title: FGF1-4_colon

city: 温州

first: sudan

last: zhang

address: 瓯海

institute: wenzhou medical university

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package.
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change >= 2 or fold change =<0.5.
Assembly: GRCm38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: colon

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

value: colon


title: FGF1-1_colon

status: Public on Mar 10 2025

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: FGF1-2_colon


title: FGF1-3_colon


title: 351-4_colon

value: DSS


title: 351-3_colon


title: RNAseq_AtT_ERPax7_Tam24h_rep2

city: Montréal

first: Juliette

middle: Emilie

last: Harris

state: Québec

address: 110 avenue des Pins O

country: Canada

institute: IRCM

library_source: genomic

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 / GRCm38 reference genome using Hisat 2.2 (--no-unal --no-mixed --no-discordant).
Bam files were created using view (-b) from SAMtools 1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools 3.5
Gene expression was assessed by integrating reads mapped to exons over transcripts length and normalized across samples with the median of ratios method.
Assembly: mm10
Supplementary files format and content: Bigwig (unit: counts per million) and tsv (unit: normalized gene expression)

molecule: genomic DNA

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
RNA was extracted from 1,000,000 cells in culture using Qiagen RNeasy Plus Mini. Ribosomal depletion was performed by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

tag: cell line

tag: cell type

value: Corticotrope

tag: genotype

value: Tam 24h


title: 351-2_colon


title: 351-1_colon


title: C3_colon

value: control


title: Tumor cell line - biological rep 1

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Pre-processing of the input sequences was done with FastQC (v0.11.6) to assess reads quality and trimmomatic to get rid of low-quality sequences. Then, reads were aligned to the mouse genome assembly (GRCm38) using the STAR software (v2.7.6a) with standard parameters, and abundances were calculated using the Subread featureCounts function (v2.0.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: polyA RNA

source_name: AKTPF

extract_protocol:
RNA was extracted from pelleted cells or tissues using the miRNeasy plus mini Kit (Qiagen/74134).
RNA sample from cultured AKTPF, liver metastases, healthy liver, and intestine of 3 mice were sent to Azenta for library preparation and sequencing with Illumina NovaSeq 2x150bp sequencing.

value: AKTPF


title: C1_colon


title: Tumor cell line - biological rep 3


title: ChIP_AtT_ERPax7_5hmC_Tam48h_Mim60h

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing RPKM/BPM) from deepTools/3.3.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: fragments per million over 10 bp bins (fpkm) or counts per million (cpm)

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept for library preparation.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Tam 48h, Mim 60h


title: Liver metastases - biological rep 3

source_name: Liver mets

value: Liver mets


title: C4_colon


title: Tumor cell line - biological rep 2


title: Healthy liver control - biological rep 2

source_name: Liver

value: Liver


title: Liver metastases - biological rep 1


title: ChIP_AtT_ERPax7_5hmC_Tam1h

value: Tam 1h


title: Healthy intestine control - biological rep 3

source_name: small intestine

value: small intestine


title: Healthy liver control - biological rep 3


title: Healthy intestine control - biological rep 2


title: Liver metastases - biological rep 2


title: Healthy intestine control - biological rep 1


title: Healthy liver control - biological rep 1


title: TA33T.Combo

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.2.0 software (10X Genomics).
All samples were merged into a single object and processed to remove cells with a low sequencing quality, those with a feature count below 600 and above 9,000, as well as cells with a fraction of mitochondrial genes higher than 10%.
Samples were demultiplexed using the hashtag information using the Seurat function HTODemux, and cells classified as HTO doublets were filtered out. At the same time, the scDblFinder (v1.16.0) package was employed to annotate doublets of cells and exclude them from the following analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample
Supplementary files format and content: Tab-separated VDJ information for each barcode

source_name: Tumor

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing. Organs were smashed into small pieces and then incubated 15min at 37°C in agitation with a tissue digestion solution composed of 1 mL IMDM (Corning) supplemented with 0.35 mg/mL collagenase type IV (Sigma-Aldrich/ SCR103), 1 mg/ml dispase II (Gibco/ 17105041) and 0.2 mg/ml DNAse (Roche/ 11284932001). The tissue was then further dissociated by pipetting and filtered using 40 μm cell strainers (Corning/ 352340). Single cell solution was washed with 30 mL of autoMACS Running Buffer (Miltenyi Biotec/130-940 091-221) and pelleted for 5min 300g 4°C to remove excess enzymes. Samples were transferred to FACS tubes, stained with surface antibody and hashtags for sample identification. Then CD45+ cells were sorted.
Library was constructed using a microfluidics-based approach on Chromium Controller (10X Genomics) using the Chromium Next-GEM Single Cell 3’ Reagent Kit v2 (10X Genomics) according to the manufacturer’s instructions. For each mouse, 30,000 CD45+ cells were sorted.  We then loaded 20,000 cells belonging to 3 mice from the same group onto the Chromium Controller (10X Genomics).

value: Tumor

value: CD45+ cells


title: TA33L.Combo

description: 10X Genomics


title: Tumor, liOVA_IL12_INFa, rep2

description: 10X Genomics

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing. Organs were smashed into small pieces and then incubated 15min at 37°C in agitation with a tissue digestion solution composed of 1 mL IMDM (Corning) supplemented with 0.35 mg/mL collagenase type IV (Sigma-Aldrich/ SCR103), 1 mg/ml dispase II (Gibco/ 17105041) and 0.2 mg/ml DNAse (Roche/ 11284932001). The tissue was then further dissociated by pipetting and filtered using 40 μm cell strainers (Corning/ 352340). Single cell solution was washed with 30 mL of autoMACS Running Buffer (Miltenyi Biotec/130-940 091-221) and pelleted for 5min 300g 4°C to remove excess enzymes. Samples were transferred to FACS tube and stained with hashtag and surface antibodies. For he staining of TCRs specific for the SIINFEKL peptide loaded on MHC class I (H2-Kb), samples were stained with an SIINFEKL-loaded MHC class I tetramer.
Library was constructed using a microfluidics-based approach on Chromium Controller (10X Genomics) using the Chromium Next-GEM Single Cell 3’ Reagent Kit v2 (10X Genomics) according to the manufacturer’s instructions. For each mouse, 30,000 CD45+ cells were pooled together with up to 2,000 barcoded tetramer+ CD8+ T cells. We then loaded 20,000 cells belonging to distinct mice from the same group.


title: Liver, liOVA_IL12_INFa, rep2

description: 10X Genomics


title: TA33L

description: 10X Genomics


title: Liver, liOVA_IL12_INFa, rep1

description: 10X Genomics


title: Tumor, liOVA_IL12_INFa, rep1

description: 10X Genomics


title: Liver, liOVA

description: 10X Genomics

value: liOVA


title: TA33T

description: 10X Genomics


title: Tumor, liOVA

description: 10X Genomics


title: Tumor, liOVA_IFNa, rep2

description: 10X Genomics


title: C2_colon


title: Tumor, liOVA_IL12, rep2

description: 10X Genomics


title: Liver, liOVA_IFNa, rep2

description: 10X Genomics


title: Tumor, liOVA_IL12, rep1

description: 10X Genomics


title: OVA.Combo

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.2.0 software (10X Genomics).
All samples were merged into a single object and processed to remove cells with a low sequencing quality, those with a feature count below 600 and above 9,000, as well as cells with a fraction of mitochondrial genes higher than 10%.
Samples were demultiplexed using the hashtag information using the Seurat function HTODemux, and cells classified as HTO doublets were filtered out. At the same time, the scDblFinder (v1.16.0) package was employed to annotate doublets of cells and exclude them from the following analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample

extract_protocol:
Cells were sorted with the Flow cytometry (FC) before sequencing. Organs were smashed into small pieces and then incubated 15min at 37°C in agitation with a tissue digestion solution composed of 1 mL IMDM (Corning) supplemented with 0.35 mg/mL collagenase type IV (Sigma-Aldrich/ SCR103), 1 mg/ml dispase II (Gibco/ 17105041) and 0.2 mg/ml DNAse (Roche/ 11284932001). The tissue was then further dissociated by pipetting and filtered using 40 μm cell strainers (Corning/ 352340). Single cell solution was washed with 30 mL of autoMACS Running Buffer (Miltenyi Biotec/130-940 091-221) and pelleted for 5min 300g 4°C to remove excess enzymes. Samples were transferred to FACS tubes. For the staining of TCRs specific for the SIINFEKL peptide loaded on MHC class I (H2-Kb), samples were stained with an SIINFEKL-loaded MHC class I tetramer.
Library was constructed using a microfluidics-based approach on Chromium Controller (10X Genomics) using the Chromium Next-GEM Single Cell 3’ Reagent Kit v2 (10X Genomics) according to the manufacturer’s instructions. For each mouse, 30,000 CD45+ cells were pooled together with up to 2,000 barcoded tetramer+ CD8+ T cells. We then loaded 20,000 cells belonging to the same sample per reaction.

value: MC38 OVA

value: LV(OVA) + LV(INFa) + LV(IL-12)


title: Liver, liOVA_IL12, rep2

description: 10X Genomics


title: Liver, liOVA_IL12, rep1

description: 10X Genomics


title: Tumor, liOVA_IFNa, rep1

description: 10X Genomics


title: Liver, liOVA_IFNa, rep1

description: 10X Genomics


title: SIINFEKL

description: 10X Genomics


title: SIINFEKL.Combo

description: 10X Genomics

value: LV(li.SIINFEKL) + LV(INFa) + LV(IL-12)


title: OVA

description: 10X Genomics

value: LV(OVA)


title: WT4

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

data_processing:
Sequence alignment with the mouse genome (GRCm38), sequence counting and quality control were performed using the nf-core/rnaseq pipeline
RNA-seq data were analyzed using R Bioconductor (3.5.4) and DESeq2 package (1.40.1).
Assembly: GRCm38
Supplementary files format and content: Gene count in tsv format

source_name: Lung

extract_protocol:
Total RNA was extracted with the standard TRIzol RNA extraction protocol. RNA quality and quantity were evaluated using a 2100 bioanalyzer (Agilent) and the Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher, R11490).
One hundred nanograms of RNA was used to generate the libraries using the TruSeq Stranded mRNA kit (Illumina, 20020594). These libraries were sequenced on an Illumina NovaSeq sequencer on an SP flow cell.

treatment_protocol: Eighteen-week-old CD45.1/CD45.2 IMDTR mice were anesthetized and irradiated, then mice were reconstituted by i.v. administration of 107 BM cells from congenic Tgfbr2fl/fl (wild-type, WT) or Lyz2Cre Tgfbr2fl/fl (knock-out, KO) mice. After 1 month, CD45.1.2 Cx3cr1-DTR i.p injected 50ng DT. Lung interstitial macrophage were isolated from CD45.1.2 Cx3cr1-DTR after 10 days DT by sony MA900.

