title: Myc.low.Methionine.low_3

city: San Francisco

first: Sensen

last: Lin

state: CA California

address: HSW 760, UCSF Parnassus, 513 Parnassus Ave, San Francisco

institute: UCSF

description: normalized counts

data_processing:
reads quality was viewed by fastqc
filter and trim of reads, fastp
fastp --detect_adapter_for_pe -q 20 -u 50 -n 5
mapping with STAR
STAR --genomeDir /Mus_musculus.GRCm39 --readFilesCommand gunzip -c outFilterIntronMotifs RemoveNoncanonical --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Bam sort and index, samtools
quality control, rseqc
reads counting, htseq
htseq-count --stranded=reverse --order=name --idattr=gene_id --type=exon --mode=union --format=bam --additional-attr=gene_name ~/Mus_musculus.GRCm39.104.gtf > quantification_result.txt
quantification with Deseq2
enrichment, clusterProfiler
gseGO(ont ="ALL", pvalueCutoff = 0.05, OrgDb ="org.Mm.eg.db", pAdjustMethod = "BH")
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: normalized counts were provided in file "counts_normalized.csv"

source_name: liver

growth_protocol: Cells were cultured with DMEM, 200 µM methionine

extract_protocol:
total RNA was extracted with Qiagen RNA extraction kit
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina

treatment_protocol: Cells were treated with DMEM containing 10 µM or 200 µM methionine for 24h

value: liver

value: cancer cells

value: MYC off

value: methionine 10 µM, 24h


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR5.LC14) rep 1

status: Public on Oct 06 2022

type: SRA

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description:
IDLV_AAVS1.tsv
Exp10_LTR5LC14_A001_2733.IDLV.PGK.GFP_BM

library_source: genomic

data_processing:
Library strategy: SLiM-PCR, custom amplicon sequencing
FASTQ files processed by RAAVIoli software
Custom software for matrix creation
Genome_build: Hg19 + custom reference AAV genome or IDLV genome
Supplementary_files_format_and_content: Data matrix if integrations (rows) observed in specific samples (columns) and quantified by the number of cells (values).

molecule: genomic DNA

organism: Homo sapiens

source_name: IDLV PGK GFP

extract_protocol:
gDNA was sheared using a Covaris E220 Ultrasonicator (Covaris Inc.), generating fragments with a target size of 1,000 bp.
The fragmented DNA was subjected to end repair, 3’ adenylation and ligation (NEBNext® Ultra™ DNA Library Prep Kit for Illumina, New England Biolabs) to custom linker cassettes (LC) (Integrated DNA Technologies). LC sequences containing 8-nucleotide barcode for sample identification. Ligation products were subjected to 35 cycles of exponential PCR with primers complementary to different regions of the AAV or IDLV genomes and to the LC. For each set of AAV or IDLV specific primers, the procedure was performed in technical replicates (n = 2-3) using 80-100 ng of sheared DNA/each. Next, ten additional PCR cycles were done to include sequences required for sequencing and a second 8-nucleotide DNA barcode. PCR products were quantified by qPCR using the Kapa Biosystems Library Quantification Kit for Illumina, following the manufacturer’s instructions. qPCR was performed in triplicate on each PCR product diluted 10:3, and the concentrations were calculated by plotting the average Ct values against the provided standard curve. The amplification products were sequenced by Illumina Next/Novaseq platforms (Illumina).

tag: tissue

value: BM

tag: vector

value: IDLV

tag: vector id

tag: subject


title: Myc.low.Methionine.low_2

country: USA

description: normalized counts

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SCC06_1e-4_B_vbc

city: Boston

first: Arpiar

last: Saunders

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
SCC06
single-cell RNA profiling using 3' counting

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on either an Illumina MiSeq, NextSeq 500 or NovaSeq6000
Sequencing Reads were aligned against a custom genome containing the GRCm38.81 mouse build; the rabies virus genome (SAD-B19-dG-EGFP) and AAV elements using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows)
Viral barcodes (VBCs) were amplified from sequenced EGFP mRNAs. Raw VBC sequences ascertained from viral genomes or scRNA-seq data (RM) were collapsed (RB) using custom algorithms. UMIs were used count/collapse VBC sequences within the context of a cell (XC)
Assembly: GRCm38.81 + custom genomes for SAD-B19-dG-EGFP and AAV elements
Supplementary files format and content: digital gene expression

molecule: total RNA

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_B_vbc]

extract_protocol:
Saunders and Macosko et al. 2018 Cell
10x Genomics 3' RNA (v2 or v3 chemistry) & this study (for viral barcode processing/sequencing)
10x Genomics 3' RNA & this study (for viral barcode processing/sequencing)

treatment_protocol: Cells were dissociated from in vitro synaptic cultures, FACS to enrich for those cells infected by rabies virus and scRNA-seq libraries were generated using 10x Genomic v2 or v3 platforms

tag: strain


title: A375_THZ531_rep3

city: Montreal

first: Philippe

middle: P.

