condition

value: bone marrow chimeras


title: RNA-Seq, Sham, Left atria, Day 9, Replicate 2

description: Library name: Sample 2

value: Sham


title: Sham-Gfp-NAc, replicate1

value: Egfp


title: Bo_Bacill_3610_1

description:
Library name: Bo_Bacill_3610_1
COND_coculture_vs_COND_control_all_3610.xlsx


title: RNA-Seq, Sham, Left atria, Day 9, Replicate 4

description: Library name: Sample 4


title: D17-CL-E-BR1-TR1

description: 3-prime RNAseq

value: Rc3h1+2 fl/fl; CD4cre(het) -> Kras-LSL-G12D mut/+; Ptf1a-cre(het)


title: TAC, Left atria, Day 9, Replicate 2

description: Library name: Sample 6

data_processing:
reads were mapped to mouse genome mm10 from UCSC using STAR v2.5.3 . Aligned reads were then filtered by mapping quality with Samtools (1.5), retaining those with a quality score greater than 30. Stringtie (v1.3.3) was used to generate a transcriptome with known and novel transcripts for each sample. BigWig files were generated from BAM files with deeptools using CPM normalizatiion.
Assembly: mm10
Supplementary files format and content: stringtie GTF files with TPMs
Supplementary files format and content: CPM normalized bigWigs

extract_protocol:
RNA was prepared with a TRIzol-based extraction protocol, and isolated using a Qiagen RNeasy Mini Column.
Libraries for non-coding RNA profiling were generated using Lexogen library preparation kit. Polyadenylated transcripts were removed using the Lexogen CORALL PolyA selection module and ribosomal RNA was removed with Lexogen Ribocop rRNA depletion kit. Libraries for the remaining non-coding RNAs were prepared with the Lexogen Total RNA-seq library prep kit.

value: TAC


title: RNA-Seq, Sham, Left atria, Day 9, Replicate 1

description: Library name: Sample 1


title: Bacillus_2

description:
Library name: Bacillus_2
COND_coculture_vs_COND_control_all_3610.xlsx


title: siScramble non-gene targetting control #3

value: Non-gene targetting control


title: D16-CL-C-BR1-TR1

description: 3-prime RNAseq


title: TAC, Left atria, Day 9, Replicate 1

description: Library name: Sample 5


title: CTRL #1


title: siScramble non-gene targetting control #2


title: Bacillus_1

description:
Library name: Bacillus_1
COND_coculture_vs_COND_control_all_3610.xlsx


title: Sham-Gfp-NAc, replicate3

value: Nucleus Accumbens


title: siScramble non-gene targetting control #1


title: D15-CL-D-BR1-TR1

description: 3-prime RNAseq


title: Sham, Left atria, Day 9, Replicate 4

description: Library name: Sample 4

value: Heart, left atria


title: siCBLL1 Estrogen #3

growth_protocol: MCF-7 cells were maintained at 37C and 5% CO2 in phenol red containing RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin-glutamine, 2 mM L-Glutamine and 1 mM sodium pyruvate.

treatment_protocol: siRNA-mediated functional depletion of CBLL1 was performed in vehicle (ethanol) and estrogen treated MCF-7 breast cancer cells grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS. ON-TARGETplus siRNA–SMART pools for Human CBLL1 (GE DharmaconTM) and ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.

value: CBLL1 depleted treated with estrogen


title: siCBLL1 #1


title: TAC, Left atria, Day 9, Replicate 3

description: Library name: Sample 7


title: Sham, Left atria, Day 9, Replicate 3

description: Library name: Sample 3


title: Sham, Left atria, Day 9, Replicate 2

description: Library name: Sample 2


title: 2D_D15_rep3

city: Lisboa

first: Alice

last: Borges

address: Av. Rovisco Pais

country: Portugal

institute: IBB

description: Library name: sample 39

data_processing:
3D: Raw reads were filtered by removing reads containing (1) adapters, (2) N > 10% (N represents base that could not be determined) and (3) low quality (when Qscore - Quality value - of over 50% bases of the read is <= 5). Paired-end clean reads were mapped to hg38 reference genome using HISAT2 software. Counts were obtained using Featurecounts. 2D: Sample read quality, reads mapping and counting were performed by a standard protocol from BlueBee Genomics Platform. For each sample individually, the pipeline includes reads trimming using BBDuk, alignment against genomic sequence using STAR aligner, gene read counting using HTSeq and quality control using RSeQC.
Assembly: grch38
Supplementary files format and content: comma-delimiyed file includes  raw gene counts for every gene and every sample

growth_protocol: Human induced pluripotent stem cells (iPS-DF6-9-9T.B, WiCell Bank, Wisconsin, USA) were maintained in mTeSR™1 medium (STEMCELL Technologies™) supplemented 1:200 (v/v) with penicillin/streptomycin (Gibco™, Thermo Fisher Scientific) on Matrigel-coated (Corning®) six-well culture plates in humidified incubators at 37ºC and 5% CO2. Culture medium was changed daily. Cell passaging was performed every three to four days when reaching a confluency ~70% using 0.5 mM EDTA (Invitrogen™, Thermo Fisher Scientific)

extract_protocol:
organoids: Total RNA from cells of dissociated liver organoids was extracted using High Pure RNA Isolation Kit following the provided instructions. 2d culture: For sample collection at selected time points, culture medium was removed, and cells were washed with PBS. Then cells were incubated with Accutase® solution (Sigma-Aldrich®, #A6964) in the case of hiPSCs or 0.25% (v/v) trypsin-EDTA (Gibco™, #R001100) in PBS for differentiated cells, both at 37ºC for 7 min. Culture medium was added to inactivate enzymatic digestion and cells were homogenized and centrifuged at 200 xg for 3 min. The cell pellet was washed with PBS and centrifuged again at 200 xg for 3 min. After removing the PBS, cell pellet was stored at -80ºC until further analysis. Total RNA was extracted using the High Pure RNA Isolation Kit (Roche, #11828665001) following the provided instructions.
3d organoid: Illumina NovaSeq 6000 system with a paired end 150 bp strategy; 2D cells: Libraries were prepared using Lexogen QuantSeq 3′mRNA-Seq Library Prep. Kit FWD for Illumina using standard protocols.Sequencing was performed using Illumina HiSeq (50 cycle’s protocol) or NextSeq (75 cycle’s protocol) platforms

treatment_protocol: 3D differentiation: For liver organoid generation cells were seeded in a vertical-wheel bioreactor PBS Mini 0.1L (PBS Biotech,USA), 27 rpm, at a density of 250 000 cells/mL in 60 mL of mTeSR™1 supplemented with 10μM ROCKi Y-27632 (STEMCELL Technologies™). 24h after inoculation, full medium volume was replaced, and aggregates were maintained in mTeSR™1 without ROCKi at 25 rpm. For definitive endoderm differentiation, RPMI 1640 medium (Gibco™) supplemented with 1% (v/v) B-27™ minus insulin (Gibco™) and 1:200 (v/v) penicillin/streptomycin (Gibco™) was used as differentiation medium. On day 0 of differentiation, differentiation medium was supplemented with 10ng/mL or 100 ng/mL of Activin A (PeproTech) and 6 μM of CHIR99021 (CHIR, Stemgent™) and agitation speed set to 30 rpm. After 24h, total media was replaced, and agitation speed changed to 33 rpm. For hepatic induction (day 3 of differentiation) cells were cultured in differentiation medium additionally supplemented with 10 ng/mL of FGF2 (PeproTech) and 20 ng/mL of BMP4 (PeproTech). From day 6 to day 20, cells were refreshed every three days with hepatocyte culture medium (HCM) BulletKit™ (Lonza) without the addition of human epidermal growth factor (hEGF). Medium was supplemented with 10 ng/mL oncostatin M (OSM, R&D Systems™), 0.1 μM dexamethasone (Dex, Sigma-Aldrich) and 20ng/mL of hepatic growth factor (HGF, Sigma-Aldrich).  2D differentiation: For hiPSC differentiation into definitive endoderm, Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco™, #21875034) was used as basal medium. RPMI was supplemented with 1% (v/v) B-27™ minus insulin (Gibco™, #A1895601) and supplemented 1:200 (v/v) with penicillin/ streptomycin (Gibco™, #15140122). At day 0 (D0) of differentiation, basal medium was supplemented with 100 ng/mL of Activin A (PeproTech, #120-14P), 1 mM of sodium butyrate (NaB, Sigma-Aldrich®, #B5887) and 50 ng/mL of Wnt3a (R&D Systems™, #5036-WN) or 2 µM of CHIR99021 (CHIR, Stemgent™, #04-0004). At day 1 and 2, basal medium was again supplemented with 100 ng/mL of Activin A. Cells continued to be cultured in RPMI 1640 medium supplemented with 1% (v/v) B-27™ minus insulin and 1:200 (v/v) with penicillin/ streptomycin, from D3 to D5 of differentiation. At D3, for hepatic induction, medium was additionally supplemented with 10 ng/mL of FGF2 (PeproTech, #100-18B) and 20 ng/mL of BMP4 (PeproTech, #120-05ET). From D6 to D20, cells were refreshed every three days with hepatocyte culture medium (HCM) BulletKit™ (Lonza, #CC-3198) without the addition of human epidermal growth factor (hEGF). Medium was supplemented with 10 ng/mL of oncostatin M (OSM, R&D Systems™, #295-OM), 0.1 µM of dexametasone (Dex, Sigma-Aldrich®, #D4902) and 20 ng/mL of hepatic growth factor (HGF, Sigma-Aldrich®, #H1404). Working volume throughout differentiation was 1 mL per well."

