title: DF3.ADAR_DF3.IP.flag_Rep1

description:
DF_FLAG_IP_DESeq2.txt
DF3_ADAR_editing_results.txt

extract_protocol:
Cell lysates (25mM Tris-Cl pH7.4; 150mM NaCl; 2.5mM EDTA, 0.5mM DTT; 0.5% NP-50) were used for RIP using Monoclonal anti-FLAG M2 antibody. Total RNA was extracted from a fraction of the cell lysate (Input samples) or eluted from antibody coupled beads using 1mL of TRIZOL reagent (Thermo) and the RNA was extracts according to the manufacturer’s protocol. RNA was resuspended in Nuclease-Free water. Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNaseI treatment to remove any contaminating DNA.
For each sample 150ng of total RNA was used for library preparation. Library construction was performed using the NEBNEXT Ultra II Directional RNA-Seq kit and the NEBNext rRNA Depletion Kit.

treatment_protocol: Expression of YTHDF-ADAR was induced by treating cells with 1 ug/mL of doxycycline for 24 h. Cells were transfected with YTHDF1-, YTHDF2-, YTHDF3-ADAR,-3xFLAG containing plasmids by lipofection using Fugene HD.

tag: rip-antibody

value: Monoclonal anti-FLAG M2 (MilliporeSigma F3165)

tag: sample type

value: RIP-seq


title: DF1.ADAR_DF1.APOBEC1_Rep1

status: Public on Oct 28 2022

type: SRA

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

country: USA

institute: Duke University School of Medicine

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF1_ADAR.bed
DF1_APOBEC1.bed

library_source: transcriptomic

data_processing:
Raw sequencing reads from RNA-seq libraries were trimmed with Flexbar (v3.5.0) with the following parameters: --adapter-preset TruSeq --zip-output GZ -qf i1.8
Trimmed reads were aligned to the Ensembl GRCh38 (hg38) primary assembly, supplemented with the rat Apobec1 sequence, using STAR (v2.7.7) in paired-end mode with the following options: --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMattributes All --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5. Duplicate reads were then marked with STAR using the following options: --runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti.
Editing sites for each YTHDF fusion proteins were identified in Gencode V36 annotated transcripts with Bullseye v1.3.0 using the following parameters: --minEdit 2.5 --maxEdit 99 --editFoldThreshold 1.5 --EditedMinCoverage 10 --ControlMinCoverage 10 --MinEditSites 3
For STAMP, editing sites found in at least 2 biological replicates and with at least 1.5 fold editing over cells expressing APOBEC1 alone are selected.
For TRIBE, editing sites found in at least 4 biological replicates for YTHDF1 and YTHDF2 or 3 replicates for YTHDF3, and with at least 3 fold editing over cells expressing ADAR alone  are selected.
Assembly: hg38
Supplementary files format and content: bed file with the position of editing sites identified in TRIBE-STAMP for each YTHDF protein fusion proteins

molecule: total RNA

organism: Homo sapiens

source_name: Cultured cells

growth_protocol: Cells were grown in DMEM containing 10% Fetal bovine serum.

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNAseI treatment to remove any contaminating DNA.
For each sample 500ng of total RNA was used for library preparation. Library construction was performed using the NEBNEXT Ultra II Directional RNA-Seq kit and the NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: Expression of YTHDF-APOBEC1 was induced by treating cells with 1 ug/mL of doxycycline for 24 h. Cells were transfected with YTHDF1-, YTHDF2-, YTHDF3-ADAR, ADAR alone or APOBEC1 alone containing plasmids by lipofection using Fugene HD.

tag: cell type

value: HEK293T cells

tag: strain

tag: transfection

tag: library type

value: RNAseq


title: DF3.ADAR_DF2.IP.flag_Rep2

data_processing:
Raw sequencing reads from RNA-seq libraries were trimmed with Flexbar (v3.5.0) with the following parameters: --adapter-preset TruSeq --zip-output GZ -qf i1.8
Trimmed reads were aligned to the Ensembl GRCh38 (hg38) primary assembly, supplemented with the rat Apobec1 sequence, using STAR (v2.7.7) in paired-end mode with the following options: --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMattributes All --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5. Duplicate reads were then marked with STAR using the following options: --runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti.
Editing sites for each YTHDF fusion proteins were identified in Gencode V36 annotated transcripts with Bullseye v1.3.0 using the following parameters: --minEdit 2.5 --maxEdit 99 --editFoldThreshold 1.5 --EditedMinCoverage 10 --ControlMinCoverage 10 --MinEditSites 3
Raw gene counts were calculated using featureCounts v2.0.1 with the following options: -O -M -p --ignoreDup -t exon -g gene_id. RNA enrichment in RIP samples over input was measured with DESeq2.
For TRIBE, an editing score defined as the cummulative some of editing frequency at each called editing site was calculated for each annotated ensembl transcript. Editing frequencies were used for fitting in a quasibinomial glm to calculate log2foldchange and wald statistic for each conditions.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: Result of DESeq2 analysis for enrichment in each YTHDF RIP samples
Supplementary files format and content: Tab separated file containing the result of differential editing analysis performed with Bullseye using a quasibinomial GLM.


title: DF3.ADAR_DF2.IP.flag_Rep1


title: DF1.ADAR_DF1.APOBEC1_Rep2


title: DF2.ADAR_DF1.APOBEC1_Rep1

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF2_ADAR.bed
DF1_APOBEC1.bed


title: DF3.ADAR_DF3.IP.flag_Rep2


title: DF3.ADAR_DF3.IP.flag_Rep3


title: DF3.ADAR_DF3.Input.flag_Rep2

value: Input


title: DF3.ADAR_DF2.IP.flag_Rep3


title: DF3.ADAR_DF3.Input.flag_Rep1


title: DF3.ADAR_DF2.Input.flag_Rep3


title: DF3.ADAR_DF1.Input.flag_Rep1


title: DF2.ADAR_DF3.IP.flag_Rep2

description:
DF_FLAG_IP_DESeq2.txt
DF2_ADAR_editing_results.txt


title: DF2.ADAR_DF3.IP.flag_Rep3


title: DF2.ADAR_DF2.IP.flag_Rep2


title: DF3.ADAR_DF2.Input.flag_Rep2


title: DF2.ADAR_DF2.Input.flag_Rep3


title: DF2.ADAR_DF2.Input.flag_Rep2


title: DF3.ADAR_DF1.IP.flag_Rep3


title: DF3.ADAR_DF1.IP.flag_Rep2


title: DF2.ADAR_DF2.IP.flag_Rep1


title: DF2.ADAR_DF1.IP.flag_Rep2


title: DF1.ADAR_DF2.APOBEC1_Rep1

description:
library was sequenced using 150bp paired-end (_151PE) and 250bp paired-end (_251PE) protocols.
DF1_ADAR.bed
DF2_APOBEC1.bed


title: DF2.ADAR_DF1.IP.flag_Rep1


title: DF3.ADAR_DF2.Input.flag_Rep1


title: DF3.ADAR_DF1.IP.flag_Rep1


title: DF3.ADAR_DF1.Input.flag_Rep2


title: DF2.ADAR_DF3.IP.flag_Rep1


title: DF1.ADAR_DF3.IP.flag_Rep3

description:
DF_FLAG_IP_DESeq2.txt
DF1_ADAR_editing_results.txt


title: DF3.ADAR_DF1.Input.flag_Rep3


title: DF2.ADAR_DF3.Input.flag_Rep1


title: DF3.ADAR_DF3.Input.flag_Rep3


title: DF1.ADAR_DF3.IP.flag_Rep2


title: DF2.ADAR_DF3.Input.flag_Rep3


title: DF1.ADAR_DF3.IP.flag_Rep1


title: DF2.ADAR_DF3.Input.flag_Rep2


title: DF2.ADAR_DF2.IP.flag_Rep3


title: DF2.ADAR_DF2.Input.flag_Rep1


title: DF2.ADAR_DF1.IP.flag_Rep3


title: DF1.ADAR_DF3.Input.flag_Rep1


title: DF2.ADAR_DF1.Input.flag_Rep3


title: DF1.ADAR_DF2.Input.flag_Rep3


title: DF1.ADAR_DF2.IP.flag_Rep1


title: DF1.ADAR_DF2.Input.flag_Rep2


title: DF2.ADAR_DF1.Input.flag_Rep2


title: DF1.ADAR_DF1.Input.flag_Rep3


title: DF1.ADAR_DF1.IP.flag_Rep1


title: DF1.ADAR_DF1.IP.flag_Rep2


title: DF2.ADAR_DF1.Input.flag_Rep1


title: DF1.ADAR_DF3.Input.flag_Rep3


title: DF1.ADAR_DF3.Input.flag_Rep2


title: DF1.ADAR_DF2.IP.flag_Rep3


title: DF1.ADAR_DF2.IP.flag_Rep2


title: fwa_H3.1_myc_ChIPseq

status: Public on Oct 27 2022

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: ChIP-seq data of H3.1 myc in fwa

library_source: genomic

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: tair10
Supplementary files format and content: bigWig
Supplementary files format and content: peak

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis floral tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants

extract_protocol: ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).

tag: tissue

value: floral tissue

tag: developmental stage

value: 5-6 weeks

tag: antibody

value: anti-myc

tag: target protein


title: fwa_H3.3_myc_ChIPseq

description: ChIP-seq data of H3.3 myc in fwa


title: ZF-ASF1B_H3.1_myc_ChIPseq_DNA_input

description: ChIP-seq data of H3.1 myc in ZF-ASF1B DNA input


title: fwa_myc_control_DNA_input

description: ChIP-seq data of myc control of H3.1 and H3.3  in fwa DNA input


title: fwa_myc_control

description: ChIP-seq data of myc control of H3.1 and H3.3  in fwa


title: ZF-ASF1B_H3.1_myc_ChIPseq

description: ChIP-seq data of H3.1 myc in ZF-ASF1B


title: DF1.ADAR_DF2.Input.flag_Rep1


title: asf1a1b_H3.3_Flag_ChIPseq_rep-2

description: ChIP-seq data of H3.3 flag in asf1a1b replicate 2

value: anti-FLAG M2 (Sigma)


title: H31_H33_flag_control_rep-2

description: ChIP-seq data of flag control of H3.1 and H3.3 replicate 2


title: DF1.ADAR_DF1.Input.flag_Rep2


title: DF1.ADAR_DF1.Input.flag_Rep1


title: ZF-ASF1B_H3.3_myc_ChIPseq_DNA_input

description: ChIP-seq data of H3.3 myc in ZF-ASF1B DNA input


title: DF1.ADAR_DF1.IP.flag_Rep3


title: Col-0_H3.3_Flag_ChIPseq_rep-2

description: ChIP-seq data of H3.3 flag in Col-0 replicate 2


title: Col-0_H3.1_Flag_ChIPseq_rep-2

description: ChIP-seq data of H3.1 flag in Col-0 replicate 2


title: fwa_H3.3_myc_ChIPseq_DNA_input

description: ChIP-seq data of H3.3 myc in fwa DNA input


title: Mouse forelimb motor neurons - RNA-seq 1 [Limb_MN-6]

status: Public on Oct 24 2022

city: Seoul

first: DongAhn

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Quality of RNA-seq raw reads were checked with FastQC (v. 0.11.9). Next, the raw data was trimmed for low quality and illumina truseq adapter sequences using trimmomatic-0.39 with the following options: “ILLUMINACLIP:[AdapterFile]:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50”. The resulting clean reads were aligned to GRCm38 for mouse and GRCg6a for chick with STAR (v. 2.7.5a) and were quantified using featureCounts.
To account for different gene length in multiple species, RPKM normalization implemented in python bioinfokit was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated file with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Forelimb motor neurons

extract_protocol:
Spinal cords of Hb9-GFP (Jackson laboratory) were dissociated and GFP+ MNs were manually collected. The regions for forelimb MNs were visualized under a fluorescence dissection scope and separated from other neurons using a sharp scalpel. The spinal cords were digested with pronase for 30min at RT.
The sequencing library was prepared using the TruSeq RNA sample prep Kit (Illumina, CA).