value: Lung

tag: strain

value: Macrophage

value: WT

tag: age

value: 12-16 Weeks

tag: Sex

value: female


title: K04

value: TgfBetar2 KO


title: WT3


title: WT2


title: CD45 cells, AB13086

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_invivo_p.txt

source_name: MC38 tumor

growth_protocol: MC38 cells were grown in full RPMI medium supplemented with 10 mM HEPES, 2 mM L-glutamine, 10% FBS, 1mM sodiumpyruvate, 1% P/S, 1x non-essential amino acids

extract_protocol:
Tumor-infiltrating leukocytes were isolated using mechanical (gentleMACS C tube, Miltenyi Biotec) enzymatic digestion (RPMI medium with 0.1 mg/ml DNase I (Sigma-Aldrich) and 1 mg/ml Collagenase IV (Sigma-Aldrich)) for 15 min at 37°C. Cells were strained through a 100 µm cell strainer, washed with ice-cold PBS-EDTA (0.2 mM EDTA, 0.5% BSA) and centrifuged for 5 min at 300 x g at 4°C and resuspendend in PBS-EDTA
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)
single-cell RNA-sequencing for gene expression quantitation

treatment_protocol: Mice with s.c. MC38 tumors were intratumorally injected with either 30 µl PBS or 2-3mg/kg CpG-siRNA conjugates every other day

value: MC38 tumor


title: CD45 cells, AB13082


title: CD45 cells, AB13079


title: CD45 cells, AB13081


title: CD45 cells, AB13080


title: CD45 cells, AB13084


title: CD45 cells, AB13085


title: CD45 cells, AB13078


title: CD45 cells, AB13077


title: CD45 cells, AB13076


title: CD45 cells, AB13074


title: CD45 cells, AB13075


title: CD45 cells, AB13073


title: K02


title: CD45 cells, AB13069


title: CD45 cells, AB13068


title: CD45 cells, AB13071


title: CD45 cells, AB13066


title: K03


title: K01


title: CD45 cells, AB13064


title: WT1


title: CD45 cells, AB13067


title: CD45 cells, AB13063


title: CD45 cells, AB13065


title: CD45 cells, AB13072


title: CD45 cells, AB13062


title: CD45 cells, AB13083


title: CD45 cells, AB13061


title: CD45 cells, AB13056


title: CD45 cells, AB13054


title: CD45 cells, AB13058


title: CD45 cells, AB13059


title: CD45 cells, AB13052


title: CD45 cells, AB13055


title: CD45 cells, AB13060


title: CD45 cells, AB13051


title: CD45 cells, AB13047


title: CD45 cells, AB13070


title: CD45 cells, AB13049


title: CD45 cells, AB13044


title: CD45 cells, AB13048


title: CD45 cells, AB13043


title: CD45 cells, AB13042

value: PBS


title: CD45 cells, AB13039


title: CD45 cells, AB13040


title: CD45 cells, AB13041


title: CD45 cells, AB13045


title: CD45 cells, AB13037


title: CD45 cells, AB13036


title: CD45 cells, AB13035


title: CD45 cells, AB13038


title: CD45 cells, AB13057


title: CD45 cells, AB13033


title: CD45 cells, AB13032


title: CD45 cells, AB13034


title: CD45 cells, AB13030


title: CD45 cells, AB13029


title: CD45 cells, AB13031


title: CD45 cells, AB13028


title: CD45 cells, AB13026


title: CD45 cells, AB13025


title: CD45 cells, AB13050


title: CD45 cells, AB13046


title: CD45 cells, AB13024


title: CD45 cells, AB13053


title: CD45 cells, AB12927

source_name: Tumor draining lymph node

value: Tumor draining lymph node


title: CD45 cells, AB12924


title: CD45 cells, AB13023


title: CD45 cells, AB13027


title: CD45 cells, AB12923


title: CD45 cells, AB12921


title: CD45 cells, AB12925


title: CD45 cells, AB12919


title: CD45 cells, AB12918


title: CD45 cells, AB12916


title: CD45 cells, AB12917


title: CD45 cells, AB12929


title: CD45 cells, AB12915


title: CD45 cells, AB12914


title: CD45 cells, AB12913


title: CD45 cells, AB12920


title: CD45 cells, AB12908


title: CD45 cells, AB12910


title: CD45 cells, AB12907


title: CD45 cells, AB12909


title: CD45 cells, AB12906


title: CD45 cells, AB12928


title: CD45 cells, AB12904


title: CD45 cells, AB12905


title: CD45 cells, AB12926


title: CD45 cells, AB12901


title: CD45 cells, AB12903


title: CD45 cells, AB12900


title: CD45 cells, AB12922


title: CD45 cells, AB12902


title: CD45 cells, AB12897


title: CD45 cells, AB12899


title: CD45 cells, AB12894


title: CD45 cells, AB12896


title: CD45 cells, AB12912


title: CD45 cells, AB12891


title: CD45 cells, AB12890


title: CD45 cells, AB12889


title: CD45 cells, AB12911


title: CD45 cells, AB12888


title: CD45 cells, AB12887


title: CD45 cells, AB12780


title: CD45 cells, AB12779


title: CD45 cells, AB12778


title: CD45 cells, AB12777


title: CD45 cells, AB12776


title: CD45 cells, AB12775


title: CD45 cells, AB12774


title: CD45 cells, AB12773


title: CD45 cells, AB12898


title: CD45 cells, AB12771


title: CD45 cells, AB12772


title: CD45 cells, AB12895


title: CD45 cells, AB12770


title: CD45 cells, AB12768


title: CD45 cells, AB12769


title: CD45 cells, AB12893


title: CD45 cells, AB12766


title: CD45 cells, AB12765


title: CD45 cells, AB12767


title: CD45 cells, AB12762


title: CD45 cells, AB12764


title: CD45 cells, AB12763


title: CD45 cells, AB12892


title: CD45 cells, AB12761


title: CD45 cells, AB12759


title: CD45 cells, AB12754


title: CD45 cells, AB12752


title: CD45 cells, AB12756


title: CD45 cells, AB12750


title: CD45 cells, AB12755


title: CD45 cells, AB12753


title: CD45 cells, AB12746


title: CD45 cells, AB12748


title: CD45 cells, AB12747


title: CD45 cells, AB12745


title: CD45 cells, AB12749


title: CD45 cells, AB12743


title: CD45 cells, AB12744


title: CD45 cells, AB12742


title: BMDMs, AB9387

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_KO_screen_p.txt

source_name: bone marrow derived macrophages

growth_protocol: 8 weeks old female CAS9-expressing C57BL/6 mice were sacrificed and bone marrow was isolated and cultured in the presence of human MCSF to generate BMDMs. Day 2 of culture, cells were transduced with lentiviruses expressing different guides in an arrayed screen fashion

extract_protocol:
24 hours after IL4 treatment, cells were isolated using Accutase and then washed and sorted in FACS to pre-prepared SPID-seq plates (Yofe et al. 2023)
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)
single-cell RNA-sequencing for gene expression quantitation

treatment_protocol: murine IL-4 was added to the cells on day 6 (20ng/ml)

