title: H3K9me2_kaku4

first: Zhen

last: Su

address: #2 Yuanmingyuan Xilu

institute: China Agricultural University

data_processing:
All clean ChIP-seq reads were mapped to the Arabidopsis genome TAIR10 using BOWTIE2 software with default parameters. The MACS program was used to shift the reads to identify peaks.
RNA-seq data with 3 biological replicates were generated. The paired-end clean reads of RNA-seq were aligned to the reference genome (TAIR10) by TopHat2 v2.0.9 software. FPKM values were calculated using Cufflinks.
Supplementary files format and content: bw
Supplementary files format and content: FPKM

source_name: 4wk leaves

extract_protocol:
A native chromatin immunoprecipitation (ChIP) was performed using antibody of histone modification essentially as described with minor modification (Nagaki et al. 2003).
ChIP-seq libraries were constructed by Shanghai Jiayin Biotechnology Co., Ltd and sequenced using the Illumina system Novaseq 6000 with a 150-bp read length.

value: 4wk leaves


title: 55_Residual_Disease

status: Public on Feb 29 2024

type: SRA

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description:
All_Sample_Raw_Counts.csv
All_Samples_TMM_log2_CPM.csv

library_source: transcriptomic

data_processing:
Fastq files have been trimmed of adapters using TrimGalore, then aligned to hg38 using STAR (v2.4.2a).
FASTQC has also been run on each of the samples. Genes with 0 counts across all samples were filtered out.
The gene-level counts from all studies were then normalized using TMM with edgeR. Log2 transformed TMM-normalized counts per million [log2 (TMM-CPM + 1)] were used for analysis.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts of each sample
Supplementary files format and content: csv file includes TMM normalized log2 (CPM+1) value of each sample

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor tissue

extract_protocol:
Total RNA was isolated from 295 formalin-fixed paraffin-embedded (FFPE) tissue specimens; each sample consisted of seven 4µm sections scraped from individual slides. Paraffin wax was removed with two rounds of xylene extraction. Samples were incubated in lysis buffer containing proteinase-K, and RNA was purified using miRNeasy FFPE (QIAGEN) kits following the manufacturer’s recommended procedure. RNA purity and concentration were measured by UV absorbance. RNA integrity (fragment size) was assessed using a 2100 Bioanalyzer (Agilent Technologies) and RNA 6000 Nano and 6000 Pico kits. DV200 values (% fragments > 200 bases) were calculated using the 2100 Bioanalyzer Expert Software (Agilent Technologies). DV200 values ranged from 7 to 66% with 221 samples having a value ≥ 30%.
Libraries were prepared using the Illumina RNA with Enrichment, Tagmentation protocol (Illumina) with the Illumina Exome Panel - Enrichment Oligos (Illumina). Libraries were profiled on a Bioanalyzer (Agilent) and quantified with an NGS Quantification Kit (Roche/Kapa Biosystems) using a StepOnePlus Real Time PCR Workstation (Thermo/ABI).

tag: tissue

value: Breast tumor tissue

tag: disease state

value: early-stage HER2-positive breast cancer

tag: genotype

value: WT

tag: treatment

tag: patient id

tag: her2 heterogeneity

value: No

tag: pcr


title: interscapular brown adipose tissue, 10day cold exposed, Mafbf/f, 3

city: Tsukuba

first: Michito

last: Hamada

state: Ibaraki

address: 1-1-1 Tennodai,

department: Department of Anatomy and Embryology

country: Japan

institute: University of Tsukuba

description: Single bam file generated for each sample using STAR, from paired-end two separate fastq files

data_processing:
STAR version=STAR_2.6.1a_08-27
Sequence read were alligned and mapped using default paramaters of STAR version STAR_2.6.1a_08-27
Read count performed by STAR
Normalization and DEG analysis done by edgeR tool
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each Sample

organism: Mus musculus

source_name: interscapular brown adipose tissue

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
Library construction and RNA seq peformed by University of Tsukuba, RNA seq service

value: interscapular brown adipose tissue

tag: strain

tag: cell type

value: tissue

value: Mafbf/f

value: 10 days, 4 degree cold exposure


title: 59_site2_core2

value: Pre-treatment


title: 54_site1_core2

value: Yes


title: H3K27me3_kaku4

city: Beijing

department: College of Biological Sciences

country: China

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana


title: 54_site1_core1


title: 53_site2_core2


title: 59_site1_core2


title: 53_site1_core1


title: H3K27me3_WT

value: col


title: 52_site1_core2


title: 52_site2_core2


title: Fibroblasts,meninges,C1,negative

city: Pavia

first: Matteo

last: Bordoni

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option.
Differental expression analysis for mRNA and lncRNA was performed using R package DESeq2
Assembly: HG19
Supplementary files format and content: fastq.gz

source_name: meninges

growth_protocol: MFs and SFs were isolated from meninges and skin fragments derived from 6 human brain donors.

extract_protocol:
Total RNA was isolated from MFs and SFs using Trizol® reagent. The specifications from the manufacturer were followed.
Lexogen CORALL Total RNA-seq Library Prep Kit,  using 500 ng total RNA. Qualities of sequencing libraries were assessed with 4200 TapeStation with the D1000 High sensitivity Kit. RNA processing has been carried out using Illumina NextSeq 550 Sequencing.

treatment_protocol: Cells were positively or negatively selected using Anti-fibroblasts magnetic beads.

value: meninges

tag: cell line

value: Fibroblasts

value: negative


title: Fibroblasts,meninges,C1,positive

value: positive


title: Fibroblasts,skin,C1,positive

source_name: skin

value: skin


title: 51_site2_core1


title: H3K4me3_kaku4

value: 4wk leaves


title: Fibroblasts,meninges,C6,positive


title: 51_site1_core2

value: Breast tumor tissue


title: 55_site1_core1

value: early-stage HER2-positive breast cancer


title: 50_site1_core2

value: WT


title: 50_site2_core2

value: No


title: 49_site2_core2


title: Library 4 mRNA

city: Leuven

first: Bart

last: De Strooper

address: Herestraat 49 box 602

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description:
10x Genomics
Mancuso2022_RNAcounts.mtx.gz
Mancuso2022_RNAcounts_genes.txt
Mancuso2022_RNAcounts_cellbarcodes.txt
Mancuso2022_NormExpr.mtx.gz
Mancuso2022_NormExpr_genes.txt
Mancuso2022_NormExpr_cellbarcodes.txt

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: Genome build: Human reference, hg19 (Ensembl 87), downloaded from 10x Genomics pre-built Cell Ranger reference packages (3.0.0).
Supplementary files format and content: *.mtx.gz: Raw or SCT normalised gene expression counts per cell in a gzipped tab-separated values file.
Supplementary files format and content: *genes.txt: row names (genes) for raw or SCT normalised gene expression matrices, in txt files.

source_name: Brain

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F, Apphu/hu or AppNL-G-FApoE-/-  mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
In this manuscript, we generated a total of 20 libraries containing 95 biological replicates for single cell RNA sequencing. In brief, we sorted 15000-20000 alive human microglia (CD11b+, hCD45+) per mouse and adjusted the final concentration to 1000 cells/µl. Out of each mouse, 2000 sorted cells were loaded into the Chromium Next GEM Chip G (PN #2000177). Since all the individual replicates were hashed using TotalSeqTM-A cell hashing antibodies, we pooled different samples into the same library. Libraries were prepared using manufacturer’s instructions (CG000204 Chromium Next GEM Single Cell 3’ Reagent Kits v3.1). For hashtag oligo libraries, we followed manufacturers’ instructions (BioLegend - TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR. Libraries were sequenced on a HiSeq4000 or NovaSeq6000 (Illumina) platform with the recommended read lengths by 10X Genomics workflow targeting 90% mRNA and 10% hashtag library (50,000 reads/cell).

value: Brain

value: Microglia

tag: mouse host genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

tag: human cells gender

value: male

tag: mouse host gender

value: female and male

tag: timepoint

value: 6 months

tag: injection

tag: multiplexed samples

tag: samples used for this study


title: H3K4me3_WT

tag: tissue

value: col


title: Fibroblasts,skin,C6,positive


title: Fibroblasts,meninges,C3,positive

value: meninges


title: TN3

city: Shanghai

first: wenbin

last: wei

address: NO.639 Zhizaoju Road,Huangpu District

institute: Shanghai Ninth People 's Hospital, Shanghai Jiao Tong UniversitySchool of Medicine

description: trigeminal nerve of trigeminal neuralgia

data_processing:
The Space Ranger software pipeline provided by 10×Genomics displayed the capture area of tissue in the chip by image processing algorithm, and distinguishes reads of each Spot according to spatial barcode information.STAR, a genomic comparison software, was integrated to calculate the total number of spots, the number of pair reads in each Spot, the number of detected genes and the number of UMIs, so as to evaluate the quality of the samples.
Assembly: Rnor6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every spot

organism: Rattus norvegicus

source_name: trigeminal neuralgia

extract_protocol:
OCT-embedded rat trigeminal nerve were cryosectioned coronally to a thickness of 10 μm. Tissue sections were layered onto the visium spatial tissue optimization slide containing oligonucleotides for mRNA capture (10x Genomics, Pleasanton, CA, USA).A Master Mix containing reverse transcription (RT) reagents and fluorescently labeled nucleotides is added on top of the tissue sections, resulting in fluorescently labeled cDNA synthesis. Tissue is enzymatically removed, leaving behind fluorescent cDNA covalently linked to oligonucleotides on the slide. Fluorescent cDNA is visualized under fluorescence imaging conditions verified using the Visium Imaging Test Slide. Fluorescent cDNA is visualized under fluorescence imaging conditions verified using the Visium Imaging Test Slide. H&E and fluorescence images are compared. The permeabilization time that results in maximum fluorescence signal with the lowest signal diffusion is optimal.
The polyadenylation mRNA released by the covered cells is captured by the primers of the lattice. RT Master Mix containing the reverse transcription reagent was added to the penetrating tissue slice. After incubation with the reagent, full-length cDNA with spatial barcodes generated from polyadenylation mRNA on a slide can be obtained. The second strand synthesis Mix reagent is added to the tissue section area on the slide to initiate second strand cDNA synthesis. After the cDNA was transferred from the slide, the full-length cDNA was amplified by PCR and sufficient amount was obtained for the construction of the library. The cDNA was enzymatically cleaved and fragmented. DNA library was constructed by End Repair and A-tail. The constructed library was sequenced using lllumina novaseq 6000.