value: Forelimb motor neurons

value: 13.5 day mouse embryo


title: Mouse forelimb motor neurons - RNA-seq 3 [Limb_MN-8]


title: fwa_H3.1_myc_ChIPseq_DNA_input

description: ChIP-seq data of H3.1 myc in fwa DNA input


title: Reh_dCas9-KRAB+sgCtrl_r2_RNA-Seq

status: Public on Oct 22 2022

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

data_processing:
RNA-Seq quantification was performed with Salmon 0.11.3. A salmon index (-k 31) was generated from Ensembl release 75 transcripts.
Transcript-level expression was then quantified (salmon quant -l --incompatPrior --validateMappings) from paired-end RNA-Seq data.
Assembly: hg38 / ENSEMBL 2014
Supplementary files format and content: Salmon transcript quantification files

source_name: Reh cell line

growth_protocol: All cell lines were cultured in RPMI 1640 + Glutamax supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1 mM sodium pyruvate, and 55 micromolar 2-mercaptoethanol

extract_protocol:
RNA was isolated via RNEasy columns with on-column DNAase digestion.
RNA-seq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina per manufacturer’s instructions

treatment_protocol: DoxOn vector-transduced Reh cell populations (tagBFP or ETV6) were induced with 500 ng/ml doxycycline (dox) for 48 hours prior to harvest for RNA-Seq. Reh cell populations with stable integration of dox-inducible dCas9-KRAB were transduced with fluorescent reporter sgRNA vectors against ERG promoter or non-targeting, were sorted, and then were induced with 500 ng/ml doxycycline (dox) for 72 hours prior to harvest for RNA-Seq

tag: cell line

value: Reh

value: B-lymphoblastic leukemia cell line

tag: transgene

tag: drug treatment

value: doxycycline

tag: data type

value: RNA-Seq


title: Reh_dCas9-KRAB+sgCtrl_r1_RNA-Seq


title: NALM6_ERG_ChIP-Seq

data_processing:
Paired-end reads were aligned to hg38 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to retain only paired reads in a proper pair (flags: 0x1, 0x2), and to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800).
Reads were filtered to retain only read-pairs mapping to <=2 sites genome-wide (X0 tag <=2 for both reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg38
Supplementary files format and content: bigwig (hg38 fragment coverage, normalized to fragments per million post-filtering)

source_name: NALM6 cell line

extract_protocol:
Twenty million cells were cross-linked in PBS + 1% formaldehyde for 10 minutes at 37C (TFs), quenched with 1/20th volume of 2.5M glycine, washed twice in cold PBS with protease inhibitors, and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g, and resuspended in cold SDS lysis buffer (0.3% SDS for H3K27ac and 1% SDS for TFs, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes. Nuclei were fragmented on a Q800R2 Sonifier (QSonica) as follows: three cycles of amplitude = 50, pulse times: 30s on / 30s off, total on time = 3:20 m, temperature = 80C (histone marks) or two cycles of amplitude = 70, pulse times: 45s on / 15s off, total on time = 8:50 m, temperature = 40C (TFs). Samples were diluted 1:3 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4°C overnight with 2-5 ug of antibody. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After reversal of cross-linking, RNase and proteinase K treatment were performed and DNA was purified with Ampure XP beads for library preparation. Input sample was prepared by the same approach without immunoprecipitation.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated (Quick T4 DNA ligase, NEB) to barcoded illumina adaptors (Single-Indexed Adapter Kit, KAPA, #KK8700). Each reaction was followed by clean-up with AMPure XP beads. Ligation products were amplified by PCR for 14-18 cycles with illumina indexing primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection.

value: ChIP-Seq

tag: chip-seq antibody

value: ERG (Cell Signaling Technologies # 97249)


title: AT1_ERG_ChIP-Seq

source_name: AT1 cell line


title: ZF-ASF1B_H3.3_myc_ChIPseq

description: ChIP-seq data of H3.3 myc in ZF-ASF1B


title: Reh_dCas9-KRAB+sgERG_r1_RNA-Seq


title: Reh_dCas9-KRAB+sgERG_r2_RNA-Seq


title: SEM_ETV6_Atlas_ChIP-Seq

source_name: SEM cell line

value: SEM

value: ETV6 (Atlas Antibodies #HPA000264)


title: Reh_ETV6_Atlas_ChIP-Seq


title: Exp2, st16-foxa1MO

status: Public on Oct 18 2022

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

country: Germany

institute: University Freiburg Medical Center

data_processing:
Quality control was done using FastQC v0.11.5
paired-end reads were mapped to Xenopus laevis genome assembly v9.2 using RNA STAR v2.6.0b-1
featureCounts v1.6.3 was used to count uniquely mapped reads per gene
statistical analysis of differential gene expression was conducted in DEseq2 v1.22.1
Assembly: X. laevis v9.2 genome assembly
Supplementary files format and content: tabular results files derived from DESeq2 (column names:  GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj)
Supplementary files format and content: GEO-XenIDSymbol_Walentek_2022 contains GeneIDs and Gene Names

organism: Xenopus laevis

source_name: epidermis, animal cap explant, st16

growth_protocol: Explants were cut from the animal portion of stage 8 Xenopus laevis embryos in 1x Modified Barth's Saline (MBS), then they were maintained in the medium for at least 1 hour to heal. After healing of explants, they were transferred to 0.5x MBS containing 0.1% of Gentamycin and cultured in that medium until they reached the indicated stage.

extract_protocol:
Total RNA was extracted using the standard Trizol protocol.
500 ng total RNA per sample was used, poly-A selection and RNA-sequencing library preparation was done using non strand massively-parallel cDNA sequencing (mRNA-Seq) protocol from Illumina, the TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation. Quality and integrity of RNA was assessed with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (Advanced Analytical #DNF-471). All samples selected for sequencing exhibited an RNA integrity number over 8. For accurate quantitation of cDNA libraries, the QuantiFluor™dsDNA System from Promega was used. The size of final cDNA libraries was determined using the dsDNA 905 Reagent Kit (Advanced Bioanalytical #DNF-905) exhibiting a sizing of 300 bp on average. Libraries were pooled and paired-end 100bp sequencing on a HiSeq4000 was conducted at the Vincent J. Coates Genomics Sequencing Lab, University of California at Berkeley.

treatment_protocol: Control embryos remained untreated, while suh-dbm (100ng/ul), suh-dbm+dnmcidas (100ng/ul each), nicd (120ng/ul), and foxa1MO (3pmol) samples were injected 4 times into the animal hemisphere at four-cell stage with indicated mRNA/MO concentrations.

tag: exp

value: epidermis, animal cap explant

tag: genotype

value: wt

tag: treatment

value: foxa1 MO injected


title: asf1a1b_H3.1_Flag_ChIPseq_rep-2

description: ChIP-seq data of H3.1 flag in asf1a1b replicate 2

value: floral tissue


title: UoCB6_ETV6_Atlas_ChIP-Seq

source_name: UoCB6 cell line


title: Exp2, st32-foxa1MO

source_name: epidermis, animal cap explant, st32


title: Exp2, st10.5-foxa1MO

source_name: epidermis, animal cap explant, st10.5


title: Exp2, st25-nicd

source_name: epidermis, animal cap explant, st25

value: nicd mRNA injected


title: Colon B6+Colon B6 CR

status: Public on Oct 25 2022

city: Basel

first: Costanza

last: Borrelli

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zürich

description:
multiplexed in run Eos_revisionB6, Sample Tag 8 = ColonB6
multiplexed in run Eos_revisionB6, Sample Tag 9 = ColonB6CR

library_source: transcriptomic single cell

data_processing:
raw FASTQ processing on the Seven Bridges Genomics platform with default parameters
Assembly: mm9
Supplementary files format and content: cell x read count matrix as .st data, convert to sparse matrix with function on github repository

molecule: polyA RNA

source_name: mixed sample (non-demultiplexed)

extract_protocol:
magnetic enrichment (MACS) based on anti-SiglecF-Pe and anti-PE magnetic beads or anti-CD45 microbeads (for B6)
BD Rhapsody: WTA kit and Mouse Multiplexing Kit

treatment_protocol: when indicated, mice where infected with C.rodentium by gavage

value: Colon

value: CD45+ cells enriched by MACS

value: steadystate + C.Rodentium infection


title: Exp2, st10.5-nicd


title: Exp2, st32-suh-dbm+dnmcidas

value: suh-dbm + dnmcidas mRNA injected


title: Exp2, st16-suh-dbm+dnmcidas


title: Adipose+Lung+Uterus

description:
multiplexed in run Eos_revision, Sample Tag 3 = Adipose
multiplexed in run Eos_revision, Sample Tag 1 = Lung
multiplexed in run Eos_revision, Sample Tag 5 = Uterus

value: Adipose tissue + Lung + Uterus

value: SiglecF+ eosinophils enriched by MACS

value: steadystate


title: Reh_dCas9-KRAB+sgCtrl_r3_RNA-Seq

value: Reh

value: B-lymphoblastic leukemia cell line

value: doxycycline

value: RNA-Seq


title: UoCB6_input

value: input chromatin


title: Exp2, st25-suh-dbm

value: epidermis, animal cap explant

value: suh-dbm mRNA injected


title: NALM6_ETV6_Atlas_ChIP-Seq

value: ChIP-Seq

value: ETV6 (Atlas Antibodies #HPA000264)


title: Exp2, st25-ctrl

value: wt

value: control


title: Exp2, st10.5-suh-dbm


title: Exp2, st16-ctrl


title: Exp2, st25-foxa1MO

value: foxa1 MO injected


title: CHIP_mild

status: Public on Oct 19 2022

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

data_processing:
Raw sequencing outputs were automatically converted to fastq file by the sequencer built-in software
raw fastq files were de-multiplexed into relative fastq files for each samples with truncated index sequence through splitBarcode version 0.1.6 provided by MGI Tech.
The demultiplexed files were aligned using cellranger count (v3.0.2; --r1-length 28 --r2-length 91) to cellranger reference GRCh38 (v 3.0.0).
Assembly: hg38
Supplementary files format and content: gene expression count matrix, cell barcode information, and gene name list in gzfile format

source_name: PBMC

extract_protocol:
polyA RNA was extracted using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
droplet based single cell RNA seq: The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.