value: bone marrow derived macrophages


title: BMDMs, AB9388


title: BMDMs, AB9385


title: BMDMs, AB9386


title: CD45 cells, AB12741


title: BMDMs, AB9384


title: BMDMs, AB9381


title: CD45 cells, AB12760


title: BMDMs, AB9380


title: BMDMs, AB9382


title: BMDMs, AB9383


title: BMDMs, AB9379


title: CD45 cells, AB12751


title: BMDMs, AB9376


title: BMDMs, AB9378


title: BMDMs, AB9373


title: BMDMs, AB9370


title: BMDMs, AB9372


title: BMDMs, AB9368


title: BMDMs, AB9369


title: BMDMs, AB9377


title: BMDMs, AB9375


title: BMDMs, AB9371


title: BMDMs, AB9364


title: BMDMs, AB9363


title: BMDMs, AB9374


title: BMDMs, AB9362


title: BMDMs, AB9360


title: BMDMs, AB9359


title: BMDMs, AB9357


title: BMDMs, AB9358


title: BMDMs, AB9366


title: BMDMs, AB9356


title: BMDMs, AB9355


title: BMDMs, AB9354


title: BMDMs, AB9353


title: BMDMs, AB9352


title: BMDMs, AB9351


title: BMDMs, AB9349


title: BMDMs, AB9350


title: BMDMs, AB9348


title: BMDMs, AB9347


title: BMDMs, AB9346


title: BMDMs, AB9367


title: BMDMs, AB9365


title: BMDMs, AB9341


title: BMDMs, AB9342


title: BMDMs, AB9339


title: BMDMs, AB9345


title: BMDMs, AB9340


title: BMDMs, AB9336


title: BMDMs, AB9338


title: BMDMs, AB9335


title: BMDMs, AB9333


title: BMDMs, AB9332


title: BMDMs, AB9331


title: BMDMs, AB9328


title: BMDMs, AB9330


title: BMDMs, AB9329


title: BMDMs, AB9323


title: BMDMs, AB9327


title: BMDMs, AB9322


title: BMDMs, AB9326


title: BMDMs, AB9325


title: BMDMs, AB9324


title: BMDMs, AB9319


title: BMDMs, AB9320


title: BMDMs, AB9318


title: BMDMs, AB9321


title: BMDMs, AB9317


title: BMDMs, AB9344


title: BMDMs, AB9315


title: BMDMs, AB9343


title: BMDMs, AB9314


title: BMDMs, AB9313


title: BMDMs, AB9316


title: BMDMs, AB9334


title: BMDMs, AB9312


title: BMDMs, AB9310


title: BMDMs, AB9309


title: BMDMs, AB9311


title: BMDMs, AB9307


title: BMDMs, AB9308


title: BMDMs, AB9306


title: BMDMs, AB9305


title: BMDMs, AB9303


title: BMDMs, AB9302


title: BMDMs, AB9304


title: BMDMs, AB9301


title: BMDMs, AB9299


title: BMDMs, AB9296


title: BMDMs, AB9295


title: BMDMs, AB9293


title: BMDMs, AB9292


title: BMDMs, AB9298


title: BMDMs, AB9294


title: BMDMs, AB9291


title: BMDMs, AB9290


title: BMDMs, AB9300


title: BMDMs, AB9297


title: BMDMs, AB9288


title: BMDMs, AB9287


title: BMDMs, AB9283


title: BMDMs, AB9286


title: BMDMs, AB9281


title: BMDMs, AB9280


title: BMDMs, AB9282


title: BMDMs, AB9289


title: BMDMs, AB9279


title: BMDMs, AB9284


title: BMDMs, AB9276


title: BMDMs, AB9278


title: BMDMs, AB9275


title: BMDMs, AB9277


title: BMDMs, AB9274


title: BMDMs, AB9271


title: BMDMs, AB9273


title: BMDMs, AB9268


title: BMDMs, AB9266


title: BMDMs, AB9270


title: BMDMs, AB9267


title: BMDMs, AB9263


title: BMDMs, AB9261


title: BMDMs, AB9264


title: BMDMs, AB9265


title: BMDMs, AB9285


title: BMDMs, AB9255


title: BMDMs, AB9253


title: BMDMs, AB9260


title: BMDMs, AB9251


title: BMDMs, AB9254


title: BMDMs, AB9252


title: BMDMs, AB9259


title: BMDMs, AB9250


title: BMDMs, AB9258


title: BMDMs, AB9256


title: BMDMs, AB9272


title: BMDMs, AB9257


title: BMDMs, AB9247


title: BMDMs, AB9249


title: BMDMs, AB9244


title: BMDMs, AB9245


title: BMDMs, AB9246


title: BMDMs, AB9243


title: BMDMs, AB9241


title: BMDMs, AB9262


title: BMDMs, AB9239


title: BMDMs, AB9248


title: BMDMs, AB9240


title: BMDMs, AB9237


title: BMDMs, AB9238


title: BMDMs, AB9235


title: BMDMs, AB9234


title: BMDMs, AB9236


title: BMDMs, AB9233


title: BMDMs, AB9232


title: BMDMs, AB9230


title: BMDMs, AB9231


title: BMDMs, AB9229


title: BMDMs, AB9228


title: BMDMs, AB9224


title: BMDMs, AB9223


title: BMDMs, AB9227


title: BMDMs, AB9221


title: BMDMs, AB9225


title: BMDMs, AB9222


title: BMDMs, AB9218


title: BMDMs, AB9220


title: BMDMs, AB9242


title: BMDMs, AB9226


title: BMDMs, AB9217


title: BMDMs, AB9219


title: BMDMs, AB9214


title: BMDMs, AB9213


title: BMDMs, AB9212


title: BMDMs, AB9211


title: BMDMs, AB9209


title: BMDMs, AB9210


title: BMDMs, AB9208


title: BMDMs, AB9207


title: BMDMs, AB9216


title: BMDMs, AB9215


title: BMDMs, AB9203


title: BMDMs, AB9205


title: cd1

city: Bethesda

first: Joana

middle: A

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

country: USA

institute: NIH/NCI

description: Library name: Sample 4

data_processing:
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library. Sequencing was performed on NextSeq 2000 with PE100 sequencing. Reads were trimmed using cutadapt (v 4.7) and mapped to GRCm39 genome using STAR aligner (2.7.11b). Read alignments were counted using Subread featureCounts (v 2.0.3). Differentially expressed genes were identified with DEseq2 (R 3.6.0).
Assembly: GRCm39
Supplementary files format and content: Gene_counts.txt, count table

source_name: Placenta

extract_protocol:
RNA was isolated from E18.5 Ago2+/+ and Ago2D598A/D598A placentas using TRIzol reagent (Thermo Fisher Scientific #15596018) and treated with TURBO DNA-free kit (Thermo Fisher Scientific #AM1907)
Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing

value: Placenta

tag: developmental stage


title: BMDMs, AB9202


title: BMDMs, AB9204


title: wt3

description: Library name: Sample 3


title: BMDMs, AB9206


title: P0+8d, purmorphamine-treated Pparg-cKO vs DMSO-treated Pparg-cKO, repl. #1

type: RNA

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2500 ng of each fluorescently labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values (for each channel independently) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:  normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: DMSO-treated Pparg-cKO

label_protocol: 200 ng of total RNA equivalents were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1), reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using the RNeasy kit (QIAGEN) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from P0 pups and cultured on transwell membranes for 8 d in medium contraining 2 µM purmorphamine or in medium without purmorphamine.

value: NMRI

value: Pax2-cre/+; Pparg (fl/fl)

value: male

tag: Stage

tag: culture period

value: 8 d

value: ureter

source_name: purmorphamine-treated Pparg-cKO

value: 2 µM purmorphamine


title: cd3

description: Library name: Sample 6


title: wt1

description: Library name: Sample 1


title: wt2

description: Library name: Sample 2


title: BMDMs, AB9200


title: LL76, low light conditions (20 µmol-2.s-1), standard temperature (21 °C), replica 2

city: Gent

first: Marieke

last: Dubois

address: Technologiepark 71

institute: PSB, Vlaams Instituut voor Biotechnologie (VIB)

data_processing:
FastQC (Qalaxy Version 0.65)
Trimmomatic (Galaxy version 0.32.3 )
Salmon (Galaxy version 0.72)
Assembly: TAIR10
Supplementary files format and content: Each "sampleX_XXX.tabular" contains the normalized counts (Transcripts Per Million) per sample.

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: A.thaliana seeds were surface sterilized in ethanol, and stratified  for three days (4 °C, dark conditions). Seedlings were cultivated in AR-36L growth chambers (Percival Scientific Inc, Perry, IA, USA) under short-day photoperiod (65% relative humidity; 21/19 °C day/night temperatures, photon flux density (PPFD) 100 µmol.m-2.s-1 provided by fluorescent tubes Philips TL-D) using an Araponics hydroponic system (Araponics, Liege Belgium) in a half-strength Murashige and Skoog media

extract_protocol:
RNeasy Plant Mini kit (Qiagen)
The library construction was performed at the Nucleomics Core Facility (VIB, Leuven, Belgium, www.nucleomics.be). Library preparation was performed with the RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Plants that reached the growth stage L(1.06) were divided into four sub-groups (>42) and cultivated at the following conditions: (i) S-PPFD at (100 µmol.m-2 .s-1 ), 21°C (S); (ii) low-PPFD (at 20 µmol.m-2 .s-1 ; LL), 21 °C; (iii) S-PPFD at 4°C (C) and (iv) low-PPFD, 4°C (CLL) and harvested after 3 hours of treatment

value: Leaf

value: Col-0, wild type

value: low light conditions, (20 umol.m-2.s-1), standard temperature (21 °C)


title: LL13, low light conditions, (20 µmol-2.s-1), standard temperature (21 °C), replica 1


title: E18.5 ureters, Pparg-cKO vs control, rep2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2500ng of each fluorescently labelled cRNA were used for hybridization.

source_name: control 2

label_protocol: 200ng of total RNA were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E18.5 embryos.

value: Pparg(fl/?)

source_name: Pparg-cKO 2

value: Pax2-cre/+; Pparg(fl/fl)


title: E18.5 ureters, Pparg-cKO vs control, rep1

source_name: control 1

value: female

source_name: Pparg-cKO 1


title: P0+8d, purmorphamine-treated control vs DMSO-treated control, repl. #1

source_name: DMSO-treated control 1

value: Pparg (fl/?)

source_name: purmorphamine-treated control


title: BMDMs, AB9199


title: E16.5 ureters, Pparg-cKO vs control, rep1

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2300ng of each fluorescently labelled cRNA were used for hybridization.

label_protocol: 50ng of total RNA were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and reaction volumes were halved, and just one round of T7 amplification was conducted.

treatment_protocol: Ureters were mechanically dissected from E16.5 embryos.


title: LL139, low light conditions (20 µmol-2.s-1), standard temperature (21 °C), replica 3


title: P0+8d, purmorphamine-treated control vs DMSO-treated control, repl. #2

source_name: DMSO-treated control 2


title: P0+8d, purmorphamine-treated Pparg-cKO vs DMSO-treated Pparg-cKO, repl. #2


title: BMDMs, AB9197


title: CON10, standard light conditions (100 µmol-2.s-1), standard temperature  (21 °C), replica 1

value: standard light conditions (100 umol.m-2.s-1), standard temperature (21 °C)


title: cd2

description: Library name: Sample 5


title: BMDMs, AB9195


title: CON136, standard light conditions (100 µmol-2.s-1), standard temperature  (21 °C), replica 3


title: BMDMs, AB9196


title: CL138, low light conditions, (20µmol-2.s-1), low temperature (4 °C), replica 3

value: low light conditions, (20 umol.m-2.s-1), low temperature (4 °C)


title: BMDMs, AB9194

value: bone marrow derived macrophages


title: BMDMs, AB9192


title: E16.5 ureters, Pparg-cKO vs control, rep2


title: CON73, standard light conditions (100 µmol-2.s-1), standard temperature  (21 °C), replica 2


title: C74, standard light conditions (100 µmol-2.s-1), low temperature (4 °C), replica 2

value: standard light conditions (100 umol.m-2.s-1), low temperature (4 °C)


title: C137, standard light conditions (100 µmol-2.s-1), low temperature (4 °C), replica 3


title: BMDMs, AB9191


title: BMDMs, AB9198


title: CL12, low light conditions, (20 µmol-2.s-1), low temperature (4 °C), replica 1


title: BMDMs, AB9187


title: BMDMs, AB9185


title: BMDMs, AB9186


title: BMDMs, AB9184


title: BMDMs, AB9189


title: C11, standard light conditions (100 µmol-2.s-1, low temperature (4 °C), replica 1


title: BMDMs, AB9182


title: BMDMs, AB9181


title: CL75, low light conditions, (20 µmol-2.s-1), low temperature (4 °C), replica 2


title: BMDMs, AB9180


title: BMDMs, AB9193


title: BMDMs, AB9179


title: BMDMs, AB9201


title: BMDMs, AB9178


title: BMDMs, AB9176


title: BMDMs, AB9177


title: BMDMs, AB9174


title: BMDMs, AB9175


title: BMDMs, AB9172


title: BMDMs, AB9190


title: BMDMs, AB9170


title: AML Patient 30862

city: Toronto

first: Andy

last: Zeng

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre

description:
Library name: MLL_30862
10X Genomics

data_processing:
Single cell RNA-seq data were aligned and quantified using the Cell Ranger (v5.0.1) pipeline against genome GRCh38.
Assembly: hg38
Supplementary files format and content: Filtered count matrices from Cell Ranger (v5.0.1).