value: trigeminal neuralgia

value: Wild type


title: 49_site1_core1

tag: disease state

value: Pre-treatment

value: Yes


title: HC

description: trigeminal nerve of negative control

tag: genotype


title: TN2


title: 48_Residual_Disease

tag: treatment


title: Fibroblasts,skin,C3,positive

value: skin

value: Fibroblasts

value: positive


title: H3K9me2_WT

value: 4wk leaves


title: 47_site2_core1

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT

tag: patient id

value: No


title: TN1


title: 47_site1_core2

tag: her2 heterogeneity


title: 47_Residual_Disease

tag: pcr


title: Fibroblasts,meninges,C5,positive


title: 46_site2_core1


title: XZ0839, liver, CCL4 administration, Input

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

institute: Nanjing agricultural university

data_processing:
Reads were quality controlled using FastQC (v0.11.5) and TrimGalore (v0.6.0).
rRNA sequence were removed by using bowtie2(v2.3.4.1) with --ungz or --un-conc-gz parameter.
The retained reads were aligned to GRCm38/mm10 by HISAT2 (v2.2.1) with default parameters.
Bigwig files were obtained by using bamCoverage function in deepTools (v3.5.1) and visualized in IGV (v11.0.19).
Read counts were quantified by using featureCounts (v1.6.0).
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA quality and integrity were assessed by NanoDrop ND 1000 spectrophotometry and agarose gel electrophoresis. Dynabeads Oligo (dT)25 was employed to isolate the mRNA containing PolyA in total RNA pool. The isolated mRNA was then sonicated into fragments of 150-200 bp through 30 cycle of ultrasound, with each cycle comprising 30 s on and 30 s off.   A total of 50 ng of fragmented mRNA was used as input. In the immunoprecipitation (IP) process, 25 μL of protein G beads (NEB, Cat. S1430) were pre-incubated with 1 μL of anti-m6Aantibody (NEB, Cat. E1610S) in reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) at 4°C for 30 min. Following this, a 250 μL mixture containing 950 ng of mRNA, 50 μL IP buffer (750 mM NaCl, 50 mM Tris-HCl, 0.5% NP-40), and 5 μL RNA inhibitor was added to antibody and incubated for 1 h at 4℃. Subsequently, beads were washed sequentially in the following solutions: twice in reaction buffer, twice in low salt buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), and twice in high salt buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). RNA was then eluted from beads with 100 μL of buffer RLT (QIAGEN, Cat. 1015762) by incubation for 1 min and then purified using a clean and concentrate RNA kit according to the manufacturer’s protocol. (Zymo research, Cat. R1017).
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara), according to the manufacturer’s protocol.
m6a-seq

value: liver

value: CCL4 administration

tag: fraction

value: Input


title: 46_site2_core2


title: Fibroblasts,meninges,C6,negative

value: negative


title: XZ0838, liver, CCL4 administration, Input


title: 46_Residual_Disease


title: Fibroblasts,meninges,C5,negative

value: meninges


title: Fibroblasts,skin,C5,positive


title: 45_site2_core1


title: 48_site1_core3


title: XZ0837, liver, CCL4 administration, Input


title: 45_site1_core1


title: XZ0836, liver, control, Input

value: control


title: 48_site1_core1


title: 44_site2_core1


title: Fibroblasts,skin,C4,positive


title: XZ0835, liver, control, Input


title: 42_site1_core1


title: Fibroblasts,skin,C2,positive


title: Fibroblasts,meninges,C2,positive


title: 43_site1_core2


title: 42_site2_core1


title: XZ0834, liver, control, Input


title: 40_site2_core2


title: XZ0830, liver, CCL4 administration, immunoprecipitation

value: immunoprecipitation


title: 40_site1_core1

value: Pre-treatment


title: XZ0829, liver, CCL4 administration, immunoprecipitation


title: 38_site1_core2

value: Yes


title: 39_site2_core1


title: XZ0828, liver, CCL4 administration, immunoprecipitation


title: 39_site1_core2


title: XZ0827, liver, control, immunoprecipitation


title: Fibroblasts,meninges,C4,positive


title: XZ0826, liver, control, immunoprecipitation


title: 44_site1_core1


title: 37_Residual_Disease


title: 43_site2_core1


title: 36_site2_core1


title: 36_site1_core1


title: 37_site1_core2


title: 35_site2_core1


title: XZ0825, liver, control, immunoprecipitation


title: E18 IL10KO mom LK LPS 3 hrs

city: New York

first: Melissa

last: Proven

state: NY

institute: Columbia Unversity

data_processing:
The demulitplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fetal liver

extract_protocol:
Cells were FACS-sorted into HBSS containing 2% FBS and transferred to the Columbia Genome Center Single Cell Analysis Core for microfluidic processing, library preparation, and sequencing.
Library was performed according to the manufacturer's instructions (Chromium Single Cell 3' Library and Gel Bead Kit v.2, 10X Genomics).

value: fetal liver

tag: age

tag: Sex

value: pooled male and female

tag: cell type

value: Linneg cKitpos

value: 3 hr in vivo LPS


title: 34_site2_core2

value: Breast tumor tissue


title: 34_site1_core2

value: early-stage HER2-positive breast cancer


title: 33_site2_core1

value: WT


title: E18 IL10KO mom LK PBS


title: 33_site1_core1

value: No


title: 40_Residual_Disease


title: 33_Residual_Disease


title: 32_site1_core2


title: 32_site2_core2


title: Adult LK LPS 3 hrs

source_name: bone marrow

value: bone marrow

value: 8-12 weeks

value: C57BL/6 wildtype


title: 38_site2_core1


title: 37_site2_core2


title: 31_site1_core1


title: 30_site2_core1


title: 31_Residual_Disease


title: 30_site1_core2


title: Adult LK PBS

value: PBS-exposed


title: 29_site1_core1


title: 28_site2_core1


title: 29_Residual_Disease


title: E18 LK LPS 16 hrs

value: 16 hr in vivo LPS


title: E18 LK PBS


title: 35_site1_core2


title: 28_site1_core1


title: 28_Residual_Disease


title: 25_site2_core2


title: E18 WT mom LK LPS 3 hrs


title: XNES1_LacZ_H3K4me3

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

data_processing:
Reads were aligned to the human and yeast genomes (hg38 and R64-1-1 respectively) using bowtie2 (–local –very-sensitive- local –no-mixed –no-discordant –phred33 -I 10 -X 700)
BAM files were indexed using samtools (version 1.12) and converted to bigwig files using deeptools bamCoverage (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Bigwigs for genome browser visualization
Library strategy: CUT&RUN

source_name: NPC

extract_protocol:
CUT&RUN analysis was done following the protocol described in Skene&Henikoff  2018 (Skene & Henikoff, 2017). 300.000 cells were used to do the analysis.
Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual indexed adapters (KAPA).

tag: individual

tag: dx

value: XDP

tag: cell type_at_ko/kd

value: NPC

tag: condition

value: Control

tag: target gene

value: LacZ

tag: batch

value: batchG

tag: antibody


title: XNES1_LacZ_IgG


title: 25_site1_core2

tag: tissue

tag: disease state

value: Pre-treatment


title: XNES1_KD_H3K4me3

value: CRISPRi

value: DNMT1+ZNF91 KD


title: E18 WT mom LK PBS

value: fetal liver

value: pooled male and female

value: Linneg cKitpos

tag: genotype

tag: treatment

value: 3 hr in vivo LPS


title: 27_site2_core1

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT

tag: patient id

tag: her2 heterogeneity

value: No

value: Yes


title: Adult LK LPS 16 hrs

value: bone marrow

value: 8-12 weeks

value: C57BL/6 wildtype

value: 16 hr in vivo LPS


title: 24_site2_core1

tag: pcr


title: E18 LK LPS 3 hrs

tag: age


title: CNES1_LacZ_IgG

value: Control

value: NPC

value: LacZ

value: batchG


title: dKOPRMT, replicate 1, RNA-seq

city: London

first: Eric

last: So

address: School of Cancer and Pharmaceutical Sciences

country: United Kingdom

institute: KCL

data_processing:
The raw reads were trimmed using trim galore (version 0.6.6) (Kreuger F. Babraham Bioinformatics - Trim Galore), and aligned to the mouse reference genome GRCm38 using STAR (version 2.7.6a) (Dobin et al., 2013).
The featureCounts tool was used to summarize read counts across the genes (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: dKO HSPCs

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
Library preparation was performed using Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7760L).

value: dKO HSPCs

value: dKO transduced with PRMT1 WT


title: 31_site2_core1

value: Pre-treatment


title: dKOMut, replicate 2, RNA-seq

value: dKO transduced with an enzymatically dead mutant of PRMT2


title: 23_site1_core2

value: Breast tumor tissue


title: 24_site1_core1

value: early-stage HER2-positive breast cancer


title: CNES1_LacZ_H3K4me3


title: 23_site2_core1

value: WT


title: 22_site2_core1

value: No


title: dKOMut, replicate 1, RNA-seq

value: dKO transduced with an enzymatically dead mutant of PRMT1


title: 22_site1_core1

value: Yes


title: 21_site1_core2


title: 21_site1_core1


title: dKOEV, replicate 2, RNA-seq

value: dKO transduced with Empty Vector control


title: dKOPRMT, replicate 2, RNA-seq


title: CNES1_KD_H3K4me3

value: CRISPRi

value: DNMT1+ZNF91 KD


title: 21_Residual_Disease


title: dKOEV, replicate 1, RNA-seq


title: 165_site1_core1


title: WTEV, replicate 2, RNA-seq

value: WT transduced with Empty Vector control


title: 165_site2_core2


title: sample2_frozen

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

description: RNA libraries created from cryopreserved, thawed, then sorted CD45+ cells from the same subject as fresh

data_processing:
Sequencing data was demultiplexed into separate per library fastq files using the mkfastq command of the cell ranger 6.0.0 pipeline (10x Genomics)
Reads in fastq files were aligned to the GRCh38 transcriptome and creation of feature barcode matrices using cell ranger 6.0.0 (10x Genomics)
Secondary analysis of the feature barcode matrices was performed using the Seurat package (Hao, 2021) within the R statistical computing environment. Cells were filtered for quality, normalized, scaled and clustered in an ubiased manner to generate a UMAP plot.
Assembly: GRCh38
Supplementary files format and content: filtered cell barcode by gene matrices

source_name: Mid-secretory (implantation window) endometrium

extract_protocol:
Endometrial tissue was grossly dissected and washed in PBS, then finely minced before being digested in a shaking 37°C water bath for 15-30 mins in sterile medium containing 0.28WU/mL Liberase TM (Roche, Catalog  # 05401127001) and 30ug/mL DNase (Roche, catalog # 10104159001)]. A large-bore transfer pipet was used to pipet tissue up and down during digestion to break down tissue. Digested tissue was pelleted, subjected to RBC lysis, and then filtered through a 70μm filter. For the fresh tissue, cells were immediately processed within 2 hours for flow sorting. Cryopreserved samples were similarly processed within 2 hours, and frozen in cryotubes at a concentration of 1x107/mL in 1mL of freezing medium, consisting of 90% RPMI (ThermoFisher, Catalog # 11875085), 10% DMSO (Sigma, Catalog # D2650-100mL), and 1mg/mL BSA (Sigma, A9418)]. Sample was frozen in a Mr.Frosty freezing container for 24 hours before being placed in a -120℃ freezer. Immediately prior to flow sorting, cryovials were thawed for 30 seconds in a 37ºC water bath and immediately washed in PBS to remove DMSO.
Next-generation sequencing libraries were prepared using the 10× Genomics Chromium Single Cell 3’ Library and Gel Bead kit v3, per manufacturer’s “Chromium Single Cell Reagent Kits” protocol. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on the Illumina NextSeq500  sequencer in a paired-end, single indexing run. Sequencing targeted 20,000 mean reads per cell.

