title: Dataset2_SARS-CoV2 double-infected replicate 3

description:
replicate 3
Brunello2_BrCov-ND3

value: double-infected


title: MT1205_AGG1

status: Public on Dec 22 2021

type: SRA

city: Stanford

first: Christopher

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 via 2-pass mapping with the STAR aligner (v2.6.1d).
Estimates of gene expression were generated using RSEM (v1.2.30) with standard input parameters.
The differentially expressed genes between different tumor genotypes were called by DESeq2 (v1.26.0) using transcript abundance estimates imported via tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Median of ratios normalized (DESeq2) counts across all samples; Differential expression analysis output from DESeq2; RSEM gene-level outputs for each library, which can be imported into R with tximport.

molecule: total RNA

organism: Mus musculus

source_name: Neoplastic cells isolated from lung tumors by FACS

growth_protocol: Lung tumors were initiated via intratracheal delivery of Lenti-sgRNA/Cre (sgNeo1/sgNT/sgNeo2/Cre (sgInert), Lenti-sgLkb1/Cre (sgLkb1), or Lenti-sgCebpa/sgCebpb/sgCebpd/Cre (sgCebpa/b/d)) in 60 µL PBS. Lung tumors were developed for 17 weeks.

extract_protocol:
Microdissected lung tumors were dissociated with collagenase IV, dispase, and trypsin at 37 °C for 30 min. After dissociation, the samples were maintained on ice, in the presence of 2 mM EDTA and 1 U/mL DNase to prevent aggregation. For the sorting of neoplastic cells, the dissociated cells were stained with antibodies against CD45 (BioLegened, 103112), CD31 (BioLegend, 303116), F4/80 (BioLegend, 123116), and Ter119 (BioLegend, 116212) to exclude hematopoietic and endothelial cells (lineage-positive (Lin+) cells). DAPI was used to exclude dead cells. FACSAria sorters (BD Biosciences) were used for cell sorting.RNA was purified using RNA/DNA Allprep kit (Qiagen, 80284). RNA quality was assessed using the RNA6000 PicoAssay for the Agilent 2100 Bioanalyzer.
Two to ten nanograms of total RNA served as input for the preparation of RNA-Seq libraries using the Trio RNA-Seq, Mouse rRNA kit (Tecan Genomics: 0507-32). Libraries were constructed per the manufacturer’s instructions. Purified libraries were assessed using the Agilent High Sensitivity DNA kit (Agilent Technologies: 5067-4626).

tag: virus

value: Lenti-sgCebpa/sgCebpb/sgCebpd/Cre

tag: Sex

value: Female

tag: label


title: HUc101pre

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

label: biotin

organism: Homo sapiens

extract_protocol: RNA was isolated using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks.

tag: patient

tag: tissue

value: liver biopsy

value: Baseline


title: HUc100pre

scan_protocol: Refer to the NanoString nCounter Assay System Manual.


title: AW96_STM470

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: fibrosis stage

tag: pls risk prediction

value: Intermediate


title: Dataset2_SARS-CoV2 double-infected replicate 2

city: Zurich

first: Moritz

last: Schaefer

address: Otto-Stern-Weg 7

department: Biology

country: Switzerland

institute: ETH Zurich

description:
replicate 2
Brunello2_BrCov-ND2

library_source: genomic

data_processing:
Library strategy: CRISPR Screen
FastQ files were obtained as provided by the sequencing facility
The MAGeCK-VISPR pipeline (v0.5.6) was employed to map R1-reads to sgRNA-library and for all downstream analyses
Genome_build: Brunello library

molecule: genomic DNA

source_name: HEK293-hACE2 cells

extract_protocol:
DNA STAT-60 Kit
Genomic DNA was extracted from each sample (detailed extraction methods are described in supplemental methods). The sgRNA regions were then amplified and indexed for Illumina sequencing using a one-step PCR method and primers specific to the LentiCRISPRv2-based Brunello libraries. Primers and indices used for the generation of amplicon libraries are listed in Table S1. Brunello  DNA samples were amplified in ten 100 µl reactions using the NEBNext High-Fidelity 2X Master Mix Kit (New England Biolabs), 0.5 µM of forward and reverse primers and 10 µg of DNA template per reaction with the following program: initial denaturation at 98°C for 3 min, 24 cycles of denaturation at 98°C for 10 s, annealing 60°C for 15 s and extension 72°C for 25 s, and final extension at 72°C for 2 min. 256 bp amplicons were quantified on a 2% agarose gel stained with SYBR Safe (Invitrogen), using the Gel Doc quantification software (Bio-Rad).
Amplicons were first pooled in an equimolar fashion and then the pools were gel-extracted using the PureLink Quick Gel Extraction Kit (Thermo Fisher Scientific). The sequencing was carried out at the Interdisciplinary Center for Biotechnology Research (ICBR; University of Florida) using a NovaSeq 6000 sequencer (Illumina). The Brunello amplicons were sequenced using the S4 2X150 cycles Kit (Illumina)

treatment_protocol: human HEK293T-hACE2 cells (Genecopoeia) were transduced with the Brunello sgRNA library. For each screen, 1.2x108 cells were transduced with lentivirus-packaged sgRNA library at MOI 0.3 in the presence of 8 μg/ml polybrene (Sigma) to achieve ~500-fold overrepresentation of each sgRNA. After 48 h, 0.6 µg/ml puromycin (Gibco) was added to eliminate non-transduced cells and cultures were expanded in Matrigel-coated (Corning) T300 flasks. Control replicates were collected at this time to determine input library composition and additional replicates were infected with SARS-CoV-2 or OC43 at the indicated MOIs. Cells surviving initial infections were collected when they had expanded to confluency. A portion of each replicate was stored in DNA/RNA Shield (Zymo Research) at -80°C for genomic DNA extraction and the remaining cells were reseeded and reinfected at the indicated MOIs.

tag: single or double infected

tag: moi


title: AW95_STM348

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: Dataset2_SARS-CoV2 double-infected replicate 1

description:
replicate 1
Brunello2_BrCov-ND1


title: AW106_STM388

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Low


title: HUc099pre

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: HUc098pre


title: AW105_STM332


title: Day 0 replicate 4

description:
replicate 4
Brunello1_T0puro4

data_processing:
Library strategy: CRISPR screen
FastQ files were obtained as provided by the sequencing facility
The MAGeCK-VISPR pipeline (v0.5.6) was employed to map R1-reads to sgRNA-library and for all downstream analyses
Genome_build: Brunello library

extract_protocol:
Quick-DNA Midiprep Plus Kit (Zymo Research)
Genomic DNA was extracted from each sample (detailed extraction methods are described in supplemental methods). The sgRNA regions were then amplified and indexed for Illumina sequencing using a one-step PCR method and primers specific to the LentiCRISPRv2-based Brunello libraries. Primers and indices used for the generation of amplicon libraries are listed in Table S1. Brunello DNA samples were amplified in ten 100 µl reactions using the NEBNext High-Fidelity 2X Master Mix Kit (New England Biolabs), 0.5 µM of forward and reverse primers and 10 µg of DNA template per reaction with the following program: initial denaturation at 98°C for 3 min, 24 cycles of denaturation at 98°C for 10 s, annealing 60°C for 15 s and extension 72°C for 25 s, and final extension at 72°C for 2 min. 256 bp amplicons were quantified on a 2% agarose gel stained with SYBR Safe (Invitrogen), using the Gel Doc quantification software (Bio-Rad).
Amplicons were first pooled in an equimolar fashion and then the pools were gel-extracted using the PureLink Quick Gel Extraction Kit (Thermo Fisher Scientific). The sequencing was carried out at the Interdisciplinary Center for Biotechnology Research (ICBR; University of Florida) using a NovaSeq 6000 sequencer (Illumina). The Brunello amplicons were sequenced using the S4 2X150 cycles Kit (Illumina)

tag: cell line

value: uninfected

tag: single or double infection


title: MT1161_AGG1


title: MT1161_AGG2


title: HUc097pre


title: AW98_STM373


title: HUc096pre


title: MT1231_AGG1

value: Male


title: Day 0 replicate 3

description:
replicate 3
Brunello1_T0puro3


title: Day 0 replicate 2

description:
replicate 2
Brunello1_T0puro2


title: HUc095pre


title: AW103_STM468


title: MT1136_AGG2


title: Day 0 replicate 1

description:
replicate 1
Brunello1_T0puro1


title: MT1203_AGG1


title: AW102_STM046


title: MT1136_AGG1


title: AW101_STM407


title: OC43 single-infected replicate 5

description:
replicate 5
Brunello1_OC43-st-5

value: single-infected


title: HUc093pre


title: AW100_STM482


title: Lkb1_AGG2


title: HUc092pre


title: Lkb1_AGG1


title: MT1139_AGG2


title: HUc091pre


title: Cebp_AGG2


title: AW94_STM381


title: AW93_STM483


title: Cebp_AGG1B


title: AW104_STM464


title: Cebp_AGG1A


title: HUc090pre


title: HUc089pre


title: HUc094pre


title: AW92_STM111


title: OC43 single-infected replicate 1

description:
replicate 1
Brunello1_OC43-st-1


title: AW91_STM377


title: HUc088pre


title: OC43 double-infected (MOI 0.1) replicate 3

description:
replicate 3
Brunello1_OC43-nd-0point1-5

value: MOI 0.1


title: OC43 single-infected replicate 4

description:
replicate 4
Brunello1_OC43-st-4


title: rSP84

description: Non-Restored

growth_protocol: Lung tumors were initiated via intratracheal delivery of Lenti-Cre in 60 µL PBS. Lung tumors were developed for 24-27 weeks for Trp53 wild-type tumors, and 16-19 weeks for Trp53-deficient tumors.

treatment_protocol: Lkb1XTR mice were subjected to treatment with either corn oil vehicle or tamoxifen (4 mg doses in 200 µL corn oil) for two weeks prior to harvesting lung tumors.

tag: genotype

tag: treatment

value: Tamoxifen

tag: cohort

value: Non-Restored


title: OC43 double-infected (MOI 0.1) replicate 2

description:
replicate 2
Brunello1_OC43-nd-0point1-2


title: HUc087pre


title: OC43 double-infected (MOI 0.1) replicate 1

description:
replicate 1
Brunello1_OC43-nd-0point1-1


title: rSP81

description: Non-Restored


title: AW90_STM409


title: AW89_STM455


title: tSP106

description: Restored; Trp53Δ/Δ

value: Restored; Trp53delta/delta


title: OC43 single-infected replicate 3

description:
replicate 3
Brunello1_OC43-st-3


title: OC43 single-infected replicate 2

description:
replicate 2
Brunello1_OC43-st-2


title: OC43 double-infected (MOI 0.01) replicate 3

description:
replicate 3
Brunello1_OC43-nd-0point01-5


title: HUc086pre


title: HUc085pre


title: OC43 double-infected (MOI 0.01) replicate 2

description:
replicate 2
Brunello1_OC43-nd-0point01-2


title: AW87_STM082


title: HUc084pre


title: rSP78

description: Restored

value: Restored


title: SARS-CoV2 single-infected replicate 4

description:
replicate 4
Brunello1_Cov-st-4


title: HUc082pre


title: OC43 double-infected (MOI 0.01) replicate 1

description:
replicate 1
Brunello1_OC43-nd-0point01-1


title: rSP79

description: Restored


title: AW86_STM472


title: rSP77

description: Restored


title: HUc081pre


title: AW85_STM349


title: rSP76

description: Non-Restored

value: Vehicle


title: SARS-CoV2 single-infected replicate 3

description:
replicate 3
Brunello1_Cov-st-3


title: HUc080pre


title: SARS-CoV2 single-infected replicate 2

description:
replicate 2
Brunello1_Cov-st-2


title: AW84_STM474


title: AW83_STM461


title: SARS-CoV2 single-infected replicate 1

description:
replicate 1
Brunello1_Cov-st-1


title: rSP73

description: Non-Restored


title: AW88_STM363


title: AW82_STM444


title: HUc078pre


title: SARS-CoV2 double-infected ext. (MOI 0.1) replicate 3

description:
replicate 3
Brunello1_Cov-nd-ext-0point1-3

value: double-infected ext.