last: Roux

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cance

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.7.1a
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 32 transcript annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

growth_protocol: A375 and Colo829 were respectively maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 4.5 g/liter glucose and in Roswell Park Memorial Institute Medium (RPMI), supplemented with 10% fetal bovine serum, 100 IU/mL penicillin and 100 µg/mL streptomycin under 37°C/5%CO2 condition.

extract_protocol:
TriZol +  RNeasy mini kit (Qiagen)
Kapa RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific)

treatment_protocol: Melanoma cell line were treated during 6 hours with DMSO or THZ531 at 500 nM

tag: cancer

value: melanoma cell line


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR53.LC10) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR53LC10_A001_2733.IDLV.PGK.GFP_BM


title: Myc.low.Methionine.low_1

description: normalized counts


title: A375_THZ531_rep2


title: SCC06_1e-4_A_vbc

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_A_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR31.LC9) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR31LC9_A000_2733.IDLV.PGK.GFP_BM


title: Myc.high.Methionine.low_3

description: normalized counts

value: MYC on


title: SCC06_1e-3_B_vbc

source_name: Striatal-Cortex Co-Culture Experiment 6, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC06_1e-3_B_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR91.LC6) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR91LC6_A001_2733.IDLV.PGK.GFP_BM


title: Myc.high.Methionine.low_2

description: normalized counts


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR23.LC5) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR23LC5_A000_2733.IDLV.PGK.GFP_BM


title: A375_THZ531_rep1


title: WTTm

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
NOT PROVIDED; REQUESTED
Assembly: R64
Supplementary files format and content: Bigwig files providing coverage for all samples. All values are normalized to total number of reads.

organism: Saccharomyces cerevisiae

source_name: wild-type

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For ER stress induction , tunicmycin (Tm) was added to a final concentration of 1 µg/ml for 2 H .

extract_protocol: Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript.

treatment_protocol: Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3). Cells were broken and extracts were prepared as described in the original publication.

value: wild-type

value: 1 µg/ml tunicamycin for 2 H

tag: molecule subtype

value: Rpb1 immunoprecipitated nascent RNA


title: A375_Ctl_rep3


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR17.LC1) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR17LC1_A000_2733.IDLV.PGK.GFP_BM


title: Myc.high.Methionine.low_1

description: normalized counts


title: Colo829_Ctl_rep1


title: Myc.low.Methionine.high_2

description: normalized counts

value: methionine 200 µM, 24h


title: A375_Ctl_rep1


title: Myc.low.Methionine.high_3

description: normalized counts


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR57.LC94) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR57LC94_A001_2733.IDLV.PGK.GFP_BM


title: SCC06_1e-3_A_vbc

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC06_1e-3_A_vbc]


title: Myc.low.Methionine.high_1

description: normalized counts


title: A375_Ctl_rep2


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR41.LC2) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR41LC2_A001_2733.IDLV.PGK.GFP_BM


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR35.LC93) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR35LC93_A000_2733.IDLV.PGK.GFP_BM


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR87.LC90) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR87LC90_A001_2733.IDLV.PGK.GFP_BM


title: rheumatoid arthritis fibroblast-like synoviocytes, SiATF6α, Day3, rep1

city: Ji'nan

first: Wang

address: #6699,Qingdao Road

country: China

institute: Biomedical Sciences College & Shandong Medicinal Biotechnology Centre

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: rheumatoid arthritis synovial tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rheumatoid arthritis synovial tissue

value: synoviocytes

value: ATF6{alpha} knockdown

value: RA FLSs were transfected with the ATF6α-siRNA (siATF6α) for 72 h at the presence of TNF-α (10 ng/mL) and IL-1β (10 ng/mL)