value: Sort-purified CD45+ cells from mid-secretory (implantation window) endometrium

value: Cryopreserved at -80C then thawed


title: sample1_fresh

description: RNA libraries created from fresh, sorted CD45+ cells from the same subject as frozen/cryopreserved

value: Mid-secretory (implantation window) endometrium

value: Fresh


title: 164_site2_core1


title: 164_site1_core2


title: 163_site2_core2


title: 163_site1_core1


title: WTEV, replicate 1, RNA-seq

value: dKO HSPCs


title: Bcat_KO, replicate 2, RNA-seq

source_name: LSK cells

value: LSK cells

value: beta-catenin knockdown


title: 162_site1_core1

value: Breast tumor tissue

value: Pre-treatment


title: 162_Residual_Disease

value: early-stage HER2-positive breast cancer

value: WT


title: AECs, S2_infection, 400nM_Ganetespib, rep2

city: Berlin

first: Luiz Gustavo

last: Teixeira Alves

address: Hannoversche Strasse 28

country: Germany

institute: MDC Berlin

data_processing:
Reads were aligned to the human reference genome hg38 (GRCh38) and the hamster genome (MesAur1.0) using hisat2.
Gene expression was quantified using the package featureCounts from Rsubread and analyzed by DESeq2.
Differentially expressed genes were defined by an absolute fold change in mRNA abundance greater than 1.5 (log2 fold change of 0.58 - using DESeq2 shrunken log2 fold changes) and an adjusted p-value of less than 0.05 (Benjamini-Hochberg corrected)
Assembly: hg38 and MesAur1.0
Supplementary files format and content: tab-delimited text files including raw values or normalized values for each Sample

source_name: distal lung tissue

growth_protocol: AECs were isolated from distal lung tissue and co-cultivated with gamma-irradiated mitotically inactivated NIH3T3 mouse embryonic fibroblasts (MEFs) in a 3:1 mixture of Ham’s F-12 nutrient mix (Life technologies) and DMEM supplemented with 5 % FCS, 0.4 µg/mL hydrocortisone (Sigma-Aldrich), 5 µg/mL recombinant human insulin (Sigma-Aldrich), 8.4 ng/mL cholera toxin (Sigma-Aldrich), 24 µg/mL Adenine (Sigma-Aldrich), 10 ng/mL recombinant human epidermal growth factor (Invitrogen), 0.1 µM Dibenzazepine (DBZ; Tocris) and 9 µM Y27632 (Miltenyi Biotec). Differentiation was induced by additional treatment with 3 µM CHIR-99021 (Sigma), 10 ng/ml keratinocyte growth factor (KGF; Invitrogen), 10 ng/ml fibroblast growth factor (FGF)-10 (Invitrogen), 100 µM 3-isobutyl-1-methylxanthine (Sigma), 100 µM 8- Bromoadenosine 3’,5’-cyclic monophosphate (Biolog), 25 nM Dexamethasone (Sigma) and 20 µM DBZ for 3 days. Two days prior to infection, the primary cells were separated from the MEFs by differential trypsinization and subsequently seeded in cell culture vessels in DMEM with 10% FCS, 1% non-essential amino acids, 1%, L-glutamine and 1% sodium pyruvate

extract_protocol:
RNA isolation was performed using Trizol reagent according to the manufacturer’s instructions and RNA extracted with
Libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Treatment with Ganetespib was done prior to infection with SARS-CoV-2 for characterization of its protective functions. AECs were treated with different concentrations of Ganetespib, ranging from 12.5 nM to 800 nM in a log2 scale

value: distal lung tissue

value: alveolar epithelial cells

value: 400nM Ganetespib


title: 161_site2_core2

value: No


title: AECs, S2_infection, 400nM_Ganetespib, rep1


title: 161_site1_core2


title: Bcat_KO, replicate 1, RNA-seq


title: dKO, replicate 2, RNA-seq

value: beta-catenin/Hoxa9 knockdown


title: 161_Residual_Disease


title: 160_site2_core1

value: Yes


title: 160_site1_core1


title: AECs, S2_infection, 200nM_Ganetespib, rep1

value: 200nM Ganetespib


title: dKO, replicate 1, RNA-seq


title: 159_site2_core2


title: 159_Residual_Disease


title: AECs, S2_infection, 800nM_Ganetespib, rep2

value: 800nM Ganetespib


title: WT, replicate 2, RNA_seq


title: 158_site2_core1


title: WT, replicate 1, RNA_seq


title: AECs, S2_infection, 100nM_Ganetespib, rep1

value: 100nM Ganetespib


title: 158_site1_core2


title: AECs, S2_infection, 800nM_Ganetespib, rep1


title: WT_PRMT1, replicate 2, RNA_seq

value: WT for PRMT1 experiment


title: 158_Residual_Disease


title: 157_site1_core2


title: 157_site2_core2


title: AECs, S2_infection, 50nM_Ganetespib, rep2

value: 50nM Ganetespib


title: WT_PRMT1, replicate 1, RNA_seq

value: LSK cells


title: 156_site1_core2


title: 156_site2_core2


title: AECs, S2_infection, 50nM_Ganetespib, rep1


title: PRMT1_KO, replicate 2, RNA-seq

value: PRMT1 knockdown


title: AECs, S2_infection, 200nM_Ganetespib, rep2


title: 154_site2_core1

value: Breast tumor tissue


title: AECs, S2_infection, 25nM_Ganetespib, rep2

value: 25nM Ganetespib


title: 155_site1_core2

value: early-stage HER2-positive breast cancer

value: Pre-treatment


title: 155_site2_core1

value: WT


title: PRMT1_KO, replicate 1, RNA-seq


title: AECs, S2_infection, 25nM_Ganetespib, rep1

value: distal lung tissue

value: alveolar epithelial cells


title: 154_site1_core2

value: No


title: AECs, S2_infection, 12.5nM_Ganetespib, rep2

value: 12.5nM Ganetespib


title: AECs, S2_infection, 100nM_Ganetespib, rep2


title: HOXA9_KO, replicate 2, RNA-seq

value: HOXA9 knockdown


title: 153_site1_core1

value: Yes


title: 153_site2_core2


title: 153_Residual_Disease


title: HOXA9_KO, replicate 1, RNA-seq


title: AECs, S2_infection, 12.5nM_Ganetespib, rep1


title: 151_site2_core2


title: 151_site1_core2


title: AECs, S2_infection, rep2

value: DMSO


title: 150_site2_core2


title: 150_site1_core2


title: 149_site2_core2


title: 148_site2_core2


title: Syn.RARg.IgG.veh.1.sorted.rmdup.BAM

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Cistromes were analyzed with csaw with different size windows for transcription factors or histone modifications, along with TF motif analyses (MotifDb). In order to find potential transcription factor binding enrichment within cistromes, GIGGLE was utilized to query the complete human transcription factor ChIP-seq dataset collection (10,361 and 10,031 datasets across 1,111 transcription factors and 75 histone marks, respectively) in Cistrome DB. Prostate specific filtering limited analysis to 681 datasets across 74 TFs and 238 datasets across 19 HMs. For each query dataset, we determined the overlap of each transcription factor cistrome. Putative co-enriched factors were identified by assessment of the number of time a given factor was observed in the top 200 most enriched datasets relative to the total number of datasets for that factor in the complete Cistrome DB (> 1.2 FC enrichment over background). For prostate specific analysis, overlaps across datasets were averaged for each factor.
Within each cistrome (e.g. H3K27ac, or AR) the treatments were compared to IgG, with the results indicated as the target (e.g. AR) and treatment (e.g. DHT) in the  file name.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Cistromes were analyzed with Rsubread/csaw along with TF motif analyses (MotifDb) all in R
Assembly: hg38
Supplementary files format and content: bed files
Library strategy: CUT&RUN

source_name: prostate

growth_protocol: Cells were grown to 70% confluence and briefly, 0.5x106 cells in triplicate were treated for DHT (10nM, 6h) or CD437 (400 nM, 6h). For TACC1, the pLenti-CMV-TACC1-C term RFP vector was transiently overexpressed for 48h followed by similar drug treatments and sustained protein expression confirmed.  Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol:
Harvested cells were washed with pre-activated Concanavalin A-coated beads mixed with antibody overnight at 4°C. CUTANA pAG-MNase (EpiCypher) was incubated with sample for 10 minutes at room temperature.
Sequencing libraries prepared from immunopreciptiated DNA
Fragmented DNA samples was purified using the Monarch DNA Clean up Kit (New England Biolabs). The libraries were prepared from 5-10ng purified CUT&RUN-enriched DNA, using the NEB Ultra II Library Prep Kit (New England Biolabs) per manufacturer's instructions and sequenced using Hiseq 4000 PE 150bp. Transcription factor modifications for sub-nucleosomal size (<120bp) DNA fragments were undertaken as per protocol.

treatment_protocol: Cells were grown to 70% confluence and briefly, 0.5x106 cells in triplicate were treated for DHT (10nM, 6h) or CD437 (400 nM, 6h). Cells were treated with nocodozole (60 ng/ml, 18h)  to bring abour ~70% cells in G2/M and then treated with DHT or vehicle as above.  For TACC1, the pLenti-CMV-TACC1-C term RFP vector was transiently overexpressed for 48h followed by similar drug treatments and sustained protein expression confirmed.  Cell lines were authenticated by STR profiling and confirmed mycoplasma free.  CUT&RUN was undertaken with antibodies to GFP (for RARgamma), AR, H3K27ac, H3S10P and IgG.

value: prostate

tag: cell line

value: RARg

tag: chip antibody

value: IgG

value: nocodozole (60 ng/ml, 18h), then Vehicle


title: AECs, S2_infection, rep1

tag: cell type


title: Syn.RARg.IgG.veh.3.sorted.rmdup.BAM


title: 148_site1_core2


title: AECs, Mock_infection, 800nM_Ganetespib, rep2

value: 800nM Ganetespib


title: Syn.RARg.IgG.veh.2.sorted.rmdup.BAM


title: 149_site1_core2

value: Breast tumor tissue


title: Syn.RARg.IgG.DHT.3.sorted.rmdup.BAM

value: nocodozole (60 ng/ml, 18h), then DHT (10nM, 6h)


title: 147_site2_core1

value: early-stage HER2-positive breast cancer


title: Syn.RARg.IgG.DHT.2.sorted.rmdup.BAM


title: AECs, Mock_infection, 800nM_Ganetespib, rep1


title: AECs, Mock_infection, rep2


title: 145_site2_core2

value: Pre-treatment


title: Syn.RARg.IgG.DHT.1.sorted.rmdup.BAM


title: 145_site1_core2

value: WT


title: AECs, Mock_infection, rep1

value: distal lung tissue


title: 144_site2_core1


title: Syn.RARg.AR.DHT.3.sorted.rmdup.BAM

value: AR


title: 144_site1_core2

value: No


title: AlvMac, S2_infection,Ganetespib, rep2_3

source_name: bronchoalveolar lavage

growth_protocol: Alveolar macrophages were isolated from bronchoalveolar lavage performed for routine diagnostic purposes in patients. Cells were washed twice in cold PBS, then resuspended at 10^6/ml in RPMI 1640/10 % FCS/penicillin/streptomycin. Untreated alveolar macrophages were placed into 24-well tissue culture plates and allowed to adhere for 2 h. Cell monolayer was washed three times to remove nonadherent cells and antibiotics and cultured in RPMI 1640/10 % FCS

treatment_protocol: Treatment with Ganetespib was done prior to infection with SARS-CoV-2 for characterization of its protective functions. Alveolar macrophages were treated for 16 h with 100 nM of Ganetespib