title: rSP71

description: Restored


title: HUc079pre


title: rSP66

description: Non-Restored; Trp53Δ/Δ

value: Non-Restored; Trp53delta/delta


title: AW81_STM335


title: HUc077pre


title: AW80_STM490


title: SARS-CoV2 double-infected ext. (MOI 0.1) replicate 2

description:
replicate 2
Brunello1_Cov-nd-ext-0point1-2


title: HUc076pre


title: rSP60

description: Restored; Trp53Δ/Δ


title: SARS-CoV2 double-infected ext. (MOI 0.1) replicate 1

description:
replicate 1
Brunello1_Cov-nd-ext-0point1-1


title: rSP62

description: Non-Restored


title: HUc075pre


title: AW78_STM473


title: SARS-CoV2 double-infected ext. (MOI 0.01) replicate 3

description:
replicate 3
Brunello1_Cov-nd-ext-0point01-3


title: AW79_STM458


title: rSP59

description: Non-Restored


title: rSP75

description: Non-Restored


title: HUc074pre


title: SARS-CoV2 double-infected ext. (MOI 0.01) replicate 2

description:
replicate 2
Brunello1_Cov-nd-ext-0point01-2


title: rSP58

description: Non-Restored


title: HUc073pre


title: AW76_WCA132


title: AW77_STM262

value: High


title: SARS-CoV2 double-infected ext. (MOI 0.01) replicate 1

description:
replicate 1
Brunello1_Cov-nd-ext-0point01-1


title: HUc072pre


title: rSP56

description: Restored

value: Female


title: HUc071pre

value: liver biopsy


title: SARS-CoV2 double-infected (MOI 0.1) replicate 3

description:
replicate 3
Brunello1_Cov-nd-0point1-3

value: double-infected


title: AW74_WCA203


title: HUc070pre

value: Baseline


title: SARS-CoV2 double-infected (MOI 0.1) replicate 2

description:
replicate 2
Brunello1_Cov-nd-0point1-2


title: rSP52

description: Non-Restored


title: SARS-CoV2 double-infected (MOI 0.1) replicate 1

description:
replicate 1
Brunello1_Cov-nd-0point1-1


title: HUc069pre


title: rSP50

description: Non-Restored; Trp53Δ/Δ


title: AW75_WCA147

value: Intermediate


title: SARS-CoV2 double-infected (MOI 0.01) replicate 3

description:
replicate 3
Brunello1_Cov-nd-0point01-3


title: SARS-CoV2 double-infected (MOI 0.01) replicate 2

description:
replicate 2
Brunello1_Cov-nd-0point01-2


title: AW73_WCA035


title: SARS-CoV2 double-infected (MOI 0.01) replicate 1

description:
replicate 1
Brunello1_Cov-nd-0point01-1


title: AW71_WCA135


title: rSP47

description: Non-Restored


title: HUc067pre


title: AW70_WCA186


title: rSP57

description: Restored


title: HUc066pre


title: AW69_WCA198


title: ZR1532

description: wild-type

value: wild-type


title: HUc065pre


title: AW68_STM417


title: Month 6 in vivo maturation (STZ)

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

description:
M6_STZ
features.tsv.gz

data_processing:
Sample de-multiplexing, alignment, filtering, and UMI counting were performed with 10x Genomics Cell Ranger (v3.1) pipeline.
The reads were mapped to a hybrid of human and mouse reference genomes (GRCh38.98 and GRCm38.98).
The UMI counts were filtered with DropletUtils to remove empty droplets, mouse cells and mouse transcripts from the data.
The filtered counts were analyzed with Seurat.
Genome_build: GRCh38.98, GRCm38.98
Supplementary_files_format_and_content: Single cell read count matrix (matrix.mtx), cell barcode (barcodes.tsv), gene names (features.tsv).

molecule: polyA RNA

source_name: stem cell derived islet cells

growth_protocol: Human embryonic cell line H1 was cultured on Matrigel-coated plates in E8 medium and passaged using EDTA. To prepare the differentiation experiments, near-confluent plates of stem cells were dissociated using EDTA and seeded on new Matrigel coated plates in E8 supplemented with 0.5-uM Rho-Associated kinase inhibitor to achieve confluent plates.

extract_protocol:
SC-islets were incubated with 1:1 mix of TrypLe and 10x Trypsin – EDTA for 10 min in +37°C. Disassociation media was neutralized by adding 3x volume 0.5% FBS in PBS and strained through a 30-um filter to remove cell clusters. Finally, the cells were resuspended in PBS+0.04% BSA, washed, counted and diluted to a 1x10^6 cells/ml concentration for encapsulation.
10x Genomics Chromium Single Cell 3’ RNAseq platform using the Chromium Next GEM Single Cell 3' Gene Expression (version 3.1 chemistry).

treatment_protocol: To start the differentiations, the medium was changed to D0 medium 24h post-seeding. The differentiation was carried out using a 7-stage protocol combined from several publications (Pagliuca 2014, Rezania 2014, Nostro 2015, patent WO2017222879A1), with stage 7 medium containing CMRL1066 supplemented with BSA, sodium pyruvate, glutmax, ITS-X, ZnSO4, heparin, Trace elements A and B and lipid concentrate with added aurora kinase inhibitor ZM447439 (ZM), tri-iodothyronine (T3) and N-acetyl cysteine (NAC). On the 3rd day of S4 culture, the planar pancreatic epithelium was dissociated using TrypLE and seeded to microwells (AggreWell 400, Stemcell technologies) at a density of 800-1000 cells per microwell. On the 1st day of S6 culture the SC-islets were transferred from the microwells to suspension culture placed on rotator spinning at 95 RPM. Media changes were performed daily until the 1st day of S6 culture and every two to three days thereafter.

tag: originating cell line

tag: developmental stage

value: streptozotocin

tag: maturation environment

value: implanted


title: HUc064pre


title: Month 6 in vivo maturation (CTRL)

description:
M6_CTRL
features.tsv.gz

value: control


title: Month 3 in vivo maturation (E7)

description:
M3_E7
features.tsv.gz


title: rSP48

description: Restored

value: Tamoxifen


title: ZR1354

description: wild-type

value: Male


title: ZR1518

description: wild-type


title: HUc068pre


title: AW72_WCA334


title: JB3844-Bulk

description: Restored; Trp53Δ/Δ

value: Restored; Trp53delta/delta


title: AW66_STM266

value: Low


title: AW65_STM273


title: Month 3 in vivo maturation (E1)

description:
M3_E1
features.tsv.gz


title: AW64_STM438


title: Month 3 in vivo maturation (B1)

description:
M3_B1
features.tsv.gz


title: ZR1534

description: wild-type


title: HUc061pre


title: HUc063pre


title: JB3839-Bulk

description: Non-Restored; Trp53Δ/Δ

value: Vehicle


title: AW63_STM422


title: AW62_STM296


title: JB3839-T1

description: Non-Restored; Trp53Δ/Δ


title: HUc059pre


title: JB3455-Bulk

description: Restored; Trp53Δ/Δ


title: Month 1 in vivo maturation (H1)

description:
M1_H1
features.tsv.gz


title: HUc060pre


title: Month 1 in vivo maturation (A7)

description:
M1_A7
features.tsv.gz


title: JB3453-T1

description: Non-Restored; Trp53Δ/Δ


title: Stage 7 week 6, in vitro (exp23)

description:
S7_exp23
features.tsv.gz

value: S7 week 6

value: in vitro


title: AW59_WCA078


title: AW60_STM437


title: HUc058pre


title: HUc062pre


title: HUc057pre


title: AW58_WCA145

value: High


title: Stage 7 week 6, in vitro (exp22)

description:
S7_exp22
features.tsv.gz


title: JB3453-Bulk-a04

description: Non-Restored; Trp53Δ/Δ

value: Non-Restored; Trp53delta/delta

value: Female


title: AW56_WCA168


title: AW55_WCA127


title: HC1844

description: Amplicon library derived from lentiviral barcodes integrated within genomic DNA of the lungs

data_processing:
Library strategy: Tuba-seq
Each read is expected to contain an 8-nucleotide sgID region followed by a 30-nucleotide barcode (BC) region (GCNNNNNTANNNNNGCNNNNNTANNNNNGC), and each of the 20 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
The sgID region corresponds to the sgRNA encoded within the Lenti-sgRNA/Cre vector that initiated a given tumor. We require a perfect match between the sequence in the forward read and one of the known sgIDs included within the Lenti-sgRNA/Cre pool.
We require the forward and reverse read to agree completely within the 30 nucleotide sequence to be further processed. Any tumors that are within a Hamming distance of two from a larger tumour is regarded as spurious, as they are likely to result from sequencing or PCR errors, and thus are excluded from downstream analyses.
The tumor size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmark spike-in cell lines (5.00E+05 cells for each benchmark cell line) added to each sample prior to lung homogenization/digestion and genomic DNA extraction.
Supplementary_files_format_and_content: Summary of all tumors in the study, including the identity and genotype of the originating mouse of origin, the sgID and clonal identifier, read count, and tumor size.

source_name: tumor-bearing lung

growth_protocol: Lung tumors were initiated via intratracheal delivery of 60 µL of a Lenti-sgRNA/Cre pool. Lung tumors were developed for 15 weeks.