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
Frozen mononuclear cells from AML samples were thawed, counted and enriched for live cells by depletion of dead cells (Miltenyi Biotec, catalog number 130-090-101). Isolated live cells were washed three times with 1X Phosphate-Buffered Saline (PBS, calcium and magnesium free) containing 0.04% weight/volume BSA (Thermo Fisher Scientific, catalog number AM2616) and automatedly counted by the Countess 3 Automated Cell Counter (Thermo Fisher Scientific) and manually by the Neubauer hemocytometer.
From each sample, we calculated the volume of cells to load to have a desired recovery target of 8,000-10,000 cells and loaded on Chromium Next GEM Chip G (10X Genomics; PN-2000177) with reagents from Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 (10X Genomics; PN-1000165), following standard manufacturer's protocols for gel beads-in-emulsion (GEMs) generation, barcoding, cDNA amplification and gene expression library construction. Final library quality was assessed using High Sensitivity D1000 ScreenTape (5067- 5584) with High Sensitivity D1000 Reagents (5067- 5585) at the Agilent 2200 TapeStation system. Illumina-ready dual index libraries were sequenced at the recommended depth and aiming at 50,000 reads/cell at the Hartwell Center at St Jude Children’s Research Hospital (SJCRH) on the Illumina NovaSeq according to manufacturer's recommendations.

value: Bone marrow

tag: disease

value: AML

value: Male


title: BMDMs, AB9188


title: BMDMs, AB9169


title: BMDMs, AB9171


title: AML Patient 29538

description:
Library name: MLL_29538
10X Genomics

value: Female


title: BMDMs, AB9168


title: BMDMs, AB9183


title: AML Patient 29512 (Patient Derived Xenograft)

description:
Library name: MLL_29512_PDX
10X Genomics


title: BMDMs, AB9165


title: BMDMs, AB9166


title: AML Patient 29532

description:
Library name: MLL_29532
10X Genomics


title: AML Patient 28855

description:
Library name: MLL_28855
10X Genomics

value: Acute erythroid leukemia (AEL)


title: BMDMs, AB9164


title: AML Patient 28830

description:
Library name: MLL_28830
10X Genomics


title: AML Patient 28824

description:
Library name: MLL_28824
10X Genomics


title: BMDMs, AB9173


title: AML Patient 17844

description:
Library name: MLL_17844
10X Genomics


title: BMDMs, AB9161


title: AML Patient 30886

description:
Library name: MLL_30886
10X Genomics


title: AML Patient 16703

description:
Library name: MLL_16703
10X Genomics


title: BMDMs, AB9158


title: AML Patient 17746

description:
Library name: MLL_17746
10X Genomics


title: IE_SE12_5

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

description: Library name: DSP-1001660009542-G-H05

library_source: other

data_processing:
DCC files generated from raw fastq sequencing data was converted to GeomxTools class oject in R, followed by quaility control, data normalizaton, unsupervised analysis, differential expressed gene identification and data visulization
Assembly: nanostring whole gene transcripts panel (not align to genome)
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: gene panel file
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Colon

extract_protocol:
After incubation and hybridization of the GeoMx reagents along with visualization reagents to slide-mounted formalin-fixed paraffin-embedded tissue, the DSP scans the slides and presents a high-quality image for region of interest (ROI) selection guided by immunofluorescent marker positivity. The oligonucleotide tags are released from user-selected regions of the tissue with focused UV light based on the user region and segmentation selections. The digital micromirror device of the DSP instrument tunes the UV light with 1-μm resolution, allowing great flexibility for region selection including irregularly shaped and noncontinuous segments.
library was sequenced on Illumina Novaseq6000 sequencer with paired end 50nt mode

value: Colon

value: Neutrophils

tag: batch

value: raw


title: BMDMs, AB9160


title: AML Patient 17843

description:
Library name: MLL_17843
10X Genomics


title: LP12_3

description: Library name: DSP-1001660009542-G-H01


title: IE_SE12_4

description: Library name: DSP-1001660009542-G-H03


title: BMDMs, AB9159


title: BMDMs, AB9167


title: AML Patient 14666

description:
Library name: MLL_14666
10X Genomics

value: Acute Myeloid Leukemia (AML)


title: IE_SE12_2

description: Library name: DSP-1001660009542-G-G11


title: BMDMs, AB9157


title: BMDMs, AB9154


title: BMDMs, AB9155


title: LP11_5

description: Library name: DSP-1001660009542-G-F11


title: BMDMs, AB9152


title: IE_SE12_1

description: Library name: DSP-1001660009542-G-G09


title: IE_SE11_3

description: Library name: DSP-1001660009542-G-F07


title: BMDMs, AB9153


title: BMDMs, AB9163


title: BMDMs, AB9151


title: BMDMs, AB9162


title: IE_SE11_4

description: Library name: DSP-1001660009542-G-F09


title: BMDMs, AB9150


title: BMDMs, AB9149


title: IE_SE11_2

description: Library name: DSP-1001660009542-G-F05


title: IE_SE11_1

description: Library name: DSP-1001660009542-G-F03


title: IE_SE10_4

description: Library name: DSP-1001660009542-G-E11


title: BMDMs, AB9156


title: IE_SE10_3

description: Library name: DSP-1001660009542-G-E09


title: BMDMs, AB9147


title: IE_SE10_5

description: Library name: DSP-1001660009542-G-F01


title: BMDMs, AB9148


title: BMDMs, AB9146


title: BMDMs, AB9145


title: BMDMs, AB9144


title: BMDMs, AB9143


title: IE_SE10_2

description: Library name: DSP-1001660009542-G-E07


title: BMDMs, AB9142


title: BMDMs, AB9141


title: LP9_4

description: Library name: DSP-1001660009542-G-E01


title: BMDMs, AB9140


title: BMDMs, AB9139


title: LP9_2

description: Library name: DSP-1001660009542-G-D09


title: BMDMs, AB9137


title: IE_SE8_5

description: Library name: DSP-1001660009542-G-C07


title: IE_SE8_4

description: Library name: DSP-1001660009542-G-C05


title: BMDMs, AB9138


title: IE_SE8_3

description: Library name: DSP-1001660009542-G-C03


title: LP9_1

description: Library name: DSP-1001660009542-G-D07


title: BMDMs, AB9135


title: BMDMs, AB9134


title: IE_SE8_2

description: Library name: DSP-1001660009542-G-C01


title: IE_SE8_1

description: Library name: DSP-1001660009542-G-B11


title: IE_SE10_1

description: Library name: DSP-1001660009542-G-E05


title: BMDMs, AB9133


title: BMDMs, AB9132


title: BMDMs, AB9131


title: LP9_5

description: Library name: DSP-1001660009542-G-E03


title: IE_SE7_5

description: Library name: DSP-1001660009542-G-B09


title: IE_SE7_3

description: Library name: DSP-1001660009542-G-B05


title: LP7_4

description: Library name: DSP-1001660009542-G-B07


title: BMDMs, AB9130


title: BMDMs, AB9129


title: IE_SE7_1

description: Library name: DSP-1001660009542-G-B01


title: IE_SE7_2

description: Library name: DSP-1001660009542-G-B03


title: BMDMs, AB9128


title: LP6_4

description: Library name: DSP-1001660009542-G-A11


title: LP9_3

description: Library name: DSP-1001660009542-G-D11


title: BMDMs, AB9127


title: BMDMs, AB9136


title: IE_SE6_2

description: Library name: DSP-1001660009542-G-A07


title: IE_SE6_3

description: Library name: DSP-1001660009542-G-A09


title: BMDMs, AB9123


title: BMDMs, AB9124


title: BMDMs, AB9122


title: LP6_1

description: Library name: DSP-1001660009542-G-A03


title: BMDMs, AB9121


title: IE_SE5_4

description: Library name: DSP-1001660009541-F-G08


title: IE_SE5_5

description: Library name: DSP-1001660009541-F-G10


title: BMDMs, AB9120


title: IE_SE5_3

description: Library name: DSP-1001660009541-F-G06


title: BMDMs, AB9119


title: IE_SE5_1

description: Library name: DSP-1001660009541-F-G02


title: BMDMs, AB9118


title: IE_SE4_6

description: Library name: DSP-1001660009541-F-F12


title: LP5_2

description: Library name: DSP-1001660009541-F-G04


title: IE_SE4_5

description: Library name: DSP-1001660009541-F-F10


title: IE_SE4_4

description: Library name: DSP-1001660009541-F-F08


title: BMDMs, AB9114


title: IE_SE4_2

description: Library name: DSP-1001660009541-F-F04


title: BMDMs, AB9113


title: BMDMs, AB9112


title: IE_SE4_3

description: Library name: DSP-1001660009541-F-F06


title: BMDMs, AB9117


title: BMDMs, AB9111


title: BMDMs, AB9126


title: LP3_5

description: Library name: DSP-1001660009541-F-E02


title: IE_SE4_1

description: Library name: DSP-1001660009541-F-F02


title: BMDMs, AB9110


title: BMDMs, AB9109


title: LP3_3

description: Library name: DSP-1001660009541-F-D10


title: LP3_4

description: Library name: DSP-1001660009541-F-D12


title: BMDMs, AB9108


title: BMDMs, AB9107


title: LP3_2

description: Library name: DSP-1001660009541-F-D08


title: LP3_1

description: Library name: DSP-1001660009541-F-D06


title: BMDMs, AB9106


title: BMDMs, AB9115


title: IE_SE2_5

description: Library name: DSP-1001660009541-F-A10


title: IE_SE2_4

description: Library name: DSP-1001660009541-F-A08


title: IE_SE2_3

description: Library name: DSP-1001660009541-F-A06


title: BMDMs, AB9105


title: BMDMs, AB9104


title: BMDMs, AB9103


title: BMDMs, AB9102


title: IE_SE2_2

description: Library name: DSP-1001660009541-F-A04


title: BMDMs, AB9101


title: BMDMs, AB9100


title: LP1_4

description: Library name: DSP-1001660009540-E-A09


title: IE_SE1_5

description: Library name: DSP-1001660009540-E-A11


title: LP1_3

description: Library name: DSP-1001660009540-E-A07


title: BMDMs, AB9098


title: LP1_2

description: Library name: DSP-1001660009540-E-A05


title: IE_SE1_1

description: Library name: DSP-1001660009540-E-A03


title: BMDMs, AB9097


title: BMDMs, AB9096


title: IPF-derived airway organoids_#3_DQzG_5uM_72h

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA77416

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT2 ver.2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: lung

extract_protocol:
Total RNA was isolated from  NHBE cells and IPF-derived airway organoids with RNAiso Plus reagent (Cat. #9109, Takara, Shiga, Japan) following the manufacturer’s instruction.
The reverse transcription to cDNA was performed using GenNext RamDA-seq Single Cell Kit and the library was prepared using Nextera XT DNA Library Preparation Kit.

value: lung

value: Airway organoids


title: BMDMs, AB9094


title: IPF-derived airway organoids_#3_NC

description: Library name: GA77415


title: BMDMs, AB9093


title: NHBE_DQzG_5uM_48h

description: Library name: GA77412

value: NHBE cells


title: IPF-derived airway organoids_#3_DQzG_5uM_48h

description: Library name: GA77414


title: BMDMs, AB9092


title: BMDMs, AB9091


title: NHBE_Control

description: Library name: GA77411


title: IE_SE2_1

description: Library name: DSP-1001660009541-F-A02


title: BMDMs, AB9090


title: NHBE_DQzG_5uM_24h

description: Library name: GA77410


title: BMDMs, AB9089


title: HEK293T-DGCR8-E518K (21A4) small RNA library replicate 2

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
First, adapter sequences were removed from sequencing reads using cutadapt (Martin 2011) (cutadapt --a AGATCGGAAGAGCACACGTCT -A GATCGTCGGACTGTAGAACTCTGAAC).
The trimmed paired-end reads were then joined using fastq-join (10.2174/1875036201307010001) (fastq-join -p 5), and low quality reads were removed using fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.14) (fastq_quality_filter -q 30 -p 90).
The remaining reads were next mapped to reference human genome (GRCh38) using bowtie2 (Ben Langmead and Salzberg, 2012) in the local alignment mode (bowtie2 --local -p 4 --score-min L,-4,2 --ma 2 -k 5).
Reads mapped to miRNA loci at both ends within the range from -4 to +4 to the annotated sites deposited in miRBase (Kozomara et al. 2019) were collected for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated TSV file containing the relative expression level of each pri-miRNA in each sample normalized to the expression of 257 DROSHA-independent pri-miRNAs.