tag: source

value: foreskin fibroblasts

value: iPSC-derived hepatic cells

tag: mode of_growth

value: 2D monolayer

tag: time

value: 15 days


title: 2D_D15_rep2

description: Library name: sample 38


title: siCBLL1 Estrogen #2

value: Cell line

value: Breast cancer


title: 2D_D15_rep1

description: Library name: sample 37


title: D13-CL-A-BR1-TR1

description: 3-prime RNAseq


title: siCBLL1 Estrogen #1


title: W12-CL-G-BR1-TR1

description: 3-prime RNAseq

value: Rc3h1+2 fl/fl; CD4cre(neg) -> Kras-LSL-G12D mut/+; Ptf1a-cre(het)


title: 2D_D12_rep3

description: Library name: sample 36

value: 12 days


title: 2D_D12_rep2

description: Library name: sample 35


title: Y-1_fixed_nuclei_histone_DMOG_2

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

description: Library name: Sample8

data_processing:
An inhouse pipeline was created to perform the CUT &TAG analyses. Briefly, bowtie2 v2.4.2 [1] was run using the parameters “--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 2” using the Mus_musculus.GRCm39.111.gtf and  Mus_musculus.GRCm39.dna_sm.primary_assembly.fa files from ENSEMBL [2] database.
samtools v1.15.1 [3] was used to filter, sort and index the bam files.
bamCoverage command from deepTools v3.5.6[4] command line software package was used to create normalized bigwig files from the filtered and sorted  bam files.
Assembly: GRCm39
Supplementary files format and content: CPM normalized bigwig files
Library strategy: CUT&Tag

source_name: Y-1 Adrenocortical Cells

growth_protocol: The murine Y-1 adrenocortical cell line was cultured in Dulbecco´s Modified Eagle’s Medium (DMEM/F12; Thermo Fisher Scientific, #31330-038), which was supplemented with 10% Fetal Calf Serum (FCS; Thermo Fisher Scientific, #10500-064), 2.5% horse serum (Biowest, #S0910-500), and 1% penicillin-streptomycin (Thermo Fisher Scientific, #15140122)

extract_protocol:
Cells were treated with 1 mM DMOG-containing or control medium for 24 hours under standard growth culture conditions and CUT&Tag libraries were prepared using HIF-1α antibodies. Briefly, Y-1 cells were cultured for 24 hours in the presence of 1 mM DMOG or under control conditions. The cells were washed with 1x PBS and treated with trypsin-EDTA (Thermo Fisher Scientific, #15400054) for 4 minutes at 37°C in a cell culture incubator. Trypsin was quenched with cell culture medium and detached cells were transferred to a 15 ml tube and pelleted for 5 minutes at 491 g. The cells were then resuspended in fresh cell culture medium and washed with 1x PBS. Cell pellet was resuspended in ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine) supplemented with Roche Complete Protease Inhibitor EDTA-Free tablets (Merck, #11836170001) at ½ volume of the starting culture and incubated for 10 minutes on ice. The cell nuclei were pelleted by centrifugation (4 minutes, 1300 g, 4°C) and resuspended in ice-cold 1x PBS. Nuclei were crosslinked with 0.1% formaldehyde (16% (w/v) formaldehyde; Thermo Fisher Scientific, #28906) for 2 minutes at room temperature and the reaction was quenched by glycine solution (70 mM final concentration). Fixed nuclei were then washed with 0.5 ml of nuclei wash buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine) supplemented with Roche Complete Protease Inhibitor EDTA-Free tablets and counted. The nuclear pellet was then resuspended in nuclei wash buffer at a concentration of 1 million nuclei per ml, aliquoted and stored at -80°C until use. The frozen nuclei were thawed at room temperature for 30 minutes and bound to ConA-coated magnetic beads (BioMag Plus Concanavalin A; Bangs Laboratories, #BP531), which were pre-equilibrated with binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) in 0.5 ml tubes (3.5 µl beads per 50,000 nuclei) for 10 minutes rotating at room temperature. The supernatant was removed and anti-HIF-1α primary antibody solution (Cayman Chemicals, #10006421) in antibody buffer (CUT&Tag wash buffer with 0.1% BSA) was added at 1:50 dilution. The beads were rotated with the primary Ab solution for 2 hours at RT followed by overnight incubation at 4°C. Next, the supernatant was removed and guinea pig α-rabbit secondary antibody (Antibodies online, #ABIN101961) solution, 1:100 in CUT&Tag wash buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor EDTA-Free tablets; Merck, #11836170001) was added to the beads. The beads were rotated for 1 hour at RT and the supernatant was removed. The beads were then washed with 0.5 ml of CUT&Tag wash buffer and the pA-Tn5 adapter complex (Epicypher, #15-1117) in 300 wash buffer (20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor EDTA-Free tablets; Merck, #11836170001) was added at 1:20. The complex was rotated with the beads for 2 hours at RT and the supernatant was removed. The beads were washed with 0.5 ml of 300 wash buffer and resuspended in CUT&Tag tagmentation buffer (300 wash buffer with 10 mM MgCl2). The samples were incubated for 1 hour at 37°C and cooled down to 8°C in a PCR cycler. The supernatant was removed and beads were washed with TAPS wash buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA). The Tn5 complex was released with 5 µl SDS release solution (10 mM TAPS pH 8.5, 0.1% SDS) at 58°C for 1 h in a PCR cycler. Subsequently, 15 µl Triton neutralisation solution (0.67% Triton X-100) was added per sample.
PCR reactions were run on the CUT&Tag samples (gap filling: 5 minutes, 58°C; 5 minutes, 72°C; initial denaturation: 30 s, 98°C; 11 cycles of denaturation 10 s, 98°C; and annealing and elongation 10s, 60°C; final elongation: 1 minute, 72°C; hold 8°C) with barcoded primers using the NEBNext High Fidelity 2x PCR mix (New England Biolabs, #M0541L). DNA was cleaned up with SPRI beads (AMPure XP Bead-Based Reagent; Beckman Coulter, #A63880) for 10 minutes at RT, washed twice with 80% ethanol and eluted with 10 mM Tris-HCl pH 8 for 1 hour at RT. The libraries were subjected to size selection to enrich for fractions between 170 and 700 bp (Fragment Analyzer, Advanced Analytical) and sequenced (Illumina next generation sequencing) at the DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden.

treatment_protocol: For HIF hydroxylase (PHD) inhibition, dimethyloxalylglycine (DMOG; Biomol, Cay71210-100) in 1x PBS was added to the growth medium at 1 mM final concentration for 24 or 48 hours (solvent only was used as control).