value: blood

tag: patient type

value: CHIP


title: Exp2, st32-nicd

value: nicd mRNA injected


title: CHIP_uninfected


title: Exp1, st10.5-foxa1MO


title: Mouse forelimb motor neurons - RNA-seq 2 [Limb_MN-7]

value: Forelimb motor neurons

value: 13.5 day mouse embryo


title: Exp2, st16-nicd


title: Reh_dCas9-KRAB+sgERG_r3_RNA-Seq

value: Reh

tag: cell type


title: Exp2, st25-suh-dbm+dnmcidas

value: suh-dbm + dnmcidas mRNA injected


title: Exp1, st16-suh-dbm+dnmcidas


title: Exp2, st10.5-suh-dbm+dnmcidas


title: Exp2, st32-suh-dbm


title: Exp1, st32-foxa1MO


title: Exp1, st32-suh-dbm


title: Exp1, st25-suh-dbm


title: Exp2, st16-suh-dbm


title: Exp2, st32-ctrl


title: Liver D10 KO, rep2

status: Public on Oct 17 2022

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: counts.txt

source_name: Liver in vivo D10

growth_protocol: cells were isolated from mouse liver at day 10 post tamoxifen induction

extract_protocol:
Mice were intravital injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with tamoxifen to induce gene deletion

value: Erg and Fli1 double knockout

value: Liver

value: Liver in vivo ECs

tag: age


title: Exp1, st16-foxa1MO

value: epidermis, animal cap explant


title: Exp1, st25-foxa1MO


title: Exp1, st32-suh-dbm+dnmcidas


title: Exp1, st32-nicd


title: Exp1, st25-nicd


title: Exp1, st10.5-nicd


title: Exp1, st25-suh-dbm+dnmcidas


title: Exp1, st16-nicd


title: Liver D10 KO, rep1


title: Exp2, st10.5-ctrl


title: Exp1, st10.5-suh-dbm+dnmcidas


title: Exp1, st16-suh-dbm

value: suh-dbm mRNA injected


title: Exp1, st10.5-suh-dbm


title: Exp1, st32-ctrl


title: Exp1, st25-ctrl


title: Exp1, st16-ctrl


title: Liver D10 KO, rep3


title: Exp1, st10.5-ctrl


title: RING2/RING1B/RNF2_ChIP_in_ESC

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

description:
Sample 4
61-D0-RNF2_0621_bam_peaks.narrowPeak

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 .
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 1-13, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and "merge500bp" imply merging the peaks within the distance of 1 kb and 500 bp, since MACS2 sometimes splits long peaks, verified in UCSC tracks.

source_name: Human embryonic stem cells

growth_protocol: Human ESC lines H7 were maintained on Matrigel-coated plates (Growth Factor Reduced, BD Biosciences) in mTeSR Medium (STEMCELL Technologies). The medium was changed every day.

extract_protocol:
Chromatin immunoprecipitation (ChIP) and ChIP-seq were performed as described previously (Lan et al., 2007; Niu et al., 2021). Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.125 M glycine for 10 minutes; then, the cell pellets were wash twice by cold PBS, and then resuspended in high salt Lysis buffer (50 mM HEPES/KOH, pH 7.5, 500 mM NaCl, 1% Trixon-X 100, 0.05% SDS, 10 mM EDTA, and proteinase inhibitors), and sonicated with Qsonica (Misonix) to shear the chromatin into 200- to 400-bp lengths. Chromatin was immunoprecipitated with the indicated antibodies overnight and MagPoly protein A/G magnetic beads (Smart, Changzhou, China) for 2 hours. Then the beads were washed 3 times of high salt lysis buffer, 3 times of low salt buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40, 0.5% Na-Deoxycholate), once of 50mM HEPES/KOH, pH 7.5, and DNA was eluted in elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) with Proteinase K (Invitrogen-Thermo Fisher, Waltham, MA) in 72℃ for 3 hours. DNA was isolated by MinElute PCR Purification Kit (QIAGEN 28006). RNA-seq: Total RNA was isolated using TRIzol (Life Technologies). Non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module (Excell Bio, Shanghai, China), and sequencing libraries were prepared with the TrueLib mRNA Library Prep Kit for Illumina (ExCell Bio, Shanghai, China). Hi-C: 1,000,000 Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.2 M glycine for 5 minutes; then, the cell pellets were wash twice by ice cold PBS, and then resuspended in 300 μl of ice cold Hi-C lysis buffer (10 mM Tris-HCl 8.0, 10 mM NaCl, 0.2% NP40, cOmplete Ultra protease inhibitors) and incubated on ice for 15 min. Samples were then centrifuged and washed once with 500 μl of ice cold Hi-C lysis buffer. Nuclei were centrifuged (2,500 g for 5 min at 4℃) and permeabilized by resuspending them in 20 μl of 0.5% SDS and incubating at 62℃ for 10 min with shaking (1,000 rpm). SDS was quenched by adding 58 μl of nuclease-free water and 10 μl of 10% Triton X-100 and incubated at 37℃ for 15 min with shaking (1,000 rpm). Chromatin was digested by adding 100 U of DpnII and 10 μl of 10x DpnII buffer for 2 hours at 37℃ with rotation. DpnII was heat-inactivated at 62℃ for 20 min. The overhangs generated by the restriction enzyme were filled-in by adding a mix of  0.4 mM biotin-dATP (10 μl; PicoHeliex), 10 mM dCTP/dGTP/dTTP (0.5 μl of each dinucleotide), and 5 U/μl DNA polymerase I，Large（Klenow）Fragment (8 μl; New England Biolabs), and incubated for 90 min at 37℃ with rotation. DNA fragments were ligated in 10X T4 DNA ligase buffer (5 μl), 10mM dATP(10 μl), 10 mg/mL BSA (1.5 μl) and 400 U/μl T4 DNA ligase (1.5 μl; NEB) by incubating 8 hours at 20℃. Protein and RNA were digested by adding 5 μl of 20 mg/mL Proteinase K (Thermo Scientific), 10 mg/ml RNase A (2 μl ; Thermo Scientific), 20 μl of 10% SDS and 25 μl of nuclease-free water and incubated at 65℃ with shaking (1,000 rpm) for 8 hours. Phenol-Chloroform-Isoamyl alcohol (25:24:1; Solarbio) extracted DNA was resuspended in 110 μl of 10mM Tris pH 8.0 and incubated for 15 min at 37℃. Samples were sheared using a Qsonica sonicator (6 cycles, each 30 s, 80% duty). DNA size was selected with VAHTS DNA Clean Beads (Vazyme Biotech, Nanjing, China) to get 250 – 500 bp length of DNA fragments dissolved in 300 μl of 10mM Tris pH 8.0. Biotinylated DNA fragments were pulled down using Streptavidin MagPoly Beads (30 μl; Smart Lifesciences, Changzhou, China) supplemented with 300μl of 2X binding buffer (10mM Tris pH 7.5, 1mM EDTA, 2M NaCl) and incubated in 25℃ with rotation for 15 min. The biotinylated DNA fragments on streptavidin beads were washed twice with 600 μl of Tween Wash buffer (5mM Tris pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) incubated in 55℃ with shaking (800 rpm) for 2min. The Hi-C DNA libraries were prepared as directed by the protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China).
ChIP DNA libraries, input DNA libraries and HiC DNA libraries were prepared as directed by protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China).

treatment_protocol: hESCs were differentiated into beating cardiomyocytes using a small-molecule-based monolayer method that has been described previously (Lian et al., 2012). Briefly, hESCs at ~90% confluence were incubated with differentiation basal medium comprising RPMI 1640 medium (Corning Cellgro) and B27 supplement minus insulin (Invitrogen). 6 μM GSK-3β inhibitor CHIR99021 (Selleck Chem) was added into differentiation basal medium for 2 days. After 2 days, the medium was changed to differentiation basal medium minus CHIR99021 for 24 h, followed by differentiation basal medium supplemented with 5 μM Wnt inhibitor IWR-1 (Selleck Chem) for 2 days, then differentiation basal medium for another 2 days, and finally changed to CDM3 medium containing RPMI 1640 supplemented with BSA and ascorbic acid (Figure S1B). Beating cells should be observed at around day 8 after differentiation. Monolayers of CMs derived from hESCs (hESC-CMs) were cultured for defined days and subsequently dissociated for experimental use using TrypLE Express (Life Technologies). Specific day time point of five selected stages are day 0 (hESC), day 2 (mesoderm, MES), day 4 (cardiac progenitor, CP), day12 (cardiomyocyte, CM), and day 35 (mature CM).

value: Human embryonic stem cells

value: Wild type

tag: chip antibody

value: Rabbit Polyclonal anti-RNF2, Bethyl, A302-869A; RRID:AB_10632773


title: Liver D10 Control, rep3

value: Wild Type


title: H3K4me3_ChIP_in_CPC_rep2

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 or MACS1.4.
Assembly: hg19
Supplementary files format and content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks called by MACS2 using corresponding ChIP-seq data and input data, and blacklist regions were filtered out. In these narrowPeaks files, "merge1k" implies merging the peaks within the distance of 1,000 bp, since MACS2 sometimes splits long peaks, which is verified in UCSC tracks. q0.001, q0.0001 and p0.001 indicate the q value and p value cutoff of ChIP-seq peaks, which is verified in UCSC tracks.

source_name: Human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: Rabbit mAb anti-H3K4me3 (Cell Signaling Technology, Cat# 9751)


title: Liver D10 Control, rep2


title: ATACseq_Chd8cHet_2

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
Assembly: mm10
Supplementary files format and content: wig files were generated by MACS14

source_name: mouse E14.5 NPCs

extract_protocol: ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 50,000 sorted cells from the mouse cortex in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.

treatment_protocol: ATAC-seq: For GFP+ NPC sorting, single cell suspension was prepared from E14.5 control and Chd8 cKO mouse cortices with papain dissociation, and cells were resuspended in PBS with 2 mM EDTA and 0.5% BSA for sorting.

tag: sample type

value: Chd8 cHet

tag: genotype/variation

value: Chd8 c/+, Emx1-cre, ccGFP

value: FACS sorted GFP+ NPCs


title: RING2/RING1B/RNF2_ChIP_in_CPC_rep2

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 or MACS1.4.
Assembly: hg19
Supplementary files format and content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks called by MACS2 using corresponding ChIP-seq data and input data, and blacklist regions were filtered out. In these narrowPeaks files, "merge500" implies merging the peaks within the distance of 500 bp, since MACS2 sometimes splits long peaks, which is verified in UCSC tracks.

value: Human cardiac progenitor cells (day 4 post differentiation from ESCs)


title: Liver D10 Control, rep1

tag: tissue


title: RING1A_ChIP_in_MESP1-KO_CPC_rep2

description: Sample 40

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 or MACS1.4.
Assembly: hg19
Supplementary files format and content: "10_Flag-MESP1_0.1_220620_m1-black.peaks.bed"  is  tab-delimited text files for ChIP-seq peaks in Sample 38, which is called by macs 1.4. ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 39 and 40, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and  imply merging the peaks within the distance of 1 kb, since MACS2 sometimes splits long peaks, verified in UCSC tracks.