value: bronchoalveolar lavage

value: alveolar macrophages

value: 100nM Ganetespib


title: 143_site2_core1


title: Syn.RARg.AR.DHT.2.sorted.rmdup.BAM


title: 143_Residual_Disease


title: 142_site2_core1

value: Yes


title: AlvMac, S2_infection,Ganetespib, rep2_2


title: 142_site1_core1


title: Syn.RARg.AR.DHT.1.sorted.rmdup.BAM

value: prostate


title: AlvMac, S2_infection,Ganetespib, rep2_1


title: Syn.RARg.H3S10p.DHT.3.sorted.rmdup.BAM

value: RARg


title: 141_site2_core2


title: AlvMac, S2_infection, rep2_3

value: DMSO


title: 147_site1_core2


title: 142_Residual_Disease


title: AlvMac, S2_infection, rep2_2


title: 139_site2_core1


title: 138_site2_core1


title: 139_site1_core2


title: 138_site1_core2


title: 137_site2_core2


title: Syn.RARg.AR.veh.3.sorted.rmdup.BAM

value: nocodozole (60 ng/ml, 18h), then Vehicle


title: AlvMac, S2_infection, rep2_1


title: Syn.RARg.H3S10p.DHT.1.sorted.rmdup.BAM


title: AlvMac, Mock_infection,Ganetespib, rep2_3


title: 141_site1_core2


title: Syn.RARg.H3S10p.DHT.2.sorted.rmdup.BAM


title: 136_Residual_Disease


title: 136_site2_core2


title: Syn.RARg.AR.veh.1.sorted.rmdup.BAM


title: AlvMac, Mock_infection,Ganetespib, rep2_2


title: Syn.RARg.AR.veh.2.sorted.rmdup.BAM


title: 134_site2_core2


title: 136_site1_core2


title: AlvMac, Mock_infection,Ganetespib, rep2_1


title: Syn.RARg.RARg.veh.3.sorted.rmdup.BAM


title: 134_site1_core2


title: AlvMac, Mock_infection, rep2_3


title: 134_Residual_Disease


title: 133_site1_core1


title: Syn.RARg.RARg.veh.2.sorted.rmdup.BAM


title: AlvMac, Mock_infection, rep2_2


title: 131_site2_core1


title: 131_site1_core2


title: Syn.RARg.RARg.veh.1.sorted.rmdup.BAM


title: 130_site2_core2


title: AlvMac, Mock_infection, rep2_1


title: 130_site1_core2


title: 130_Residual_Disease


title: AlvMac, S2_infection,Ganetespib, rep1_3


title: Syn.RARg.H3S10p.veh.1.sorted.rmdup.BAM


title: AlvMac, S2_infection,Ganetespib, rep1_2


title: 129_site1_core2


title: Asy.RARg.IgG.veh.3.sorted.rmdup.BAM

value: IgG


title: 128_site2_core1

value: Breast tumor tissue


title: AlvMac, S2_infection,Ganetespib, rep1_1


title: 127_site2_core1


title: 128_site1_core1


title: Asy.RARg.IgG.veh.2.sorted.rmdup.BAM


title: 127_site1_core2


title: 127_Residual_Disease


title: Asy.RARg.IgG.veh.1.sorted.rmdup.BAM


title: 126_site2_core1


title: AlvMac, S2_infection, rep1_2


title: 129_site2_core2


title: AlvMac, S2_infection, rep1_1


title: 125_site2_core2


title: 126_Residual_Disease


title: Asy.RARg.IgG.DHT.2.sorted.rmdup.BAM

value: DHT (10nM, 6h)


title: 125_site1_core1

value: early-stage HER2-positive breast cancer


title: Asy.RARg.IgG.DHT.1.sorted.rmdup.BAM


title: 125_Residual_Disease


title: 124_site2_core1

value: Pre-treatment


title: Syn.RARg.H3S10p.veh.3.sorted.rmdup.BAM


title: 124_site1_core2

value: WT


title: AlvMac, Mock_infection,Ganetespib, rep1_2


title: AlvMac, Mock_infection,Ganetespib, rep1_1


title: Asy.RARg.AR.DHT.3.sorted.rmdup.BAM


title: 123_site2_core1


title: AlvMac, S2_infection, rep1_3


title: Asy.RARg.AR.DHT.2.sorted.rmdup.BAM


title: 123_Residual_Disease


title: 122_site2_core1


title: AlvMac, Mock_infection,Ganetespib, rep1_3


title: AlvMac, Mock_infection, rep1_3


title: 122_site1_core2


title: Asy.RARg.IgG.DHT.3.sorted.rmdup.BAM


title: 121_site1_core1


title: Asy.RARg.H3S10p.DHT.3.sorted.rmdup.BAM


title: Asy.RARg.AR.DHT.1.sorted.rmdup.BAM


title: 120_site2_core1


title: 120_site1_core1


title: 121_Residual_Disease


title: Asy.RARg.H3S10p.DHT.2.sorted.rmdup.BAM


title: T42

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Sequencing reads were mapped using STAR against the human genome reference (hg19), and gene level quantification was performed with featureCounts. Total counts mapped to protein-coding genes were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: Comma-separated values (CSV) file with featureCounts for protein-coding genes

source_name: Colorectal cancer primary

extract_protocol:
RNA was isolated using the Roche KAPA Stranded RNA-Seq kit with RiboErase according to the manufacturer protocol
Roche KAPA Stranded RNA-Seq kit with RiboErase

value: Colorectal cancer primary

tag: Sex

value: Male

tag: age of_diagnosis

tag: tumor stage

value: IV

value: Adenocarcinoma

value: FOLFOX

tag: description (mutations)

value: Unavailable


title: 118_site2_core2

source_name: Breast tumor tissue

value: No

value: Yes


title: 119_site2_core2


title: T41

source_name: Colorectal cancer liver met

value: Colorectal cancer liver met

value: Unspecified

value: KRAS, APC


title: 123_site1_core1


title: 118_site1_core1


title: Asy.RARg.H3S10p.DHT.1.sorted.rmdup.BAM

value: prostate

value: RARg


title: 117_site2_core2

value: Breast tumor tissue


title: T40

value: FOLFIRI/cetux


title: T39

value: Female


title: 117_site1_core2

value: early-stage HER2-positive breast cancer

value: WT

value: Pre-treatment


title: AlvMac, Mock_infection, rep1_2

value: bronchoalveolar lavage

value: alveolar macrophages

value: DMSO


title: 116_site2_core2


title: 116_site1_core2


title: 121_site2_core2


title: T38

value: IV

value: Adenocarcinoma

value: FOLFOX, FOLFIRI/Bevacizumab

value: KRAS, PIK3CA, APC, RB1, NOTCH1


title: 116_Residual_Disease

value: No


title: 115_site2_core2


title: T37

value: Colorectal cancer liver met

value: Male


title: Asy.RARg.AR.veh.2.sorted.rmdup.BAM

value: prostate

value: RARg

value: AR

value: Vehicle


title: Asy.RARg.RARg.veh.3.sorted.rmdup.BAM


title: 115_site1_core1

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer


title: AlvMac, Mock_infection, rep1_1


title: Asy.RARg.RARg.veh.2.sorted.rmdup.BAM


title: 114_site2_core1

value: WT

value: Pre-treatment

value: Yes


title: Asy.RARg.AR.veh.3.sorted.rmdup.BAM


title: T36

value: Female

value: FOLFOX/Bevacizumab, experimental

value: TP53, KDR


title: 114_site1_core2


title: 113_site2_core1


title: T35

value: IV

value: Adenocarcinoma

value: FOLFIRI/Bevacizumab

value: TP53, KRAS, PTEN, PIK3R1


title: 113_site1_core2

value: No


title: Asy.RARg.H3S10p.veh.3.sorted.rmdup.BAM

value: prostate


title: 111_site2_core1


title: T34

value: Colorectal cancer primary

value: II

value: Unavailable; MLH1 and PMS2 deletion


title: Asy.RARg.AR.veh.1.sorted.rmdup.BAM

value: RARg

value: AR

value: Vehicle


title: Asy.RARg.H3S10p.veh.2.sorted.rmdup.BAM


title: 110_site2_core2

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT

value: Pre-treatment


title: T33

value: Female

value: FOLFOX, RT, FOLFIRI/cetux


title: 110_site1_core2


title: Asy.RARg.H3S10p.veh.1.sorted.rmdup.BAM


title: 109_site2_core1

value: Yes


title: TACC1.RARg.CD.K3.2.sorted.rmdup.BAM


title: 109_site1_core2


title: T31

value: Male

value: IV

value: Adenocarcinoma

value: FOLFIRI/Bevacizumab

value: KRAS, APC, TP53, NF1, FBXW7


title: T32

value: Colorectal cancer primary

value: II


title: 108_site1_core1

value: No


title: TACC1.RARg.CD.K3.1.sorted.rmdup.BAM

value: prostate


title: 106_site2_core2


title: T30

value: Colorectal cancer liver met


title: Asy.RARg.RARg.veh.1.sorted.rmdup.BAM

value: RARg

value: Vehicle


title: TACC1.RARg.CD.K3.3.sorted.rmdup.BAM


title: T29

value: XELOX, xeloda

value: APC, TP53, KRAS, PIK3CA, KDR


title: 105_site2_core2

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT

value: Pre-treatment


title: 105_site1_core1


title: TACC1.RARg.DHT.K27.2.sorted.rmdup.BAM

value: DHT (10nM, 6h)


title: 104_site2_core1

value: Yes


title: 111_site1_core2


title: 104_site1_core2


title: 103_site2_core2


title: 110_Residual_Disease


title: T27

value: Female

value: IV

value: Adenocarcinoma

value: FOLFOX plus/minus Bevacizumab, PVE, Y90, 5FU/Bevacizumab, FOLFIRI + cetux

value: Unavailable but KRAS/NRAS/BRAF WT


title: TACC1.RARg.DHT.K27.3.sorted.rmdup.BAM

value: prostate


title: 103_Residual_Disease

value: No


title: 103_site1_core2


title: T26

value: Colorectal cancer liver met

value: FOLFIRI/Bevacizumab, FOLFOX/cetux

value: TP53, APC, BRCA1, PIK3CA


title: 102_site2_core1


title: TACC1.RARg.M.K27.2.sorted.rmdup.BAM

value: Vehicle


title: T25

value: TP53, KRAS, ATM


title: 102_Residual_Disease

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer


title: 108_site2_core1

value: WT

value: Pre-treatment


title: TACC1.RARg.M.K27.1.sorted.rmdup.BAM


title: 102_site1_core1


title: T24

value: Male

value: Capecitabine/RT, FOLFOX, FOLFIRI

value: KRAS, TP53


title: 101_site1_core2


title: TACC1.RARg.M.K27.3.sorted.rmdup.BAM


title: 100_site2_core1


title: T28

value: IV

value: Adenocarcinoma

value: KRAS, TP53, PIK3CA, APC


title: T23

value: Female

value: FOLFOX, RT, then phase I

value: KRAS, TP53, CDKN2A, SMAD4


title: TACC1.RARg.CD.RARg.2.sorted.rmdup.BAM

value: prostate

value: RARg


title: 100_Residual_Disease

value: No


title: T22

value: Colorectal cancer liver met

value: FOLFOX

value: TP53, APC


title: TACC1.RARg.DHT.K27.1.sorted.rmdup.BAM

value: DHT (10nM, 6h)


title: U2OS_siMYBL1-siMYBL2_rep2

city: Leipzig

first: Robin

last: Kohler

address: Semmelweisstr. 14

department: Medical School

institute: University Leipzig

data_processing:
Adapter trimming was performed with cutadapt v4.4
Trimmed reads were mapped to hg38 using salmon v1.10.1
Differential gene expression between samples was analyzed separately for HCT116 and U2OS cells with DEseq2 1.40.
Assembly: hg38

extract_protocol:
RNA extraction was performed using the Zymo Direct-zol RNA miniprep kit.
library construction was performed by GENEWIZ/Azenta