source_name: HEK293T DGCR8-E518K

extract_protocol:
The total RNAs were isolated from the cells by using TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
The small RNA fraction was separated from extracted total RNA using 12% denaturing urea-PAGE and was purified using the IPA precipitation method. Small RNA libraries were then prepared using NEBNext® Small RNA Library Prep Set for Illumina (E7330S) with the purified small RNA fraction as input. The final dsDNA libraries were subjected to a next-generation sequencing platform in a paired-end sequencing mode.

value: HEK293T DGCR8-E518K

value: culture cells


title: HEK293T-DGCR8-E518K (21A4) small RNA library replicate 3


title: BMDMs, AB9088


title: BMDMs, AB9099


title: HEK293T-DGCR8-E518K (21A4) small RNA library replicate 1


title: HEK293T-DGCR8-KO (1A5) small RNA library replicate 2

source_name: HEK293T DGCR8-KO

value: HEK293T DGCR8-KO


title: HEK293T-DGCR8-KO (1A5) small RNA library replicate 3


title: HEK293T-DGCR8-KO (1A5) small RNA library replicate 1


title: BMDMs, AB9086

source_name: bone marrow derived macrophages

value: bone marrow derived macrophages


title: BMDMs, AB9087


title: BMDMs, AB9084


title: HEK293T-WT small RNA library replicate 3


title: BMDMs, AB9083


title: HEK293T-WT small RNA library replicate 2


title: BMDMs, AB9095


title: HEK293T-WT small RNA library replicate 1


title: BMDMs, AB9082


title: BMDMs, AB9081


title: HEK293T-DGCR8-KO mRNA library replicate 1

data_processing:
As recommended by the manufacturer, due to the low quality of Read 2, only data of Read 1 were utilized in the analysis.
Firstly, polyA tail, 3p adapter, and the first 12 nt in the 5p end of sequencing reads were removed using cutadapt (Martin 2011) (cutadapt -m 18 -u 12 -n 2 -a A{18} --discard-untrimmed).
Low quality reads were then removed using fastq_quality_filter from http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.14 (fastq_quality_filter -Q33 -q 30 -p 80).
The remaining reads were mapped to reference human genome GRCh38 using STAR version 2.7.11a (10.1093/bioinformatics/bts635) (STAR --runThreadN 4 --outSAMmultNmax 1 --outFilterMultimapNmax 20  --outFilterMismatchNmax 3 --alignSJDBoverhangMin 7 --outSAMattributes NH HI AS nM jI).
The mapped reads were then annotated using bedtools intersect (Quinlan and Hall, 2010) with reference mRNA genomic loci obtained from Ensembl (Martin et al. 2023). The raw read count of each gene in each sample was normalized by the read count of GAPDH which was used as an internal control of gene expression.
Assembly: GRCh38
Supplementary files format and content: Tab-separated TSV file containing the relative expression level of each gene in each sample normalized to the expression of GAPDH.

extract_protocol:
The total RNAs were isolated from the cells by using TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
Total RNA were extracted from cultured cells using Trizol. The mRNA libraries were then prepared using Collibri™ 3' mRNA Library Prep Kit for Illumina™ Systems (A38110024). The DNA libraries were then subjected to paired-end next-generation sequencing runs.


title: HEK293T-DGCR8-E518K mRNA library replicate 1


title: BMDMs, AB9079


title: HEK293T-WT mRNA library replicate 1

description: WT


title: BMDMs, AB9078


title: ARPE-19 MGME1-/-, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ApaLI, Dox induced for 12 hours, rep #2

city: New York

first: Yi

last: Fu

state: New York

address: 430 E 67th Street – RRL 1141

institute: MSKCC

description: ARPE-19 MGME1-/-, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ApaLI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #2

data_processing:
Deletions and duplications were called using MitoSAlt34, a pipeline that classifies deletions that overlap with replication origins as duplications with the assumption that mtDNA deletions with altered replication origins are unlikely to be propogated. We applied the default filtering criteria: cluster threshold = 5, break threshold = -2, hplimit = 0.01, deletion threshold min = 30, breakspan = 15, split distance threshold = 5, score threshold = 80, and evalue threshold = 0.00001.
Assembly: hg38
Supplementary files format and content: Table S1.xlsx

source_name: eye

extract_protocol: 50,000 cells were collected and frozen in 10% DMSO in culture media in -80°C before submission to the Integrated Genomics Operation (IGO) core at Memorial Sloan Kettering Cancer Center. Library preparation followed standard ATAC-seq protocol without nuclei isolation (Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature methods 10, 1213-1218. 10.1038/nmeth.2688.).

value: eye

value: retinal pigmental epithelial cells

value: MGME1-/-, constitutive mito-Ku and mito-LigD, Dox-inducible mito-ApaLI

value: Dox induced for 12hr, Dox removed for 5 days


title: BMDMs, AB9080


title: ARPE-19 MGME1-/-, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ApaLI, Dox induced for 12 hours, rep #1

description: ARPE-19 MGME1-/-, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ApaLI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #1


title: ARPE-19 MGME1-/-, inducible mito-ApaLI, Dox induced for 12 hours, rep #2

description: ARPE-19 MGME1-/-, inducible mito-ApaLI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #2

value: MGME1-/-, Dox-inducible mito-ApaLI


title: ARPE-19 MGME1-/-, inducible mito-ApaLI, Dox induced for 12 hours, rep #1

description: ARPE-19 MGME1-/-, inducible mito-ApaLI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #1


title: BMDMs, AB9076


title: BMDMs, AB9074


title: BMDMs, AB9085


title: BMDMs, AB9077


title: BMDMs, AB9075


title: ARPE-19 POLG-p.D274A homozygous clone mix, mito-T4, transfected with mitoScaI, Day 5

data_processing:
Deletions and duplications were called using MitoSAlt34, a pipeline that classifies deletions that overlap with replication origins as duplications with the assumption that mtDNA deletions with altered replication origins are unlikely to be propogated. We applied the default filtering criteria: cluster threshold = 5, break threshold = -2, hplimit = 0.01, deletion threshold min = 30, breakspan = 15, split distance threshold = 5, score threshold = 80, and evalue threshold = 0.00001.
Assembly: hg38
Supplementary files format and content: Exp2_processed.xlsx

value: POLG p.D274A homozygous

value: transfected with mito-ScaI


title: ARPE-19 MGME1 depleted by CRISPR, mito-T4, transfected with mitoScaI, Day 4

value: MGME1 knockout by CRISPR


title: BMDMs, AB9073


title: ARPE-19, inducible mito-ScaI, no Dox treatment, rep #2

description: ARPE-19, inducible mito-ScaI, no Dox treatment, replicate #2

data_processing:
Deletions and duplications were called using MitoSAlt, a pipeline that classifies deletions that overlap with replication origins as duplications with the assumption that mtDNA deletions with altered replication origins are unlikely to be propogated. We applied the default filtering criteria: cluster threshold = 5, break threshold = -2, hplimit = 0.01, deletion threshold min = 30, breakspan = 15, split distance threshold = 5, score threshold = 80, and evalue threshold = 0.00001.
Assembly: hg38
Supplementary files format and content: Exp1_processed.xlsx

value: wildtype

value: no treatment


title: BMDMs, AB9071


title: BMDMs, AB9070


title: ARPE-19, inducible mito-ScaI, no Dox treatment, rep #1

description: ARPE-19, inducible mito-ScaI, no Dox treatment, replicate #1


title: BMDMs, AB9069


title: ARPE-19 mito-T4, transfected with mitoScaI, Day 3


title: BMDMs, AB9068


title: ARPE-19, inducible mito-ScaI, Dox induced for 12 hours, rep #2

description: ARPE-19, inducible mito-ScaI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #2


title: ARPE-19, inducible mito-ScaI, Dox induced for 12 hours, rep #1

description: ARPE-19, inducible mito-ScaI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #1


title: BMDMs, AB9067


title: ARPE-19, constitutive mito-T4, inducible mito-ScaI, no Dox treatment, rep #1

description: ARPE-19, constitutive mito-T4, inducible mito-ScaI, no Dox treatment, replicate #1


title: BMDMs, AB9066


title: BMDMs, AB9065


title: ARPE-19, constitutive mito-T4, inducible mito-ScaI, Dox induced for 12 hours, rep #2

description: ARPE-19, constitutive mito-T4, inducible mito-ScaI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #2


title: BMDMs, AB9064


title: BMDMs, AB9063


title: BMDMs, AB9062


title: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, no Dox treatment, rep #1

description: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, no Dox treatment, replicate #1


title: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, no Dox treatment, rep #2

description: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, no Dox treatment, replicate #2


title: BMDMs, AB9072


title: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, Dox induced for 12 hours, rep #2

description: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #2


title: BMDMs, AB9061


title: BMDMs, AB9058


title: BMDMs, AB9059


title: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, Dox induced for 12 hours, rep #1

description: ARPE-19, constitutive mito-Ku, constitutive mito-LigD, inducible mito-ScaI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #1


title: BMDMs, AB9055


title: BMDMs, AB9057


title: Patient_#1_NGFR+ cells (Basal cells)

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT2 ver.2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was isolated from primary cells with RNAiso Plus reagent (Cat. #9109, Takara, Shiga, Japan) following the manufacturer’s instruction.
The reverse transcription to cDNA was performed using GenNext RamDA-seq Single Cell Kit and the library was prepared using Nextera XT DNA Library Preparation Kit.

value: lung

value: Basal

tag: patient


title: BMDMs, AB9056


title: Patient_#2_NGFR+ cells (Basal cells)


title: Patient_#1_HTll-280+ cells (AT2 cells)


title: ARPE-19, constitutive mito-T4, inducible mito-ScaI, no Dox treatment, rep #2

description: ARPE-19, constitutive mito-T4, inducible mito-ScaI, no Dox treatment, replicate #2


title: Patient_#2_HTll-280+ cells (AT2 cells)


title: Alveolar organoids_#3_NV

extract_protocol:
Total RNA was isolated from organoids with RNAiso Plus reagent (Cat. #9109, Takara, Shiga, Japan) following the manufacturer’s instruction.
The reverse transcription to cDNA was performed using GenNext RamDA-seq Single Cell Kit and the library was prepared using Nextera XT DNA Library Preparation Kit.