extract_protocol:
Lung tissue was extracted temporarily frozen for later processing. Prior to tissue homogenization and proteinase K digestion, each lung sample was spiked with three cell lines bearing known barcodes (5.00E+05 cells of each cell line). Genomic DNA was then isolated by phenol-chloroform extraction followed by ethanol precipitation from the total lung tissue of each mouse.
One-step PCR targeting lentiviral barcodes to append Illumina adapters, unique dual indices for multiplexing, and six to nine random bases to increase sequence complexity.
Custom Amplicon Library (Tuba-seq)


title: HC1882


title: HUc056pre

value: liver biopsy


title: Stage 7 week 3, in vitro (D25)

description:
S7_D25
features.tsv.gz

value: S7 week 3


title: Stage 7 week 3, in vitro (D20)

description:
S7_D20
features.tsv.gz


title: HUc053pre

value: Baseline


title: HUc054pre


title: HC1909


title: AW54_WCA013


title: AW53_WCA053


title: HUc052pre


title: HC1911


title: HUc051pre


title: Stage 7 week 0, in vitro (B5)

description:
S6_B5
features.tsv.gz

value: S7 week 0


title: Stage 7 week 0, in vitro (B3)

description:
S6_B3
features.tsv.gz


title: Stage 7 week 0, in vitro (A11)

description:
S6_A11
features.tsv.gz


title: HUc055pre


title: AW51_WCA093

value: Intermediate


title: AW50_WCA080


title: HC1887


title: HC1905


title: Stage 5 in vitro (NT)

description:
S5_NT
features.tsv.gz


title: HC1875


title: HUc049pre


title: AW49_WCA092


title: Month 1 in vivo maturation (H6)

description:
M1_H6
features.tsv.gz

value: implanted


title: Stage 5 in vitro (DT)

description:
S5_DT
features.tsv.gz

value: doxycycline


title: Stage 7 week 3, in vitro (D18)

description:
S7_D18
features.tsv.gz

value: control


title: JB3453-Bulk-g03

description: Non-Restored; Trp53Δ/Δ


title: HUc048pre


title: AW48_WCA089


title: HC1843

value: Male


title: HC1845


title: AW47_WCA018


title: MT1505


title: AW52_WCA063


title: HUc050pre


title: HUc045pre


title: AW46_WCA183


title: HUc047pre


title: MT1504


title: HUc044pre


title: MT1503


title: AW42_WCA204


title: HUc043pre


title: MT1502


title: HUc042pre


title: MT1499


title: HUc041pre


title: HUc039pre


title: AW38_WCA161


title: AW40_WCA185


title: HUc038pre


title: CM2309


title: CM2363


title: HUc037pre


title: CM2495


title: AW45_WCA171


title: CM2312


title: AW30_WCA009


title: AW31_WCA369


title: HUc034pre


title: MT1164


title: HUc035pre


title: MT1118


title: AW41_WCA094


title: HUc036pre


title: AW29_WCA126


title: AW28_WCA179


title: MT1048


title: AW37_WCA140


title: AW27_WCA201


title: AW34_WCA384


title: HUc112post

value: Follow-up


title: MT1122


title: AW26_WCA370


title: CM2364


title: HUc109post


title: MT1163


title: AW25_WCA395


title: MT1180


title: AW24_WCA305


title: HUc107post


title: HUc108post


title: CM2604


title: MT0926


title: HUc106post


title: AW23_WCA315


title: MT1040


title: MT1041


title: AW21_WCA155


title: HUc105post


title: HUc104post


title: HUc110post


title: AW22_WCA319


title: AW20_WCA367


title: HUc103post


title: AW19_WCA396


title: MT1045


title: HUc102post


title: MT0876


title: AW17_WCA136


title: AW18_WCA129


title: HUc101post


title: MT1047


title: AW16_WCA234


title: HUc100post


title: HUc099post


title: CM2556


title: AW15_WCA386


title: HUc098post


title: AW14_WCA390


title: HUc097post


title: MT1042


title: CM2609


title: AW13_WCA393


title: Control 2

city: Durham

first: Preetish

last: Kadur Lakshminarasimha Murthy

state: NC

address: 101 Science Dr

institute: Duke University

description: Control

data_processing:
Drop-seq data generated in this study were analysed using dropSeqPipe as described in (Kobayashi et al., 2020). Briefly, reads were aligned to mm10 genome and UMI counts were obtained. Counts were imported into Seurat for further analysis. Data were normalised using SCTransform before performing PCA and UMAP dimensional reductions, and identifying clusters. Non-epithelial cells were excluded from the analysis based on the expression of Pecam1, Ptprc, Pdgfra, Pdgfrb and Acta2. Cell barcodes of interest were used as input to velocyto.py program (La Manno et al., 2018) and further analysis were performed as described in (Kobayashi et al., 2020).
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix

source_name: lung

extract_protocol:
Lungs were collected from two CK 6w and 6 CC (control) mice injected with 4 doses of tamoxifen. Tissues were dissociated and a single cell suspensions were subjected to immune cell depletion using CD45 microbeads as described previously. fGFP+ cells were enriched by performing FACS in “yield-sort” mode. This mode is suitable to enrich populations found in small numbers, however, also results in contamination from other fGFP- cell types. The number of fGFP+ cells in each lung is small and a minimum of 100,000 cells are necessary for scRNA-seq, hence the ‘yield-sort’ mode was chosen. fGFP+ cell enriched suspensions from all controls were pooled but the two tumour samples were handled separately. Cells were then resuspended in 0.01% BSA in PBS.
scRNA-seq was performed using Drop-seq protocol (Macosko et al., 2015) with modifications described in (Kobayashi et al., 2020). Libraries were sequenced on HiSeq in 150 bp PE configuration.

tag: strain

value: mixed

value: Control


title: CM2548

tag: Sex


title: Control 1

description: Control


title: HUc095post


title: Treatment arm, before treatment w/ netazapeptde, patient 12, condition sample 9, overall sample 33

city: New York

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

description:
b9a.trt.t1.p17.ay033
Treatment arm, before treatment with netazapeptde, patient 12, condition sample 9, overall sample 33

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fastq format with bcl2fastq (version 2.2.0).
Reads were mapped to the genome with Rsubread
Reads in each gene were counted with featureCounts
Genome_build: Grch37.2
Supplementary_files_format_and_content: Xlsx file with raw counts for each gene

source_name: Treatment arm

extract_protocol:
Extraction was performed with Qiagen's miRNeasy micro kit
The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent)..
The average RNA Integrity Number (RIN) was 8.9 and the minimum was 7.5
PolyAAA pulldown, amplification, and labeling was performed with the TruSeq Stranded mRNA kit.

treatment_protocol: Subjects took netazpeptide 25 mg or placebo daily for 12 weeks,

tag: patient #

tag: sample number for condition

tag: sample number overaal

value: netazapeptde 25mg.

tag: time

value: before treatment


title: HUc094post

tag: patient

tag: tissue


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 12 condition sample 9, overall sample 34

description:
b9b.trt.t2.p17.ay034
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 12 condition sample 9, overall sample 34

value: after 12 weeks of treatment


title: H3k27me3-WT-2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Library strategy: Cut&Tag
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome using the align function of RSubread 2.2.6.
Read counts were summarized by Entrez Gene ID using the featureCounts function of Rsubread 2.6.1 and Rsubread's built-in NCBI annotation. The supplementary file GenewiseCounts.tsv.gz provides the gene-level counts for all the samples.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length and the number of reads mapping to that gene and their promoter region (trimmed at 3000bp upstream).

source_name: Alveolar macrophage

extract_protocol:
Alveolar macrophages sorted from the lung of wt or Suz12cKO mouse were bound to concanavalin A cated magnetic beads (Bags laboratories) and were subjected for immunoprecipitation with 1ul (0.5μg) of primary antibody (anti-H3K27me3 Abcam)
Hyperactive in situ ChIP Library Prep Kit was purchased from Vazyme and libraries were generated following manufacturer recommendations.

tag: background strain

value: Lung

tag: cell type

value: Alveolar macrophage

tag: transgenic mouse genotype

value: Wild type

tag: primary antibody

value: anti-H3K27me3 Abcam


title: HUc093post

value: liver biopsy


title: MT1038

tag: genotype


title: Brain CD45+ cells, Cd300a-fl/fl Lyz2-cre, 3 hr after MCAO

city: Tsukuba

first: Akira

last: Shibuya

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

country: Japan

institute: University of Tsukuba

data_processing:
Read alignment and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: Brain CD45+ cells

extract_protocol:
To isolate the brain cells, mice were sedated under deep anesthesia and perfused with PBS transcardially. Collected brain tissues were transferred to dounce homogenizer with 3.5ml of RPMI-1640 and grinded using loose and tight plunger. Homogenates were filtered through 70 micrometre cell strainer and then subjected to Percoll (GE Healthcare) gradient centrifugation. Cells were collected from the interlayer between 40% and 70% Percoll layers. Collected cells were filtered through 70 micrometre nylon mesh to obtain single-cell suspensions and PI-CD45+ hematopoietic cells were sorted by flow cytometry.
10X Genomics, Chromium Single Cell 3’ Library and Gel Bead Kit v3.

treatment_protocol: Transient cerebral ischemia (MCAO) was induced using the intraluminal filament technique. A silicon-coated nylon monofilament (Doccol Corporation) was inserted into the right internal carotid artery and left in situ for 60 min. Operation time per animal did not exceed 15 min. During the MCAO procedure, mice were kept on the 40°C heater and after 60 min, the inserted monofilament was withdrawn to allow reperfusion. We only included mice that showed reduction of blood flow of right middle cerebral artery which confirmed by doppler ultrasound.

value: Brain CD45+ cells

value: Cd300a-fl/fl Lyz2-cre


title: H3k27me3-WT-1


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 12 condition sample 8, overall sample 24

description:
b8b.trt.t2.p12.ay024
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 12 condition sample 8, overall sample 24

tag: treatment


title: Treatment arm, before treatment w/ netazapeptde, patient 12, condition sample 8, overall sample 23

description:
b8a.trt.t1.p12.ay023
Treatment arm, before treatment with netazapeptde, patient 12, condition sample 8, overall sample 23


title: HUc092post


title: HUc091post


title: H3k27me3-ko-2

value: Suz12 cKO


title: CM2786

value: Female


title: Brain CD45+ cells, Cd300a-fl/fl Lyz2-cre, 1 hr after MCAO


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 10, condition sample 7, overall sample 20

description:
b7b.trt.t2.p10.ay020
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 10, condition sample 7, overall sample 20


title: CK_6_weeks

value: Kras mutant


title: HUc090post


title: HUc096post


title: H3k27me3-ko-1


title: Treatment arm, before treatment w/ netazapeptde, patient 10, condition sample 7, overall sample 19

description:
b7a.trt.t1.p10.ay019
Treatment arm, before treatment with netazapeptde, patient 10, condition sample 7, overall sample 19


title: WT-LC-1

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome using the align function of RSubread 2.4.3.
Read counts were summarized by Entrez Gene ID using the featureCounts function of Rsubread 2.6.0 and Rsubread's built-in NCBI annotation. The supplementary file GenewiseCounts.tsv.gz provides the gene-level counts for all the samples.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length and the number of reads mapping to that gene.

extract_protocol:
RNA libraries were extracted from 5000 purified Langerhans cells from the skin of one week old mice
mRNA reverse transcription and cDNA libraries were prepared using the ultra-low input RNA-seq protocol from Takara following the manufacturer’s instructions

value: Skin


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 9, condition sample 6, overall sample 18

description:
b6b.trt.t2.p9.ay018
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 9, condition sample 6, overall sample 18


title: Brain CD45+ cells, Cd300a-fl/fl, 1 hr after MCAO


title: Brain CD45+ cells, Cd300a-fl/fl Lyz2-cre, naïve


title: HUc089post

value: Follow-up


title: WT-Langerhans-cell-2


title: HUc088post


title: Treatment arm, before treatment w/ netazapeptde, patient 9, condition sample 6, overall sample 17

description:
b6a.trt.t1.p9.ay017
Treatment arm, before treatment with netazapeptde, patient 9, condition sample 6, overall sample 17


title: E9.5_PGC_Rep2

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

data_processing:
Clean reads were mapped to the Mus musculus mm10 reference genome using Bowtie2 (population) or Hisat2 (a few cells).
Reads were assigned and counted to genes using the RSEM.
The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: E9.5PGC_TPM_pESC.csv. This file contains all samples TPM value of all genes

source_name: 9.5 day Embryo Primordial germ cells

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Isolated from E9.5 mouse embryo by SSEA1 antibody, no treatment

value: 9.5 day Embryo Primordial germ cells


title: Suz12-ko-LC-2


title: Brain CD45+ cells, Cd300a-fl/fl, naïve


title: Suz12-ko-LC-1


title: HUc087post


title: HUc086post


title: HUc085post


title: Brain CD45+ cells, Cd300a-fl/fl, 3 hr after MCAO


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 7, condition sample 5, overall sample 14

description:
b5b.trt.t2.p7.ay014
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 7, condition sample 5, overall sample 14


title: Primary chondrocytes - mutant FLAG-SP7

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

data_processing:
Fastq files were trimed by Trimmomatic-0.33 with follwing options: LEADING:20 TRAILING:20 MINLEN:50 CROP:50 HEADCROP:10
ChIP-seq reads were aligned to the mm9 genome assembly using  bowtie 1.2.2 with follwing options: -v 2 -m 1
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the input control
Genome_build: mm9
Supplementary_files_format_and_content: peak bed file

source_name: Primary chondrocytes

growth_protocol: Primary mouse chondrocytes isolated from proximal tibia and distal femur of 7 day old male mice cardiomyocytes were cultured in DMEM/F12 media supplemented with 10% FBS, P/S, and 50 μg/mL ascorbic acid at 37C and 5% CO2

extract_protocol:
Protein-DNA complexes were crosslinked with 1% formaldehyde, Lysates were clarified from sonicated nuclei and Protein-DNA complexes were purified with FLAG antibody.
SMARTer ThruPLEX DNA-seq Kit (R400428, Takara Bio)

treatment_protocol: On the day of infection, the retrovirus-containing cell culture media (produced by transfecting ECO cells with retroviral plasmids) were filtered with a 0.45um membrane filter, mixed 1:1 with full chondrocyte, and supplemented with 8ug/ml polybrene. Chondrocytes infected twice with the media (once in the morning and second time overnight or longer). Successful retroviral infection was indicated by GFP signal in cells after incubation (close to 100% infection efficiency).