tag: time


title: TACC1.RARg.CD.RARg.1.sorted.rmdup.BAM


title: U2OS_siMYBL1-siMYBL2_rep1


title: U2OS_siMYBL2_rep2


title: TACC1.RARg.CD.RARg.3.sorted.rmdup.BAM


title: T20

value: FOLFOX, FOLFIRI/Bevacizumab

value: TP53, RNF43


title: U2OS_siMYBL2_rep1


title: TACC1.RARg.M.RARg.2.sorted.rmdup.BAM

value: Vehicle


title: U2OS_siMYBL1_rep1


title: T19

value: Male

value: FOLFIRI, FOLFOXIRI, Bevacizumab, cetuximab, phaseI


title: U2OS_siCtrl_rep2

description:
U2OS_siMYBL1.csv
U2OS_siMYBL2.csv
U2OS_siMYBL1-siMYBL2.csv

value: siCtrl


title: U2OS_siCtrl_rep1


title: T18

value: IV

value: Adenocarcinoma

value: FOLFOX/Bevacizumab, FOLFIRI

value: TP53, KRAS


title: 101_site2_core1

value: Breast tumor tissue

value: early-stage HER2-positive breast cancer

value: WT

value: Pre-treatment


title: HCT116_siMYBL1-siMYBL2_rep2


title: TACC1.RARg.M.RARg.3.sorted.rmdup.BAM

value: prostate

value: RARg


title: 100_site1_core2

value: No


title: T17

value: Colorectal cancer liver met

value: FOLFIRI/Bevacizumab, RT, regorafenib

value: TP53, APC


title: HCT116_siMYBL2_rep1


title: TACC1.RARg.DHT.AR.2.sorted.rmdup.BAM

value: AR

value: DHT (10nM, 6h)


title: T16

value: Colorectal cancer primary

value: Male

value: II

value: BRAF,  MLH1 promoter hypermethylation


title: TACC1.RARg.DHT.AR.1.sorted.rmdup.BAM


title: HCT116_siMYBL1_rep1


title: HCT116_siCtrl_rep2

description:
HCT116_siMYBL1.csv
HCT116_siMYBL2.csv
HCT116_siMYBL1-siMYBL2.csv

value: siCtrl


title: HCT116_siMYBL2_rep2


title: T21

value: IV

value: Adenocarcinoma

value: FOLFOX/Bevacizumab


title: HCT116_siCtrl_rep1


title: TACC1.RARg.DHT.AR.3.sorted.rmdup.BAM


title: T14

value: Unavailable


title: U2OS_siMYBL1_rep2


title: TACC1.RARg.M.RARg.1.sorted.rmdup.BAM

value: prostate

value: Vehicle


title: Airway_Day7_HoechstHigh_3 [airway]

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

data_processing:
Sequenced reads of the Hoechst-high (Edge) or Hoechst-low (Center) cells were trimmed using fastp (S. Chen et al. 2018), and the trimmed reads were aligned to GRCh38 using STAR 2.7.1a (Dobin et al. 2013).
Transcripts per million (TPM) values were calculated using RSEM (B. Li and Dewey 2011).
Assembly: hg38
Supplementary files format and content: patterning_PAL+_Center_Edge.txt: Tab-delimited text file includes count values and TPM for each sample.

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round shaped cell-attachment areas 100 or 200 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at cell density 3x10^5 cells/well. The LPs were differentiated into airway epithelial cells in the medium as the following steps: “PAL(-)” medium made of PneumaCult-ALI medium (Veritas, ST-05001) containing 500nM hydrocortisone, 10 μM heparin, and 10 μM Y27632 for initial two days and thereafter PAL(+) medium made of PAL(-) medium supplemented with 10 mM DAPT. Each medium was changed every two days.

extract_protocol:
Total RNA of Hoechst-high or Hoechst-low cells isolated by FACS was extracted using RNeasy micro (Qiagen).
1 ng of the total RNA was reverse transcribed and amplified for 11 cycles using SMART-Seq HT (Clontech Laboratories, Z4456N). The amplified cDNA was used for preparation of sequencing libraries using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131).

value: Airway epithelial cells

tag: cell population

value: HoechstHigh cell population in micro-patterned culture

tag: time point


title: Airway_Day7_HoechstHigh_2 [airway]


title: TACC1.RARg.M.AR.2.sorted.rmdup.BAM

tag: tissue


title: Airway_Day7_HoechstHigh_1 [airway]


title: T13

value: Colorectal cancer liver met

tag: genotype


title: TACC1.RARg.M.AR.1.sorted.rmdup.BAM

tag: treatment


title: Airway_Day7_HoechstLow_3 [airway]

value: HoechstLow cell population in micro-patterned culture


title: Airway_Day7_HoechstLow_2 [airway]


title: T12

value: FOLFIRI/Bevacizumabacizumab

value: KRAS, NOTCH3, FBXW7


title: HCT116_siMYBL1-siMYBL2_rep1


title: Airway_Day7_HoechstLow_1 [airway]


title: LungProgenitor_3 [airway]

description: Carboxypeptidase M (CPM) was used as a surface-antigen protein of the lung progenitor cells.

value: iPSC-derived CPM+


title: T11

value: Female

value: APC, TP53


title: HCT116_siMYBL1_rep2


title: T15

value: Colorectal cancer primary

value: FOLFIRI/Bevacizumab, Regorafenib

value: TP53, APC


title: T10

value: Male

value: IV

value: Adenocarcinoma

value: TP53, KRAS


title: LungProgenitor_2 [airway]


title: RARg.CD.K3.3.sorted.rmdup.BAM

value: prostate

value: RARg


title: LungProgenitor_1 [airway]


title: RARg.CD.K3.2.sorted.rmdup.BAM


title: 126_site1_core2

value: Breast tumor tissue

tag: disease state

value: early-stage HER2-positive breast cancer

value: WT

value: Pre-treatment

tag: patient id

value: No


title: T9

value: Colorectal cancer liver met

value: FOLFOX

value: TP53, KRAS, FLT3


title: Alveolar_Day14_HoechstHigh_2 [alveolar]

data_processing:
Sequenced reads of the Hoechst-high (Edge) or Hoechst-low (Center) cells were trimmed using fastp (S. Chen et al. 2018), and the trimmed reads were aligned to GRCh38 using STAR 2.7.1a (Dobin et al. 2013).
Transcripts per million (TPM) values were calculated using RSEM (B. Li and Dewey 2011).
Assembly: hg38
Supplementary files format and content: patterning_DCIK+3i_Center_Edge.txt: Tab-delimited text file includes count values and TPM for each sample.

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round shaped cell-attachment areas in 100 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities 1x10^5 cells/well. The LPs were differentiated into alveolar epithelial cells in DCIK+3i medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning), and 50 U/mL Penicillin/Streptomycin.

value: Alveolar epithelial cells

value: HoechstHigh cell population in micro-patterned culture


title: Alveolar_Day14_HoechstHigh_1 [alveolar]


title: T8

value: Female

value: FOLFOX/Bevacizumab, 5-FU/Bevacizumab, trastuzumab, pertuzumab, iri/cetux

value: TP53, PIK3CA, ERBB2


title: RARg.DHT.K3.3.sorted.rmdup.BAM

value: DHT (10nM, 6h)


title: T7

value: Male

value: IV

value: Adenocarcinoma

value: FOLFOX/Bevacizumab

value: KRAS, APC, SMAD4


title: Alveolar_Day14_HoechstLow_2 [alveolar]

value: HoechstLow cell population in micro-patterned culture


title: Alveolar_Day8_HoechstHigh_3 [alveolar]


title: Alveolar_Day14_HoechstLow_1 [alveolar]


title: Alveolar_Day14_HoechstLow_3 [alveolar]


title: Alveolar_Day14_HoechstHigh_3 [alveolar]


title: TACC1.RARg.M.AR.3.sorted.rmdup.BAM

value: prostate

value: AR

value: Vehicle


title: Alveolar_Day8_HoechstHigh_1 [alveolar]


title: Alveolar_Day8_HoechstHigh_2 [alveolar]


title: T5

value: Colorectal cancer liver met

value: Xeloda/Bevacizumab, RT

value: KRAS, TP53, PIK3CA, APC


title: RARg.DHT.K3.1.sorted.rmdup.BAM

value: RARg


title: Alveolar_Day8_HoechstLow_2 [alveolar]

value: Alveolar epithelial cells


title: RARg.M.K3.3.sorted.rmdup.BAM


title: Alveolar_Day8_HoechstLow_3 [alveolar]


title: Alveolar_Day8_HoechstLow_1 [alveolar]


title: LungProgenitor_3 [alveolar]

value: iPSC-derived CPM+


title: RARg.M.K3.2.sorted.rmdup.BAM


title: T3

value: Female

value: FOLFIRI/Bevacizumab

value: APC, TP53, NRAS


title: T4

value: Colorectal cancer primary

value: II

value: Unavailable


title: LungProgenitor_2 [alveolar]


title: RARg.M.K3.1.sorted.rmdup.BAM


title: LungProgenitor_1 [alveolar]


title: T2

value: IV

value: Adenocarcinoma

value: FOLFOX/Bevacizumab, Xeloda

value: TP53, KRAS, NOTCH1, ARID1A, FBXW7


title: RARg.DHT.K3.2.sorted.rmdup.BAM

value: prostate

value: DHT (10nM, 6h)


title: T6

value: Colorectal cancer liver met

value: FOLFOX

value: Unavailable but KRAS/NRAS/BRAF WT


title: RARg.M.RARg.3.sorted.rmdup.BAM

value: RARg

value: Vehicle


title: WT3 day 210 ROs

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

data_processing:
The BCL files were de-multiplexed using CellRanger mkfastq version 3.01 and then aligned and quantify them against the human reference genome GRCh38 using Cellranger count.
We performed quality control checks for each sample in R for each sample and removed any cells with fewer than 1000 reads or 500 genes or greater than 10% mitochondrial reads. Any cells which expressed haemoglobin genes were also removed from the analysis. Doublets were predicted using DoubletFinder and filtered from the data.
The Seurat R package (version 4.3.0) was then used to process the data prior to integration. Firstly the raw data was normalised using the standard parameters.
Assembly: GRCh38
Supplementary files format and content: counts.csv: Comma-separated values file containing filtered count matrix for each cell.
Supplementary files format and content: md.csv: Comma-separated values file with metadata for each cell, contains cell identification.

source_name: Retinal organoid

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech).
Libraries generated using the Chromium Single Cell 3’ Library & Gel Bead Kit (version 3, 10x Genomics).
Single-cell RNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000.

value: Retinal organoid

tag: developmental stage

value: Day 210

value: No mutation


title: RP13-2 day 210 ROs

value: PRPF8 H2309P


title: T1

value: Male

value: APC, TP53, KRAS


title: Cas9- RP13-2 day 210 ROs


title: RARg.M.RARg.2.sorted.rmdup.BAM


title: RARg.M.RARg.1.sorted.rmdup.BAM


title: RP13-1B day 210 ROs


title: Cas9- RP13-1C day 210 ROs


title: RP13-1A day 210 ROs


title: RARg.CD.RARg.3.sorted.rmdup.BAM


title: Cas9- RP13-1A day 210 ROs


title: N841_2

description: Total cell RNA

source_name: Large intestine; Colon

growth_protocol: All cell lines were maintained either in RPMI-1640 or DMEM medium with 10% FBS, 100 units/mL penicillin and 100 µg/mL streptomycin at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
RNA was isolated using the Roche KAPA Stranded RNA-Seq kit with RiboErase for cell lines according to the manufacturer protocol
Roche KAPA Stranded RNA-Seq kit with RiboErase

treatment_protocol: Not applicable

value: Large intestine; Colon

value: CCD 841 CoN

value: WT

value: Normal


title: RARg.CD.RARg.2.sorted.rmdup.BAM

value: prostate


title: WNT3A rep 3

city: Düsseldorf

first: Jörg

last: Distler

address: Merowingerplatz 1A

department: Department of Rheumatology

institute: University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University

description:
WNT3A.txt
Sample 30

data_processing:
Reads were checked and filtered by FastQC and Trimmomatic
Reads were mapped to human genome (hg38) by HISAT2
Uniquely mapped reads were assigned to annotated genes with htseq (gencode.v35.annotation)
Assembly: hg38
Supplementary files format and content: text document containing raw counts from each group of sample

source_name: Primary dermal fibroblast

growth_protocol: The fibroblasts were cultured in DMEM/F12 with 10% FBS, 1% penicillin-streptomycin, 2 mM l-glutamine and 2.5 μg ml−1 amphotericin B until reaching 90% confluence. Cells were trysinized and seeded to 6-well plates (3 x 105 cell/well). The plates were incubated for 24 hours at 37oC, 5% CO2.