value: Y-1 Adrenocortical Cells

value: WT


title: Sham, Left atria, Day 9, Replicate 1

description: Library name: Sample 1

value: Sham


title: siCBLL1 Vehicle #3

value: CBLL1 depleted treated with vehicle


title: W11-CL-F-BR1-TR1

description: 3-prime RNAseq

value: primary tumor cell lines

value: bone marrow chimeras


title: 2D_D12_rep1

description: Library name: sample 34


title: Y-1_fixed_nuclei_histone_DMOG_1

description: Library name: Sample7


title: siCBLL1 Vehicle #2


title: D17-Ti-BR1-TR1

description: 3-prime RNAseq

source_name: Primary tumor tissue

value: Primary tumor tissue

value: Rc3h1+2 fl/fl; CD4cre(het) -> Kras-LSL-G12D mut/+; Ptf1a-cre(het)


title: siCBLL1 Vehicle #1


title: D13-CL-B-BR1-TR1

description: 3-prime RNAseq


title: 2D_D9_rep3

description: Library name: sample 33

value: 9 days


title: Y-1_fixed_nuclei_histone_control_1

description: Library name: Sample5


title: D16-Ti-BR1-TR1

description: 3-prime RNAseq


title: Y-1_fixed_nuclei_histone_control_2

description: Library name: Sample6


title: W15-CL-H-BR1-TR1

description: 3-prime RNAseq


title: siScramble non-gene targetting Estrogen #3

value: Non-targeting scramble control treated with estrogen


title: siScramble non-gene targetting Estrogen #2


title: D15-Ti-BR1-TR1

description: 3-prime RNAseq


title: PE 2um #1

value: whole body

value: polyethylene


title: Y-1_fixed_nuclei_HIF-1_DMOG_1

description: Library name: Sample3


title: 2D_D9_rep2

description: Library name: sample 32

value: foreskin fibroblasts

value: iPSC-derived hepatic cells

value: 2D monolayer


title: 2D_D9_rep1

description: Library name: sample 31


title: D13-Ti-BR1-TR1

description: 3-prime RNAseq


title: D14-Ti-BR1-TR1

description: 3-prime RNAseq


title: Y-1_fixed_nuclei_HIF-1_DMOG_2

description: Library name: Sample4


title: 2D_D7_rep2

description: Library name: sample 29

value: 7 days


title: siScramble non-gene targetting Vehicle #3

value: Cell line

value: Breast cancer

value: Non-targeting scramble control treated with vehicle


title: siScramble non-gene targetting Vehicle #2


title: 2D_D7_rep1

description: Library name: sample 28


title: siScramble non-gene targetting Vehicle #1


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, Anterior prostate, Tamoxifen 4 weeks, scRNAseq, No Multiplexing

city: New York City

first: Dan

last: Li

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

description:
Library name: TYA4weeks
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Data files were demultiplexed using cellranger multi command, version is 7.0.0
Assembly: mm10
Supplementary files format and content: comma-separated read counts

source_name: Anterior prostate

extract_protocol:
Prostate cells sorted from intact or castrated and DHT treated wild-type or Ar knockout mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 3’ GEM Library and Gel Bead kit.
The hashing protocol described in BioLegend website (https://www.biolegend.com/en-us/products/totalseq-b0301-anti-mouse-hashtag-1-antibody-17771), and a 3’ gene expression library (https://www.10xgenomics.com/instruments/chromium-x)

value: primary cells

value: Anterior prostate

value: 4 weeks after Tamoxifen

tag: library type

value: mRNA

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: 2D_D3_rep3

description: Library name: sample 27

value: 3 days


title: W15-Ti-BR1-TR1

description: 3-prime RNAseq

value: Primary tumor tissue

value: Rc3h1+2 fl/fl; CD4cre(neg) -> Kras-LSL-G12D mut/+; Ptf1a-cre(het)

value: bone marrow chimeras


title: MECP2T203M

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

country: China

institute: Beijing Institute of Basic Medical Sciences

data_processing:
After obtaining the raw sequencing data, reads were aligned to the hg38 human reference genome, and gene-level unique molecular identifier (UMI) counts were obtained using 10x Genomics Cell Ranger (version 5.0.0). For quality control, we kept cells with more than 500 genes, more than 2000 reads and mitochondrial fraction less than 0.2 for subsequent analysis. In addition, genes detected less than 5 cells were removed for further analysis. The expression matrix was converted to a Seurat object using Seurat package (version 4.0.1)(Hao et al. 2021). We ﬁrstly selected high variable genes by using the FindVariableGenes function with log-mean expression values. We then reduced the dimensionality of our data by principle component analysis (PCA) and Tsne using functions, RunPCA and the RunTSNE. Clustering was performed by FindClusters function with default parameters, and resolutions set from 0.5 to 1.5. To annotate cell population clusters to known cell types, we assessed expression of known cell type-specific marker genes identified from previous literature. 4 different cell types and 4,160 cells were kept for downstream analysis. Unbiased spatial mapping of all cells was performed using VoxHunt (version 1.0.1) (Fleck et al. 2021). The transcriptome profiles were compared with E13.5 mouse brains from the Allen Brain Institute.
Assembly: hg38 human reference genome
Supplementary files format and content: cell ranger result files

extract_protocol:
Briefly, 5-7 cerebral organoids were dissociated into a single-cell suspension via incubation with 1 mL tryp-LE (Life Technologies, Thermo Fisher Scientific) for 35 minutes at 37°C with gentle agitation every 5–8 minutes, followed by 3 washes with 2% FBS in DPBS and gentle titration using a P200 pipette.
Cell suspension approximately 10,000 cells was loaded onto a Chromium Single Cell 3’ controller (10x Genomics) to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics). The libraries were then sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) strategy.

treatment_protocol: Day 30 organoids were prepared for scRNA-Seq. Briefly, 5-7 cerebral organoids were dissociated into a single-cell suspension via incubation with 1 mL tryp-LE (Life Technologies, Thermo Fisher Scientific) for 35 minutes at 37°C with gentle agitation every 5–8 minutes, followed by 3 washes with 2% FBS in DPBS and gentle titration using a P200 pipette.

value: induced pluripotent stem cell


title: W14-Ti-BR1-TR1

description: 3-prime RNAseq


title: siScramble non-gene targetting Estrogen #1

value: Non-targeting scramble control treated with estrogen


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 weeks, Multiplexing

description:
Library name: TYCD2w_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

molecule: protein

source_name: whole prostate

value: whole prostate

value: 2 weeks after Tamoxifen, castrate 2 weeks, DHT 2 weeks

value: Hashtag-derived oligonucleotide (HTO)

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1 (mouse replicate 1), TotalSeq-B0302 anti-mouse Hashtag 2 (mouse replicate 2), TotalSeq-B0303 anti-mouse Hashtag 3 (mouse replicate 3)

value: Tmprss2CreERT2, lsl-EYFP


title: MECP2


title: 2D_D3_rep1

description: Library name: sample 25

value: foreskin fibroblasts

value: iPSC-derived hepatic cells

value: 2D monolayer


title: W13-Ti-BR1-TR1

description: 3-prime RNAseq


title: 2D_D3_rep2

description: Library name: sample 26


title: ATAC MECP2T203M-2

data_processing:
ATAC-seq data were aligned to the GRCh38 reference genome (version 40) using BWA (version 0.7.17), followed by sorting and indexing of bam files using SAMtools (version 1.3.1)(Danecek et al. 2021), and annotation of PCR duplicates using the Picard (version 2.23.8) MarkDuplicates function. All mitochondrial reads were removed using SAMtools. Peak calling was performed using MACS (version 2.2.7.1).
Assembly: GRCh38 reference genome (version 40)
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq libraries (replicates, n = 3) were generated from transposed DNA using the Nextera DNA Library Preparation Kit (Illumina) according to the manufacturer’s recommendations.
ATAC-seq libraries were further purified using the MinElute PCR Purification Kit (Qiagen) and sequenced on Novaseq 6000 using PE150 with an average of 80 million reads per sample.

treatment_protocol: The human iPSC cell line, iPSCs-WC30 (gift from Dr. Yuejun Chen at the CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), were cultured on a feeder of irradiated mouse embryonic fibroblasts (MEFs) in the embryonic stem cell (ESC) medium consisting of Dulbecco’s Modified Eagle’s medium/Nutrient Mixture F-12 (DMEM/F-12), 1× Non-Essential Amino Acids (NEAA), 0.5× Glutamax, 0.1 mM 2-Mercaptoethanol, and 4 ng/mL fibroblast growth factor-2 (FGF-2). Cells were fed daily with ESC medium and passaged weekly by Dispase II till electroporation.


title: D12-Ti-BR1-TR1

description: 3-prime RNAseq

value: Rc3h1+2 fl/fl; CD4cre(het) -> Kras-LSL-G12D mut/+; Ptf1a-cre(het)