source_name: MESP1 knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: MESP1 -/-

tag: antibody

value: Rabbit Polyclonal anti-RING1A, Cell Signaling Technology, 2820; RRID:AB_2177962


title: RING2/RING1B/RNF2_ChIP_in_CPC

description:
Sample 5
73-D4-RNF2_0621_bam_peaks.narrowPeak


title: input_CPC

description:
Sample 13
68-D4-RING1A_0621-black.narrowPeak
73-D4-RNF2_0621_bam_peaks.narrowPeak
75_RING1_D4_WT-hESC_200908-black.narrowPeak


title: input_ESC

description:
Sample 12
14-D0-RING1A_0621_bam_peaks.narrowPeak
61-D0-RNF2_0621_bam_peaks.narrowPeak


title: RING1A_ChIP_in_WT_CPC (re-sequenced)

description:
Sample 36
75-RING1_D4_WT_20.09.08+21.11.16-black.merge1kb.narrowPeak

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2 in pair-end mode.
ChIP-seq peaks were called by MACS2 .
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 1-13, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and "merge500bp" imply merging the peaks within the distance of 1 kb and 500 bp, since MACS2 sometimes splits long peaks, verified in UCSC tracks.


title: H3K27ac_ChIP_in_WT_CPC_rep2

value: Rabbit polyclonal anti-H3K27ac (Millipore, Cat# 07-360)


title: RING1A_ChIP_in_CPC_rep1

description:
Processed data:
68-D4-RING1A_0621-black.narrowPeak
68-D4-RING1A_0621_merge500bp-black.narrowPeak
68-D4-RING1A_0621_q0.0001-blacklist.narrowPeak


title: H3K27ac_ChIP_in_RING1A-KO_CPC_rep2

source_name: RING1 knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: RING1A knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: RING1A -/-


title: RING1A_ChIP_in_WT_CPC_rep2

description: Sample 39


title: RING1A_ChIP_in_ESC_rep2


title: FLAG-MESP1_ChIP_in_Dox+MESP1_CPC_rep2

description: Sample 38

source_name: Dox induced FLAG-MESP1 overexpressed human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: Dox induced FLAG-MESP1 overexpressed human cardiac progenitor cells ( day 4 post differentiation from ESCs)

value: Rabbit mAb anti-DYKDDDDK Tag (D6W5B) , Cell Signaling Technology, 14793


title: mRNA-seq_WT_D6_CPC_rep1

description:
Sample 27
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
RNA-seq data were mapped to the human genome hg19 using hisat2 and assembled by homer to get counts by million (CPM).
Differentially expressed genes were generated by DEseq2 with fold change > or = 2 and p <0.05.
Genome_build: hg19
Supplementary_files_format_and_content: "diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx" and "diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx" files are RNA-seq gene expression data (log2CPM) and differentially expressed in WT, MESP1-KO and RING1-KO CPCs for Sample 18-35.

source_name: Human cardiac progenitor cells (day 6 post differentiation from ESCs)


title: mRNA-seq_WT_D6_CPC_rep2

description:
Sample 28
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx


title: ATACseq_Chd8cHet_1


title: mRNA-seq_RING1A-KO_D6_CPC_rep3

description:
Sample 35
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx

source_name: RING1 knockout human cardiac progenitor cells (day 6 post differentiation from ESCs)


title: mRNA-seq_RING1A-KO_D4_CPC_rep2

description:
Sample 25
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: mRNA-seq_WT_D6_CPC_rep3

description:
Sample 29
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx


title: mRNA-seq_MESP1-KO_D6_CPC_rep3

description:
Sample 32
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx

source_name: MESP1 knockout human cardiac progenitor cells (day 6 post differentiation from ESCs)

value: MESP1 knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)


title: mRNA-seq_RING1A-KO_D6_CPC_rep1

description:
Sample 33
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx


title: RING2/RING1B/RNF2_ChIP_in_ESC_rep2

value: Human embryonic stem cells


title: mRNA-seq_MESP1-KO_D6_CPC_rep2

description:
Sample 31
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx


title: mRNA-seq_MESP1-KO_D4_CPC_rep3

description:
Sample 23
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: mRNA-seq_MESP1-KO_D4_CPC_rep1

description:
Sample 21
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: mRNA-seq_RING1A-KO_D6_CPC_rep2

description:
Sample 34
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx


title: RING1A_ChIP_in_ESC

description:
Processed data:
14-D0-RING1A_0621_bam_peaks.narrowPeak

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 .
RNA-seq data were mapped to human genome hg19 using hisat2 and assembled by homer to get couts by million (CPM).
Differentially expressed genes were generated by DEseq2 with fold change > or = 2 and p <0.05.
Reads were aligned and quality-controlled through HiC-Pro 2.11.1 . Next, 2 replicates of WT samples were merged, and 2 replicates of RING1-KO samples were merged. Finally, the merged allValidPairs files were converted to .hic files. Hi-C loops were called by Homer and cLoops2 and merged together. Differential enriched loops for WT and RING1-KO samples were identified by cLoops2 callDiffLoops.
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 1-13, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and "merge500bp" imply merging the peaks within the distance of 1 kb and 500 bp, since MACS2 sometimes splits long peaks, verified in UCSC tracks.  ".hic" files are HiC-Pro mapped and hicpro2juicebox.sh conveted Hi-C results for Sample 14-17. "diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx" and "diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx" files are RNA-seq gene expression data (log2CPM) and differentially expressed in WT, MESP1-KO and RING1-KO CPCs.

value: Wild type


title: mRNA-seq_MESP1-KO_D6_CPC_rep1

description:
Sample 30
diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx


title: mRNA-seq_WT_D4_CPC_rep2

description:
Sample 19
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: mRNA-seq_RING1A-KO_D4_CPC_rep1

description:
Sample 24
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: Erg Fli1 dKO Liver Ecs day 12 post tamoxifen administration 1

description:
Erg Fli1 dKO
5_45_KO_Liver_EC_S37

source_name: in vivo liver

growth_protocol: cells were isolated from mouse liver

value: endothelial cells

tag: time points

value: 12 days post tamoxifen

value: in vivo liver


title: mRNA-seq_MESP1-KO_D4_CPC_rep2

description:
Sample 22
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: Control Liver Ecs day 12 post tamoxifen administration 1

description:
control
4_43_Ctrl_Liver_EC_S36


title: H3K4me3_ChIP_in_CPC

description:
Sample 9
75_K4me3_D4_210327-black.narrowPeak

value: Rabbit mAb anti-H3K4me3 (Cell Signaling Technology, Cat# 9751)


title: mRNA-seq_WT_D4_CPC_rep3

description:
Sample 20
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: H3K27ac_ChIP_in_RING1A-KO_CPC_rep1

description:
Sample 11
73_K27ac_R1KO_D4_1213-black.narrowPeak

source_name: RING1A knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: RING1A-KO human cardiac progenitor cells (day 4 post differentiation from ESCs)


title: RING1A_ChIP_in_MESP1-KO_CPC

description:
Sample 8
78-RING1_D4_MESP1-KO_20.09.08+21.11.16-black.narrowPeak
78_RING1_D4_KO-MESP1_200908-black.narrowPeak


title: RING1A_ChIP_in_CPC_rep2

description:
Sample 3
75_R1_D4_S141+S029_190119_bam_peaks-black.narrowPeak


title: mRNA-seq_RING1A-KO_D4_CPC_rep3

description:
Sample 26
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: FLAG-MESP1_ChIP_in_Dox+MESP1_CPC

description:
Sample 6
30_Flag-MESP1_Dox0.03_D4_201012-blacklist.narrowPeak
30_Flag-MESP1_Dox0.03_D4_201012_q0.0001-blacklist.narrowPeak

source_name: Dox induced FLAG-MESP1 overexpressed human cardiac progenitor cells ( day 4 post differentiation from ESCs)


title: RING1A_ChIP_in_WT_CPC

description:
Sample 7
75-RING1_D4_WT_20.09.08+21.11.16-black.merge1kb.narrowPeak


title: mRNA-seq_WT_D4_CPC_rep1

description:
Sample 18
diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx


title: Erg Fli1 dKO Liver Ecs day 12 post tamoxifen administration 2

description:
Erg Fli1 dKO
6_46_KO_Liver_EC_S38


title: ZNF382 construct replicate 1

status: Public on Oct 15 2022

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

library_source: other

data_processing:
[Preliminary processing for each sample] Counting the number of Bound and Unbound reads for each sample. The negative logarithmic ratio of Bound and Unbound reads can be calculated as the relative binding energy for each binding sites.
[Data quality check between replicates] Cross comparison between replicate samples reveals the resolution of each sample, usually around 0.2kT for individual site.
[Specificity and methylation sensitivity analysis] The motif or specificity profile can be constructed by regression of binding energy values of select sequences, e.g., some reference site and all of its single/double variants. TFCookbook package, which contains all necessary codes to analyze the TF-DNA motif profile, can be accessed through https://github.com/zeropin/zeropin/TFCookbook.
Supplementary_files_format_and_content: For each sample, the associated csv file contains the bound and unbound reads, calculated relative bindng energy, library type, and the number of mismatches to some reference site for individual binding site. The data analysis protocol for each ZFP can be accessed through Github https://github.com/zeropin/ZFPCookbook
Library strategy: Spec-seq

molecule: other

organism: synthetic construct

source_name: Spec-seq sample to synthetic DNA library

extract_protocol:
[Recombinant protein expression protocol] We used the NEB PURExpress or E. coli(BL21) system to produce N-terminal HALO tagged ZFP constructs and noticed better success rates than previously used SUMO-tagged constructs.
[EMSA protocol] 20uL binding reactions were loaded onto 10% Tris-glycine gel in cold room and run for 50mins at 200V.
[Sequencing sample prep protocol] The bound and unbound fractions of each sample were cut separately as thin gel slice, extracted by acrylamide gel extraction buffer (soaking a 55C for more than 30mins). Each fraction of DNA pool was purified and further amplified by uniquely indexed Illumina primers set for at least 12 cycles (annealing temperature 52C, extension time 30s). All samples were pooled together for Illumina Nextseq (1X 75bp single end run).

tag: recombinant protein

value: ZNF382 construct


title: 10512R_CD80pos

status: Public on Oct 13 2022

city: New Orleans

first: James

middle: G

last: Jackson

state: LA

address: 1430 Tulane

institute: Tulane

data_processing:
DNA was run on NextSeq 500/550 Hi Output Kit and the NextSeq 500 Illumina Sequencer.
Excel, bindetect results of PD-L1-positive cells versus CD80-positive cells

source_name: Mammary tumor cells

growth_protocol: MMTV-Wnt1 tumor transplanted into C57BL6j mouse

extract_protocol:
Tumors were digested by GentleMACs, and CD80-positive cells were magnetically extracted from CD45-negative cells. 50,000 nuclei were processed for tagmentation and adaptor incorporation at accessible chromatin sites
Nextera DNA Library prep kit

treatment_protocol: Mice with transplanted tumors were treated with 5 consecutive doses of 4mg/kg doxorubicin. Tumors were harvested 48h after final dose.