value: Mouse primary chondrocytes

tag: chip antibody

value: FLAG M2 antibody (Sigma, F1804)


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 6, condition sample 4, overall sample 12

description:
b4b.trt.t2.p6.ay012
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 6, condition sample 4, overall sample 12

value: netazapeptde 25mg.


title: Primary chondrocytes - wild type FLAG-SP7


title: Suz12 WT4

extract_protocol:
RNA was isolated with the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions


title: Suz12-ko-Langerhans-cell-3


title: E9.5_PGC_Rep1


title: Primary chondrocytes - input DNA


title: Suz12 WT3


title: HUc083post


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 3, condition sample 3, overall sample 8

description:
b3b.trt.t2.p4.ay008
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 3, condition sample 3, overall sample 8

value: after 12 weeks of treatment


title: Suz12 WT2

value: Lung


title: whole fly DNA-seq

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

description: DNA-seq

data_processing:
Library strategy: DNA-seq
DNA-seq: sequencing reads were adapter clipped, names of reads were transformed using “sed -i -r 's/(@.*) 1.*$/\1\/1/g'” or “sed -i -r 's/(@.*) 2.*$/\1\/2/g'” commands and mapped onto reference genome combined with repeatmasker. Mapped reads were analyzed using PoPoolation TE2 pipeline (Kofler et al., 2016)
Te_inserts.txt file represents coordinates of transposable elements insertion obtained from PoPoolation TE2
Genome_build: dm3

organism: Drosophila melanogaster

source_name: whole flies

growth_protocol: Flies were grown at 18 °C

extract_protocol:
DNA-seq: genomic DNA was isolated from the whole flies according to the standard procedure (Maniatis et al. 1982).
DNA-seq: Paired-end library of the fragmented genomic DNA was prepared according to the Illumina standard protocol and sequenced on the Illumina HiSeq 4000 platform.

value: whole fly

tag: age

value: 2-4 days


title: Treatment arm, before treatment w/ netazapeptde, patient 3, condition sample 3, overall sample 7

description:
b3a.trt.t1.p4.ay007
Treatment arm, before treatment with netazapeptde, patient 3, condition sample 3, overall sample 7

value: before treatment


title: Suz12 WT1

value: Wild type


title: HUc081post

value: liver biopsy


title: Treatment arm, before treatment w/ netazapeptde, patient 7, condition sample 5 overall sample 13

description:
b5a.trt.t2.p7.ay013
Treatment arm, before treatment with netazapeptde, patient 7, condition sample 5 overall sample 13


title: HUc082post


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 2, condition sample 2, overall sample 4

description:
b2b.trt.t2.p2.ay004
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 2, condition sample 2, overall sample 4


title: suz12 KO5


title: slful_SFIM3

city: Wageningen

first: Xiaobing

last: Jiang

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

data_processing:
Barcoded libraries were pooled and sequenced on a NovaSeq platform (150 nt paired end reads).
Before mapping of the reads to the Solanum lycopersicum genome, raw reads were trimmed by removing adapter sequences.
Reads were mapped to the Solanum lycopersicum genome version 4.0 with RNA-Seq analysis package CLC Genomics Workbench 11 (www.clcbio.com).
Parameters mapping: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no.
Genome_build: Solanum lycopersicum genome version 4.0
Supplementary_files_format_and_content: xlsx (raw counts, flod change and p-value)

organism: Solanum lycopersicum

source_name: meristem

growth_protocol: Tomato plants were grown under normal greenhouse conditions.

extract_protocol:
Each sample (30-60 meristems) was disrupted with stainless steel beads and RNA was extracted using the InviTrap Spin Plant RNA Mini Kit (Stratec).
DNAse-treated RNA was used as template for RNA-seq library preparation (TruSeq RNA Library Prep Kit).

value: meristem

value: slful

tag: developmental stage

value: SFIM


title: HUc079post


title: suz12 KO4

value: Suz12 cKO


title: Treatment arm, before treatment w/ netazapeptde, patient 6, condition sample 4 overall sample 11

description:
b4a.trt.t1.p6.ay011
Treatment arm, before treatment with netazapeptde, patient 6, condition sample 4 overall sample 11


title: Treatment arm, before treatment w/ netazapeptde, patient 2, condition sample 2, overall sample 3

description:
b2a.trt.t1.p2.ay003
Treatment arm, before treatment with netazapeptde, patient 2, condition sample 2, overall sample 3


title: Treatment arm, after daily treatment w/ netazpeptide 25 mg for 12 wks, patient 1, condition sample 1, overall sample 2

description:
b1b.trt.t2.p1.ay002
Treatment arm, after daily treatment with netazpeptide 25 mg for 12 weeks, patient 1, condition sample 1, overall sample 2


title: HUc084post


title: slful_SFIM1


title: suz12 KO3


title: HUc078post


title: Treatment arm, before treatment w/ netazapeptde, patient 1, condition sample 1, overall sample 1

description:
b1a.trt.t1.p1.ay001
Treatment arm, before treatment with netazapeptde, patient 1, condition sample 1, overall sample 1


title: HUc046pre

value: Baseline


title: suz12 KO2


title: WT_SFIM2

value: WT


title: HUc077post

value: Follow-up


title: suz12 KO1


title: HUc076post


title: WT_SFIM3


title: Placebo arm, before treatment w/ placebo, patient 19, condition sample 10, overall sample 37

description:
b10a.trt.t1.p19.ay037
Placebo arm, before treatment with placebo, patient 19, condition sample 10, overall sample 37

source_name: Placebo arm

value: placebo


title: WT-AM-ind4

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome using the align function of RSubread 2.1.1.
Read counts were summarized by Entrez Gene ID using the featureCounts function of Rsubread 2.4.3 and Rsubread's built-in NCBI annotation. The supplementary file GenewiseCounts.tsv.gz provides the gene-level counts for all the samples.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length and the number of reads mapping to that gene.


title: HUc075post


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 18, condition sample 9, overall sample 36

description:
a9b.pla.t2.p18.ay036
Placebo arm, after daily treatment with placebo for 12 weeks, patient 18, condition sample 9, overall sample 36


title: HUc080post


title: slful_FIM3

value: FIM


title: WT_SFIM1


title: WT-AM-ind3


title: HC1891

description: Amplicon library derived from lentiviral barcodes integrated within genomic DNA of the lungs

value: Male


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 19, condition sample 10, overall sample 38

description:
b10b.trt.t2.p19.ay038
Placebo arm, after daily treatment with placebo for 12 weeks, patient 19, condition sample 10, overall sample 38

value: after 12 weeks of treatment


title: HUc074post


title: slful_FIM2


title: Placebo arm, before treatment w/ placebo, patient 18, condition sample 9, overall sample 35

description:
a9a.pla.t1.p18.ay035
Placebo arm, before treatment with placebo, patient 18, condition sample 9, overall sample 35


title: slful_FIM1


title: WT-AM-ind2

value: Lung


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 16, condition sample 8, overall sample 32

description:
a8b.pla.t2.p16.ay032
Placebo arm, after daily treatment with placebo for 12 weeks, patient 16, condition sample 8, overall sample 32


title: HUc073post


title: HUc072post


title: WT-AM-ind1


title: slful_TM2

value: TM


title: Suz12-AM-ind3


title: HUc070post


title: HUc071post


title: Suz12-AM-ind2


title: slful_TM1


title: slful_VM3

value: VM


title: Suz12-AM-ind1


title: Placebo arm, before treatment w/ placebo, patient 15, condition sample 7, overall sample 29

description:
a7a.pla.t1.p15.ay029
Placebo arm, before treatment with placebo, patient 15, condition sample 7, overall sample 29

value: before treatment


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 14, condition sample 6, overall sample 28

description:
a6b.pla.t2.p14.ay028
Placebo arm, after daily treatment with placebo for 12 weeks, patient 14, condition sample 6, overall sample 28


title: HSC_Repl1

city: Cambridge

first: Eva

last: Fast

state: MA

address: 1 Portland st

institute: Pfizer

description: control Replicate 1

data_processing:
scRNA-Seq: For HSC_Repl1 cellranger (v2.1.0) was used for demultiplexing and count matrix generation. For stimulation scRNA-Seq experiment Cellranger (v3.0.1) command ‘mkfastq’ was used to demutliplex raw base call (BCL) files into individual samples and separate cDNA fastq files and HTO surface fastq files. The cellranger ‘count’ command was used with default options to generate count matrices from cDNA fastq files.
scRNA-Seq: For HTO surface libraries, fastq files split into different lanes but from the same read (e.g. L001_R2, L002_R2) were combined using 'cat'. Reads shorter than 26bp were filtered using 'cutadapt'. CITE-Seq 'count' (version 1.4.3) was used to generate surface count by cell matrices from the HTO surface fastq libraries using the following barcodes: MPP - GGTCGAGAGCATTCA, MPP1 - ACCCACCAGTAAGAC, MPP2 - CTTGCCGCATGTCAT, MPP3/4 - AAGCATTCTTCACG and expected cell numbers per conditions: control - 5064 cells, dmPGE2 - 6497 cells, GCSF - 5297 cells, indo - 4665 cells and pIC - 5035 cells. Final pooled HTO/cDNA dataset including all stimulated HSC and MPP conditions is available here: https://mouse-hsc.cells.ucsc.edu.
scATAC-Seq: For scATAC-seq cellranger-atac mkfastq and count (1.2.0) was used for demultiplexing, alignment and generation of the fragment file. To generate the count matrix MACS2 was run with default parameters (keeping duplicates) on the aligned reads. Resulting peak summits were extended to 300 bp and this peak file was used to extract a count matrix from the fragment file via a custom script (see https://github.com/evafast/scrnaseq_paper).
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq matrixes are defined by barcode, features (both .tsv) and count matrix (.mtx)
Supplementary_files_format_and_content: scATAC-Seq count matrixes can be generated with peak (.bed) and fragments file (.tsv). Barcode file (.tsv) indicates cell identities and .csv file provides metadata.

source_name: FACS sorted bone marrow

growth_protocol: All cells were isolated from 9-12 week old male and female mice pooled at equal ratios. For treatment with niche stimulants and for scATAC-seq mice were ordered from Jackson Laboratories (C57BL/6J, #00664). Mice were kept for at least one week in the animal facility before initiating experiments. Control HSC replicate 1 (HSC_Repl1) is derived from the following mouse strain (Jackson Laboratories #016617) which carries a GFP transgene and was bred in house.