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 weeks, RNAseq

description:
Library name: TYCD2w
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: primary cells

value: mRNA


title: 2D_D7_rep3

description: Library name: sample 30

value: 7 days


title: 2D_D1_rep3

description: Library name: sample 24

value: 1 day


title: Y-1_fixed_nuclei_HIF-1_control_2

description: Library name: Sample2

value: Y-1 Adrenocortical Cells

value: WT


title: W12-Ti-BR1-TR1

description: 3-prime RNAseq

value: Primary tumor tissue

value: Rc3h1+2 fl/fl; CD4cre(neg) -> Kras-LSL-G12D mut/+; Ptf1a-cre(het)

value: bone marrow chimeras


title: Y-1_fixed_nuclei_HIF-1_control_1

description: Library name: Sample1


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 days, Multiplexing

description:
Library name: TYCD2d_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: whole prostate

value: 2 weeks after Tamoxifen, castrate 2 weeks, DHT 2 days


title: W11-Ti-BR1-TR1

description: 3-prime RNAseq


title: W10-Ti-BR1-TR1

description: 3-prime RNAseq


title: ATAC MECP2T203M-1

value: induced pluripotent stem cell


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 days, RNAseq

description:
Library name: TYCD2d
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Tmprss2CreERT2, lsl-EYFP


title: 2D_D1_rep2

description: Library name: sample 23

value: foreskin fibroblasts


title: Tmprss2CreERT2, lsl-EYFP, Anterior prostate, Tamoxifen 4 weeks, scRNAseq, No Multiplexing

description:
Library name: TY4weeks
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Anterior prostate

value: 4 weeks after Tamoxifen


title: 2D_D1_rep1

description: Library name: sample 22

value: iPSC-derived hepatic cells

value: 2D monolayer


title: ATAC MECP2-3


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 5 days, Multiplexing

description:
Library name: TYC5d_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: primary cells

value: 2 weeks after Tamoxifen, castrate 5 days

value: Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0301 anti-mouse Hashtag 1 (mouse replicate 1), TotalSeq-B0302 anti-mouse Hashtag 2 (mouse replicate 2), TotalSeq-B0303 anti-mouse Hashtag 3 (mouse replicate 3)


title: 2D_D0_rep3

description: Library name: sample 21

value: induced pluripotent stem cells

value: 0 days


title: BMM_LPS_DRP1

city: Nouzilly

first: ronan

last: kapetanovic

address: Centre INRAE Val de Loire

country: France

institute: INRAE - UMR ISP 1282

data_processing:
raw sequencing reads were trimmed as paired-end reads using TrimGalore! (https://github.com/FelixKrueger/TrimGalore) with default parameters
Trimmed reads were mapped with Bowtie2 (--sensitive-local) against the reference genome mm10.
Then, duplicates were removed (PicardTools, MarkDuplicates),
GC-bias was corrected (deepTools, correctGCbias (Ramirez et al., 2016) and reads were filtered for their insert size (<= 250 bp insert size).
Peaks have been called using the histone mode (-style histone).
deepTools bamCoverage generated bigwig files (normalized to RPKM) for visual inspection in a genome browser and for plotting genomic snapshots (pyGenomeTracks (Lopez-Delisle et al., 2021).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (Bed file)
Library strategy: Cut&Run

source_name: Primary Bone-Marrow Macrophages

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cut&Run was performed as earlier described (Meers et al., 2019) with minor modifications. 500,000 cultured bone marrow macrophages per Cut&Run experiment were washed 3 times in Cut&Run wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine plus fresh 1x protease inhibitor cocktail (Roche cOmplete)). 10 µL of Concanavalin A conjugated paramagnetic beads (EpiCypher) per sample were washed 2 times in Cut&Run wash buffer using a magnetic rack and activated in 10 µL binding buffer (20 mM HEPES pH 7.5, 20 mM KCl, 1 mM CaCl2, 1 mM MnCl2 + fresh 1x protease inhibitor cocktail) for 10 min. 10 µL of activated Concanavalin A beads were mixed very well with the washed cells and incubated for 10 min. After binding and 3 washes with Cut&Run wash buffer using a magnetic rack, cells were aliquoted according to the number of Cut&Run reactions into 200 µL PCR strips (500,000 cells per antibody/reaction). Then, buffer was changed (100 µL of antibody buffer (Cut&Run wash buffer with 0.025% digitonin and 2 mM EDTA)), the antibody was added (1:100), mixed very well by pipetting up and down for >10 times and incubated on a nutator at 4C overnight. The next day, samples were washed 3x on ice with 200 µL of Dig-wash buffer (Cut&Run wash buffer with 0.025% digitonin and fresh 1x protease inhibitor) using a magnetic rack. According to the number of samples, 20x pAG-MNase (EpiCypher) stock was diluted using Dig-wash buffer to 1x. Cells were resuspended with 50 µL of 1x pAG-MNase, mixed well and incubated on ice for 30 minutes. After 3 washes with 200 µL Dig-wash buffer each using a magnetic rack, cells were resuspended in 50 µL of cold Dig-wash buffer and 1 µL of 100 mM CaCl2 was directly added and mixed very well. The Cut&Run reaction was carried out for 2 hours on ice and stopped by adding 33 µL of 2x stop solution (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.025% digitonin, 100 µg/mL RNase A (Qiagen), 50 µg/mL glycogen (Thermo Scientific)). After mixing the samples very well, small fragments were released by incubating the samples in a thermo cycler at 37°C for 10 min. Cells were separated on a magnetic rack and the supernatant was used for DNA purification using the DNA clean & concentrator kit (Zymo) according to the manufacturer’s instruction. The concentration of the eluted DNA was measured using a Qubit Fluorometer.
Not more than 30 ng of DNA was used for preparing the NGS-library using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The temperature for the end repair reaction was lowered to 58C for 45 min and 1.25 µL of 3 µM adaptor was used afterwards in the ligation step. For the PCR amplification, annealing and extension was combined to one step (65C for 10 seconds). In total, 12 PCR cycles were used. Afterwards, DNA was purified twice using 1x vol of MagBind TotalPure NGS (Omegabiotek) and analyzed on a DNA Bioanalyzer High Sensitivity Chip. NGS-libraries were pooled and sequenced on an Illumina NextSeq 500 (15-20 M reads per sample, 2x 38bp PE).

treatment_protocol: Treated with LPS (100 ng.ml) for 5h

tag: strain

value: Primary Bone-Marrow Macrophages

tag: chip antibody

value: Anti-DRP1 Ser637 (Rabbit, CST, #4867S)


title: ATAC MECP2-2


title: 2D_D0_rep2

description: Library name: sample 20


title: ATAC MECP2-1


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, Multiplexing

description:
Library name: TYC2w_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: whole prostate

value: 2 weeks after Tamoxifen, castrate 2 weeks


title: BMM_LPS_ATF5

value: Anti-ATF5 (Rabbit, Abcam, #ab184923)


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 5 days, RNAseq

description:
Library name: TYC5d
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA

value: Tmprss2CreERT2, lsl-EYFP


title: ME-2 Ribo-seq

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Low quality reads were filtered by fastp. Raw reads containing over 50 % of low quality bases or over 10 % of N bases were removed. Adapter sequences were trimmed. Reads with length between 20-40 bp were retained for subsequent analysis. Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed.
Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2-pass setting enabled. The reads mapped to classical noncoding RNAs (including long noncoding RNAs, microRNA precursors) were abandoned. Then remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment.
Three-nucleotide periodicity was plotted using the riboWaltz R package as described. Read counts in the open reading frame of coding genes was calculated by software RSEM, and the gene expression level was normalized by using FPKM method.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of false discovery rate (FDR) < 0.05 and log2 fold change > 1.
Assembly: GRCH38/hg38
Library strategy: Ribo-seq

source_name: mesendoderm cells

growth_protocol: The hESC (Line H9, passages 39–55, Shanghai Chuan Qiu Biotechnology Co.,Ltd.) were cultured on a feeder layer of mouse embryonic fibroblast (MEFs). The MEFs were treated with mitomycin C (10 μg/mL) for 3 h. The hESC medium consisted of Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12), 0.1 mM β–mercaptoethanol, 1 % GlutaMaxTM, Knockout serum replacement (KSR), 10 ng/mL basic fibroblast growth factor 2 and 1 % Nonessential amino acid solution (NEAA).