value: tumor cells

value: CD80-positive cells magnetically sorted from tumor

tag: genome build


title: 10512R_PDL1pos

extract_protocol:
Tumors were digested by GentleMACs, and PD-L1-positive cells were magnetically extracted from CD45-negative cells. 50,000 nuclei were processed for tagmentation and adaptor incorporation at accessible chromatin sites
Nextera DNA Library prep kit

value: PDL1-positive cells magnetically sorted from tumor


title: ZNF382 construct replicate 2


title: 10500R_CD45neg

data_processing:
DNA was run on NextSeq 500/550 Hi Output Kit and the NextSeq 500 Illumina Sequencer.
Excel, bindetect results of PD-L1-positive cells versus CD45-negative cells

extract_protocol:
Tumors were digested by GentleMACs, and CD45-negative cells magnetically extracted. 50,000 nuclei were processed for tagmentation and adaptor incorporation at accessible chromatin sites
Nextera DNA Library prep kit

treatment_protocol: No treatment

value: CD45-negative cells magnetically sorted from tumor


title: 10512L_PDL1pos


title: MMTV_Wnt1_TCell_Doxo_CTLA4

data_processing:
Data were processed using CellRanger for UMI processing and filtering
Feature matrix

extract_protocol:
Tumors were digested by GentleMACs, and CD4/8-positive T cells magnetically extracted
Barcoded, single-cell beads in emulsion were made and reverse transcribed according to manufacturer instructions (Chromium Single Cell 3' Reagents Kit)

treatment_protocol: Mice with transplanted tumors were treated with 5 consecutive doses of 4mg/kg doxorubicin. 48h later, mice were treated with 200ug anti-CTLA4 and 200ug IgG control once every 72h, for three total doses. Tumors were harvested 24h after final dose.

value: T_Cells harvested from mammary tumor

value: Doxorubicin and anti-CTLA4 treated

value: GRCm38 - mm10


title: 10500L_CD45neg


title: MMTV_Wnt1_TCell_Doxo_IgG

treatment_protocol: Mice with transplanted tumors were treated with 5 consecutive doses of 4mg/kg doxorubicin. 48h later, mice were treated with 400ug IgG control once every 72h, for three total doses. Tumors were harvested 24h after final dose.

value: Doxorubicin and IgG treated


title: 10512L_CD80pos


title: MMTV_Wnt1_TCell_Doxo48h

value: Doxorubicin treated (48 hour harvest)


title: MMTV_Wnt1_TCell_Doxo_Combo

treatment_protocol: Mice with transplanted tumors were treated with 5 consecutive doses of 4mg/kg doxorubicin. 48h later, mice were treated with 200ug anti-CTLA4 and 200ug anti-PD-1 once every 72h, for three total doses. Tumors were harvested 24h after final dose.

value: Doxorubicin and anti-PD1/CTLA4 treated


title: MMTV_Wnt1_TCell_Unt

value: No treatment


title: MMTV_Wnt1_TCell_Doxo_PD1

treatment_protocol: Mice with transplanted tumors were treated with 5 consecutive doses of 4mg/kg doxorubicin. 48h later, mice were treated with 200ug anti-PD1 and 200ug IgG control once every 72h, for three total doses. Tumors were harvested 24h after final dose.

value: Doxorubicin and anti-PD1 treated


title: 4226-Prol-1

data_processing:
RNA-seq was performed using BGISEQ-500, single-end 50-bp, 20 million reads per sample
Excel, gene expression matrix of contol, doxo-rx, IFNg-rx, and doxo plus IFNg-rx

source_name: Mammary tumor cell line

growth_protocol: Cells cultured from an MMTV-Wnt1 tumor in full DMEM media

extract_protocol:
RNA was harvested by trizol extraction
Library construction was performed by BGI

value: mammary tumor cells


title: 4226-Prol+IFN-3

treatment_protocol: Cells were treated with 10ng/ml of rIFNg. Cells were harvested 24h later.

value: IFNg treated


title: MMTV_Wnt1_Immune_Unt_2

extract_protocol:
Tumors were digested by GentleMACs, and CD45-positive cells magnetically extracted
Barcoded, single-cell beads in emulsion were made and reverse transcribed according to manufacturer instructions (Chromium Single Cell 3' Reagents Kit)

value: CD45+ immune cells harvested from mammary tumor


title: 4226-Prol-3


title: 4226-Prol+IFN-2


title: MMTV_Wnt1_Immune_Doxo_2

value: Doxorubicin treated


title: MMTV_Wnt1_Immune_Unt_1


title: 4226-Doxo+IFN-3

treatment_protocol: Cells were treated with 750nM of doxorubicin for 24h. Media was then replaced. 6d later, cells were treated with 10ng/ml of rIFNg. Cells were harvested 24h later.

value: Doxorubicin and IFNg treated


title: 4226-Doxo-1

treatment_protocol: Cells were treated with 750nM of doxorubicin for 24h. Media was replaced and cells harvested 7d later


title: 4226-Prol+IFN-1


title: 4226-Doxo-2


title: 4226Doxo2_ATAC

data_processing:
DNA was run on NextSeq 500/550 Hi Output Kit and the NextSeq 500 Illumina Sequencer.
Excel, bindetect results of doxo-rx versus control

extract_protocol:
50,000 nuclei from 4226 cells were processed for Tn5-transposase-mediated tagmentation and adaptor incorporation at accessible chromatin sites.
Nextera DNA Library prep kit


title: 4226-Doxo+IFN-2


title: 4226Prolif2_ATAC


title: 4226-Doxo+IFN-1


title: 4226Doxo1_ATAC


title: 4226Prolif1_ATAC


title: 4226-Prol-2


title: MMTV_Wnt1_Immune_Doxo_1


title: 4226-Doxo-3


title: RNAseq.HUH7.C12.Rep1

status: Public on Oct 11 2022

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Cut & Tag, ATAC-Seq, and human RNA-seq samples were sequenced with the Illumina NextSeq 500 technology, and VERO RNA-seq samples were sequenced with Illumina NovaSeq 6000 technology.
RNAseq reads were aligned to the reference genomes hg19 and chlSab2 (NCBI annotation release 100), using STAR aligner v2.7.3a [1] with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts, and bigWig files were generated using the deeptools v3.1.3 bamCoverage function [2] with the normalizeUsingRPKM parameter.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: chlSab2, NCBI annotation release 100, hg19
Supplementary files format and content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes.

growth_protocol: Vero E6 cells were grown in DMEM (Gibco, 11960-44), supplemented with 10% FBS (Gibco), 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
Omni-ATAC protocol was used to probe DNA accessibility with slight modifications covered below 54. 100,000 cells per sample were trypsinized and washed with cold PBS to remove trypsin. Cell pellets were lysed in 50μl cold resuspension buffer (RSB) supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v) (RSB recipe: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2). Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and nuclei were pelleted at 500g for 10 min at 4°C after incubating on ice for 3 minutes. Nuclei were resuspended in 50μl transposition reaction mix containing 25 μl 2X Tagment DNA buffer (Illumina), 2.5μl Tn5 transposase, 16.5μl 1X PBS, 0.5μl 1% digitonin (final 0.01% v/v), 0.5μl 10% Tween-20 (final 0.1% v/v), and 5μl nuclease-free water. Transposition reaction was incubated at 37°C for 30 min with constant shaking (1000 rpm) on a thermomixer. Tagmented DNA was purified using the Qiagen MinElute Reaction Cleanup Kit. Standard ATAC-seq amplification protocol with 7 cycles of amplification was used to amplify tagmented libraries. Libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
RNAs were extracted using Direct-zol RNA MiniPrep Kit and submitted to the Yale Center for Genome Analysis for library preparation. RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 instrument with the goal of at least 25 × 106 reads per sample. Reads were aligned to reference genome chlSab2, NCBI annotation release 100, using STAR aligner v2.7.3a(Dobin et al., 2013) with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts. Differential expression was obtained using the R package DESeq2 v1.32(Dobin et al., 2013; Love et al., 2014). Bigwig files were generated using deeptools v3.1.3(Ramírez et al., 2016) with parameter --normalizeUsing RPKM
CUT&Tag was carried out using a protocol developed by Epicypher in 8-strip PCR tubes with slight modifications as described below. Briefly, Concanavalin A (ConA) coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were stored on ice until used. 300,000 cells/sample were trypsinized and pelleted by centrifugation at room temperature (600g for 3 min). Cells were lysed using cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche) for 2 min. Nuclei were pelleted by centrifugation (600g for 3 min), resuspended in 100ul/sample Resuspension buffer (20 mM HEPES–KOH, pH 7.9, 150mM NaCl supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor) and incubated with activated ConA beads at room temperature for 15 min. The nuclei-ConA bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 0.5ug primary antibody/sample. Following overnight incubation at 4°C on a nutator, supernatant was discarded, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. The ConA-nuclei complexes were then incubated with Digitonin 150 buffer supplemented with 0.5ug/sample Secondary antibody for 1hr at room temperature on a nutator. They were then washed with Digitonin 150 Buffer twice before resuspension in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, protease inhibitor, and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample and incubated on a nutator for 1hr at room temperature. Following incubation, beads were washed twice with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out according to Epicypher’s protocol.
RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were packaged in 293TX cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Vero E6 cells were lentivirally infected with either Empty vector, SMARCA4 WT or SMARCA4 K785R for 24h and then selected with 5ug/ml Puromycin for 4 days. Cells were harvested for genomics experiments using standard protocols. For Huh7.5 and Calu3 Compound 12 (C12) treatment studies, cells were treated with DMSO vehicle or 1.25uM C12 for 3 days.

tag: cell line

value: wild type + Compound 12


title: RNAseq.HBEC.C12.Rep2

source_name: HBEC

value: HBEC


title: CutAndTag.HUH7.DMSO.SMARCC1

value: wild type + DMSO

tag: cut&tag antibody

value: Rabbit anti-SMARCC1 (D7F8S);  11956S


title: RNAseq.CALU3.C12.Rep1


title: CutAndTag.HUH7.DMSO.SMARCA4

value: Rabbit anti-SMARCA4 (D1Q7F);  49360S


title: RNAseq.CALU3.DMSO.Rep1


title: RNAseq.CALU3.DMSO.Rep2


title: RNAseq.CALU3.C12.Rep2


title: CutAndTag.HUH7.C12.H3K27ac

value: Rabbit anti-H3K27ac (D5E4); 8173S


title: RNAseq.HBEC.C12.Rep1


title: RNAseq.HUH7.DMSO.Rep1


title: RNAseq.HUH7.DMSO.Rep2


title: RNAseq.HUH7.C12.Rep2


title: RNAseq.HBEC.DMSO.Rep1


title: CutAndTag.HUH7.DMSO.IgG

value: Rabbit anti-IgG; 2729


title: CutAndTag.HUH7.C12.IgG


title: CutAndTag.HUH7.C12.SMARCA4


title: CutAndTag.HUH7.DMSO.ARID1A

value: Rabbit anti-ARID1A (D2A8U);  12354S


title: CutAndTag.HUH7.DMSO.H3K27ac


title: CutAndTag.HUH7.C12.SMARCC1


title: CutAndTag.CALU3.DMSO.SMARCC1


title: CutAndTag.CALU3.DMSO.SMARCA4


title: CutAndTag.CALU3.DMSO.IgG


title: CutAndTag.CALU3.DMSO.H3K27ac


title: CutAndTag.CALU3.DMSO.HNF1A

value: Rabbit anti-HNF1A; ab272693


title: CutAndTag.CALU3.DMSO.ARID1A


title: CutAndTag.HUH7.C12.ARID1A


title: CutAndTag.CALU3.C12.SMARCA4


title: CutAndTag.CALU3.C12.HNF1A


title: CutAndTag.HUH7.DMSO.HNF1A


title: RNAseq.HBEC.DMSO.Rep2


title: ATACseq.CALU3.DMSO.Rep1


title: CutAndTag.HUH7.C12.HNF1A


title: Small Cell Ovarian cancer GTFB1170, position D

status: Public on Oct 10 2022

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description:
Primary Tumor (pT): pT1a: Tumor limited to one ovary (capsule intact) or fallopian tube, no tumor on ovarian or fallopian tube surface; no malignant cells in ascites or peritoneal washings; Regional Lymph Nodes (pN): pN1b: Metastasis more than 10 mm in greatest dimension; FIGO Stage (2015 FIGO Cancer Report): IIIA1(ii): Metastasis >10 mm in greatest dimension
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-066 position D1