extract_protocol:
Total RNA was extracted from adherent cells using the Nucleo Spin RNA isolation kit (Macherey-Nagel).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol:
Starve the cells with serum-free DMEM/F12 for 24 hours at 37oC, 5% CO2.
Cells were pretreated with JNK inhibitor SP600125 (Sigma-Aldrich, Steinheim, Germany) at 125 nM for 4 hours, the ROCK inhibitor Y27632 (Sigma-Aldrich) at 1 µM for 1 hour, the TGFβRI kinase inhibitor SD-208 (Tocris, Nordenstadt, Germany) at 3 µM for 4 hours, ITGAV inhibitor CWHM12 (BOC Sciences, Shirley, NY, USA) at 1 µM for 1 hour, or actin polymerization inhibitor Cytochalasin D (Abcr, Karlsruhe, Germany) at 10 µM for 1 hour.
Cells were incubated with recombinant WNT5A protein (100 ng/ml) (R&D Systems, Wiesbaden-Nordenstadt, Germany), recombinant TGFβ (10 ng/ml) (PeproTech, Hamburg, Germany) or recombinant WNT3A protein (100 ng/ml) (R&D Systems, Wiesbaden-Nordenstadt, Germany) for 48 hours at  37oC, 5% CO2.

tag: donor

value: donor 3

value: Primary dermal fibroblast

tag: pre-treatment

value: no

tag: pretreatment time

value: WNT3A (100ng/ml)

value: 48 hours


title: N841_1

description: Total cell RNA

tag: cell line

tag: cell type


title: WNT3A rep 2

description:
WNT3A.txt
Sample 29

value: donor 2


title: HCT116.dil4

description: Mixed total cell RNA - 50% HCT 116/50% CCD 841 CoN

source_name: Colon

value: Colon

value: HCT 116 & CCD 841 CoN

value: Adenocarcinoma/Normal


title: Control rep 6

description:
for experiments related to WNT3A
Control_1.txt
Sample 27


title: Control rep 5

description:
for experiments related to WNT3A
Control_1.txt
Sample 26


title: RARg.CD.RARg.1.sorted.rmdup.BAM

value: RARg

tag: chip antibody


title: RARg.M.AR.3.sorted.rmdup.BAM

value: AR

value: Vehicle


title: WNT3A rep 1

description:
WNT3A.txt
Sample 28

value: donor 1


title: HCT116.dil3

description: Mixed total cell RNA - 10% HCT 116/90% CCD 841 CoN


title: RP13-1C day 210 ROs

value: Retinal organoid

value: Day 210

value: PRPF8 H2309P


title: WNT5A_Actin-i rep 3

description:
WNT5A_Actini.txt
Sample 24

value: Cytochalasin D 10 µM

value: 1 hour

value: WNT5A (100ng/ml)


title: Control rep 4

description:
for experiments related to WNT3A
Control_1.txt
Sample 25

value: Primary dermal fibroblast

value: no


title: RARg.M.AR.2.sorted.rmdup.BAM

value: prostate


title: WNT5A_Actin-i rep 2

description:
WNT5A_Actini.txt
Sample 23

value: donor 2

value: 48 hours


title: HCT116.dil2

description: Mixed total cell RNA - 1% HCT 116/99% CCD 841 CoN

value: Colon

value: HCT 116 & CCD 841 CoN

value: WT


title: WNT5A_Actin-i rep 1

description:
WNT5A_Actini.txt
Sample 22


title: WNT5A_ITGAVi rep 3

description:
WNT5A_ITGAVi.txt
Sample 21

value: donor 3

value: CWHM12 1 µM


title: HCT116.dil1

description: Mixed total cell RNA - 0.1% HCT 116/99.9% CCD 841 CoN

value: Adenocarcinoma/Normal


title: RARg.DHT.AR.3.sorted.rmdup.BAM

value: RARg

value: AR

value: DHT (10nM, 6h)


title: HCT116_3

description: Total cell RNA

value: Large intestine; Colon

value: HCT 116

value: Adenocarcinoma


title: RARg.M.AR.1.sorted.rmdup.BAM

value: Vehicle


title: N841_3

description: Total cell RNA

value: CCD 841 CoN

value: Normal


title: WNT5A_ITGAVi rep 2

description:
WNT5A_ITGAVi.txt
Sample 20

value: donor 2

value: Primary dermal fibroblast

value: 1 hour

value: WNT5A (100ng/ml)


title: WNT5A_ITGAVi rep 1

description:
WNT5A_ITGAVi.txt
Sample 19

value: donor 1

value: 48 hours


title: HCT116_2

description: Total cell RNA

value: WT


title: WNT5A_ROCKi rep 3

description:
WNT5A_ROCKi.txt
Sample 18

value: donor 3


title: RARg.DHT.AR.2.sorted.rmdup.BAM

value: prostate

value: RARg


title: HCT116_1

description: Total cell RNA


title: WNT5A_ROCKi rep 1

description:
WNT5A_ROCKi.txt
Sample 16


title: WNT5A_ROCKi rep 2

description:
WNT5A_ROCKi.txt
Sample 17


title: RARg.DHT.AR.1.sorted.rmdup.BAM

value: AR

value: DHT (10nM, 6h)


title: WNT5A_SD208 rep 3

description:
WNT5A_SD208.txt
Sample 15

value: SD208 3 µM

value: 4 hours


title: HT29.dil4

description: Mixed total cell RNA - 50% HT-29/50% CCD 841 CoN

value: Colon

value: HT-29 & CCD 841 CoN

value: Adenocarcinoma/Normal


title: WNT5A_SD208 rep 2

description:
WNT5A_SD208.txt
Sample 14

value: donor 2


title: WNT5A_SD208 rep 1

description:
WNT5A_SD208.txt
Sample 13

value: Primary dermal fibroblast


title: HT29.dil3

description: Mixed total cell RNA - 10% HT-29/90% CCD 841 CoN


title: RARg.M.IgG.2.sorted.rmdup.BAM

value: IgG

value: Vehicle


title: liver, KO2, CCL4, replicate2, scRNA-seq

data_processing:
The demultiplexing，barcoded processing，gene counting and aggregation were made using the cell Ranger software v6.1.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Single-cell RNA-seq was performed following the protocol established by Gene Denovo Biotechnology Co. (Guangzhou, China).9 In brief, the cell suspension derived from mouse liver was centrifuged at 50 g for 2 min, resulting in the separation of hepatocytes settling at the bottom, while nonparenchymal cells (NPCs) were mainly remained in the supernatant suspension.9 A small amount of single cell suspension was mixed with equal volume of 0.4% trypan blue staining solution and counted using Counter ® II Automated Cell Counter.
The mixture, including gel beads with barcode, cells, and enzymes, was separated by oil in the reservoir to form GEMs (Gel Beads In Emulations). Subsequently, gel beads dissolved, releasing the captured sequence containing Barcode sequence. RNA was reverse transcribed to produce cDNA, following the 10×Genomics single cell 3’ library construction V3 protocol. Quantification and pooling were carried out using the ABI One-Step Plus Real-Time PCR System (Life Technologies). 9 High-throughput sequencing was performed in PE150 sequencing mode on the Illumina sequencing platform.

value: liver

value: Ythdf3 knockout

value: CCL4 administration


title: WNT5A_JNKi rep 2

description:
WNT5A_JNKi.txt
Sample 11

value: WNT5A (100ng/ml)

value: 48 hours


title: WNT5A_JNKi rep 3

description:
WNT5A_JNKi.txt
Sample 12

value: donor 3


title: liver, KO1, CCL4, replicate1, scRNA-seq


title: RARg.M.IgG.1.sorted.rmdup.BAM

value: prostate

value: RARg


title: HT29.dil1

description: Mixed total cell RNA - 0.1% HT-29/99.9% CCD 841 CoN

value: WT


title: HT29.dil2

description: Mixed total cell RNA - 1% HT-29/99% CCD 841 CoN


title: Mock.DHT.K3.3.sorted.rmdup.BAM

value: DHT (10nM, 6h)


title: HT29_3

description: Total cell RNA

value: Large intestine; Colon

value: Adenocarcinoma


title: liver, WT2, CCL4, replicate2, scRNA-seq


title: liver, WT1, CCL4, replicate1, scRNA-seq


title: TGFβ rep 3

description:
TGFB.txt
Sample 9

value: no

value: TGFβ (10ng/ml)


title: HT29_2

description: Total cell RNA


title: Mock.DHT.K3.2.sorted.rmdup.BAM


title: WNT5A_JNKi rep 1

description:
WNT5A_JNKi.txt
Sample 10

value: donor 1

value: Primary dermal fibroblast

value: 4 hours


title: xz50, liver, Input

extract_protocol:
The liver tissue was lysed and homogenized at 4℃ for 1 h in buffer solution consisting of 1% SUPERaseln, 1% protease inhibitor cocktail, 150 mM KCl, 0.5 mM DTT, 2 mM EDTA, 10 mM Tris-HCl, and 0.5% NP-40. After centrifugation at 12,000 rpm for 10 min, the supernatant was collected in a 1.5 mL centrifuge tube. To preserve the input, 50 μL of lysate was stored in 1 mL Trizol at -80℃.  For immunoprecipitation, 5 μg of the YTHDF3 antibody was combined with 40 μL of protein A beads (Sigma), dissolved in 140 μL of PBST buffer (PBS and 0.05% Tween), and incubated for 1 h at 4°C. As a control, 5 μg of normal rabbit IgG was added to another 40 μL of protein A beads in parallel. Half of liver lysate was added to protein A-anti YTHDF3 mixture, while the other half was added to protein A-IgG mixture. After thorough mixing, the mixture was continuously agitated for 3 h at 4°C. The mixture underwent eight washes with 500 μL ice-cold NT2 buffer (200 mM NaCl, 1% SUPERaseln, 1% protease inhibitor cocktail, 50 mM Tris-HCl, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT).  To elute the samples, 100 μL of protease K buffer (150 mM NaCl, 12.5 mM EDTA, 2%(w/v) SDS, 100mM Tris-HCl) and 20 μL thermo protease K were added to each sample, followed by incubation at 55℃ for 40 min. Using a magnetic separator, the supernatant was collected, and Trizol was added to preserve it as IP sample. RNA was extracted from both input and IP samples for sequencing purpose.
The library was generated using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara) with three biological replicates for each sample.