extract_protocol:
Whole Bone marrow was isolated from femur, tibia, hip and vertebrae via gentle crushing using a mortar and pestle. Stem and progenitor cells were enriched via lineage depletions (Miltenyi Biotech, 130-090-858). For treatment with niche stimulants cells were FAC-sorted  into the following populations: HSCs (Lin-, c-Kit+, Sca1+, CD48-, CD150+, CD34-), MPP1s (Lin-, c-Kit+, Sca1+, CD48-, CD150+, CD34+), MPPs (Lin-, c-Kit+, Sca1+, CD48-, CD150-), MPP2s (Lin-, c-Kit+, Sca1+, CD48+, CD150+), and MPP3/4s (Lin-, c-Kit+, Sca1+, CD48+, CD150-). Sorted MPPs were each labeled with different hashtag oligonucleotide (HTO) conjugated antibodies (Biolegend, TotalSeq™-A Cell Hashing). After 30min incubation cells were washed and the four MPP samples were pooled at equal ratios into a single MPP sample per condition (control, dmPGE2, pIC, GCSF, indo) for library preparation.
scRNA-Seq: Library for HSC_Repl1 were processed according to manufacturer’s recommendations (10X Genomics V2, CG00052 Rev B). Libraries were sequenced on a Next-seq 500 using a 75 cycle kit. Libraries for stimulated HSC and MPP scRNA-Seq samples were processed according to manufacturer’s recommendations (10X Genomics V3, CG000185 Rev B) through Post Gem-RT Cleanup – Dynabeads (step 2.1). At the cDNA amplification step (Step 2.2) an HTO additive primer was added to the amplification mix and steps 2.3A and 2.3B (using 70 µL of SPRI beads) were followed exactly to separate HTOs from cDNAs. cDNA library preparation was finished according to 10x Genomics recommendations. Purified HTO fraction was amplified using SI PCR primer and TruSeq D70x_s indexes according to HTO antibody manufacturer instructions (Biolegend).
scATAC-Seq: For ATAC-seq nuclei were isolated from HSCs and MPPs (pooled MPP, MPP1, MPP2 and MPP3/4) according to manufacturer's recommendations (CG000169 Rev D - Low Cell Input Nuclei Isolation). ScATAC-Seq libraries were prepared using manufacturers recommendations (10x Chromium Single Cell ATAC , CG000168 Rev B). ScRNA-Seq libraries form niche stimulation experiment and scATAC-Seq libraries were sequenced on a NOVAseq 6000 using a 100 cycle kit.

treatment_protocol: For the niche stimulation scRNA-Seq experiment the following treatments were used: Indomethacin (Sigma, 6mg/l) was administered for 7 days in acidified drinking water to maintain stability. Mice were injected with the following drugs and euthanized after 2 hours: Poly(I:C) HMW (Invivogen), IP injection 10mg/kg. G-CSF Recombinant Human Protein (Thermo fisher), IP injection, 0.25mg/kg. DmPGE2 (Cayman), SC injection, 2mg/kg.

value: HSC

value: control

tag: strain


title: HUc069post

value: liver biopsy


title: slful_VM2

value: meristem

value: slful


title: HK5 [miRNA-seq]

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
Raw data was demultiplexed with bcl2fastq (v2.20.0.422)
Raw fastq files were trimmed adapters using cutadapt (v1.12) and filtered low-quality reads using FASTX-Toolkit (0.0.14); Quality control of raw and clean reads were performed using FastQC (v0.11.5).
Clean reads were mapped to Atlantic salmon genome assembly ICSASG_v2 (GCF_000233375.1) by miRDeep package (v2.0.0.x) subcommand mapper.pl, mapped reads were counted by quantifier.pl from the same package with inputing salmon hairpin miRNA and mature miRNA sequences from miRBase (release 22).
Read counts were extracted and all samples were merged into one matrix
Differential miRNA expression analysis was performed using DESeq2 (v1.20.0), and plot visualization was achieved using R packages ggplot2 (v3.2.1) and pheatmap (v1.0.12).
Genome_build: ICSASG_v2
Supplementary_files_format_and_content: Tab-delimited matrix containing read counts of each individual samples

organism: Salmo salar

source_name: head kidney

growth_protocol: Atlantic salmon post smolts of about 70 g were purchased from a commercial producer (Sundsfjord Smolt, Nygårdsjøen, Norway) and maintained at the Research Station of Nord University, Bodø, Norway. Fish were fed a commercial feed (Ewos Micro, Ewos AS, Bergen, Norway) to satiation, and reared in a flow-through sea water system (temperature: 7-8°C, dissolved oxygen saturation: 87-92 %, 24-h light cycle). The fish (average 550g) were starved for 24 h and were sacrificed with an overdose of MS-222. Head kidney (HK) and distal intestine (DI) samples were then collected. Immune cells from head kidney (HK) and distal intestine (DI) were isolated and grown at 12°C in Leibovitz’s L-15 Medium. The osmolality of cell culture media was adjusted to 380 mOsm by adding a solution consisting of 5% (v/v) 0.41 M NaCl, 0.33 M NaHCO3 and 0.66 (w/v) D-glucose.

extract_protocol:
Total RNA was extracted from adherent intestinal cells (AICs) or adherent head kidney cells (AKCs) (< 500,000 cells) using PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The quality and quantity of the isolated total RNA were assessed using Agilent RNA high sensitivity screen tape kits and Bioanalyzer 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA).
Fifty ng from the extracted RNA that was used for mRNA sequencing was employed for library preparation using the NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific, Austin, Texas, United States) following the manufacturer’s protocol. Briefly, RNA was ligated with the NEXTflex 3’ 4N and 5’ 4N Adenylated adapters. Then, the RNA was reverse transcribed into first-strand cDNA. The cDNA was amplified with NEXTflex universal and barcoded primers on a thermocycler (Applied Biosystem Thermocycler, NY, United States) employing 25 cycles, and the conditions for each cycle were: 95 °C for 2 min; 95 °C for 20 s, 60 °C for 30 s, 72 °C for 15 s; 72 °C for 2 min. For PAGE size selection, 5 µL of 6X gel loading dye was added to each PCR product and the mixture was loaded on 10 % TBE-PAGE gel (Thermo Fisher Scientific, Oslo, Norway). Then, miRNA was isolated from the ~150 bp gel band. After size selection, the quality and quantity of individual libraries were ensured using Agilent RNA high sensitivity screen tape kits and Bioanalyzer 2200 TapeStation system.

treatment_protocol: The fish were starved for 24 h and were sacrificed with an overdose of MS-222 (80 mg/L). Head kidney (HK) and distal intestine (DI) samples were then collected. Immune cells from DI and HK were extracted and grown at 12°C in Leibovitz’s L-15 Medium (L-15). The isolated DI or HK leukocytes were allowed to adhere on a petri dish with 2 mL L-15+ for 2 days at 12°C. After removing the supernatant containing non-adherent cells, the adherent cells on petri dish were detached by washing three times with 1.5 mL ice-cold PBS supplemented with 5 mM EDTA. The cells were centrifuged (500 × g, 5 min, 4°C) and re-suspended with 2 mL L-15+.

value: adherent cells from head kidney


title: slful_VM1


title: miRNA-Seq: keloid fibroblasts with blank plasmid knock-down

city: Harbin

first: Yuhong

last: Wang

state: Heilongjiang

address: NO 23 Youzheng Street

country: China

institute: First Hospital of Harbin Medical University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: miRBase Release 22
Supplementary_files_format_and_content: Supplementary_files_format_and_content:

source_name: keloids

growth_protocol: Fresh excised keloid samples were immediately punched into mini cube explants for further grinding into tiny pieces and primarily cultured. All fresh keloid mini explants were washed with phosphate-buffered saline (PBS; Cultilab, SP, Brazil), penicillin (100 Ul/ml; Gibco, Carlsbad, CA, USA) and streptomycin (100 µm/ml; Gibco). Mini explants were incubated in Dulbecco’s modified Eagle’s medium (DMEM; Cultilab) for surface adherence. Consistent culture was conducted in DMEM adding 15% fetal bovine serum (FBS; Cultilab), penicillin (100 UI/ml; Gibco) and streptomycin (100 µg/ml; Gibco).

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.onymous patients affected with chronic keloids underwent keloid excision surgery. Keloid explants were collected from each patient under aseptic conditions. It was flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

treatment_protocol: Primary cultured keloid fibroblasts (Passages 2–3) were used for siRNA interference using transfection approach. All siRNAs were designed and offered as commercial products from Sigma-Aldrich (Shanghai, China). Three 100 nM siRNA plasmids targeting HOXA11-AS were simultaneously transfected into two keloid fibroblasts (samples 1 and 2) respectively. Normal keloid fibroblasts were overtaken as a blank sample 0. Significantly reduced expres- sion of HOXAS-11 was validated using real-time PCR between HOXA11-AS-knockdown keloid fibroblasts and normal keloid fibroblasts. Simultaneously, plasmids harboring scram- bled nonspecific RNAs were transinfected as a positive control (sample 3). A blank plasmid harboring no siRNA was transfected as a negative control (sample 4).

value: primary cultured keloid- derived fibroblasts

value: keloids

tag: disease state

value: three keloid patients

value: with blank plasmid knock-down


title: HK6 [miRNA-seq]


title: Placebo arm, before treatment w/ placebo, patient 14, condition sample 6, overall sample 27

description:
a6a.pla.t1.p14.ay027
Placebo arm, before treatment with placebo, patient 14, condition sample 6, overall sample 27

tag: patient #

value: placebo


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 13, condition sample 5, overall sample 26

description:
a5b.pla.t2.p13.ay026
Placebo arm, after daily treatment with placebo for 12 weeks, patient 13, condition sample 5, overall sample 26

tag: sample number for condition


title: HK4 [miRNA-seq]


title: miRNA-Seq: keloid fibroblasts with nonspecific plasmid knock-down

value: with nonspecific plasmid knock-down


title: slful_TM3


title: WT_FIM3

value: WT

value: FIM


title: Placebo arm, before treatment w/ placebo, patient 16, condition sample 8, overall sample 31

description:
a8a.pla.t1.p16.ay031
Placebo arm, before treatment with placebo, patient 16, condition sample 8, overall sample 31

tag: sample number overaal


title: Placebo arm, before treatment w/ placebo, patient 13, condition sample 5, overall sample 25

description:
a5a.pla.t1.p13.ay025
Placebo arm, before treatment with placebo, patient 13, condition sample 5, overall sample 25

tag: time


title: miRNA-Seq: keloid fibroblasts with HOXA11-AS knock-down 2

value: with HOXA11-AS knock-down


title: WT_FIM2


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 15, condition sample 7, overall sample 30

description:
a7b.pla.t2.p15.ay030
Placebo arm, after daily treatment with placebo for 12 weeks, patient 15, condition sample 7, overall sample 30

value: after 12 weeks of treatment


title: HK3 [miRNA-seq]