data_processing:
Libraries were sequenced on a NovaSeq (Illumina) instrument at the University of Colorado Genomics Shared Resource. Sequencing files were inputted into the SpaceRanger (version 1.3.0) software to assign the tissue location and gene expression values using the GRCh38-3.0.0 transcriptome and GRCh38-2020-A probe set from 10x genomics.
Processed files were loaded into the Seurat (v4.0.4) package using Read10X_Image and Read10X_Spatial. These were then normalized using the SCT normalization.
Dimensionality reduction was performed using RunPCA and RunUMAP while clusters were identified with FindNeighbors and FindClusters.
Cell types were identified using clustifyr (v1.2.0) using Characterizing the tumor microenvironment of metastatic ovarian cancer by single-cell transcriptomics (GSE147082) and the pan cancer database (https://lambrechtslab.sites.vib.be/en/pan-cancer-blueprint-tumour-microenvironment-0) as a reference
To determine spots containing multiple cells, SpatialCluster and SpatialEnhance from BayesSpace (v1.0.0) were used. Spots containing "multiple"cells were removed and processing (dimensionality reduction, clustering, and cell type identificationz) were repeated.
All code to reproduce analysis available at https://github.com/kwells4/Bitler_visium_ovary
Assembly: GRCh38
Supplementary files format and content: All samples have a tar.gz file that contains all image files associated with the sample, raw counts for each spot, normalized counts for each spot, and the associated metadata file containing clustering and cell type information.

source_name: Ovary

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tumor tissue was sectioned onto a Visium Spatial Expression Slide (Serial Number: V10D07-67, 10X Chromium) and was visualized via H&E. RNA within the tissue was hybridized to barcoded probes.
10x genomics Visium library prep for FFPE human samples following the standard protocol. Each Visium Spatial Gene Expression Slide contains Capture Areas with gene expression spots that include primers required to capture the probes. Tissue sections placed on these Capture Areas are deparaffinized, stained, and decrosslinked, as described in Deparaffinization & Staining Demonstrated Protocols – CG000409 or CG000410. The RNA-probe complexes were amplified using KAPA qPCR and AMP (Cat. # 2000047)kits. Indexed primers are used from Dual Index Plate TS Set A (Cat. # 3000511).
Visium FFPE probe

value: Ovary

tag: Sex

value: Female

tag: histological diagnosis

value: Undifferentiated SMARCA4/SMARCA2-deficient malignant neoplasm


title: Ovarian tumor GTFB1230, position D

description:
Primary Tumor (pT): pT3c: Macroscopic peritoneal metastasis beyond pelvis more than 2 cm in greatest dimension with or without metastasis to the retroperitoneal lymph nodes (includes extension of tumor to capsule of liver and spleen without parenchymal involvement of either organ); Regional Lymph Nodes (pN): pN1b: Metastasis more than 10 mm in greatest dimension; FIGO Stage (2015 FIGO Cancer Report): IIIC: Macroscopic peritoneal metastases beyond the pelvic brim >2 cm in greatest dimension, with or without metastases to the retroperitoneal nodes
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-047 position D1

value: High grade serous carcinoma (11 cm) involving ovarian surface and parenchyma, and fallopian tube serosa, arising in a background of serous tubal intraepithelial carcinoma


title: ATACseq.HUH7.C12.Rep2

tag: genotype


title: Ovarian cancer tumor GTFB1191, position B

description:
Primary Tumor (pT): pT3c: Macroscopic peritoneal metastasis beyond pelvis more than 2 cm in greatest dimension with or without metastasis to the retroperitoneal lymph nodes (includes extension of tumor to capsule of liver and spleen without parenchymal involvement of either organ); Regional Lymph Nodes (pN): pN1b: Metastasis more than 10 mm in greatest dimension; FIGO Stage (2015 FIGO Cancer Report): IIIC: Macroscopic peritoneal metastases beyond the pelvic brim >2 cm in greatest dimension, with or without metastases to the retroperitoneal nodes
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-066 position B1

value: high grade serous ovarian carcinoma


title: CutAndTag.CALU3.C12.IgG


title: Ovarian tumor 955, position A

description:
Primary Tumor pT3c [IIIC]: Peritoneal metastasis beyond pelvis more than 2 cm in greatest dimension (omental metastases); Regional Lymph Nodes pNX: Cannot be assessed; No nodes submitted or found
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-047 position A1

value: grade 3 serous fallopian tube carcinoma


title: Ovarian cancer tumor GTFB1154 position A

description:
y (posttreatment); Primary Tumor (pT): pT3c: Macroscopic peritoneal metastasis beyond pelvis more than 2 cm; in greatest dimension with or without metastasis to the retroperitoneal lymph nodes; Regional Lymph Nodes (pN): pNX: Regional lymph nodes cannot be assessed
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-066 position A1


title: Human meningoma, QM153

city: San Francisco

first: William

last: Chen

address: 1450 3rd Street, HD 402

institute: UCSF

data_processing:
Transcript quantification was performed with Kallisto (v0.46.2)
Assembly: GRCh38.96.gtf
Supplementary files format and content: TSV files containing abundance outputs from Kallisto, including estimated counts and TPM

source_name: Meningioma

extract_protocol:
Frozen meningiomas were mechanically lysed using a TissueLyser II (QIAGEN) according to the manufacturer’s instructions. RNA were extracted from lysed tissue using the AllPrep DNA/RNA/miRNA Universal Kit (#80224, QIAGEN). RNA quality were initially assessed using a NanoDrop One (Thermo Fisher Scientific). RNA samples with 260/280 values less than 1.8 or 260/230 values less than 1.6 were cleaned using the RNA Cleanup protocol from the RNeasy Mini Kit (#74106, QIAGEN).
library preparation was performed using the TruSeq Standard mRNA Kit (#20020595, Illumina)

value: Meningioma


title: Human meningoma, QM173


title: ATACseq.HUH7.C12.Rep1


title: CutAndTag.CALU3.C12.ARID1A


title: ATACseq.CALU3.DMSO.Rep2


title: ATACseq.HUH7.DMSO.Rep1


title: ATACseq.HUH7.DMSO.Rep2


title: Omentum tumor 1191, position C

description:
Primary Tumor (pT): pT3c: Macroscopic peritoneal metastasis beyond pelvis more than 2 cm in greatest dimension with or without metastasis to the retroperitoneal lymph nodes (includes extension of tumor to capsule of liver and spleen without parenchymal involvement of either organ); Regional Lymph Nodes (pN): pN1b: Metastasis more than 10 mm in greatest dimension; FIGO Stage (2015 FIGO Cancer Report): IIIC: Macroscopic peritoneal metastases beyond the pelvic brim >2 cm in greatest dimension, with or without metastases to the retroperitoneal nodes
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-047 position C1

value: Omentum


title: ATACseq.CALU3.C12.Rep2

value: wild type + Compound 12


title: CutAndTag.CALU3.C12.H3K27ac


title: Human meningoma, QM414


title: Omentum 1180, position B

description:
Primary Tumor (pT): ypT3c: Macroscopic peritoneal metastasis beyond  pelvis more than 2 cm in greatest dimension with or without metastasis to the retroperitoneal lymph nodes (includes extension of tumor to capsule of liver and spleen without parenchymal involvement of either organ); Regional Lymph Nodes (pN): pNX: Regional lymph nodes cannot be assessed; FIGO Stage (2015 FIGO Cancer Report): IIIC: Macroscopic peritoneal metastases beyond the pelvic brim >2 cm in greatest dimension, with or without metastases to the retroperitoneal nodes
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-047 position B1


title: Human meningoma, QM420


title: Human meningoma, QM400


title: Human meningoma, QM405


title: Human meningoma, QM401


title: Human meningoma, QM411


title: ATACseq.CALU3.C12.Rep1


title: CutAndTag.CALU3.C12.SMARCC1


title: Small Cell Ovarian cancer GTFB1170, position C

description:
Primary Tumor (pT): pT1a: Tumor limited to one ovary (capsule intact) or fallopian tube, no tumor on ovarian or fallopian tube surface; no malignant cells in ascites or peritoneal washings; Regional Lymph Nodes (pN): pN1b: Metastasis more than 10 mm in greatest dimension; FIGO Stage (2015 FIGO Cancer Report): IIIA1(ii): Metastasis >10 mm in greatest dimension
FFPE sample, use 10x human FFPE probe set. Visium slide V10D07-066 position C1