extract_protocol:
The hESC, NEP and ME cells were treated with CHX (100 ug/ml, Sigma, St Louis, MO, USA) for 5 min to freeze the translating ribosomes. The ribosomal profiling technique was carried out as reported previously, with a few modifications as described below. The resuspended extracts in lysis buffer were transferred to new microtubes, pipetted several times and incubated on ice for 10 min. Then cells were triturated ten times through a 26-G needle. The lysate was centrifuged at 20000 g for 10 min at 4 °C, and the supernatant was collected. To prepare RFs, 10 µl of RNase I (NEB, Ipswich, MA, USA) and 6 µl of DNase I (NEB, Ipswich, MA, USA) were added to 400 µl of lysate, which was then incubated for 45 min at room temperature with gentle mixing on a Nutator mixer. Nuclease digestion was stopped by adding 10 µL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Size exclusion columns (illustraMicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27- 5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600 g for 4 min at room temperature. 100 μL of digested RFs were added to the column and centrifuged at 600 g for 2 min. Next, 10 μL 10 % (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research; R1017). The rRNA was removed using the method reported previously. Briefly, short (50–80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme, Nanjing, Jiangsu, China).
After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no. E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160 bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM X10.

treatment_protocol: For differentiation of hESCs into NEP cells, hESCs were dissociated with dispase and seeded on the mitomycin C treated mouse embryonic fibroblast cells. On the following day (D1), the hESC medium was replaced with NEP medium, including DMEM/F12 and neurobasal medium (1:1) with 0.1 mM ascorbic acid, 1 X N2 supplement, 1 X B27 supplement, 3 μM CHIR99021, 1 % GlutaMaxTM, 2 μM DMH1 and 2 μM SB431542 for 6 days. For differentiation of ME cells, the hESC medium was changed to advanced RPMI1640, supplemented with 1x penicillin/streptomycin, CHIR99021 (5 μM) and 1 % GlutaMaxTM for 36 h.

value: mesendoderm cells

tag: developmental stage

value: differentiation for 36 h


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, scRNAseq

description:
Library name: TYC2w
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: RNA MECP2T203M-3

data_processing:
Clean reads were aligned to the GRCh38 reference genome (version 40) using HISAT2 (version 2.2.1)(Kim et al. 2015, 2019; Pertea et al. 2016). HTSeq (version 0.12.4)(Anders et al. 2015) was used to count the number of reads mapped in each annotated gene based on the mapping results. R package DESeq2 (version 1.26.0)(Love et al. 2014) was used to calculate DEGs with the cutoff values of FDR< 0.05 and |Log2 (fold change)| > 1. Then a ranked list of genes significantly upregulated or downregulated in expression analyzed for their enriched Gene Ontology (GO) (p<0.05) using clusterProfiler (version 3.14.3).
Assembly: GRCh38 reference genome (version 40)
Supplementary files format and content: tab-delimited text files include reads count  values for each Sample

extract_protocol:
Following a standard protocol, total RNA from day-30 organoids was extracted using a TRIzol reagent kit (Invitrogen, Thermo Fisher Scientific). RNA integrity was checked on an Agilent 4200 TapeStation to conduct quality control (Agilent Technologies).
Library construction and high-throughput RNA-Seq were performed with Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) strategy.

value: induced pluripotent stem cell


title: 2D_D0_rep1

description: Library name: sample 19

value: foreskin fibroblasts

value: 2D monolayer


title: U87-MG cell line, α-SYN protofibrils treatment, 24 hours_6

city: Bengakuru

first: Sangeetha

last: Nath

state: Karnataka

address: MAHE Bengaluru, BSF Campus, Govindapura

department: Manipal Institute of Regenerative Medicine

country: India

institute: Manipal Academy of Higher Education

description: Library name: Sample 9

data_processing:
Raw sequence reads were subjected to FastQC (v0.12.1) to assess read quality and reads were further trimmed using Trimmomatic (v0.39)
The trimmed reads were aligned to the reference genome GRCh38 using HISAT2 (v2.2.1) in a stand-alone custom analysis pipeline
The aligned reads were quantified to generate raw counts using feature Counts (v2.0.8). Raw counts were further normalized and differential expression analysis was performed using DESeq 2 (v1.40.2).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: U87-MG cell lines were cultured in Dulbecco’s Modified Eagle Medium, supplemented with 10% Fetal Bovine Serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Trizol-choloform method of RNA isolation protocol
The screened RNA samples were pooled to generate a paired-end cDNA library using NEBNext® UltraTM II Directional RNA Library Prep Kit and further processed for sequencing

treatment_protocol: U87-MG cell lines were treated with 1 µM α-SYN protofibrils at 37°C, 5% CO₂ for durations between 3 - 24 hours

value: human glioblastoma cell line

value: α-SYN protofibrils treatment, 24 hours


title: RNA MECP2T203M-2


title: ME-1 Ribo-seq


title: RNA MECP2T203M-1


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 weeks, RNAseq

description:
Library name: TYACD2w
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: primary cells

value: 2 weeks after Tamoxifen, castrate 2 weeks, DHT 2 weeks

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 weeks, Multiplexing

description:
Library name: TYACD2w_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0301 anti-mouse Hashtag 1 (mouse replicate 1), TotalSeq-B0302 anti-mouse Hashtag 2 (mouse replicate 2), TotalSeq-B0303 anti-mouse Hashtag 3 (mouse replicate 3)


title: NEP-1 Ribo-seq

source_name: neuroepithelial progenitors cells

value: neuroepithelial progenitors cells

value: differentiation for 6 days


title: U87-MG cell line, α-SYN protofibrils treatment, 24 hours_4

description: Library name: Sample 7


title: U87-MG cell line, α-SYN protofibrils treatment, 24 hours_5

description: Library name: Sample 8


title: hESC-2 Ribo-seq

value: human embryonic stem cells


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 days, RNAseq

description:
Library name: TYACD2d
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: whole prostate

value: 2 weeks after Tamoxifen, castrate 2 weeks, DHT 2 days

value: mRNA


title: U87-MG cell line, α-SYN protofibrils treatment, 3 hours_2

description: Library name: Sample 5

value: α-SYN protofibrils treatment, 3 hours


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, DHT 2 days, Multiplexing

description:
Library name: TYACD2d_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: ATAC MECP2T203M-3

value: induced pluripotent stem cell


title: RNA MECP2-2


title: BMM_LPS_H3K27Ac

value: Primary Bone-Marrow Macrophages

value: Anti-H3K27Ac  (Rabbit, Diagenode, #C15410196)


title: U87-MG cell line, α-SYN protofibrils treatment, 3 hours_3

description: Library name: Sample 6

value: human glioblastoma cell line


title: RNA MECP2-3


title: RNA MECP2-1


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 5 days, Multiplexing

description:
Library name: TYAC5d_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: 2 weeks after Tamoxifen, castrate 5 days


title: U87-MG cell line, α-SYN protofibrils treatment, 3 hours_1

description: Library name: Sample 4


title: RNA_rep4

city: Ann Arbor

first: Arushi

last: Varshney

state: MI

address: 100 Washtenaw Ave

institute: University of Michigan

data_processing:
We processed this data through a custom pipeline to quantify barcode counts within each sample (RNA, gDNA) separately while accounting for sequencing errors. We extracted 20-bp barcodes and 15-bp unique molecular identifiers (UMIs) with cutadapt and umitools, respectively. We used starcode-umi to cluster UMIs and correct for PCR amplification bias. We then clustered and counted barcodes using starcode with an edit distance of 0.
We matched individual barcodes to the barcode pairing dictionary. We retained all barcodes with at least 5 RNA and 5 gDNA counts. For the entire library (not published here), we used DESeq2 to perform normalization and to quantify overall fragment level activity and allelic bias between paired fragments. For the barcodes published here, we used a Wilcoxon-rank test to test for statistically significant differences in activity between alleles or between each allele and negative controls. We used aggregated mean activity for the negative control fragments rather than testing each separately. For plotting purposes, we transformed counts to transcripts per million and plotted log2(RNA/DNA).
Assembly: Custom synthetic barcode sequences
Supplementary files format and content: File "bc_dictionary.txt" is a tab-delimited text file containing the barcodes and corresponding oligo names for the library used here. File "lhcnm2-mpra-counts.txt" is a tab-delimited text file containing the counts for each barcode (rows) for each sample (columns).
Library strategy: MPRA barcode amplicon sequencing

source_name: Skeletal muscle

extract_protocol:
We used the Qiagen AllPrep RNA/DNA kit to isolate genomic DNA and total RNA from each sample. We performed two separate DNase treatments of the total RNA to remove DNA contamination.
We constructed sequencing libraries for the RNA and gDNA samples separately. We used a custom primer to reverse transcribe GFP RNA from total RNA, then performed nested PCR to add sequencing adapters and Illumina indexes. For gDNA samples, we used a similar set of primers to target integrated GFP sites and used nested PCR to add sequencing adapters and indexes.