value: Alveolar organoids

value: Control


title: Alveolar organoids_#3_MIR205HG OE

value: MIR205HG overexpressing


title: BMDMs, AB9053


title: BMDMs, AB9052


title: BMDMs, AB12235

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_invitro_p.txt

growth_protocol: 8 weeks old C57BL/6 mice were sacrificed and bone marrow was isolated and cultured in the presence of human MCSF in C10 medium to generate BMDMs. At day 2, medium was replaced with fresh medium and MCSF .

extract_protocol:
24 hours after treatment, cells were isolated using Accutase and then washed and sorted in FACS to pre-prepared SPID-seq plates (Yofe et al. 2023)
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)
single-cell RNA-sequencing for gene expression quantitation

treatment_protocol: At day 6, cells were treated with murine IL4, TGFb, IL13, IL10, IFNg or left untreated


title: Alveolar organoids_#2_NV


title: Alveolar organoids_#2_MIR205HG OE


title: BMDMs, AB12234


title: ARPE-19, constitutive mito-T4, inducible mito-ScaI, Dox induced for 12 hours, rep #1

description: ARPE-19, constitutive mito-T4, inducible mito-ScaI, Dox induced for 12 hours, harvested 5 days post Dox removal, replicate #1


title: Alveolar organoids_#1_MIR205HG OE


title: BMDMs, AB12226


title: BMDMs, AB12233


title: Alveolar organoids_#1_NV


title: NHBE_sgMIR205HG_#2

value: NHBE

value: MIR205HG knock down


title: BMDMs, AB12225

value: bone marrow derived macrophages


title: NHBE_sgMIR205HG_#1


title: NHBE_NV


title: BMDMs, AB12224


title: NHBE_NC


title: BMDMs, AB12223


title: BMDMs, AB12222


title: BMDMs, AB9054


title: IPF-derived airway organoids_#3

value: IPF-derived airway organoids


title: IPF-derived airway organoids_#2


title: BMDMs, AB12221


title: Alveolar organoids_#3


title: BMDMs, AB12220


title: Alveolar organoids_#2


title: BMDMs, AB12219


title: IPF-derived airway organoids_#1


title: BMDMs, AB12216


title: Alveolar organoids_#1


title: BMDMs, AB12215


title: BMDMs, AB12214


title: BMDMs, AB12213


title: BMDMs, AB12212


title: mESC_H3K27me2

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
CUT&Tag and CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed and reads trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to either the mm10 version of Mus musculus genome or the hg38 version of the human genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates
Assembly: hg38
Supplementary files format and content: BigWig files were created based on coverage at 100 bp windows genome-wide, which was calculated as the number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads). 2800000000 was a number chosen arbitrarily.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag in SU-DIPG-IV cells: Nuclei were prepared from SU-DIPG-IV cells, and up to 5x105 cells were used per individual CUT&Tag reaction using CUT&Tag V3 (https://www.protocols.io/view/cut-amp-tag-direct-for-whole-cells-with-cutac-x54v9mkmzg3e/v3). pAG-Tn5 was purchased from Epicypher (Durham, North Carolina), and H3K27me3 antibody was purchased from Cell Signalling Technologies (#9733). Rabbit Isotype IgG control (ab172730) was purchased from Abcam. Antibodies were used at 1:100 dilution. Sequencing was performed on an Illumina NextSeq 500 using a P1/100 cycle kit with 50bp paired-end reads, targeting 10 million reads per sample. CUT&Tag in HEK293: Genome-wide H3K27me3 domain changes were profiled using the CUT&Tag protocol adapted from EpiCypher. Cells were harvested via 0.25% trypsin-EDTA solution and counted using 0.4% trypan blue stain and Countess automated cell counter. A single-cell suspension was prepared by washing cells with cold 1x PBS and resuspending 1.0 x 106 cells in 1 mL cold nuclear extraction buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1% Triton x-100, 20% glycerol, & 0.5 mM spermidine), then incubated on ice for 10 minutes to isolate nuclei. Biomag Plus Concanavalin A beads were activated with two washes of cold bead activation buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, & 1 mM MnCl22). After activation, beads were added to aliquots of 0.1 x 106 isolated nuclei and incubated at room temperature for 10 minutes. Nuclei:bead samples were resuspended in 50 µL cold Antibody150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, & protease inhibitors) followed by the addition of 0.5 µg of anti-H3K27me3 (#9733S, Cell Signaling Technology). To facilitate primary antibody binding, samples were incubated on nutator at room temperature for 1 hour. Samples were resuspended in 50 µL Digitonin150 buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors) followed by the addition of 0.5 µg CUTANA anti-rabbit secondary antibody (#13-1047, EpiCypher). Samples were then incubated on nutator at room temperature for 1 hour to facilitate binding, followed by two washes with 200 µL cold Digitonin300 buffer (20 mM HEPES-KOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, & protease inhibitors). The tagmentation reaction was performed by resuspending samples in 50 µL cold Tagmentation buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, & protease inhibitors) and incubating at 37°C in thermocycler for 1 hour. Samples were washed with 50 µL TAPS buffer (10 mM TAPS pH 8.5 & 0.2 mM EDTA) then resuspended in 5 µL SDS Release buffer (10 mM TAPS pH 8.5 & 0.1% SDS) to quench the tagmentation reaction and release adaptor-tagged DNA fragments into solution. After incubating samples at 58°C in thermocycler for 1 hour, 15 µL SDS Quench buffer (0.67% Triton x-100), 2 µL i5 universal primer (EpiCypher), 2 µL i7 barcoded primer (EpiCypher), 0.005 ng Escherichia coli spike-in DNA (made in-house), and 25 µL NEBNExt High Fidelity 2x PCR Master Mix were added to each sample for library construction with the following PCR protocol: 5 minutes at 58°C, 5 minutes at 72°C, 45 seconds at 98°C, 14 cycles of 15 seconds at 98°C and 10 seconds at 60°C, with a final extension for 1 minute at 72°C. Libraries were checked for quality using the Qubit dsDNA HS Assay kit and TapeStation High Sensitivity DNA assay kit and then sequencing was performed using Novaseq 6000 (Novogene) to generate 150 bp paired-end reads.
Library were constructed by tagmentation followed by PCR as described in the extract protocol.


title: mESC_H2AK119ub


title: DMSO_K27


title: Chiron_K27

value: 0.5 uM of Chir-124 for 48 hours


title: Async IgG CUT&RUN

description: CUT&RUN of IgG in asynchronous mESC

data_processing:
CUT&Tag and CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed and reads trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to either the mm10 version of Mus musculus genome or the hg38 version of the human genome using bowtie2. Samtools and bedtools were used for processing aligned reads from sam to bed files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates
Assembly: mm10, dm6 (spike in)
Supplementary files format and content: Coverage at 100 bp windows genome-wide was calculated as the number of reads that mapped at that window, normalized by the factor N: N = 10000/(Total number of mapped spike-in reads). 10000 was a number chosen arbitrarily.
Library strategy: CUT&RUN

source_name: mESC

extract_protocol:
Genome-wide H3K27me3 domain changes were determined using the CUT&RUN protocol adapted from Hainer & Fazzio. Cells were harvested via 0.25% trypsin-EDTA solution and counted using 0.4% trypan blue stain and Countess automated cell counter (Invitrogen). A single-cell suspension was then prepared to achieve 0.5 x 10^6 cells in 1 mL cold nuclear extraction buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton x-100, & 20% glycerol). Isolated nuclei were pelleted via centrifugation at 2000 rpm and 4°C for 5 minutes, then resuspended in 600 µL cold nuclear extraction buffer. Biomag Plus Concanavalin A beads (Bangs Laboratories) were activated via two washes with 1 mL cold binding buffer (20 mM HEPES-KOH pH 7.5, 10 mM KCl, 1 mM CaCl2, & 1 mM MnCl2) using a magnetic rack, with 150 µL bead slurry used for each sample of 0.5 x 106 cells. After the final wash, beads were resuspended in 300 µL cold binding buffer. While gently vortexing, nuclei were added to activated beads and then incubated on a rotating platform at 4°C for 10 minutes to facilitate nuclei binding. Nuclei:bead samples were resuspended in 1 mL blocking buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 2 mM EDTA, & protease inhibitors) and incubated at room temperature for 5 minutes. After blocking, samples were washed with 1 mL wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA, & protease inhibitors) then resuspended in 250 µL wash buffer. While gently vortexing, 5 µg of anti-H3K27me3 (#9733S, Cell Signaling Technology) in 250 µL wash buffer was added to each sample. Antibody binding was facilitated by incubating samples on a rotating platform at 4°C overnight. Samples were washed twice with 1 mL cold wash buffer and then resuspended in 250 µL cold wash buffer. While gently vortexing, 2.5 µL of CUTANA pAG-MNase (EpiCypher) was added, and samples were incubated at 4°C for 1 hour to facilitate binding. After incubation, samples were washed twice with 1 mL cold wash buffer and resuspended in 50 µL cold wash buffer. While gently vortexing, 3 µL 0.1 M CaCl2 was added to each sample. Samples were briefly flicked to mix and then incubated on ice for 30 minutes after which the pAG-MNase was inactivated by adding 50 µL 2x STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, & 0.05% digitonin) supplemented with RNase A (ThermoFisher Scientific), proteinase K (ThermoFisher Scientific), glycogen (VWR), and spike-in DNA generated from MNase digestion of Drosophila S2 cells. Released fragments were cleaned up by incubating samples at 37°C for 20 minutes, followed by centrifugation at 16000xg and 4°C for 5 minutes. The resulting supernatant was mixed with 3 µL 10% SDS and 2.5 µL proteinase K solution, followed by incubation at 70°C for 10 minutes. To purify MNase-digested DNA fragments, samples underwent phenol-chloroform extraction. The final resulting aqueous phase was transferred and incubated with 2 µg glycogen and 750 µL ethanol at -20°C overnight. DNA was pelleted by centrifugation at 16000xg, air-dried, and then resuspended in 0.1x TE buffer. DNA fragments were checked for quality using the Qubit dsDNA HS Assay kit (Invitrogen) and TapeStation High Sensitivity DNA assay kit (Agilent).
Sequencing libraries of DNA fragments isolated following CUT&RUN were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs; New England BioLabs). Libraries were checked for quality using the Qubit dsDNA HS Assay kit and TapeStation High Sensitivity DNA assay kit. Sequencing was performed using a NovaSeq 6000 with Illumina 150 bp paired-end reads at the Genomics Shared Resource, University of Colorado Cancer Center.