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 11,  condition sample 4, overall sample 22

description:
a4b.pla.t2.p11.ay022
Placebo arm, after daily treatment with placebo for 12 weeks, patient 11,  condition sample 4, overall sample 22


title: WT_FIM1


title: miRNA-Seq: keloid fibroblasts with HOXA11-AS knock-down


title: HK2 [miRNA-seq]


title: miRNA-Seq: keloid fibroblasts


title: WT_TM3

value: TM


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 8, condition sample 3, overall sample 16

description:
a3b.pla.t2.p8.ay016
Placebo arm, after daily treatment with placebo for 12 weeks, patient 8, condition sample 3, overall sample 16


title: Placebo arm, before treatment w/ placebo, patient 11, condition sample 4,  overall sample 21

description:
a4a.pla.t1.p11.ay021
Placebo arm, before treatment with placebo, patient 11, condition sample 4,  overall sample 21

value: before treatment


title: WT_TM2


title: Normal_Epcam+_BRPC-19-056

data_processing:
ATAC-seq data were processed using the pipeline developed in (Koh et al., 2016) with default parameters. 75 bp PE reads were trimmed to 50 bp PE using FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) before analysing them. Reads were aligned to mm10 (mouse) or GRCh38 (human) genome using Bowtie 2 (Langmead and Salzberg, 2012). Duplicate and mitochondrial reads were removed. And peaks were called using MACS2 software. Peaks were annotated using HOMER (Heinz et al., 2010).
Genome_build: mm10/GRCh38
Supplementary_files_format_and_content: Peak file

extract_protocol:
Mice were anaesthetised using Avertin. Skin and muscular layers were cut to expose the abdominal and thoracic cavities. Descending aorta was cut to exsanguinate and euthanise the animal. Cold PBS was perfused through the cardiac right ventricle to flush the blood out of the lungs. Lungs were then removed and inflated with 4% PFA and fixed overnight at 40C in PFA for histology. For isolation of live primary cells, lungs were instead inflated with lung/tumour dissociation buffer (Miltenyi Biotec), cut into small pieces and incubated at 370C for 30 minutes (normal lung) or 45 minutes (lung with neoplastic growth). A single cell suspension was obtained by mechanically dissociating using gentleMACS (Miltenyi Biotec) dissociator and passing the samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). To isolate AEC2 cells from CC mice, Lysotracker dye was used as described in (der Velden et al., 2013). Briefly, dissociated lung cells were resuspended in DMEM/F12 containing Lysotracker (1 µL dye in 14 mL medium) and incubated at 370C for 30 minutes. Human normal lung and cancer samples were stored on ice in DMEM/F12 medium supplemented with 2% FBS until dissociation. Samples were dissociated using human tumour dissociation kit (Miltenyi Biotec) following the manufacturer’s recommendation. A single cell suspension was obtained by passing the dissociated samples through a 70 µm filter. RBCs were lysed by resuspending the cells in ACK lysis buffer and leucocytes were depleted by using anti-CD45 microbeads (Miltenyi Biotec). Samples were resuspended in PBS supplemented with 10% FBS and incubated with anti-EpCAM antibodies for 10 minutes at room temperature. Samples were then washed once in PBS supplemented with 10% FBS. Primary cells were isolated by FACS using SONY SH800 sorter. Sytox dyes (Blue, Green, Red and AADvanced) were used to exclude dead cells.
Harvested primary cells were immediately used to prepare ATAC-seq libraries as described in (Buenrostro et al., 2013). Briefly, isolated cells were washed in PBS and resuspended in buffer containing transposase Tn5 and incubated at 370C for 30 minutes. Tagmented DNA was PCR amplified for 10-16 cycles. Mitochondrial DNA present in the libraries was cleaved using a CRISPR-Cas9 based method described in (Wu et al., 2016). sgRNA library targeting mitochondrial DNA was purchased from Addgene (#82480). In vitro transcription was performed to produce the gRNAs using MEGAshortscript Kit (Thermo Fisher Scientific). ATAC-seq libraries were treated with 10 µg Cas9 protein and 15 µg of sgRNA in a 40 µL reaction for 2 hours at 370C. The libraries were purified using Qiaquick PCR purification kit (Qiagen) and sequenced using Illumina Hi-Seq 2500 (50 bp paired end) or Next-Seq (75 bp paired end).

value: lung epithelial cell


title: Placebo arm, before treatment w/ placebo, patient 8, condition sample 3,  overall sample 15

description:
a3a.pla.t1.p8.ay015
Placebo arm, before treatment with placebo, patient 8, condition sample 3,  overall sample 15


title: DI5 [miRNA-seq]

source_name: distal intestine

value: adherent cells from distal intestine


title: WT_TM1

value: meristem


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 5, condition sample 2, overall sample 10

description:
a2b.pla.t2.p5.ay010
Placebo arm, after daily treatment with placebo for 12 weeks, patient 5, condition sample 2, overall sample 10


title: DI4 [miRNA-seq]


title: Normal_Epcam+_BRPC-18-529


title: DI3 [miRNA-seq]


title: Placebo arm, before treatment w/ placebo, patient 5, condition sample 2,  overall sample 9

description:
a2a.pla.t1.p5.ay009
Placebo arm, before treatment with placebo, patient 5, condition sample 2,  overall sample 9


title: WT_VM3

value: VM


title: WT_VM2


title: Placebo arm, after daily treatment w/ placebo for 12 wks, patient 3, condition sample 1, overall sample 6

description:
a1b.pla.t2.p3.ay006
Placebo arm, after daily treatment with placebo for 12 weeks, patient 3, condition sample 1, overall sample 6


title: Co01 spheroid cells_rep2

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

institute: Amsterdam UMC

description: Sample 2

data_processing:
All reads were mapped to the human genome (GRCh38) using HISAT2.
Gene counts (Ensembl build 92) were determined using the summarizeOverlaps function of the GenomicAlignments R package
Gene counts were normalized to FPKM (fragments per kilobase per million mapped fragments) using the DESeq2 R package
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Colorectal cancer tumor-derived spheroids

growth_protocol: Spheroid cultures were cultured in advanced DMEM/F12 (Thermo Fischer Scientific) supplemented with N2 supplement (Thermo Fischer Scientific), 2 mM L-glutamine (Lonza), 0.15% D-glucose (Sigma-Aldrich), 100 µM β-mercaptoethanol (Sigma-Aldrich), trace elements B and C (Thermo Fisher Scientific), 5 mM HEPES (Thermo Fisher Scientific), 2 µg/ml heparin (Sigma-Aldrich), 10 µg/ml insulin (Sigma-Aldrich), Epidermal Growth Factor (Peprotech, EGF, 50 ng/ml) and basic Fibroblast Growth Factor (Tebu-Bio, FGF, 10 ng/ml). Cultures were maintained in ultra-low adherent flasks (Corning) at 37 °C

extract_protocol:
Total RNA isolation was performed using the Nucleospin RNA isolation kit (Bioke) and duplicate RNA samples of Co01 cells were prepared for RNA sequencing. RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina as per manufacturer’s instructions and DNA sequencing was performed using the Illumina NextSeq 500 (GenomeScan, Leiden).

value: Colorectal cancer

value: spheroids


title: Co01 spheroid cells_rep1

description: Sample 1


title: WT_VM1


title: DI1 [miRNA-seq]


title: HK1 [miRNA-seq]

value: adherent cells from head kidney


title: DI6 [miRNA-seq]


title: PDX_Epcam+_14-405


title: DI2 [miRNA-seq]


title: Placebo arm, before treatment w/ placebo, patient 3, condition sample 1,  overall sample 5

description:
a1a.pla.t1.p3.ay005
Placebo arm, before treatment with placebo, patient 3, condition sample 1,  overall sample 5


title: Secretory floral nectary A [J.herrerae 1_0]

status: Public on Dec 21 2021

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description: RNA-Seq sample

data_processing:
Contigs assembled with Trinity v.2.12
Reads quantified using kallisto 0.46.1
Contigs mapped to Arabidopsis thaliana with NCBI’s blastn
Genome_build: N/A
Supplementary_files_format_and_content: Jaltomata_hp_tpms.xlsx

organism: Jaltomata herrerae

source_name: Nectary tissue

extract_protocol: Jaltomata procumbens and Jaltomata herrerae plants were grown in Sun Gro LC8 soil in the MAES/MDA Plant Growth Facilities at the University of Minnesota with typical daytime highs of 25C and nighttime lows of 15C. Three types of RNA samples were separately prepared in triplicate from the floral nectaries of both species, including: ‘pre-secretory’ (~24-48 hours prior to anthesis/nectar secretion), ‘secretory’ (full anthesis, at ~3-6 hours after dawn), and ‘post-secretory’ (after petal abscission). RNA from fully expanded leaf tissue was also isolated in triplicate for both species. All tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Thermo Fisher) with Plant RNA Isolation Aid (Thermo Fisher). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina NovaSeq 6000 sequencing. Twenty-four TruSeq stranded mRNA libraries were created (triplicate samples for nectaries at three timepoints each, as well as leaf tissue, for each species) and sequenced via 150 bp, paired-end runs on the NovaSeq 6000 using Rapid chemistry. All libraries were pooled and sequenced. All expected barcodes were detected and mean depth for the libraries was ≥ 20 M reads. The average quality scores were all above Q30.

value: Secretory floral nectary


title: Post-secretory floral nectary C [J.herrerae 2_2]

description: RNA-Seq sample

value: Post-secretory floral nectary


title: Leaf B [J.herrerae L_2]

description: RNA-Seq sample

source_name: Leaf tissue

value: Leaf


title: Pre-secretory floral nectary A [J.herrerae 0_0]

description: RNA-Seq sample

value: Pre-secretory floral nectary


title: Pre-secretory floral nectary C [J.herrerae 0_2]

description: RNA-Seq sample


title: Post-secretory floral nectary A [J.herrerae 2_0]

description: RNA-Seq sample


title: Secretory floral nectary B [J.herrerae 1_1]

description: RNA-Seq sample


title: TeloHAEC_CRISPRdel-SMAD3_S13

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 4.0.2.7.
The sequencing reads were processed using the nf-core RNA-seq pipeline (version 3.1; (Ewels et al. 2020)) with the hg38 genome. Genes with low expression were filtered out with the filterByExpr function of the edgeR package (version 3.24.3; (Robinson et al. 2010)) using minimum count 5 and minimum total count 15.
Genome_build: hg38
Supplementary_files_format_and_content: raw count matrix

source_name: aortic endothelial cell, immortalized

growth_protocol: Immortalized human aortic endothelial cells (teloHAECs) were purchased from ATCC and cultured in Vascular Cell Basal Medium (ATCC PCS-100-030), supplemented with Vascular Endothelial Cell Growth Kit-VEGF (ATCC PCS-100-041), 100 U/ml penicillin and 100 µg/ml streptomycin. Cells were incubated at 37°C in 5% CO2 and passaged every 3 days.

extract_protocol:
To analyze the efficiency of enhancer deletion, genomic DNA was extracted using NucleoSpin tissue kit (Macherey-Nagel, Düren, Germany) and amplified by PCR using specific primers flanking the deletion sites using DreamTaq DNA Polymerase (EP0701, Thermo Fisher Scientific). PCR products were then analyzed by electrophoresis in 1% agarose gel.  To analyze the effects of enhancer deletion on cis target gene expression, the RNA was extracted using RNeasyPlus Micro kit (QIAGEN).
RNA-Seq library preparation was carried out using QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) according to the manufacturer’s instructions. The resultant library was quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and its quality was checked with Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies). Individual libraries were pooled in equimolar ratio (4 nM total) and sequenced with the NextSeq 550 platform (Illumina, San Diego, California) with a single end high output kit using read length 86 cycles.