value: Skeletal muscle

value: Myotube


title: NEP-2 Ribo-seq


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 5 days, RNAseq

description:
Library name: TYAC5d
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: primary cells

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, Multiplexing

description:
Library name: TYAC2w_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: 2 weeks after Tamoxifen, castrate 2 weeks

value: Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0301 anti-mouse Hashtag 1 (mouse replicate 1), TotalSeq-B0302 anti-mouse Hashtag 2 (mouse replicate 2), TotalSeq-B0303 anti-mouse Hashtag 3 (mouse replicate 3)


title: RNA_rep3


title: U87-MG cell line, Control_2

description: Library name: Sample 2

value: Control


title: gDNA_rep4


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, castrate 2 weeks, RNAseq

description:
Library name: TYAC2w
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: whole prostate


title: MV411_Baseline_WT_C_T_Editor_Day_0_Rep3

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description: Library name: Sample 42

data_processing:
Data processing was performed with the genomic perturbation platform (GPP) at the Broad institute.
An internal software tool, PoolQ, deconvolutes and quantitates perturbation barcodes from multiplexed sequencing data.
Count matrix files were log normalized to standardize read counts.
The log normalized read counts for each condition after 21 days of drug treatment were compared to the log normalized read counts for each condition at the start of the screen (Day 0).
Assembly: GRCh38/hg38
Supplementary files format and content: CRISPR Base editor screen details and results in Excel .xlsx format
Library strategy: CRISPR Screen

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 1% L-glutamine at 37 °C with 5% CO2.

extract_protocol:
Genomic DNA was extracted from 5 million cells per condition with the Machery Nagel NucleoSpin Blood Kit
Library construction performed utilizing genomic perturbation platform at Broad Institute: Sangree, A.K., et al. Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2. Nat Commun 13, 1318 (2022).
Briefly, PCR amplification of unique barcodes was performed and sequencing (Hiseq 2500) performed to assess and quantify the abundance of each barcode.

treatment_protocol: Cells were treated with DMSO control or 13.8 nM DS-1594, 17.3 nM JNJ-6617, 23.4 nM KO-539, 51.6 nM SNDX-5613, 25.2 nM DSP-5336 for 21 days.

value: Overexpression of C>T base editor:TadA-CDd, SpG-SpyoCas9 (D10A), pRDB_092, addgene plasmid # #231110

value: None, baseline

tag: timepoint

value: Day 0 baseline


title: gDNA_rep3

tag: tissue


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, scRNAseq

description:
Library name: TYA
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: cell type

value: 2 weeks after Tamoxifen

value: mRNA


title: MV411_Baseline_WT_C_T_Editor_Day_0_Rep2

description: Library name: Sample 41

tag: genotype


title: U87-MG cell line, Control_1

description: Library name: Sample 1

tag: treatment


title: gDNA_rep2


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, Multiplexing

description:
Library name: TY_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Tmprss2CreERT2, lsl-EYFP


title: MV411_Baseline_WT_C_T_Editor_Day_0_Rep1

description: Library name: Sample 40


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, whole prostate, Tamoxifen 2 weeks, Multiplexing

description:
Library name: TYA_FB
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: RNA_rep1


title: sus1 mutant exposed to Congo Red 3 hours_2

type: RNA

city: Madrid

first: Raul

last: Garcia

state: Madrid

address: Plaza Ramon y Cajal s/n

department: Microbiologia y Parasitologia

institute: Universidad Complutense de Madrid

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scanner were analyzed using RMA (Robust Multichip Average) algorithm from Bioconductor software

label: biotin

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown for 3 hours

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the NucleoSpin RNA kit (Macherey-Nagel, Dueren, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown with Congo Red for 3 hours

tag: genetic background


title: sus1 mutant 3 hours_3


title: Tmprss2CreERT2, lsl-EYFP, whole prostate, Tamoxifen 2 weeks, scRNAseq

description:
Library name: TY
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: sus1 mutant exposed to Congo Red 3 hours_1


title: sus1 mutant exposed to Congo Red 3 hours_3


title: MV411_Baseline_WT_A_G_Editor_Day_0_Rep3

description: Library name: Sample 39


title: gDNA_rep1


title: sus1 mutant 3 hours_1


title: sus1 mutant 3 hours_2


title: mWAT tissue, HfiD feed 5w, HFD feed 8w female

city: Huddinge

first: Zhi

last: Peng

state: Stockholm

address: Blickagången 16

department: MedH

country: Sweden

institute: Karolinska Institutet

description: Library name: HfiD_HFD8w_female

data_processing:
The raw FASTQ files were processed with Cell Ranger version 7.0.0, and the obtained reads were aligned to the Ensembl genome (mm10). CellBender version 0.2.2 was then used to clean the raw nuclei-gene count matrices by removing ambient RNA contamination and empty droplets. The resulting count matrices were analyzed using Seurat version 5.1.0. For snRNA-seq data preprocessing, nuclei containing a total number of detected genes less than 100 or percentage of mitochondrial genes larger than 15% were filtered out. The resulting nuclei was further processed by normalizing, variable feature genes selection (selection method as VST), scaling, PCA dimension reduction, UMPA dimension reduction and clustering with resolution parameter set at 0.25. Cell clusters were manually annotated based on previously published marker genes. For adipocytes and ASPCs subclusters analysis, nuclei were subset and further processed by same procedure described above except ASPCs subclusters with resolution parameter set at 0.2. RNA velocity analysis was performed using Monocle3 version 1.3.7 and scvelo version 0.3.2 to construct predicted pseudotime trajectory in adipocytes and ASPCs. For monocle analysis, the “cluster_cells” was performed with resolution parameter set at 0.01. For scvelo analysis, unspliced and spliced RNA for each cell were extracted from all mWAT samples with cell Ranger. Through filtering, normalizing, computing moments and modeling, the velocity “stream” were visualized in PCA dimensionally reduced graphics.
Assembly: mm10
Supplementary files format and content: Expression matrix file.

source_name: mesenteric white adipose tissue (mWAT)

extract_protocol:
Nuclei isolation of mWAT for snRNA-seq Nuclei isolation was performed as previously described (Van Hauwaert et al., 2021). Adipose tissue that was connected to the small intestine and colon was collected as mWAT. The dissected tissue was minced with scissors in 500 ml nuclei isolation buffer (NIB) that contains 250 mM sucrose (Solarbio, S8271), 10 mM HEPES (Solarbio, H8090), 1.5 mM MgCl2 (Sigma-Aldrich, M8266), 10 mM KCl (Sigma-Aldrich, P5405), 0.001% IGEPAL CA-630 (NP-40) (Sigma-Aldrich, I3021), 0.2 mM DTT (Sigma-Aldrich, D9779), and 1 U/μl RNase inhibitor (Solarbio, R8061) dissolved in DEPC-treated water (Thermo Fisher, R0601). The tissue was further homogenized with a 2 ml Dounce homogenizer (Sigma-Aldrich, D8938) for three strokes with the loose pestle, before filtering through a 70-μm cell strainer (Falcon, 352350). The nuclei pellet was obtained by centrifuging the homogenate at 500 g for 5 min at 4°C, followed by another centrifugation at 300 g for 3 min at 4°C in the NIB. The nuclei were finally resuspended in 300 μl nuclei resuspension buffer containing 2% BSA (Sigma-Aldrich, A1933), 1.5 mM MgCl2, and 1 U/μl RNase inhibitor in dissolved PBS.
snRNA-seq library preparation and sequencing Nuclei suspension was stained with 7-AAD (Invitrogen, A1310) and subsequently sorted on a BD FACSMelody 4-Way Cell Sorter (BD Biosciences) with a 100-µm nozzle. Number of nuclei was assessed using a Countstar Rigel S5 Automated Cell Counter (Countstar). 20,000 nuclei per sample were loaded onto the 10x Genomics Chromium controller (10x Genomics). Libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns (10x Genomics, PN-1000121). Libraries were sequenced on an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads, aiming for a coverage of approximately 50,000 raw reads per nucleus.

value: mesenteric white adipose tissue (mWAT)

tag: Sex

value: Female


title: siMETTL14 n=3

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Assembly: GRCh38.83
Supplementary files format and content: Tab delimited text file contain gene expression in counts

growth_protocol: Cells were maintained at 37C and 5% CO2. MDA-MB-231 cells were maintained in in RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit with oncolumn DNase treatment
Illumina

treatment_protocol: siRNAs targeting METTL3 and METTL14 were used to deplete METTL3 and METTL14 in MDA-MB-231 breast cancer cells and the effects on gene expression determined.