title: Human meningoma, QM402


title: Human meningoma, QM403


title: Human meningoma, QM384


title: Human meningoma, QM385


title: Human meningoma, QM397


title: Human meningoma, QM378


title: Human meningoma, QM396


title: Human meningoma, QM370


title: Human meningoma, QM390


title: Human meningoma, QM353


title: Human meningoma, QM389


title: Human meningoma, QM344


title: Human meningoma, QM335


title: Human meningoma, QM336


title: Human meningoma, QM395


title: Human meningoma, QM311


title: Human meningoma, QM371


title: Human meningoma, QM387


title: Human meningoma, QM388


title: Human meningoma, QM308


title: Human meningoma, QM337


title: Human meningoma, QM377


title: Human meningoma, QM299


title: Human meningoma, QM406


title: Human meningoma, QM368


title: Human meningoma, QM346


title: Human meningoma, QM381


title: Human meningoma, QM373


title: Human meningoma, QM289


title: Human meningoma, QM287


title: Human meningoma, QM366


title: Human meningoma, QM361


title: Human meningoma, QM277


title: Human meningoma, QM270


title: Human meningoma, QM298


title: Human meningoma, QM345


title: Human meningoma, QM314


title: Human meningoma, QM331


title: Human meningoma, QM327


title: Human meningoma, QM255


title: Human meningoma, QM264


title: Human meningoma, QM365


title: Human meningoma, QM323


title: Human meningoma, QM259


title: Human meningoma, QM247


title: Human meningoma, QM238


title: Human meningoma, QM242


title: Human meningoma, QM222


title: Human meningoma, QM283


title: Human meningoma, QM233


title: Human meningoma, QM215


title: Human meningoma, QM276


title: Human meningoma, QM268


title: Human meningoma, QM202


title: Human meningoma, QM266


title: Human meningoma, QM263


title: Human meningoma, QM254


title: Human meningoma, QM261


title: Human meningoma, QM253


title: Human meningoma, QM251


title: Human meningoma, QM229


title: Human meningoma, QM250


title: Human meningoma, QM170


title: Human meningoma, QM230


title: Human meningoma, QM232


title: Human meningoma, QM221


title: Human meningoma, QM219


title: Human meningoma, QM209


title: Human meningoma, QM195


title: Human meningoma, QM169


title: Human meningoma, QM193


title: Human meningoma, QM197


title: Human meningoma, QM189


title: Human meningoma, QM160


title: Human meningoma, QM157


title: Human meningoma, QM240


title: Human meningoma, QM320


title: Human meningoma, QM174


title: Human meningoma, QM262


title: Human meningoma, QM182


title: Human meningoma, QM171


title: Human meningoma, QM146


title: Human meningoma, QM138


title: Human meningoma, QM137


title: Human meningoma, QM152


title: Human meningoma, QM148


title: Human meningoma, QM136


title: Human meningoma, QM116


title: Human meningoma, QM117


title: Human meningoma, QM159


title: Human meningoma, QM111


title: Human meningoma, QM101


title: Human meningoma, QM156


title: Human meningoma, QM175


title: Human meningoma, QM130


title: Human meningoma, QM99


title: Human meningoma, QM141


title: Human meningoma, QM410


title: Human meningoma, QM129


title: Human meningoma, QM121


title: Human meningoma, QM81


title: Human meningoma, QM85


title: Human meningoma, QM118


title: Human meningoma, QM84


title: Human meningoma, QM104


title: Human meningoma, QM112


title: Human meningoma, QM72


title: Human meningoma, QM133


title: Human meningoma, QM68


title: Human meningoma, QM73


title: Human meningoma, QM89


title: Human meningoma, QM107


title: Human meningoma, QM74


title: Human meningoma, QM61


title: Human meningoma, QM63


title: Human meningoma, QM35


title: Human meningoma, QM360


title: Human meningoma, QM43


title: Human meningoma, QM358


title: Human meningoma, QM369


title: Human meningoma, QM375


title: Human meningoma, QM374


title: Human meningoma, QM364


title: Human meningoma, QM10


title: Human meningoma, QM357


title: Human meningoma, QM379


title: Human meningoma, QM359


title: Human meningoma, QM348


title: Human meningoma, QM355


title: Human meningoma, QM340


title: Human meningoma, QM343


title: Human meningoma, QM339


title: Human meningoma, QM367


title: Human meningoma, QM354


title: Human meningoma, QM352


title: Human meningoma, QM351


title: Human meningoma, QM350


title: Human meningoma, QM324


title: Human meningoma, QM362


title: Human meningoma, QM341


title: Human meningoma, QM332


title: Human meningoma, QM316


title: Human meningoma, QM326


title: Human meningoma, QM333


title: Human meningoma, QM330


title: Human meningoma, QM325


title: Human meningoma, QM313


title: Human meningoma, QM321


title: Human meningoma, QM322


title: Human meningoma, QM297


title: Human meningoma, QM317


title: Human meningoma, QM304


title: Human meningoma, QM302


title: Human meningoma, QM300


title: Human meningoma, QM286


title: Human meningoma, QM315


title: Human meningoma, QM285


title: Human meningoma, QM292


title: Human meningoma, QM282


title: Human meningoma, QM280


title: Human meningoma, QM269


title: Human meningoma, QM274


title: Human meningoma, QM273


title: Human meningoma, QM318


title: Human meningoma, QM272


title: Human meningoma, QM267


title: Human meningoma, QM329


title: Human meningoma, QM258


title: Human meningoma, QM249


title: Human meningoma, QM248


title: Human meningoma, QM260


title: Human meningoma, QM245


title: Human meningoma, QM236


title: Human meningoma, QM235


title: Human meningoma, QM231


title: Human meningoma, QM226


title: Human meningoma, QM228


title: Human meningoma, QM227


title: Human meningoma, QM214


title: Human meningoma, QM218


title: Human meningoma, QM225


title: Human meningoma, QM220


title: Human meningoma, QM213


title: Human meningoma, QM211


title: Human meningoma, QM207


title: Human meningoma, QM271


title: Human meningoma, QM212


title: Human meningoma, QM205


title: Human meningoma, QM203


title: Human meningoma, QM199


title: Human meningoma, QM198


title: Human meningoma, QM256


title: Human meningoma, QM239


title: Human meningoma, QM183


title: Human meningoma, QM188


title: Human meningoma, QM187


title: Human meningoma, QM181


title: Human meningoma, QM179


title: Human meningoma, QM172


title: Human meningoma, QM164


title: Human meningoma, QM163


title: Human meningoma, QM162


title: Human meningoma, QM161


title: Human meningoma, QM158


title: Human meningoma, QM155


title: Human meningoma, QM200


title: Human meningoma, QM140


title: Human meningoma, QM139


title: Human meningoma, QM131


title: Human meningoma, QM127


title: Human meningoma, QM124


title: Human meningoma, QM119


title: Human meningoma, QM192


title: Human meningoma, QM177


title: Human meningoma, QM106


title: Human meningoma, QM105


title: Human meningoma, QM168


title: Human meningoma, QM103


title: Human meningoma, QM113


title: Human meningoma, QM109


title: Human meningoma, QM98


title: Human meningoma, QM154


title: Human meningoma, QM290


title: Human meningoma, QM102


title: Human meningoma, QM96


title: Human meningoma, QM142


title: Human meningoma, QM93


title: Human meningoma, QM92


title: Human meningoma, QM100


title: Human meningoma, QM95


title: Human meningoma, QM90


title: Human meningoma, QM94


title: Human meningoma, QM91


title: Human meningoma, QM87


title: Human meningoma, QM86


title: Human meningoma, QM79


title: Human meningoma, QM83


title: Human meningoma, QM78


title: Human meningoma, QM80


title: Human meningoma, QM76


title: Human meningoma, QM69


title: Human meningoma, QM71


title: Human meningoma, QM65


title: Human meningoma, QM67


title: Human meningoma, QM60


title: Human meningoma, QM59


title: Human meningoma, QM52


title: Human meningoma, QM49


title: Human meningoma, QM77


title: Human meningoma, QM66


title: Human meningoma, QM64


title: Human meningoma, QM62


title: Human meningoma, QM51


title: Human meningoma, QM48


title: Human meningoma, QM50


title: Human meningoma, QM47


title: Human meningoma, QM46


title: Human meningoma, QM42


title: Human meningoma, QM40


title: Human meningoma, QM39


title: Human meningoma, QM33


title: Human meningoma, QM36


title: Human meningoma, QM32


title: Human meningoma, QM28


title: Human meningoma, QM29


title: Human meningoma, QM291


title: Human meningoma, QM206


title: Human meningoma, QM25


title: Human meningoma, QM26


title: Human meningoma, QM23


title: Human meningoma, QM12


title: Human meningoma, QM20


title: Human meningoma, QM21


title: Human meningoma, QM53


title: Human meningoma, QM15


title: Human meningoma, QM24


title: Human meningoma, QM27


title: Human meningoma, QM16


title: Human meningoma, QM14


title: Human meningoma, QM8


title: Human meningoma, QM7


title: Human meningoma, QM9


title: Human meningoma, QM6


title: Human meningoma, QM2


title: Human meningoma, QM1


title: Human meningoma, QM34


title: Human meningoma, QM30


title: FVB_Telogen_IFE_rep2

status: Public on Oct 09 2022

city: New York City

first: Katherine

last: Stewart

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

description: Biological replicate 2

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm10) using either Salmon (v 1.4.0) or Bowtie2 (v 2.2.9)
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts with Tximport (v 1.12.3) in R (v 3.6.1)(Salmon aligned data) or by RSEM (v 1.2.30)(Bowtie2 aligned data).
Assembly: mm10 (UCSC release)
Supplementary files format and content: tab-delineated text files or comma separated value files contain raw counts, and tab-delineated text files or comma separated value files contain calculated TPM

source_name: mouse back skin

extract_protocol:
Cells were isolated by FACS, and collected into trizol. RNA was extracted using the Direct-zol RNA extraction kit (Zymo) following manufacturer's instructions.
RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit. Libraries were sequenced on an Illumina HiSeq 4000 or NovaSeq instrument as indicated.

tag: tumor stage

value: normal skin

tag: mouse strain

value: FVB/N

tag: mouse age

value: wild type

tag: mouse sex

tag: lentivirus injected at e9.5

tag: sorting scheme

tag: read alignment program

value: Salmon (v 1.4.0)

tag: read quantification program

value: Tximport (v 1.12.3)


title: FVB_Telogen_IFE_rep1

description: Biological replicate 1


title: Human meningoma, QM13

tag: tissue


title: Human meningoma, QM19


title: Human meningoma, QM11


title: Human meningoma, QM17


title: FVB_Telogen_HFSC_rep2

description: Biological replicate 2


title: IFE_ATAC_rep2

description: Biological replicate 2

data_processing:
The raw sequencing reads were aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome.
The aligned reads were deduplicated with Picard (v. 2.3.0) and shifted to correct for Tn5 insertion bias.
Bamfiles from biological replicates are combined with Samtools (1.9)
Peaks were called on replicate-pooled bamfiles with MACS2 (v. 2.1.1) with default settings.
Assembly: GRCm38 (mm10)
Supplementary files format and content: bedfiles of narrowpeaks called from MACS2

extract_protocol:
Cells were isolated by FACS into FACS sorting buffer. Cells were pelleted and lysed using 0.01% IGEPAL CA-630. ATAC libraries were prepared on these solubilized nuclei, according to Buenrostro et al. 2015.
Illumina Nextera, Buenrostro et al., 2015

value: 8 wks

value: WT

value: female


title: HFSC_ATAC_rep2

description: Biological replicate 2


title: HFSC_ATAC_rep3

description: Biological replicate 3


title: Human meningoma, QM3


title: IFE_ATAC_rep3

description: Biological replicate 3


title: CD25neg INFg KO 5

status: Public on Oct 06 2022

city: REHOVOT

first: Steffen

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description:
Source data Fig 7D.xlsx
Source data Fig 7C.xlsx

data_processing:
UTAP analysis (https://doi.org/10.1186/s12859-019-2728-2)
Demultiplexing
Low-quality trimmng
UMI counting
Normalization
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for every gene above 5 reads number and every sample

source_name: T cells

growth_protocol: Mice were maintained on a 12 hour light/dark cycle, with food and water provided ad libitum, and maintained under specific pathogen-free (SPF) conditions.

extract_protocol:
Mice were anesthetized with Pental (1:2 in PBS) and were perfused with PBS. Samples were homogenized on ice in ice-cold homogenization buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:100 protease inhibitor (Sigma), 200 units/ml RNasin (Promega) and 0.1 mg/ml cycloheximide (Sigma) in RNase free DDW) 10% w/v with a Dounce homogenizer (Sigma) until the suspension was homogeneous. To remove cell debris, 1 ml of the homogenate was transferred to an Eppendorf tube and was centrifuged at 10,000g and 4°C for 10 min. Supernatants were transferred to a fresh Eppendorf tube on ice, then 10μl was removed for 'input' analysis and 10µg of anti-HA antibody (H9658, Sigma) or 10µg of mouse monoclonal IgG1 antibody (Sigma, Cat# PP100) was added to the supernatant, *followed by 4 h of incubation with slow rotation in a cold room at 4 °C. Meanwhile, Dynabeads Protein G (Thermo Fisher Scientific), 100 μl per sample, were equilibrated to homogenization buffer by washing three times. At the end of 4 h of incubation with antibody, beads were added to each sample, followed by incubation overnight in cold room at 4 °C. After not more than 12 h, samples were washed three times with high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:200 protease inhibitor, 100 units/ml RNasin and 0.1 mg/ml cycloheximide in RNase free DDW), 5 min per wash in a cold room on a rotator. At the end of the washes, beads were magnetized and excess buffer was removed, 100µl Lysis Buffer  was added to the beads (Ambion Life Technologies). For Sort+aHA IP samples (RiboTag IP after sorting), 30,000 microglial cells were sorted directly into 100µl Lysis Buffer (Ambion Life Technologies) containing 10µg of anti-HA antibody (H9658, Sigma) or 10µg of mouse monoclonal IgG1 antibody (Sigma, Cat# PP100), the rest of IP was continued as above from *.
t cells were sorted from whole brain
PolyA-tailed mRNA was captured using the Dynabeads mRNA DIRECT kit (Ambion Life Technologies) according to manufacturer’s guidelines. RNA-seq libraries were constructed used a derivation of MARS-seq as described in Jaitin et al. (2014) adapted for bulk cell populations.
Mars-seq (DOI: 10.1126/science.1247651)

treatment_protocol: All mice were treated with Tamoxifen as follows: 5mg of tamoxifen (Sigma, diluted in corn oil) were administered to mice by gavage 4 times every other day at the age of 4-6 weeks.