value: liver

value: control

tag: fraction

value: Input


title: TGFβ rep 2

description:
TGFB.txt
Sample 8

value: donor 2


title: Mock.DHT.K3.1.sorted.rmdup.BAM


title: RARg.M.IgG.3.sorted.rmdup.BAM

value: IgG

value: Vehicle


title: Mock.M.K3.3.sorted.rmdup.BAM

value: prostate


title: xz49, liver, Input


title: HT29_1

description: Total cell RNA


title: TGFβ rep 1

description:
TGFB.txt
Sample 7

value: 48 hours


title: LS1034.dil4

description: Mixed total cell RNA - 50% LS1034/50% CCD 841 CoN

value: Colon

value: LS1034 & CCD 841 CoN

value: WT

value: Adenocarcinoma/Normal


title: xz48, liver, Input


title: Mock.M.K3.2.sorted.rmdup.BAM


title: LS1034.dil3

description: Mixed total cell RNA - 10% LS1034/90% CCD 841 CoN


title: WNT5A rep 3

description:
WNT5A.txt
Sample 6

value: donor 3

value: no

value: WNT5A (100ng/ml)


title: xz44, liver, CCL4 administration, Input

value: CCL4 administration


title: WNT5A rep 2

description:
WNT5A.txt
Sample 5

value: Primary dermal fibroblast


title: Mock.M.K3.1.sorted.rmdup.BAM


title: WNT5A rep 1

description:
WNT5A.txt
Sample 4

value: donor 1


title: xz42, liver, CCL4 administration, Input

value: liver


title: LS1034.dil1

description: Mixed total cell RNA - 0.1% LS1034/99.9% CCD 841 CoN


title: LS1034.dil2

description: Mixed total cell RNA - 1% LS1034/99% CCD 841 CoN


title: Control rep 3

description:
for experiments related to WNT5A or TGFβ
Control.txt
Sample 3


title: RARg.CD.K3.1.sorted.rmdup.BAM

value: RARg


title: xz43, liver, CCL4 administration, Input

value: Input


title: LS1034_3

description: Total cell RNA

source_name: Large intestine; Cecum

value: Large intestine; Cecum

value: Adenocarcinoma


title: Mock.DHT.AR.2.sorted.rmdup.BAM

value: prostate

value: AR

value: DHT (10nM, 6h)


title: Mock.DHT.AR.1.sorted.rmdup.BAM


title: xz38, liver, immunoprecipitation

value: control

value: immunoprecipitation


title: LS1034_2

description: Total cell RNA

value: WT


title: Mock.DHT.AR.3.sorted.rmdup.BAM


title: Control rep 2

description:
for experiments related to WNT5A or TGFβ
Control.txt
Sample 2

value: donor 2

value: 48 hours


title: Mock.M.AR.3.sorted.rmdup.BAM

value: Vehicle


title: LS1034_1

description: Total cell RNA


title: Control rep 1

description:
for experiments related to WNT5A or TGFβ
Control.txt
Sample 1

value: no


title: SUGP1_3

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

data_processing:
Generation of pre-trimmed FASTQ files was performed by Azenta Biosciences.
The general quality of the sequencing data was validated using FastQC (version 0.11.5).
The reads were quality trimmed using TrimGalore! (version 0.6.7) and its dependency Cutadapt (version 2.4) in paired-end mode.
The FASTQ reads were mapped to the human reference genome GRCh38 (version 102) using the STAR aligner (version 2.7.9a) that was distributed with the transcript splicing analysis software rMATS inside a Docker container, which was made available on Docker Hub.
The primary alignments of the mapped data (in the form of BAM files) were imported into the genome browser SeqMonk v1.48.0.  Gene expression was determined for each sample using the SeqMonk RNA-seq Quantitation Pipeline.  The resulting raw counts were used to identify differentially expressed genes using DESeq2 (version 1.32.0) which was launched from SeqMonk using default settings. DESeq2 was run using R (version 4.1.0 Patched (2021-06-08 r80465) - Camp Pontanezen) on a macOS operating system (version 11.6 Big Sur). Differentially expressed genes were defined as having an adjusted p-value cut-off of less than or equal to 0.05 after multiple testing correction and an absolute log2 fold change of greater than or equal to 0.5.
Pairwise splicing comparisons were performed using the rMATs v4.1.2.
Alternative polyadenylation analysis was performed using LABRAT.  Genes whose total abundance across all isoforms was less than 5 transcripts per million (TPM) in any sample were excluded from the analysis. False discovery rate (FDR) values were calculated using LABRAT's linear mixed effects model followed by multiple hypothesis correction. Isoform structures and transcript sequences were derived from GENCODE v28.
Assembly: GRCh38 (version 102)
Supplementary files format and content: Tab-delimited text file listing the raw counts of read pairs mapping to genome annotations, for all samples.

source_name: U-2 OS

growth_protocol: U-2 OS cells were maintained in McCoys 5A.  Media was supplemented with 10% (v/v) FBS and 1% (v/v) GlutaMAX (Thermo Fisher).

extract_protocol:
Approximately 1x106 U-2 OS cells per sample were harvested from an individual T25 flask and processed for RNA extraction and sequencing by Azenta Biosciences.
Performed by Azenta Biosciences.

treatment_protocol: Pre-designed crRNAs were dispensed into 384-well Pheno plates (Perkin Elmer) via an Echo 555 instrument (Labcyte) at a final concentration of 50 nM. For the genome-wide screen, automatic liquid handling was executed by docking a Steristore (HighRes), Echo 555, Multidrop combi (Thermo Fisher) and washer dispenser EL406 (Biotek) to a Star6 automation platform (HighRes). Library and assay plates were stored in the Steristore at 8°C during dispensing and were brought to room temperature before reverse transfection. Controls included in the genome screen were NTC (a pool of four pre-designed, commercially available crRNAs with at least three mismatches to potential PAM-adjacent targets in the human genome; 38 wells per plate) as neutral control, crLIS1 (a pool of four crRNAs targeting LIS1; 13 wells per plate) as positive control, and crPLK1 (a pool of four crRNAs targeting PLK1) as editing control. Cas9-transfected cells (1500 U-2 OS cells per 384-well) were reverse transfected with crRNAs with 1% (v/v) RNAiMAX (Thermo Fisher) in serum-free media dispensed via a Multidrop combi, and were incubated for 72 h before fixation.

value: U-2 OS

value: Osteosarcoma

value: crRNA targeting SUGP1


title: LOVO.dil4

description: Mixed total cell RNA - 50% LoVo/50% CCD 841 CoN

value: Colon

value: LoVo & CCD 841 CoN

value: Adenocarcinoma/Normal


title: Mock.M.AR.2.sorted.rmdup.BAM


title: xz37, liver, immunoprecipitation

value: liver


title: xz32, liver, CCL4 administration, immunoprecipitation

value: CCL4 administration


title: Mock.M.AR.1.sorted.rmdup.BAM

value: prostate

value: AR


title: xz36, liver, immunoprecipitation

value: control


title: LOVO.dil3

description: Mixed total cell RNA - 10% LoVo/90% CCD 841 CoN


title: xz30, liver, CCL4 administration, immunoprecipitation

value: immunoprecipitation


title: XCR1_3

value: crRNA targeting XCR1


title: LOVO.dil1

description: Mixed total cell RNA - 0.1% LoVo/99.9% CCD 841 CoN

value: WT


title: W1_5_3

city: Nantong

first: JingTing

last: Zhao

address: No. 99, Qingnian Middle Road, Chongchuan District

institute: Nantong Third People's Hospital

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: Keloid

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

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: KFs from the control group and those treated with HMME-SDT at 1.0 W/cm² and 1.5 W/cm² were harvested 24 hours post-treatment using TRIzol reagent.

value: Keloid

value: Keloid Fibroblasts

value: 1.5 W/cm²


title: SUGP1_2

value: U-2 OS


title: NTC_3

value: Osteosarcoma

value: Non-targeting control


title: W1_5_2


title: XCR1_2


title: W1_5_1


title: LOVO_2

description: Total cell RNA

value: Large intestine; Colon

value: LoVo

value: Adenocarcinoma


title: W1_3

value: 1.0 W/cm²


title: LOVO_3

description: Total cell RNA


title: W1_2


title: NTC_2


title: LOVO_1

description: Total cell RNA


title: SUGP1_1

value: crRNA targeting SUGP1


title: W1_1


title: XCR1_1


title: Female_ACC_WT_Untrained 3

city: Durham

first: Kristina

last: Sakers

state: NC

address: 307 Research Dr

institute: Duke University

data_processing:
Reads were first processed through FastQC (v0.11.7) to check quality
Adapters were trimmed using Trimmomatic (v0.38)
Alignment was done to mm10 using STAR aligner (v2.5.3a)
Mapped reads were counted by gene using featureCounts from Subread (v1.6.3)
Assembly: mm10
Supplementary files format and content: CSV file of all samples and fragments per kilobase per million (FPKM) in each column

source_name: Brain, anterior cingulate cortex

growth_protocol: Mice were housed in a standard 12/12h light/dark cycle with access to food and water ad libitum until training at which time animals were food deprived. See methods in manuscript for full details

extract_protocol:
RNA was harvested using TriZol RNA extraction protocol and subsequently cleaned and concentrated on a Zymo Clean and Concentrator -5 kit.
Libraries were made using the Illumina TruSeq stranded mRNA kit

treatment_protocol: Mice underwent skinner box training as described in manuscript methods

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Wild-type

tag: Sex

value: Female


title: Female_ACC_WT_Untrained 4


title: Male_ACC_KO_Untrained 4

value: Thbs1/2 KO

value: Male


title: Female_ACC_WT_Untrained 2


title: xz31, liver, CCL4 administration, immunoprecipitation

data_processing:
Reads were quality controlled using FastQC (v0.11.5) and TrimGalore (v0.6.0).
rRNA sequence were removed by using bowtie2(v2.3.4.1) with --ungz or --un-conc-gz parameter.
The retained reads were aligned to GRCm38/mm10 by HISAT2 (v2.2.1) with default parameters.
Bigwig files were obtained by using bamCoverage function in deepTools (v3.5.1) and visualized in IGV (v11.0.19).
Read counts were quantified by using featureCounts (v1.6.0).
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig

value: liver

value: WT

value: CCL4 administration

value: immunoprecipitation


title: NC_3

value: Keloid

value: Keloid Fibroblasts

value: control


title: NTC_1

value: U-2 OS

value: Osteosarcoma

value: Non-targeting control


title: SW480_exRNA

description: Total RNA from extracellular vesicles

extract_protocol:
RNA was isolated using the Roche KAPA Stranded RNA-Seq kit with RiboErase for cell lines and Invitrogen total exosome RNA & Protein Isolation kit for extracellular vesicles according to the manufacturer protocol
Roche KAPA Stranded RNA-Seq kit with RiboErase for cell lines and  SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

value: Large intestine; Colon

value: Adenocarcinoma


title: LOVO.dil2

description: Mixed total cell RNA - 1% LoVo/99% CCD 841 CoN

value: Colon

value: LoVo & CCD 841 CoN

value: Adenocarcinoma/Normal


title: Female_ACC_WT_Untrained 1

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Wild-type

value: Female


title: Female_ACC_KO_Untrained 4

value: Thbs1/2 KO


title: Male_ACC_WT_Untrained 4

value: Male


title: Library 14 cell hashing

first: Bart

last: De Strooper

institute: VIB-KU Leuven

description:
10x Genomics
Mancuso2022_RNAcounts.mtx.gz
Mancuso2022_RNAcounts_genes.txt
Mancuso2022_RNAcounts_cellbarcodes.txt
Mancuso2022_NormExpr.mtx.gz
Mancuso2022_NormExpr_genes.txt
Mancuso2022_NormExpr_cellbarcodes.txt

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: Genome build: Human reference, hg19 (Ensembl 87), downloaded from 10x Genomics pre-built Cell Ranger reference packages (3.0.0).
Supplementary files format and content: *.mtx.gz: Raw or SCT normalised gene expression counts per cell in a gzipped tab-separated values file.
Supplementary files format and content: *genes.txt: row names (genes) for raw or SCT normalised gene expression matrices, in txt files.