treatment_protocol: CRISPR-Cas9-mediated deletion of target regions was performed using the Alt-R CRISPR-Cas9 System (Integrated DNA technologies; IDT, Coralville, Iowa). Briefly, CRISPR-Cas9 single gRNAs flanking the target enhancers were designed using an online CRISPR design tool (https://eu.idtdna.com/site/order/designtool/index/CRISPR_SEQUENCE) and ordered from IDT as crRNAs. As controls, the negative control (non-targeting crRNA) and the positive control (crRNA targeting HPRT) from the Alt-R CRISPR-Cas9 Human Control Kit (IDT) were used. These crRNAs were annealed to a tracrRNA (IDT) and complexed with Cas9 endonuclease (S.p. HiFi Cas9 Nuclease V3; IDT) to form the ribonucleoprotein complex (RNP). The RNP complexes were then delivered into 150,000 teloHAEC cells per replicate by electroporation using the Neon transfection system (Invitrogen) with a 1350 V pulse of 30 ms width, following IDT CRISPR genome editing protocol for RNP electroporation with Neon Transfection system. Two days later, transfected cells were collected for RNA and gDNA extraction.

tag: cell line

value: teloHAEC

value: SMAD3 enhancer deletion

tag: experiment set

value: A


title: TeloHAEC_CRISPRdel-SMAD3_S10


title: TeloHAEC_CRISPRdel-series_B_pos_control_S64

value: CRISPR positive control

value: B


title: TeloHAEC_CRISPRdel-series_B_pos_control_S59


title: TeloHAEC_CRISPRdel-SMAD3_S11


title: TeloHAEC_CRISPRdel-SMAD3_S12


title: TeloHAEC_CRISPRdel-series_B_pos_control_S57


title: muscle_day3 of differentiation_Adeno m-cherry_rep4

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using Tac4.0.

label: Biotin

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno m-cherry 48hr treatment_rep4

label_protocol: 25 ng of total RNA is reverse transcribed following the Ovation PicoSL WTA System V2 (Tecan). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Tecan protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Tecan).

extract_protocol: The cells were collected and centrifuged. After centrifuge the pellet was lysed in RLT buffer with β-mercapto comes from the micro kit RNAeasy by Quiagen, used to extract RNA. The samples were all treated with DNAsi.

tag: tissue

value: adult muscle stem cells


title: muscle_day3 of differentiation_Adeno m-cherry_rep2

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno m-cherry 48hr treatment_rep2


title: Post-secretory floral nectary B [J.herrerae 2_1]

description: RNA-Seq sample


title: muscle_day3 of differentiation_Adeno CRE m-cherry_rep4

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno CRE m-cherry 48hr treatment_rep4


title: muscle_day3 of differentiation_Adeno CRE m-cherry_rep1

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno CRE m-cherry 48hr treatment_rep1


title: muscle_day3 of differentiation_Adeno m-cherry_rep1

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno m-cherry 48hr treatment_rep1


title: TeloHAEC_CRISPRdel-series_B_pos_control_S55


title: muscle_day3 of differentiation_Adeno CRE m-cherry_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno CRE m-cherry 48hr treatment_rep3


title: Leaf A [J.herrerae L_1]

description: RNA-Seq sample


title: muscle_day3 of differentiation_Adeno CRE m-cherry_rep2

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno CRE m-cherry 48hr treatment_rep2


title: Secretory floral nectary C [J.herrerae 1_2]

description: RNA-Seq sample


title: Pre-secretory floral nectary B [J.herrerae 0_1]

description: RNA-Seq sample


title: muscle_day3 of differentiation_Adeno m-cherry_rep3

source_name: skeletal muscle_primary myoblast isolated by FACS_day3 of differentiation_Adeno m-cherry 48hr treatment_rep3


title: TeloHAEC_CRISPRdel-series_B_neg_control_S67

value: CRISPR negative control


title: TeloHAEC_CRISPRdel-series_B_neg_control_S65


title: TeloHAEC_CRISPRdel-series_B_neg_control_S63


title: TeloHAEC_CRISPRdel-series_B_neg_control_S60


title: TeloHAEC_CRISPRdel-series_B_neg_control_S58


title: TeloHAEC_CRISPRdel-series_A_neg_control_S27


title: TeloHAEC_CRISPRdel-C2orf43_S54

value: C2orf43 (LDAH) enhancer deletion


title: TeloHAEC_CRISPRdel-series_A_neg_control_S31


title: TeloHAEC_CRISPRdel-C2orf43_S50


title: TeloHAEC_CRISPRdel-series_A_pos_control_S26


title: TeloHAEC_CRISPRdel-series_A_neg_control_S33


title: TeloHAEC_CRISPRdel-series_B_neg_control_S56


title: TeloHAEC_CRISPRdel-series_A_pos_control_S32


title: TeloHAEC_CRISPRdel-C2orf43_S53


title: TeloHAEC_CRISPRdel-C2orf43_S51


title: PEO1-OR, ATF6 shRNa, replicate 2

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

data_processing:
raw fastq files were uploaded to, aligned by, and differential genes were identified by BioJupies
Files were compressed in an HDF5 data package and uploaded to google cloud
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel File containing

growth_protocol: PEO1-OR cells were grown in RPMI 1640 with 10% fetal bovine serum and 1% Pen/Strep

extract_protocol:
Total RNA was extracting using the Qiagen RNAeasy kit
Illumina directional mRNA prep
per Novogene protocol for PE150 Illumina NGS

treatment_protocol: Cells were transduced with control or ATF6-targeting shRNA lentivirus and selected with 1ug/mL Puromycin

tag: cell type

value: Ovarian Cancer cell lines


title: TeloHAEC_CRISPRdel-series_A_pos_control_S30


title: PEO1-OR, control shRNA, replicate 2


title: PEO1-OR, control shRNA, replicate 1


title: TeloHAEC IL1b 24h rep2

data_processing:
Illumina sequencing run demultiplexing was carried out using the i5 index only, and the i7 index read (containing the UMI) was extracted as regular sequence read.
UMI-tools version 1.0.141 was used to remove any reads where the UMI did not match the expected sequence pattern RDHBVDHBVD.
The remaining reads with valid UMIs were aligned to a custom reference genome consisting of all the oligonucleotide sequences included in the library.
Alignment was performed with the STAR aligner by running the nf-core RNA-Seq pipeline version 1.4.2.
UMI deduplication was performed to the resulting BAM files using the UMI-tools default method.
Reads mapping uniquely and strand-specifically to a library oligonucleotide were summed using featureCounts (Subread Python package version 1.6.5).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw counts (UMI-deduplicated) for every sample and every oligonucleotide (sequence) in the STARR-Seq library.

source_name: teloHAEC

extract_protocol:
Cells were harvested 48 h post-transfection and total RNA was extracted using the RNeasy Midi Kit (Qiagen). PolyA RNA was purified from total RNA using Dynabeads Oligo(dT)25 beads (Invitrogen) with 2:1 bead to total RNA volume ratio. The isolated polyA RNA was treated with Turbo DNaseI (Ambion) and purified using RNeasy MinElute clean up kit (Qiagen).
Reverse transcription of reporter transcript mRNA was performed using a gene-specific primer containing a 10 nt unique molecular identified (UMI). After reverse transcription, RNA was remove by RNase A treatment and the cDNA was purified with AMPure XP beads using a 1.8:1 beads to cDNA ratio. The cDNA-s were amplified using a reporter-specific PCR amplicon targeting an exon-exon junction to minimize potential contribution from plasmid DNA. The junction PCR products were purified using AMPure XPbeads with beads to sample ratio of 0.8. A second PCR step was run to add the Illumina multiplexing indices for sequencing (NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 and 2). The final library PCR product was purified using SPRIselect beads (Beckman) with a bead to sample ratio of 0.8. Sequencing was performed on an Illumina NextSeq 500 platform as a paired-end dual-index run using the following read length setup: 37bp (insert sequence), 10bp (the UMI in place of the i7 index), 8bp (i5 index for Illumina demultiplexing), 37bp (insert sequence).

treatment_protocol: The STARR-Seq MPRA plasmid library was transfected into teloHAEC cells using the Neon transfection system (Invitrogen). Three independent replicate experiments were performed. For each replicate experiment, 9x10E7 cells were detached with trypsin, centrifuged, washed with PBS, and resuspended to Neon Resuspension Buffer R at 5x10E7 cells/ml. The cell suspension was mixed with 150 µg of STARR-Seq library plasmid DNA per ml of cell suspension and subjected to electroporation using the 100 µl Neon tip and three 1350V pulses of 10 ms width. The cells were allowed to recover from electroporation for 24 hours, after which they were separated into three groups for treatment with inflammatory stimulus (IL1β, 10 ng/ml) for either control (mock treatment), 6 h stimulus or 24 h stimulus.

value: immortalized human aortic endothelial cells

value: IL1b 24h

tag: replicate


title: Input library rep2

source_name: MPRA plasmid DNA library

tag: molecule subtype

value: plasmid DNA


title: TeloHAEC IL1b 24h rep3


title: Input library rep1


title: TeloHAEC IL1b 6h rep3

value: IL1b 6h


title: Input library rep3


title: PEO1-OR, ATF6 shRNA, replicate 1


title: TeloHAEC IL1b 24h rep1


title: TeloHAEC_CRISPRdel-series_A_pos_control_S28


title: TeloHAEC_CRISPRdel-series_B_neg_control_S61


title: TeloHAEC_CRISPRdel-series_A_neg_control_S29


title: TeloHAEC IL1b 6h rep2


title: TeloHAEC IL1b 6h rep1


title: TeloHAEC CTRL rep2

value: Control


title: TeloHAEC CTRL rep3


title: SA3-BM-CD235a+

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
Sequencing was done using the NextSeq 500/550 High Output Kit v2 (75 Cycles) (Illumina)
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 and Samtools --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.4a) and RSeQC (v2.6.4)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.24.0) were performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: bone marrow CD235a+ cells from XLSA patient

growth_protocol: For iPSCs, ReproCELL supplemented with bFGF at 37 ºC in a humidified incubator with 5% CO2. For hematopoietic differentiation, iPSCs were suspended in StemPro-34 media supplemented with glutamine, monothioglycerol, transferrin, and ascorbic acid. Cytokines and a chemical compound were utilized as follows during differentiation: on days 0-1, hBMP4 and Y27632; on days 1-4, hBMP4, hbFGF; on days 4-8, hVEGF, hbFGF, hIL-6, hIL-3, hIL-11, hSCF, and hFlt3L; and on days 8-15, hVEGF, hIL-6, hIL-3, hIL-11, hSCF, hFlt3L, hEPO; 4U/mL, and hTPO. For erythroid differentiation, FACS-sorted CD43+CD34+ iPSC-derived HPCs on day15 were plated onto OP9 cells and cultured and maintained with alpha-Minimum Essential Medium supplemented with 10% fetal calf serum, glutamine, monothioglycerol, transferrin, and ascorbic acid. The cytokines or chemical compound used during the differentiation were as follows: on days 15-20, hSCF, hFlt3L, hEPO, and hTPO; on days 20-27, hSCF and hEPO; and on days 27-34, hEPO and sodium ferrous citrate.