tag: strain

value: F1 of C57BL/6 * SJL

value: Cx3cr1-CreER:RPL22-HA:Ifngr ko/fl

tag: organ

value: brain

tag: cell type

value: T cells

tag: treatment

value: relapsing remmiting EAE


title: CD25neg INFg KO 3


title: CD25pos control 3

value: Cx3cr1-CreER:RPL22-HA:Ifngr ko/wt


title: CD25pos control 4


title: CDpos INFg KO 2


title: CD25pos control 2


title: CDpos INFg KO 5


title: CDpos INFg KO 1


title: CDpos INFg KO 4


title: CD25neg INFg KO 4


title: CD25pos control 1


title: CD25neg INFg KO 2


title: CDpos INFg KO 6


title: CDpos INFg KO 3


title: CD25neg INFg KO 1


title: CD25neg control 6


title: CD25neg control 5


title: FVB_Telogen_HFSC_rep1

description: Biological replicate 1

value: Female


title: CD25pos control 5


title: CD25neg control 4


title: CD25neg control 2


title: CD25neg control 3


title: CD25neg control 1


title: EAE INFg KO IgG 4

description: Source data Fig 5E.xlsx

source_name: microglia

value: microglia

tag: immunoprecipitation antibody

value: IgG1 isotype control (Merck PP100)


title: EAE INFg KO HA 4

description: Source data Fig 5E.xlsx

value: anti-HA (Sigma H9658)


title: EAE INFg KO Input 4

description: Source data Fig 5E.xlsx


title: EAE INFg KO HA 3

description: Source data Fig 5E.xlsx


title: EAE INFg KO Input 3

description: Source data Fig 5E.xlsx


title: EAE INFg control Input 3

description: Source data Fig 5E.xlsx


title: EAE INFg control HA 2

description: Source data Fig 5E.xlsx


title: EAE INFg KO Input 1

description: Source data Fig 5E.xlsx


title: EAE INFg KO Input 2

description: Source data Fig 5E.xlsx


title: EAE INFg control HA 3

description: Source data Fig 5E.xlsx


title: EAE INFg KO IgG 1

description: Source data Fig 5E.xlsx


title: EAE INFg control HA 4

description: Source data Fig 5E.xlsx


title: CD25neg INFg KO 6


title: EAE INFg KO HA 1

description: Source data Fig 5E.xlsx


title: EAE INFg KO HA 2

description: Source data Fig 5E.xlsx


title: EAE INFg control IgG 4

description: Source data Fig 5E.xlsx


title: EAE INFg control Input 4

description: Source data Fig 5E.xlsx


title: EAE INFg control IgG 3

description: Source data Fig 5E.xlsx


title: EAE INFg KO IgG 2

description: Source data Fig 5E.xlsx


title: EAE INFg control IgG 2

description: Source data Fig 5E.xlsx


title: EAE INFg control IgG 1

description: Source data Fig 5E.xlsx


title: EAE INFg control Input 2

description: Source data Fig 5E.xlsx


title: EAE INFg control Input 1

description: Source data Fig 5E.xlsx


title: EAE Relapse HA 4

description: Source data Fig 2C.xlsx


title: EAE INFg control HA 1

description: Source data Fig 5E.xlsx


title: EAE Relapse HA 3

description: Source data Fig 2C.xlsx


title: EAE Relapse IgG 4

description: Source data Fig 2C.xlsx


title: EAE Relapse Input 3

description: Source data Fig 2C.xlsx


title: EAE INFg KO IgG 3

description: Source data Fig 5E.xlsx


title: EAE Relapse IgG 3

description: Source data Fig 2C.xlsx


title: EAE Relapse IgG 2

description: Source data Fig 2C.xlsx


title: EAE Relapse Input 2

description: Source data Fig 2C.xlsx


title: Human meningoma, QM108

value: Meningioma


title: EAE Cure IgG 5

description: Source data Fig 2C.xlsx


title: EAE Cure HA 5

description: Source data Fig 2C.xlsx


title: EAE Relapse IgG 1

description: Source data Fig 2C.xlsx


title: EAE Cure Input 5

description: Source data Fig 2C.xlsx


title: EAE Cure Input 3

description: Source data Fig 2C.xlsx


title: EAE Cure IgG 3

description: Source data Fig 2C.xlsx


title: EAE Cure IgG 4

description: Source data Fig 2C.xlsx


title: EAE Cure Input 4

description: Source data Fig 2C.xlsx


title: EAE Cure HA 2

description: Source data Fig 2C.xlsx


title: EAE Relapse Input 1

description: Source data Fig 2C.xlsx


title: EAE Cure IgG 2

description: Source data Fig 2C.xlsx


title: EAE Relapse HA 1

description: Source data Fig 2C.xlsx


title: EAE Relapse HA 2

description: Source data Fig 2C.xlsx


title: EAE Cure HA 4

description: Source data Fig 2C.xlsx


title: EAE Remission Input 8

description: Source data Fig 2C.xlsx


title: EAE Cure Input 1

description: Source data Fig 2C.xlsx


title: EAE Cure Input 2

description: Source data Fig 2C.xlsx


title: EAE Remission HA 8

description: Source data Fig 2C.xlsx


title: EAE Remission HA 7

description: Source data Fig 2C.xlsx


title: EAE Cure HA 1

description: Source data Fig 2C.xlsx


title: EAE Cure HA 3

description: Source data Fig 2C.xlsx


title: EAE Remission Input 7

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 8

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 7

description: Source data Fig 2C.xlsx


title: EAE Cure IgG 1

description: Source data Fig 2C.xlsx


title: EAE Remission HA 6

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 6

description: Source data Fig 2C.xlsx


title: EAE Remission Input 6

description: Source data Fig 2C.xlsx


title: EAE Remission Input 5

description: Source data Fig 2C.xlsx


title: EAE Remission HA 4

description: Source data Fig 2C.xlsx


title: EAE Remission HA 3

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 2

description: Source data Fig 2C.xlsx


title: EAE Remission Input 3

description: Source data Fig 2C.xlsx


title: EAE Remission HA 1

description: Source data Fig 2C.xlsx


title: EAE Remission HA 2

description: Source data Fig 2C.xlsx


title: EAE Remission Input 2

description: Source data Fig 2C.xlsx


title: EAE Remission Input 1

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 1

description: Source data Fig 2C.xlsx


title: EAE Max IgG 6

description: Source data Fig 2C.xlsx


title: EAE Max Input 5

description: Source data Fig 2C.xlsx


title: EAE Max IgG 5

description: Source data Fig 2C.xlsx


title: EAE Remission HA 5

description: Source data Fig 2C.xlsx


title: EAE Max HA 6

description: Source data Fig 2C.xlsx


title: EAE Max HA 5

description: Source data Fig 2C.xlsx


title: EAE Max Input 6

description: Source data Fig 2C.xlsx


title: EAE Max HA 4

description: Source data Fig 2C.xlsx


title: EAE Max Input 4

description: Source data Fig 2C.xlsx


title: EAE Relapse Input 4

description: Source data Fig 2C.xlsx


title: EAE Max HA 3

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 3

description: Source data Fig 2C.xlsx


title: EAE Remission Input 4

description: Source data Fig 2C.xlsx


title: EAE Max IgG 3

description: Source data Fig 2C.xlsx


title: EAE Max IgG 2

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 4

description: Source data Fig 2C.xlsx


title: EAE Max HA 2

description: Source data Fig 2C.xlsx


title: EAE Max HA 1

description: Source data Fig 2C.xlsx


title: EAE Max Input 1

description: Source data Fig 2C.xlsx


title: EAE Initiation IgG 4

description: Source data Fig 2C.xlsx


title: EAE Initiation HA 4

description: Source data Fig 2C.xlsx


title: EAEInitiation HA 3

description: Source data Fig 2C.xlsx


title: EAE Max IgG 4

description: Source data Fig 2C.xlsx


title: EAE Max IgG 1

description: Source data Fig 2C.xlsx


title: EAE Initiation Input 4

description: Source data Fig 2C.xlsx


title: EAEInitiation HA 2

description: Source data Fig 2C.xlsx


title: EAE Initiation Input 2

description: Source data Fig 2C.xlsx


title: EAE Initiation Input 3

description: Source data Fig 2C.xlsx


title: EAE Initiation IgG 3

description: Source data Fig 2C.xlsx


title: EAE Remission IgG 5

description: Source data Fig 2C.xlsx


title: EAE Initiation IgG 2

description: Source data Fig 2C.xlsx


title: EAE Initiation HA 1

description: Source data Fig 2C.xlsx


title: EAE Initiation Input 1

description: Source data Fig 2C.xlsx


title: EAE Initiation IgG 1

description: Source data Fig 2C.xlsx


title: EAE Non immunized Input 6

description: Source data Fig 2C.xlsx


title: EAE Non immunized HA 6

description: Source data Fig 2C.xlsx


title: EAE Non immunized IgG 6

description: Source data Fig 2C.xlsx


title: EAE Max Input 3

description: Source data Fig 2C.xlsx


title: EAE Non immunized HA 5

description: Source data Fig 2C.xlsx


title: EAE Max Input 2

description: Source data Fig 2C.xlsx


title: EAE Non immunized Input 4

description: Source data Fig 2C.xlsx


title: EAE Non immunized HA 3

description: Source data Fig 2C.xlsx


title: EAE Non immunized IgG 5

description: Source data Fig 2C.xlsx


title: EAE Non immunized Input 5

description: Source data Fig 2C.xlsx


title: EAE Non immunized HA 4

description: Source data Fig 2C.xlsx


title: EAE Non immunized IgG 4

description: Source data Fig 2C.xlsx


title: EAE Non immunized IgG 2

description: Source data Fig 2C.xlsx


title: EAE Non immunized HA 2

description: Source data Fig 2C.xlsx


title: EAE Non immunized Input 3

description: Source data Fig 2C.xlsx


title: EAE Non immunized IgG 3

description: Source data Fig 2C.xlsx


title: EAE Non immunized Input 2

description: Source data Fig 2C.xlsx


title: EAE Non immunized IgG 1

description: Source data Fig 2C.xlsx


title: EAE Non immunized HA 1

description: Source data Fig 2C.xlsx