value: mESC


title: Async Thy H3K27me3 CUT&RUN Rep3

description: CUT&RUN of H3K27me3 in asynchronous mESC


title: Async Thy H3K27me3 CUT&RUN Rep2


title: Async H3K27me3 CUT&RUN Rep1


title: BMDMs, AB12217


title: 20h Thy H3K27me3 CUT&RUN Rep2

description: CUT&RUN of H3K27me3 in mESC treated with Thymidine for 20 hours

value: 2mM Thymidine 20 hours


title: 20h Thy H3K27me3 CUT&RUN Rep3


title: 20h Thy H3K27me3 CUT&RUN Rep1


title: 16h Thy H3K27me3 CUT&RUN Rep3

description: CUT&RUN of H3K27me3 in mESC treated with Thymidine for 16 hours

value: 2mM Thymidine 16 hours


title: 16h Thy H3K27me3 CUT&RUN Rep1


title: 16h Thy H3K27me3 CUT&RUN Rep2


title: 12h Thy H3K27me3 CUT&RUN Rep3

description: CUT&RUN of H3K27me3 in mESC treated with Thymidine for 12 hours

value: 2mM Thymidine 12 hours


title: mESC_H3K36me2


title: WT_ML90_CTL_2

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Gene counts and TPM's were averaged for 2 sample IDs with 2 technical replicates: ML128a&b and ML47a&b.
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

source_name: Follicular Lymphoma STAT6 wildtype (WT)

growth_protocol: Cryopreserved single-cell suspensions from human non-malignant lymph node (LN) biopsies or lymphomatous LNs were thawed, washed and depleted of CD3+ T cells and CD14+ macrophages using Miltenyi beads and columns (Miltenyi, 130-050-101 and 130-050-201)

extract_protocol:
Total RNA was purified using the Trizol reagent followed by RNAeasy column purification (Qiagen). RNA was assessed using the Bioanalyzer (Agilent #5067-1513) and a Qubit RNA High Sensitivity assay (Thermofisher # Q32855), and 2ng of RNA input was processed for sequencing using the Takara SMART-Seq  stranded kit (#634444).
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: The B lymphocytes were cultured in RPMI1640 + 10% hiFCS  for 4 h in the presence or absence of 10 ng/ml of IL4.

value: Follicular Lymphoma STAT6 wildtype (WT)

value: STAT6 wildtype


title: WT_ML79_CTL_4


title: WT_ML79_IL4_4


title: WT_ML66_IL4_6


title: WT_ML87_IL4_3


title: WT_ML69_IL4_5


title: WT_ML69_CTL_5


title: 8h Thy H3K27me3 CUT&RUN Rep 3

description: CUT&RUN of H3K27me3 in mESC treated with Thymidine for 8 hours

value: 2mM Thymidine 8 hours


title: WT_ML93_IL4_1


title: WT_ML93_CTL_1


title: WT_ML66_CTL_6


title: 8h Thy H3K27me3 CUT&RUN Rep1


title: WT_ML47b_IL4_7


title: WT_ML47b_CTL_7


title: 8h Thy H3K27me3 CUT&RUN Rep2


title: WT_ML47a_IL4_12


title: WT_ML87_CTL_3


title: WT_ML47a_CTL_12


title: 387-WT-CD

city: Munich

first: Dieter

last: Edbauer

state: Select...

address: Feodor-Lynenstr. 17

institute: DZNE

data_processing:
The raw sequencing data were initially processed using Cell Ranger software from 10x Genomics to align reads to the mouse reference genome, followed by the creation of a Seurat object. A series of quality control measures were performed on the data where doublet score was calculated on a sample level. Then clustering was performed with high resolution and clusters with more than 20% doublets were completely removed. Next, clusters with low quality cells (mitochondrial gene expression, too many/few genes/UMIs) were also fully removed. Subsequently, we performed more rigorous quality control, where we deleted the individual cells with a higher-than-average doublet score or mitochondrial content using Seurat version 4.3.0 77 in R 4.2.0.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated value files and matrix files

source_name: hippocampus

extract_protocol:
Animals were perfused with ice-cold PBS prior to brain dissection and snap frozen. Nuclei from P40 female hippocampi with acceptable RNA quality (RNA Integrity Number (RIN) > 7 with Agilent RNA 6000 Nano kit (Agilent, 50671511)) were isolated according to Frankenstein protocol for nuclei isolation from fresh and frozen tissue. Nuclei were sorted via fluorescence-activated nuclei sorting (FANS) by a DAPI+ gate and two further gates of NeuN positive and NeuN negative nuclei (anti-NeuN antibody from Abcam, ab190195), in order to obtain 5000 neurons and 5000 glia per sample, respectively.
The nuclei were processed with Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, 1000268) generate the cDNA libraries for this study. Gel Bead-in-Emulsions (GEMs) were generated with chip G (10x Genomics, 1000120) on the microfluidic platform 10x Genomics Chromium Single Cell Controller. Next, the samples were uniquely barcoded to distinguish the mRNAs (each having unique molecular identifier (UMI)) from different nuclei. The cDNA was extracted with Dynabeads MyOne SILANE beads (Invitrogen, 370-12D) and amplified by PCR. The PCR product was purified with SPRIselect reagent (Beckman Coulter, Cat #B23318). Subsequently, the 3’ gene expression library was constructed with primers for Illumina NGS platform and Dual Index Kit TT set A (10x Genomics, 1000215) which allows individual sample identification.

treatment_protocol: (2-Hydroxypropyl)-β-cyclodextrin (CAS #128446-35-5, referred to here as CD, Sigma-Aldrich H107-100G, Degree of Substitution=5) was dissolved in 30 mM citric buffer (pH 5.0) in normal saline (vehicle) to achieve a 20% concentration. Starting from P21, wildtype and transgenic mice received daily subcutaneous injections of 2 g/kg CD solution or an equivalent volume of the vehicle.

value: hippocampus

value: Ctrl

value: HPbCD


title: WT_ML30_IL4_8


title: WT_ML30_CTL_8

value: Control


title: 12h Thy H3K27me3 CUT&RUN Rep2


title: 408-TG-CD

value: GA-Nes


title: 392-WT-CD


title: WT_ML2_CTL_9


title: WT_ML2_IL4_9


title: WT_ML174_IL4_11


title: 406-TG-CD


title: 12h Thy H3K27me3 CUT&RUN Rep1


title: 185-TG-Vehicle

value: Vehicle


title: WT_ML136_IL4_10


title: 399-TG-CD


title: 397-WT-CD


title: NBC_ML95_IL4_4

source_name: Normal B cells

value: Normal B cells

value: Normal


title: 186-WT-Vehicle


title: 379-WT-CD


title: WT_ML136_CTL_10


title: NBC_ML95_CTL_4


title: NBC_ML92_CTL_3


title: NBC_ML92_IL4_3


title: 166-WT-Vehicle


title: WT_ML90_IL4_2


title: NBC_ML57_IL4_6


title: 145-TG-Vehicle


title: WT_ML174_CTL_11


title: 412-TG-CD


title: NBC_ML57_CTL_6


title: 144-TG-Vehicle


title: NBC_ML31_IL4_5


title: NBC_ML31_CTL_5


title: Kidney, spatial transcriptomics, male, Alport, nicotinamide riboside

city: Washington

first: Bryce

last: Jones

state: DC

address: 4000 Reservoir Rd NW

department: Pharmacology and Physiology

institute: Georgetown University

description:
Fresh frozen spatial transcriptome sequencing
SeuratAlport_ST_JonesB_03082024.h5Seurat

data_processing:
Space Ranger (v2.0.0) was used to perform expression analysis, mapping, counting, and clustering. Labels were transferred from snRNA-seq to ST to spatially localize the cell types based on gene expression profiles using Seurat (v.5.0.0).
Assembly: mm10-2020-A
Supplementary files format and content: The ".h5Seurat" file contains the processed spatial transcriptomic data.
Supplementary files format and content: The ".tif" files contain adjacent sections stained with periodic acid–Schiff.
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
Fresh kidneys were frozen in O.C.T. Compound, and tissues were cryosectioned (10 µm). Adjacent sections were stained with periodic acid–Schiff and imaged.
The library was constructed according to the Visium Spatial Gene Expression protocol (10x Genomics, CG000240 protocol) followed by SPRIselect cDNA cleanup (Visium CG000239 protocol).

value: Kidney

value: 25 weeks

value: male

value: Nicotinamide riboside


title: Kidney, spatial transcriptomics, male, control, nicotinamide riboside


title: Kidney, single nuclei, pooled male and female, Alport, nicotinamide riboside

data_processing:
Cell Ranger ARC was used to demultiplex and process barcoded data. Data were analyzed using Seurat (v.5.0.0).
Assembly: mm10-2020-A
Supplementary files format and content: The ".h5Seurat" file contains the processed single nuclei RNA-sequencing data.
Library strategy: snRNA-Seq

molecule: nuclear RNA

extract_protocol:
A total of 49,488 nuclei were isolated from tissue cryosections and processed as described in the Open Access article available online: https://doi.org/10.1038/s41467-023-44467-6.
The library was prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (v1.0) kit as described in the step-by-step protocol available online: dx.doi.org/10.17504/protocols.io.5qpvoby69l4o/v2.

tag: cellular compartment

value: isolated nuclei

value: pooled male and female

value: Nicotinamide Riboside


title: NBC_ML123_CTL_2


title: NBC_ML111_IL4_1


title: Kidney, spatial transcriptomics, male, control, vehicle


title: 176-WT-Vehicle


title: 167-WT-Vehicle


title: NBC_ML123_IL4_2


title: Kidney, single nuclei, pooled male and female, control, nicotinamide riboside


title: Mutant_ML55_CTL_4

source_name: Follicular Lymphoma STAT6 mutant

value: Follicular Lymphoma STAT6 mutant

value: STAT6 mutant


title: Kidney, single nuclei, pooled male and female, control, vehicle


title: Mutant_ML55_IL4_4


title: Kidney cortex, female, Alport, nicotinamide riboside, rep4

data_processing:
Sequencing files were aligned and processed with BioJupies, a webserver that automatically analyzes RNA-seq datasets and generates Jupyter Notebooks: https://doi.org/10.1016/j.cels.2018.10.007.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains raw read counts for all 32 samples.
Supplementary files format and content: Tab-delimited text file contains log CPM for all 32 samples.

source_name: Kidney cortex

extract_protocol:
Kidney cortex RNA was isolated with Qiagen RNeasy Mini Kit.
RNA was sent to Genewiz (South Plainfield, NJ, USA) for RNA-sequencing (NEBNext Ultra II RNA Library Prep Kit, poly-A selection method).