extract_protocol:
RNeasy Micro Kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

tag: differentiation stage

tag: genotype

value: mutant type

tag: sorting method

value: MACS CD235a+ sorting


title: TeloHAEC CTRL rep1

tag: treatment


title: MT1-erythroblasts-2

source_name: human iPSC derived CD235a+ erythroblasts

value: FACS CD235a+ sorting


title: MT1-erythroblasts-3

value: human iPSC derived CD235a+ erythroblasts


title: MT1-erythroblasts-4


title: contol-BM-CD235a+

source_name: bone marrow CD235a+ cells from healthy donor

value: wild type


title: MT1-erythroblasts-1


title: WT1-erythroblasts-2


title: MT1-CD43+CD34+CD38-Lin--4

source_name: human iPSC derived CD43+CD34+CD38-Lin- hematopoietic progenitor cells

value: FACS CD43+CD34+CD38-Lin- sorting


title: MT1-CD43+CD34+CD38-Lin--1

value: human iPSC derived CD43+CD34+CD38-Lin- hematopoietic progenitor cells


title: WT1-CD43+CD34+CD38-Lin--3


title: WT1-erythroblasts-1


title: WT1-CD43+CD34+CD38-Lin--1


title: MT1-CD34+-4

source_name: human iPSC derived CD34+ cells

value: human iPSC derived CD34+ cells

value: FACS CD34+ sorting


title: MT1-CD34+-3


title: WT1-CD43+CD34+CD38-Lin--2


title: MT1-CD34+-1


title: MT1-CD34+-2


title: WT1-CD34+-3


title: MT1-CD43+CD34+CD38-Lin--2


title: WT1-CD34+-2


title: MT1-iPSC4

source_name: human iPSCs

value: human iPSCs

value: iPSC

value: FACS TRA-1+ sorting


title: WT1-CD34+-1


title: MT1-iPSC3


title: WT1-erythroblasts-3


title: WT1-iPSC3


title: WT1-iPSC2


title: MT1-iPSC1


title: WT1-iPSC1


title: hiPSC-derived Neural Progenitors treated with Bezafibrate sample 3

city: Warsaw

first: Pawel

last: Gaj

address: Zwirki i Wigury 101

country: Poland

institute: Warsaw Genomics

description:
NPBEZ3
Sample from Experiment 3 of the hiPSC neural differentation

data_processing:
Reads were aligned using STAR version 2.5.3a.
Raw counts were calculated using htseq-count against Ensembl reference gennome GRCh38.88.
Normalized data counts (log2) were prepared using edgeR package in R.
Genome_build: GRCh38.88
Supplementary_files_format_and_content: Text file containing normalized read counts for all samples in the study.

growth_protocol: hiPSC (Gibco™ Human Epismal iPSC Line cat no. A18945 (ThermoFisherScientific)) was differentiated into the neural stem cells (NSC), early neural progenitos (eNP) and neural progenitors (NP) according to the protocol described by Augustyniak et al., 2017.

extract_protocol:
Total RNA was isolated from cells using ZR-Duet™ DNA/ RNA Mini Prep Kit (Zymo Rsearch) according to the manufacturers' protocols. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared with Truseq stranded mRNA (Illumina) for NGS the 1x76 bp Next Seq 500/550 high throughput 75 cycles reagent was used

treatment_protocol: hiPSC-derived Neural Progenitors (1 replicate from each 3 independent hiPSC neural differentiation) were treated with Idebenone (IDB) at dose 0.5 microM or 50 nM dose of Bezafibrate (BEZ) per 5 days according to the protocol described respectively at Augustyniak et al., 2017 and Augustyniak et al., 2019.

value: hiPSC (Gibco Human Epismal iPSC Line cat no. A18945 (ThermoFisherScientific))

tag: cell status

value: normal

tag: stage of neural differentiation

value: hiPSC differentiated into NP

value: treated with 50 nM of bezafibrate (Sigma-Aldrich) per 5 days


title: hiPSC-derived Neural Progenitors treated with Idebenone sample 3

description:
NPIDB3
Sample from Experiment 3 of the hiPSC neural differentation

value: treated with 0.5 microM of idebenone (Sigma-Aldrich) per 5 days


title: hiPSC-derived Neural Progenitors treated with Idebenone sample 2

description:
NPIDB2
Sample from Experiment 2 of the hiPSC neural differentiation


title: hiPSC-derived Neural Progenitors sample 3

description:
NP3
Sample from Experiment 3 of the hiPSC neural differentation

source_name: hiPSC-derived Neural Progenitors

value: untreated


title: hiPSC-derived Neural Progenitors treated with Bezafibrate sample 2

description:
NPBEZ2
Sample from Experiment 2 of the hiPSC neural differentiation


title: hiPSC-derived Neural Progenitors sample 2

description:
NP2
Sample from Experiment 2 of the hiPSC neural differentiation


title: hiPSC-derived early Neural Progenitors sample 3

description:
eNP3
Sample from Experiment 3 of the hiPSC neural differentation

source_name: hiPSC-derived early Neural Progenitors

value: hiPSC differenated into eNP


title: human Induced Pluripotent Stem Cells sample 1

description:
hiPSC1
Sample from Experiment 1 of the hiPSC neural differentation

source_name: human Induced Pluripotent Stem Cells

value: undifferentated hiPSC


title: hiPSC-derived Neural Stem Cells sample 1

description:
NSC1
Sample from Experiment 1 of the hiPSC neural differentation

source_name: hiPSC-derived Neural Stem Cells

value: hiPSC differenated into NSC


title: hiPSC-derived early Neural Progenitors sample 2

description:
eNP2
Sample from Experiment 2 of the hiPSC neural differentiation


title: hiPSC-derived Neural Progenitors sample 1

description:
NP1
Sample from Experiment 1 of the hiPSC neural differentation


title: human Induced Pluripotent Stem Cells sample 3

description:
hiPSC3
Sample from Experiment 3 of the hiPSC neural differentation


title: hiPSC-derived Neural Stem Cells sample 2

description:
NSC2
Sample from Experiment 2 of the hiPSC neural differentiation


title: hiPSC-derived Neural Stem Cells sample 3

description:
NSC3
Sample from Experiment 3 of the hiPSC neural differentation


title: MT1-iPSC2

value: mutant type


title: hiPSC-derived Neural Progenitors treated with Bezafibrate sample 1

description:
NPBEZ1
Sample from Experiment 1 of the hiPSC neural differentation


title: mouse_shCO_50K_2

city: PADOVA

first: SIRIO

last: DUPONT

state: PD

address: VIA BASSI 58/B

department: Department of Molecular Medicine

country: Italy

institute: University of Padua

data_processing:
trimming was performed using BBDuk from BBTools v38.87
alignment was performed with STAR 2.7.6a
quantification was performed with featureCounts 2.0.1
Genome_build: Mus Musculus GRCm38.p6 Ensembl release 102
Supplementary_files_format_and_content: raw_counts_matrix.txt is a TSV containing EnsemblID and raw counts for each condition

source_name: mouse cancer cell line

growth_protocol: D2.0R cells were routinely passaged in DMEM/F12 + 10% FBS (Corning T175 flasks)

extract_protocol:
Total RNA was isolated using a commercial kit (Norgen) with DNAse treatment to remove genomic contaminations.
Library generation was based on Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) with oligo-dT priming.
Sequencing was performed on a NextSeq500 ILLUMINA instrument and based on at least 5 million reads (75bp SE single end sequencing) for each sample.

treatment_protocol: Day 1: cells were trypsinized and seeded in full medium in 10cm-diameter tissue culture petri dishes (Corning Costar) or in 10cm-diameter petri dishes coated with poly-acrylamide hydrogels of defined stiffness (Matrigen Softwell Hydrogels). Day 2: cells were washed in ? and harvested

value: D2.0R metastatic dormant breast cancer cells

tag: strain

value: Balb/c

value: culture on 50kPa Collagen-I-coated acrylamide hydrogel


title: mouse_shCO_02K_2

value: culture on 0,2kPa Collagen-I-coated acrylamide hydrogel


title: mouse_shCO_02K_3


title: mouse_shCO_02K_1


title: mouse_shCO_50K_3


title: mouse_shCO_50K_1


title: hiPSC-derived Neural Progenitors treated with Idebenone sample 1

description:
NPIDB1
Sample from Experiment 1 of the hiPSC neural differentation


title: mouse_shCO_G_3

value: culture on tissue culture plastics


title: hiPSC-derived early Neural Progenitors sample 1

description:
eNP1
Sample from Experiment 1 of the hiPSC neural differentation


title: mouse_shCO_G_2


title: human Induced Pluripotent Stem Cells sample 2

description:
hiPSC2
Sample from Experiment 2 of the hiPSC neural differentiation


title: mouse_shCO_G_1


title: iWAT saline rep3

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

data_processing:
Quality control, quality and adapter trimming of RNA-seq libraries were performed with Trim Galore version 0.6.4_dev (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads were aligned with Rsubread version 2.6.2
Low counts genes were filtered with DEseq2 version 1.32.0
Differential expression analysis was performed with edgeR version 3.34.0
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file

source_name: mouse inguinal white adipose tissue

extract_protocol:
RNA was extracted using TRIzol (Invitrogen)
PolyA mRNA librairies were prepared from 200ng of total RNA using a NEB E6420 kit, according to the manufacturer's recommendations. Quality of the libraries was evaluated on a Bionalyzer DNA HS Chip (Agilent) and quantified using a Qubit fluorimeter (Invitrogen). The libraries were then pooled and sequenced on Illumina Nextseq500, PE40

treatment_protocol: mice were acclimated to 3 subcutaneous (s.c.) injections, distributed each 3 days, during 10 days of chow diet. For mice exposed to the GIP analogue, injections consisted of 2 pre-injections of saline followed by 1 sensitizer dose of (D-Ala2)GIP[Lys37PAL]. HFD was next introduced for 2 weeks during which mice received a total of 5 s.c. injections of saline or (D-Ala2)GIP[Lys37PAL] at 2 pmol/kg. Mice were then sacrificed and iWAT and eWAT dissected.

value: iWAT

value: saline

value: High Fat Diet introduced for 2 weeks


title: iWAT saline rep2


title: iWAT GIP rep1


title: iWAT saline rep1


title: eWAT GIP rep3

source_name: mouse epididymal white adipose tissue

value: eWAT


title: iWAT GIP rep2


title: iWAT GIP rep3


title: eWAT saline rep3


title: eWAT GIP rep1


title: eWAT saline rep2


title: eWAT GIP rep2


title: Mouse pool 6 : mTEChi knockout

city: Parkville

first: Gordon

last: Smyth

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Read-pairs were aligned to the mm10 genome using Rsubread version 1.24.1.
Read-pairs were counted for each Entrez Gene ID using Rsubread's featureCounts function and Rsubread's inbuilt mm10 gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with four columns. Columns give Entrez Gene ID, gene symbol, gene length and read count respectively. The supplementary file GenewiseCounts.txt.gz consolidates the read counts for all the samples into one file.

source_name: Thymic epithelial cells

extract_protocol:
RNA from sorted TEC subsets was isolated using the microRNeasy Micro Kit (Qiagen) with on-column DNase digestion according to manufacturer’s instructions.
First strand cDNA synthesis and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) according to the manufacturer’s instructions. Complementary DNA (cDNA) libraries were prepared and indexed separately using the Nextera XT DNA Library Preparation Kit (Illumina) following the manufacturer’s instructions. The indexed sample libraries were pooled and diluted to 1.5pM for 75 base paired-end sequencing on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per the manufacturer’s instructions.

tag: background mouse strain

value: Kat7 knockout

tag: mouse pool

tag: anatomical location

value: medullary

tag: mhcii level

value: high


title: Mouse pool 6 : cTEC knockout

value: cortical


title: Mouse pool 6 : mTEClo knockout

value: low


title: Mouse pool 5 : cTEC knockout


title: Mouse pool 4 : mTEChi knockout


title: Mouse pool 4 : mTEClo knockout


title: Mouse pool 3 : mTEClo wildtype

value: Wildtype


title: Mouse pool 3 : cTEC wildtype


title: Mouse pool 5 : mTEClo knockout