tag: cell line

value: Breast cancer

value: METTL14 knockdown


title: RNA_rep2

value: Skeletal muscle

value: Myotube


title: MV411_Baseline_WT_A_G_Editor_Day_0_Rep2

description: Library name: Sample 38


title: MV411_Baseline_WT_A_G_Editor_Day_0_Rep1

description: Library name: Sample 37


title: wild type exposed to Congo Red 3 hours_2


title: MV411_DSP-5336_WT_C_T_Editor_Day_21_Rep3

description: Library name: Sample 36

value: 21 days of treatment


title: hESC-1 Ribo-seq

value: human embryonic stem cells


title: siMETTL14 n=1


title: mWAT tissue, CD feed 5w, HFD feed 0w female

description: Library name: CD_HFD0w_female


title: wild type exposed to Congo Red 3hours_1


title: MV411_DSP-5336_WT_C_T_Editor_Day_21_Rep2

description: Library name: Sample 35


title: MV411_DSP-5336_WT_C_T_Editor_Day_21_Rep1

description: Library name: Sample 34


title: mWAT tissue, CD feed 5w, HFD feed 8w female

description: Library name: CD_HFD8w_female


title: siMETTL3 n=2

value: METTL3 knockdown


title: DF-1 cells, DH3

city: Fuzhou

first: Nelam

last: Sajjad

state: Fujian, China

address: 15 Shangxiadian road

department: Animal Science

institute: Fujian Agriculture and Forestry University

data_processing:
CLC genomic Workbench V 11.0.1
reference sequence were used for read alignment
Assembly: not provided
Supplementary files format and content: fpkm_anno.txt

organism: Gallus gallus

growth_protocol: DF-1 cells were grown in DMEM (Dulbecco’s modified Eagle’s medium, Gibco, Grand Island, NY, USA) supplemented with 10 percent FBS (Fetal Bovine Serum), streptomycin and penicillin (100U/ml, Gibco, Grand Island, NY, USA) at 37℃ with 5% CO2

extract_protocol:
Total RNA was used for the construction  of sequencing library
libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: DF-1 cells have been infected with LPAIV such as H9N2

value: Chicken embryonic fibroblasts


title: siCBLL1 #2

value: Cell line

value: CBLL1 knockdown


title: mWAT tissue, HfiD feed 5w, HFD feed 4w (rep2)

description: Library name: HfiD_HFD4w_rep2

value: Male


title: MV411_SNDX-5613_WT_C_T_Editor_Day_21_Rep3

description: Library name: Sample 33

value: Overexpression of C>T base editor:TadA-CDd, SpG-SpyoCas9 (D10A), pRDB_092, addgene plasmid # #231110


title: wild type 3 hours_3


title: siMETTL3 n=3


title: wild type 3 hours_2


title: DF-1 cells, DH2


title: mWAT tissue, HfiD feed 5w, HFD feed 0w (rep2)

description: Library name: HfiD_HFD0w_rep2


title: MV411_SNDX-5613_WT_C_T_Editor_Day_21_Rep2

description: Library name: Sample 32


title: siScramble n=3

value: Non-gene targetting control


title: mWAT tissue, CD feed 5w, HFD feed 8w (rep2)

description: Library name: CD_HFD8w_rep2


title: siMETTL3 n=1


title: MV411_SNDX-5613_WT_C_T_Editor_Day_21_Rep1

description: Library name: Sample 31


title: DF-1 cells, DC3

value: control


title: siMETTL14 n=2


title: siScramble n=2


title: U87-MG cell line, Control_3

description: Library name: Sample 3

value: human glioblastoma cell line

value: Control


title: mWAT tissue, CD feed 5w, HFD feed 4w (rep2)

description: Library name: CD_HFD4w_rep2

value: mesenteric white adipose tissue (mWAT)


title: MV411_KO-539_WT_C_T_Editor_Day_21_Rep3

description: Library name: Sample 30


title: mWAT tissue, HfiD feed 5w, HFD feed 0w female

description: Library name: HfiD_HFD0w_female

value: Female


title: mWAT tissue, HfiD feed 5w, HFD feed 8w (rep2)

description: Library name: HfiD_HFD8w_rep2


title: siScramble n=1

value: Breast cancer


title: DF-1 cells, DC2


title: mWAT tissue, CD feed 5w, HFD feed 0w (rep2)

description: Library name: CD_HFD0w_rep2


title: DF-1 cells, DH1


title: wild type 3 hours_1


title: wild type exposed to Congo Red 3hours_3


title: DF-1 cells, DC1


title: MV411_KO-539_WT_C_T_Editor_Day_21_Rep1

description: Library name: Sample 28


title: MV411_JNJ-6617_WT_C_T_Editor_Day_21_Rep3

description: Library name: Sample 27


title: MDA-MB-231 STM2457 1

growth_protocol: Cells were maintained at 37C and 5% CO2. MCF-7 were maintained in phenol-red free RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate, and  10% charcoal “depleted” FBS. MDA-MB-231 cells were maintained in in RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate and 10% fetal bovine serum (FBS).

treatment_protocol: MCF-7 cells were either treated with vehicle (DMSO) or estradiol (10nM), alone or in combination with the STM2457 (10µM) METTL3 inhibitor.  MDA-MB-231 cells were treated with either vehicle (DMSO) or STM2457 (10µM). Cells were treated twice over 6 days (day 0 and day 3) and RNA harvested on day 6. The effect on global gene expression and alternative splicing was determined by RNA sequencing.

value: Breast cancer (Triple negative)


title: Nampt cKO_Rep3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

description: Library name: KO (Nampt KO)_3

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Skin

growth_protocol: Generation of epidermis-specific Nampt cKO mice: Nampt floxed mice (C57BL/6J-Namptflox/flox) (Rongvaux A, et al. The Journal of Immunology. 2008;181(7):4685-4695) were crossed with KRT5-CreERT2 mice (C57BL/6J-Krt5CreERT2) (Horiuchi M, et al. Molecular and Cellular Biology. 2021;41(2)) to generate epidermis-specific Nampt conditional knockout (cKO) mice (Namptflox/flox; KRT5-CreERT2+). Genotyping was performed by PCR to confirm the presence of the floxed Nampt allele and CreERT2 transgene.

extract_protocol:
Total RNA was extracted from skin tissues using TRI Reagent (Sigma-Aldrich, T9424) and purified with the RNeasy Mini Kit (Qiagen, 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Tamoxifen administration: To induce Cre-mediated recombination, 8-week-old male cKO mice received intraperitoneal injections of tamoxifen (Sigma-Aldrich, T5648) dissolved in corn oil (Sigma-Aldrich, C8267) at 20 mg/mL. Tamoxifen was administered at 100 μg/g body weight once daily for five consecutive days.

value: Skin

tag: age

value: Nampt flox/flox; KRT5-CreERT2+

value: male

value: Tamoxifen


title: SD.AG8

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

description: Library name: Sample48

data_processing:
Demultiplexed sequence data were imported into QIIME2, and quality filtering was performed using DADA2 to ensure sequence quality. A total of ? reads were obtained from pre-gestational and gestational adult samples, and ? reads from postnatal samples, with an average of ? reads per sample. A feature table and representative sequence table containing amplicon sequence variants (ASVs) were generated, and ASVs with low counts were removed. A rooted phylogenetic tree was constructed to infer evolutionary relationships. Outputs from QIIME2, along with metadata, were imported into R (version 4.2.1).
Assembly: mm10
Supplementary files format and content: Rds file contains abundance counts of amplicon sequence variants (ASVs) across different samples,taxonomic classification table  and sample data
Library strategy: 16S rDNA-seq

source_name: feces

growth_protocol: C57/BL6 strain mice were purchased from Jackson Lab, Bar Harbor, ME. Mice were maintained in 12:12-h light-dark cycles and care/treatment provided according to UCLA Animal Research Committee’s approved protocol

extract_protocol:
Feces were collected from non-pregnant, age-matched females and GD19 pregnant mothers, each housed individually in separate cages. Additionally, feces were collected separately from male and female PN21 pups just before weaning.
DNA was extracted using bead beating and the Qiagen PowerSoil kit. Libraries were prepared following methods adapted from Caporaso et al. The V4 region of the 16S rRNA gene was amplified with barcoded universal primers. PCR products were purified, pooled in equimolar concentrations, and sequenced on the Illumina MiSeq platform with a 2X250 bp reagent kit for paired-end sequencing.