value: Kidney cortex

value: female


title: Mutant_ML165_CTL_2


title: Kidney cortex, female, Alport, nicotinamide riboside, rep3


title: Kidney, spatial transcriptomics, male, Alport, vehicle


title: Kidney cortex, female, Alport, nicotinamide riboside, rep1


title: Mutant_ML127_IL4_1


title: Mutant_ML127_CTL_1


title: Kidney cortex, female, Alport, vehicle, rep4


title: male parasites, rep2

city: Dallas

first: James

middle: J

last: Collins

state: Texas

address: 5323 Harry Hines Blvd

department: Department of Pharmacology

institute: UT Southwestern Medical Center

description: Library name: Sample2

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were mapped to the Schistosoma mansoni genome (v10) and read counts were obtained using STAR (v2.7.10a) GeneCounts quantification mode.
Transcripts-per-million (TPM) was calculated using the following order of operations: 1). Obtained read counts were divided by the legnth of each gene in kilobases (Reads per kilobase; RPK). 2). Sum all RPK values in a sample, then divide this number by 1,000,000 to obtain "per million" scaling factor. 3). Divide the RPK values by the "per million" scaling factor to obtain TPM.
Assembly: Schistosoma mansoni v10
Supplementary files format and content: Excel spreadsheet (xlsx.) file containing raw counts of each sample
Supplementary files format and content: Excel spreadsheet (xlsx.) file containing analysis of data generated from three replicates of male worm samples isolated from culture in Rich Media with female parasites for 72 hours. Transcripts-per-million calculated from read counts following RNA-seq of replicates of adult male parasites isolated from 72 hour culture with female parasites in Rich Media.

organism: Schistosoma mansoni

source_name: whole worm extract

growth_protocol: Adult male and female parasites cultured in Rich Media (Basch Media 169 + ascorbic acid, red blood cells, and cholesterol) at 37°C at 5% CO2 for 3 days

extract_protocol:
Total RNA was extracted using Trizol reagent and purified using a Zymo Direct-zol RNA miniprep kit before Illumina sequencing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA library preparation kit.

treatment_protocol: Freshly perfused male and female parasites were cultured in Rich Media for 72 hours before separating male and females. Only male parasites were harvested in Trizol, then stored at -80°C until further processing.

value: whole worm extract

value: Puerto Rico


title: Mutant_L128b_IL4_6


title: male parasites, rep1

description: Library name: Sample1


title: Kidney cortex, female, Alport, vehicle, rep3


title: Kidney, single nuclei, pooled male and female, Alport, vehicle


title: Kidney cortex, female, Alport, vehicle, rep2


title: NBC_ML111_CTL_1

value: Control


title: Mutant_L128b_CTL_6


title: Mutant_L128a_IL4_5


title: Mutant_ML165_IL4_2


title: Mutant_L128a_CTL_5


title: Kidney cortex, female, control, nicotinamide riboside, rep4


title: Kidney cortex, female, Alport, nicotinamide riboside, rep2


title: HEK293T,EJCEnh,SMG1i,3

first: Divya

last: Kolakada

address: 13001 E 17th Place

institute: University of Colorado Anschutz

description:
HEK293T cells with with the EJC-Enhanced NMD reporter library integrated, treated with SMG1i. Rep 3
DESeq_RNA_ARTi.csv

data_processing:
Sequencing reads were trimmed to the sequence of interest
Reads 1 and 2 were aligned. Only perfectly aligned reads were accepted
Reads were mapped to a reference file
UMIs were deduplicated and a final bed file was created of reads in the correct orientation
Occurences of each sequence was counted and put through a DESeq2 pipeline, calculating the fold change of DMSO to SMG1i and normalizing to NMD negative sequences
Assembly: N/A, custom reference file consisting of all possible sequences in NNNNNNTRRN used for mapping
Supplementary files format and content: DESeq_RNA_ART.csv: Fold changes for the sequences in the  EJC-Independent population of cells after being put though DESeq2
Supplementary files format and content: DESeq_RNA_ARTi.csv: Fold changes for the sequences in the  EJC-Enhanced population of cells after being put though DESeq2

growth_protocol: HEK293T cells were maintained in DMEM and 10% Equalfetal

extract_protocol:
RNA was harvested using TRIzol
RNA was converted into cDNA and libraries were made via a homemade library prep protocol

treatment_protocol: DMSO and SMG1i (0.5 uM) were added 24 hours before harvest

value: Human Embryonic Kidney

value: WT integrated with EJC-enhanced reporter library in a single location within the genome


title: Kidney cortex, female, Alport, vehicle, rep1

value: Vehicle


title: Yeats2_auxin_rep_2

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

description: Library name: Sample7

data_processing:
Image analysis and base calling were performed using RTA 4.12.2 and bclconvert 4.2.7.
Alignment : Reads were mapped onto mm10 assembly of Mus musculus genome using STAR v.2.5.3a
Quantification : Gene expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 102 annotations.
Differential gene expression analysis was performed using R 3.3.2 and DESeq2 v1.16.1.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: Embryonic stem cells

growth_protocol: Embryonic stem cells were grown on 0.1% gelatinized (Sigma-Aldrich, Cat# G1890) tissue-culture plates in DMEM (4.5 g/L glucose) with GlutaMAX-I supplemented with ES-tested 15% foetal calf serum (FCS, ThermoFisher Scientific, Cat# 10270-106), 0.1% β-mercaptoethanol (ThermoFisher Scientific, Cat# 31350-010), 100 U/ml penicillin, 100 μg/ml streptomycin (ThermoFisher Scientific, Cat# 15140-122), 0.1 mM non-essential amino acids (ThermoFisher Scientific, Cat# 11140-035), and 1500 U/ml leukaemia inhibitory factor (produced in-house). 3 μM CHIR99021 (Axon Medchem, Cat# 1386) and 1 μM PD0325901 (Axon Medchem, Cat# 1408) (2i) were added freshly to the medium, which was replaced every 24 h. Cells were kept in 400 µg/ml G418 for Tir1 selection. ESC numbers were assessed using a Countess II Automated Cell Counter (Invitrogen).

extract_protocol:
P3209
Total RNA extraction was performed using TRI Reagent® (Molecular Research Center Inc., Cat# TR 188), following the manufacturer's instructions. DNase I treatment was performed to prevent genomic DNA contamination using the TURBO DNA-free™ Kit (ThermoFisher Scientific, Cat# AM1907) per manufacturer's instructions.
P3209 : RNA-Seq libraries were generated from 200 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes (Illumina, San Diego, USA), according to manufacturer's instructions with minor modifications. Following ribodepletion, RNAs were fragmented at 94oC for 2 minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: Auxin (IAA, 3-Indoleacetic acid, Sigma-Aldrich I2886) was used at 500 μM for 24 h for YEATS2 and ZZZ3 depletion.

value: Embryonic stem cells


title: Zzz3_auxin_rep_1

description: Library name: Sample3


title: Control_rep_2

description: Library name: Sample2


title: Zzz3_auxin_rep_3

description: Library name: Sample5


title: Zzz3_auxin_rep_2

description: Library name: Sample4


title: Yeats2_auxin_rep_3

description: Library name: Sample8


title: Yeats2_auxin_rep_1

description: Library name: Sample6


title: Control_rep_1

description: Library name: Sample1


title: Kidney cortex, female, control, nicotinamide riboside, rep3

value: 25 weeks


title: Kidney cortex, female, control, nicotinamide riboside, rep2


title: male parasites, rep3

description: Library name: Sample3


title: MC38_aPD1_R_m16_sec3_spatial

city: Cambridge

first: Andrew

last: Kavran

state: MA

address: 250 Water Street

institute: Bristol Myers Squibb

description:
Library name: MC38_aPD1_R_m16_sec3_spatial
FFPE Spatial Transcriptomic Sequencing

data_processing:
Raw sequencing data were processed using 10X Genomics Space ranger pipeline to generate FASTQ files
Sequences were aligned to the visium mouse probeset v1 using space ranger to quantify gene expression
Assembly: Visium mouse probeset v2
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: raw_feature_bc_matrix.h5
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_positions_list.csv
Supplementary files format and content: scalefactors_json.json
Library strategy: Spatial Transcriptomics

source_name: MC38 Tumor

growth_protocol: Syngeneic tumors were grown by injecting 1 million MC38 cells subcutaneously in the right flank of 6–8-week-old female C57BL/6 mice. Sixteen mice were enrolled for study if their tumor reached 150-250 mm3 on day 16.

extract_protocol:
5 uM FFPE sections were cut on a microtome and placed on 10X Genomics Visium gene expression capture slides, and followed the Visium for FFPE manufacturer's protocol (10X Genomics CG000407|Rev D, non-cytassist) for the sample labeled "base_protocol". For the rest of the samples, there was an added permeabilization step during RNA Digestion. A blend of collagenase B and dispase enzymes (EMD Millipore Sigma #SCR140) resuspended in Hank’s Buffered Salt Solution (ThermoFisher Scientific cat# 14175095) was added to the RNase buffer and enzyme mix to a concentration of 0.4 CDU/uL in step 3.1 to improve the permeabilization of the tissue. Then, after permeabilization at step 3.1.n, the slide was washed with 2X saline-sodium citrate buffer (Millipore Sigma S6639) with 0.1% sodium dodecyl sulfate (Millipore Sigma 71736).
Libraries were constructed according to the Visium for FFPE mouse probeset manufacturer's protocol (non-cytassist)

treatment_protocol: Mice were randomly assigned to control IgG or aPD-1 treatments (n=8 per treatment) and were dosed with 200ug, on days 16 and 20 (Q4Dx2). Mice were euthanized by CO2, and tumors were harvested on day 21 and stored in ice cold PBS before processing. Each tumor was cut in half and processed by either FFPE or fresh-frozen tissue embedding. For FFPE blocks, the tumors were placed in 10% Neutral Buffered Formalin for 24-h fixation. The tumors were then processed for paraffin embedding in a Sakura VIP automated system with vacuum/pressure cycles, dehydrating in graded alcohols to xylene and then paraffin, and embedded into blocks for sectioning

value: MC38 Tumor

value: Colorectal Carcinoma


title: HEK293T,EJCEnh,SMG1i,2

description:
HEK293T cells with with the EJC-Enhanced NMD reporter library integrated, treated with SMG1i. Rep 2
DESeq_RNA_ARTi.csv

value: Kidney


title: MC38_IgG_m04_base_protocol_spatial

description:
Library name: MC38_IgG_m04_base_protocol_spatial
FFPE Spatial Transcriptomic Sequencing

value: IgG Control


title: MC38_aPD1_R_m16_sec2_spatial

description:
Library name: MC38_aPD1_R_m16_sec2_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_R_m15_sec2_spatial

description:
Library name: MC38_aPD1_R_m15_sec2_spatial
FFPE Spatial Transcriptomic Sequencing


title: Kidney cortex, female, control, nicotinamide riboside, rep1

value: Nicotinamide riboside


title: HEK293T,EJCEnh,DMSO,3

description:
HEK293T cells with with the EJC-Enhanced NMD reporter library integrated, treated with DMSO. Rep 3
DESeq_RNA_ARTi.csv

value: DMSO


title: MC38_aPD1_R_m15_sec1_spatial

description:
Library name: MC38_aPD1_R_m15_sec1_spatial
FFPE Spatial Transcriptomic Sequencing