source_name: Brain

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F, Apphu/hu or AppNL-G-FApoE-/-  mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
In this manuscript, we generated a total of 20 libraries containing 95 biological replicates for single cell RNA sequencing. In brief, we sorted 15000-20000 alive human microglia (CD11b+, hCD45+) per mouse and adjusted the final concentration to 1000 cells/µl. Out of each mouse, 2000 sorted cells were loaded into the Chromium Next GEM Chip G (PN #2000177). Since all the individual replicates were hashed using TotalSeqTM-A cell hashing antibodies, we pooled different samples into the same library. Libraries were prepared using manufacturer’s instructions (CG000204 Chromium Next GEM Single Cell 3’ Reagent Kits v3.1). For hashtag oligo libraries, we followed manufacturers’ instructions (BioLegend - TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR. Libraries were sequenced on a HiSeq4000 or NovaSeq6000 (Illumina) platform with the recommended read lengths by 10X Genomics workflow targeting 90% mRNA and 10% hashtag library (50,000 reads/cell).

value: Brain

value: Microglia

tag: mouse host genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

tag: human cells gender

value: female

tag: mouse host gender

value: female and male

tag: timepoint

value: 6 months

tag: injection

tag: multiplexed samples

tag: samples used for this study


title: NC_1

tag: tissue

value: Keloid

value: Keloid Fibroblasts

tag: treatment

value: control


title: LS123_cRNA

description: Total cell RNA

value: Large intestine; Colon

value: WT

tag: genotype

value: Adenocarcinoma


title: NC_2


title: LS123_exRNA

description: Total RNA from extracellular vesicles


title: Library 25 cell hashing

value: Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

value: male


title: Library 24 cell hashing

value: 3 months

value: Scrambled peptide, soluble amyloid-β aggregates


title: Primary nasal epithelial cells, SARS-CoV-2 Omicron Variant infected, 96hpi, rep 2

first: David

middle: Michael

last: Renner

address: 3610 Hamilton Walk

department: Microbiology

institute: University of Pennsylvania

description: Library preparation and sequencing by GeneWiz / Azenta

data_processing:
Reads were trimmed for adaptor content and low quality sequences using BBDuk v38.73 (ktrim=r k=23 mink=11 hdist=1 minlength=35 tpe tbo qtrim=20 qin=33)
Trimmed sequence reads were aligned to hg38v98 using Salmon (-p 8 --validateMappings --numBootstraps 30 --rangeFactorizationBins 4 --seqBias --gcBias)
Read count extraction and normalization were performed using DESeq2 v1.22.1
Assembly: hg38 v98
Supplementary files format and content: comma-delimited text file includes normalized counts from DESeq2 for each sample

source_name: Primary nasal

growth_protocol: Sinonasal cells from four separate donors obtained from patient donors with informed consent, per protocol approved by the University of Pennsylvania Institutional Review Board (protocol #800614), were pooled together and grown to 80% confluence in in PneumaCult™-ALI Medium (STEMCELL Technologies 05001) supplemented with heparin (STEMCELLl Technologies 07980) and hydrocortisone. Once cells reach confluency in 0.4 µM pore transwell inserts, the apical growth media is removed and the basal differentiation media is replaced every 3-4 days for a minimum of 4 weeks.

extract_protocol:
Total RNA was harvested using Rneasy Mini Plus Kit (Qiagen). 2ug of RNA was sent to Azenta Life Sciences for sequencing library preparation
poly(A) selected libraries were prepared by Azenta Life Sciences

treatment_protocol:
Mucus was washed off of apical surface of cells using PBS
Cells were infected apically with each indicated virus at MOI = 0.1 for 1 hour at 37oC
Unabsorbed virus was washed off with PBS 3 times before cells were returned to 37oC and incubated for 96 hours

value: Primary nasal

value: Nasal epithelium

value: SARS-CoV-2 Omicron Variant Infected

tag: time


title: HCT116_exRNA

description: Total RNA from extracellular vesicles

value: HCT 116


title: Library 23 cell hashing

address: Herestraat 49 box 602

value: Brain

value: Microglia


title: Primary nasal epithelial cells, SARS-CoV-2 Omicron Variant infected, 96hpi, rep 3


title: HCT116_cRNA

description: Total cell RNA


title: WiDr_cRNA

description: Total cell RNA

value: WiDr


title: Primary nasal epithelial cells, SARS-CoV-2 Delta Variant infected, 96hpi, rep 3

value: SARS-CoV-2 Delta Variant Infected


title: WiDr_exRNA

description: Total RNA from extracellular vesicles


title: Female_ACC_KO_Untrained 1

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Thbs1/2 KO

value: Female


title: Female_ACC_KO_Untrained 2


title: Library 21 cell hashing

value: female and male


title: Library 20 cell hashing

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

value: female

value: 6 months

value: all


title: LS513_exRNA

description: Total RNA from extracellular vesicles

value: Large intestine; Cecum

value: WT

value: Adenocarcinoma


title: Library 22 cell hashing

value: Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

value: male

value: 3 months

value: Scrambled peptide, soluble amyloid-β aggregates


title: SW480_cRNA

description: Total cell RNA

value: Large intestine; Colon


title: Primary nasal epithelial cells, SARS-CoV-2 Delta Variant infected, 96hpi, rep 2

value: Primary nasal

value: Nasal epithelium

value: SARS-CoV-2 Delta Variant Infected


title: Primary nasal epithelial cells, SARS-CoV-2 Delta Variant infected, 96hpi, rep 1


title: Male_ACC_WT_Untrained 3

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Wild-type

value: Male


title: Library 19 cell hashing

value: Brain

value: Microglia

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

value: female and male

value: 6 months


title: Male_ACC_WT_Untrained 1


title: HT29_exRNA

description: Total RNA from extracellular vesicles

value: WT

value: Adenocarcinoma


title: Male_ACC_WT_Untrained 2


title: Male_ACC_KO_Untrained 2

value: Thbs1/2 KO


title: Library 18 cell hashing

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F ApoE-/-

value: male


title: LS513_cRNA

description: Total cell RNA

value: Large intestine; Cecum


title: Primary nasal epithelial cells, SARS-CoV-2 Beta Variant infected, 96hpi, rep 2

value: Primary nasal

value: Nasal epithelium

value: SARS-CoV-2 Beta Variant Infected


title: Female_ACC_KO_Untrained 3

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Female


title: Primary nasal epithelial cells, SARS-CoV-2 Omicron Variant infected, 96hpi, rep 1

value: SARS-CoV-2 Omicron Variant Infected


title: HT29_cRNA

description: Total cell RNA

value: Large intestine; Colon


title: Primary nasal epithelial cells, SARS-CoV-2 Beta Variant infected, 96hpi, rep 1


title: Library 17 cell hashing

value: Brain

value: Microglia

value: all


title: Female_ACC_KO_Trained

value: Trained


title: Library 13 cell hashing

value: Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

value: female and male

value: 6 months


title: Male_ACC_KO_Trained 4

value: Thbs1/2 KO

value: Male


title: Library 12 cell hashing

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F ApoE-/-

value: male


title: SNUC1_exRNA

description: Total RNA from extracellular vesicles

value: WT

value: Adenocarcinoma


title: Female_ACC_KO_Trained 3

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)


title: Primary nasal epithelial cells, SARS-CoV-2 Alpha Variant infected, 96hpi, rep 3

value: Primary nasal

value: Nasal epithelium

value: SARS-CoV-2 Alpha Variant Infected


title: SNUC1_cRNA

description: Total cell RNA

value: Large intestine; Colon


title: Primary nasal epithelial cells, SARS-CoV-2 Alpha Variant infected, 96hpi, rep 2


title: Library 11 cell hashing

value: Brain

value: Microglia


title: LS1034_exRNA

description: Total RNA from extracellular vesicles

value: Large intestine; Cecum


title: Male_ACC_KO_Trained 3

value: Trained


title: Male_ACC_KO_Untrained 3


title: Primary nasal epithelial cells, SARS-CoV-2 Alpha Variant infected, 96hpi, rep 1


title: Male_ACC_KO_Trained 2


title: Library 9 cell hashing

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

value: female and male

value: 6 months


title: Primary nasal epithelial cells, SARS-CoV-2 Beta Variant infected, 96hpi, rep 3

value: SARS-CoV-2 Beta Variant Infected


title: Library 8 cell hashing

value: female

value: all


title: COLO201_exRNA

description: Total RNA from extracellular vesicles

value: WT

value: Adenocarcinoma


title: Primary nasal epithelial cells, SARS-CoV-2 WA/01 infected, 96hpi, rep 2

value: SARS-CoV-2 WA/01 Infected


title: Female_ACC_KO_Trained 2

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Thbs1/2 KO

value: Female


title: Library 7 cell hashing

value: Brain

value: male


title: LS1034_cRNA

description: Total cell RNA

value: Large intestine; Cecum


title: COLO201_cRNA

description: Total cell RNA

value: Large intestine; Colon


title: Male_ACC_KO_Trained 1

value: Trained

value: Male


title: Primary nasal epithelial cells, SARS-CoV-2 WA/01 infected, 96hpi, rep 1

value: Primary nasal

value: Nasal epithelium


title: LOVO_exRNA

description: Total RNA from extracellular vesicles

value: LoVo


title: Female_ACC_KO_Trained 1


title: Primary nasal epithelial cells, mock infected, 96hpi, rep 3

value: Mock Infected


title: Library 25 mRNA

value: Microglia

value: Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

value: female and male

value: 6 months


title: Primary nasal epithelial cells, mock infected, 96hpi, rep 2

value: WT


title: Library 24 mRNA

value: 3 months

value: Scrambled peptide, soluble amyloid-β aggregates


title: Library 23 mRNA

value: Brain


title: Primary nasal epithelial cells, mock infected, 96hpi, rep 1


title: K6

city: shenzhen

first: Zhonghao

last: Zhang

address: xueyuan

institute: shenzhen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: FPKM values and raw gene counts for each sample

source_name: brain

extract_protocol:
Isolated total RNA from adult microglia was used for RNA-seq analysis. cDNA library construction and sequencing were performed by Jingjie PTM BioLab (Hangzhou, China) using the Illumina platform. High-quality reads were aligned to the mouse reference genome using Hisat2 (v.2.0.5). Each sample was sequenced with a data depth of 10G. Expression levels for each of the genes were quantified by stringtie (v.2.2.0). Differential gene analysis was carried out using the DESeq2 package (v.1.20.0). Differentially expressed genes (DEGs) with ≥2-fold change and P<0.05 were identified. Gene functional annotation overrepresented by DEGs was performed using the GO (Gene Ontology) database. The gene set enrichment analysis (GSEA) was performed using the ranked list of genes based on the log-fold change obtained from the differential gene analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: strain

value: adult microglia

value: Selk-/-


title: K1 3


title: Library 22 mRNA

city: Leuven

tag: cell line

value: male


title: K2

tag: cell type


title: BMECs, POS_6, 6-h

city: Qingdao

first: Lianbin

last: Xu

address: No.700, Changcheng Road

department: College of Animal Science and Technology

institute: Qingdao Agricultural University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.20.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: ensembl_bos_taurus_ars_ucd1_2_gca_002263795_2
Supplementary files format and content: FPKM.txt

organism: Bos taurus

source_name: Mammary gland

growth_protocol: Bovine mammary epithelial cells (6 passages) were grown and maintained in DMEM-F12 medium containing 1% L-glutamine with 10% (v/v) fetal bovine serum, 5 μg/mL transferrin, 5 μg/mL insulin, 5 μg/mL prolactin, 1 μg/mL hydrocortisone, 10 ng/mL epidermal growth factor, and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA was harvested according to the Trizol/Qiazol protocol (Qiagen, Cat#79306). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Cells were cultured with DMEM-F12 medium for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)

value: DMEM-F12 medium