treatment_protocol: study was conducted with a 4-week pre-conceptional exposure to air pollutants, followed by continued exposure during gestation (GD0 to GD18), based on previous research. Mice were exposed every third day, with two exposures per period under light restraint: a) the Air Pollutant (AP) group was administered 20 μl of SRM1649b (300 μg/mouse) suspension, divided and instilled intra-nasally into each nare; b) the Control (CON) group was administered 20 μl of sterile saline, similarly instilled. Vaginal delivery was allowed for the pregnant dams, who then cared for their litters.

value: feces

tag: group

tag: gender


title: MDA-MB-231 STM2457 2

city: Nottingham

first: Nigel

last: Mongan

institute: University of Nottingham

value: Cell line


title: SD.AG9

description: Library name: Sample49


title: Nampt cKO_Rep2

description: Library name: KO (Nampt KO)_2


title: SD.AG7

description: Library name: Sample47


title: MV411_JNJ-6617_WT_C_T_Editor_Day_21_Rep2

description: Library name: Sample 26

value: 21 days of treatment


title: MDA-MB-231 Vehicle 3

value: Vehicle (DMSO)


title: Nampt cKO_Rep1

description: Library name: KO (Nampt KO)_1


title: MV411_JNJ-6617_WT_C_T_Editor_Day_21_Rep1

description: Library name: Sample 25

value: Overexpression of C>T base editor:TadA-CDd, SpG-SpyoCas9 (D10A), pRDB_092, addgene plasmid # #231110


title: MDA-MB-231 Vehicle 2


title: MV411_DS-1594_WT_C_T_Editor_Day_21_Rep3

description: Library name: Sample 24


title: SD.AG5

description: Library name: Sample45


title: MDA-MB-231 Vehicle 1


title: MDA-MB-231 STM2457 3


title: Nampt flox_Rep2

description: Library name: ff (Nampt WT)_2

value: Nampt flox/flox


title: SD.AG6

description: Library name: Sample46


title: MV411_KO-539_WT_C_T_Editor_Day_21_Rep2

description: Library name: Sample 29


title: MV411_DS-1594_WT_C_T_Editor_Day_21_Rep1

description: Library name: Sample 22


title: SD.AG4

description: Library name: Sample44


title: Nampt flox_Rep3

description: Library name: ff (Nampt WT)_3


title: MCF-7 Estradiol + STM2457 3

value: Breast cancer (ER positive)

value: Estradiol (10nM) + STM2457 (10µM)


title: SD.AG49

description: Library name: Sample43

value: Male


title: MCF-7 Estradiol + STM2457 2


title: MCF-7 Estradiol + STM2457 1


title: Nampt flox_Rep1

description: Library name: ff (Nampt WT)_1


title: SD.AG48

description: Library name: Sample42


title: MV411_DMSO_WT_C_T_Editor_Day_21_Rep2

description: Library name: Sample 20

value: DMSO


title: mWAT tissue, HfiD feed 5w, HFD feed 8w

description: Library name: HfiD_HFD8w

data_processing:
The raw FASTQ files were processed with Cell Ranger version 7.0.0, and the obtained reads were aligned to the Ensembl genome (mm10). CellBender version 0.2.2 was then used to clean the raw nuclei-gene count matrices by removing ambient RNA contamination and empty droplets. The resulting count matrices were analyzed using Seurat version 5.1.0. For snRNA-seq data preprocessing, nuclei containing a total number of detected genes less than 100 or percentage of mitochondrial genes larger than 15% were filtered out. The resulting nuclei was further processed by normalizing, variable feature genes selection (selection method as VST), scaling, PCA dimension reduction, UMPA dimension reduction and clustering with resolution parameter set at 0.25. Cell clusters were manually annotated based on previously published marker genes. For adipocytes and ASPCs subclusters analysis, nuclei were subset and further processed by same procedure described above except ASPCs subclusters with resolution parameter set at 0.2. RNA velocity analysis was performed using Monocle3 version 1.3.7 and scvelo version 0.3.2 to construct predicted pseudotime trajectory in adipocytes and ASPCs. For monocle analysis, the “cluster_cells” was performed with resolution parameter set at 0.01. For scvelo analysis, unspliced and spliced RNA for each cell were extracted from all mWAT samples with cell Ranger. Through filtering, normalizing, computing moments and modeling, the velocity “stream” were visualized in PCA dimensionally reduced graphics.
Assembly: mm10
Supplementary files format and content: Expression matrix file and loom file for velocity analysis.

value: mesenteric white adipose tissue (mWAT)


title: MCF-7 STM2457 3


title: SD.AG47

description: Library name: Sample41

value: Female


title: Nampt flox_Rep4

description: Library name: ff (Nampt WT)_4


title: MV411_DS-1594_WT_C_T_Editor_Day_21_Rep2

description: Library name: Sample 23


title: MV411_DMSO_WT_C_T_Editor_Day_21_Rep1

description: Library name: Sample 19


title: SD.AG46

description: Library name: Sample40


title: Nampt cKO_Rep4

description: Library name: KO (Nampt KO)_4


title: mWAT tissue, HfiD feed 5w, HFD feed 4w

description: Library name: HfiD_HFD4w


title: mWAT tissue, HfiD feed 5w, HFD feed 0w

description: Library name: HfiD_HFD0w


title: SD.AG45

description: Library name: Sample39


title: MV411_DSP-5336_WT_A_G_Editor_Day_21_Rep3

description: Library name: Sample 18

value: Overexpression of A>G base editor:ABE8e (V106W), SpG-SpyoCas9 (D10A), pRDA_867, addgene plasmid #231109


title: MCF-7 STM2457 1


title: mWAT tissue, CD feed 5w, HFD feed 8w

description: Library name: CD_HFD8w


title: MV411_DSP-5336_WT_A_G_Editor_Day_21_Rep2

description: Library name: Sample 17


title: MCF-7 Estradiol 3

value: Estradiol (10nM)


title: SD.AG44

description: Library name: Sample38


title: MV411_DMSO_WT_C_T_Editor_Day_21_Rep3

description: Library name: Sample 21


title: MV411_DSP-5336_WT_A_G_Editor_Day_21_Rep1

description: Library name: Sample 16


title: mWAT tissue, CD feed 5w, HFD feed 4w

description: Library name: CD_HFD4w


title: mWAT tissue, CD feed 5w, HFD feed 0w

description: Library name: CD_HFD0w


title: MCF-7 Estradiol 2


title: MV411_SNDX-5613_WT_A_G_Editor_Day_21_Rep3

description: Library name: Sample 15


title: MCF-7 Estradiol 1


title: MV411_SNDX-5613_WT_A_G_Editor_Day_21_Rep2

description: Library name: Sample 14


title: MCF-7 Vehicle 3


title: SD.AG41

description: Library name: Sample35


title: Duodenum, HFD, KO8

city: Beijing

first: Xiaowei

last: Xing

state: Beijing

address: No.1 Xian Nong Tan St. Xi Cheng District

department: Institute of Materia Medica

institute: Peking Union Medical College

description: Library name: SAMPLE 16

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Paired-end clean reads were aligned to the reference mouse Ensemble genome GRCm38 using Hisat2 v2.0.5 and counted by featureCounts v1.5.0-p3.
Differential expressed genes were analyzed using the DESeq2 R package (1.20.0). After Benjamini and Hochberg’s approach for controlling the false discovery rate, genes with an adjusted P-value < 0.05 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: Microsoft excel file includes gene counts normalized by DESeq2 for each sample

source_name: duodenal epithelium

extract_protocol:
Frozen tissues were homogenized and total RNA was extracted by TRIzol method, the integrity was assessed by Bioanalyzer 2100 system.
mRNA was purified using poly-T oligo-attached magnetic beads. NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) was used for library preparation following manufacturer's recommendations.

treatment_protocol: Ephb4 fl/fl and Ephb4-IKO mice were fed with HFD for 19 weeks. Mice were sacrificed and duodenal epithelium were collected, snap frozen in liquid nitrogen and transferred to -80 degree refrigerator.

value: duodenal epithelium

value: KO

value: fed with HFD for 19 weeks


title: MV411_SNDX-5613_WT_A_G_Editor_Day_21_Rep1

description: Library name: Sample 13


title: Duodenum, HFD, KO7

description: Library name: SAMPLE 15


title: SD.AG42

description: Library name: Sample36

value: feces


title: Duodenum, HFD, KO5

description: Library name: SAMPLE 14


title: MCF-7 STM2457 2

address: University Park

value: Cell line