title: rheumatoid arthritis fibroblast-like synoviocytes, SiATF6α, Day3, rep3


title: rheumatoid arthritis fibroblast-like synoviocytes, SiNC, Day3, rep3

value: WT

value: RA FLSs were transfected with the control siRNA(siNC) for 72 h at the presence of TNF-α (10 ng/mL) and IL-1β (10 ng/mL)


title: Myc.high.Methionine.high_2

description: normalized counts

value: liver

value: cancer cells


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR51.LC89) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR51LC89_A000_2733.IDLV.PGK.GFP_BM


title: rheumatoid arthritis fibroblast-like synoviocytes, SiNC, Day3, rep2


title: rheumatoid arthritis fibroblast-like synoviocytes, SiNC, Day3, rep1


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR37.LC85) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR37LC85_A000_2733.IDLV.PGK.GFP_BM


title: SCC06_1e-2_A_vbc

source_name: Striatal-Cortex Co-Culture Experiment 6, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC06_1e-2_A_vbc]


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR7.LC81) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC81_B003_2738.AAV.PGK.GFP_BM

source_name: AAV PGK GFP

value: AAV


title: CUTO28-ER gDNA

city: Denver

first: LOGAN

middle: C

last: TYLER

state: CO

address: 1240 Ulster St

institute: UC Anschutz Medical Campus

data_processing:
library strategy: Whole Exome Seq
Novogene utilized STAR software to map reads to the hg19 reference genome by positioning reads according to known exon-intron junctions. Raw reads were filtered to remove the following: reads of sequencing adaptors, reads that contain >10% uncertain nucleotides, and reads where low quality nucleotides (Base Quality < 5) constitute >50% of the read. Further, reads were normalized using the DESeq2 R package.
Assembly: hg19
Supplementary files format and content: ".xls" for Differentially Expressed Genes (DEG) between respective "-ER" or "-CR" and parental cell lines are provided as RNAseq processed data files.

source_name: adenocarcinoma

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% FBS. "-ER" and "-CR" cells' media were also supplemented with 500nM entrectinib or crizotinib, respectively, every 3-5 days in the media.

extract_protocol: RNA was extracted with Buffer RLT+ using Qiagen RNeasy kit. gDNA was extracted with Genomic Lysis Buffer using Zymo Quick-gDNA Mini Prep kit.

treatment_protocol: "-ER" and "-CR" cells were harvested within 3 days of entrectinib or crizotinib treatment, respectively. CUTO28 and CUTO37 samples were untreated.

value: adenocarcinoma

value: CUTO28 (TPM3-ROS1)

value: NSCLC

value: 500nM entrectinib


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR3.LC80) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR3LC80_B002_2738.AAV.PGK.GFP_BM

value: BM


title: CUTO28-CR gDNA

value: 500nM crizotinib


title: FHC, LPS + Tat (48-60) YVEEL, 6h

city: Nanjing

first: Xiangyun

last: Yan

address: 123rd Tian Fei Xiang, Mo Chou Road, Nanjing 210004

institute: Women’s Hospital of Nanjing Medical University,  Nanjing Maternity and Child Health Care Hospital

data_processing:
For RNA seq technology, the sequencing error rate will increase with the length of sequenced reads, which is a feature of illumina high throughput sequencing platforms. Generally, the sequencing error rate of a single base position should be less than 1%, that is, corresponding to Q20 filtering.
After the completion of data quality control, first compare clean reads with the reference genome, and count the comparison rate of reads between each sample and the reference genome.
Then, based on the comparison results, judge the overall construction quality of RNA seq library.
Based on the HISAT2 comparison results, HTSeq software is used to count the number of reads of each gene compared. The parameters are default. The expression level of each gene was calculated based on HTSeq calculation results. The genes with FDR ≤ 0.05 were significantly differentially expressed.
Assembly: human NBCI genome build 36
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: FHC

growth_protocol: FHC cells were cultured in DMEM: F12 Medium (Gibco, USA), supplemented with fetal bovine serum (10%, Gibco, USA) and penicillin/streptomycin (1%, Gibco, USA), cholera toxin (10 ng/ml, Sigma-Aldrich, USA) and hydrocortisone (100 ng/ml, Sigma-Aldrich, USA).

extract_protocol:
Total RNA was extracted from cultured cells using Trizol Reagent (Invitrogen, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Lipopolysaccharides (LPS, 50 μg/ml, Sigma-Aldrich, USA) was used to establish NEC in vitro cell model. Tat (48-60) YVEEL were pretreated at different concentrations (40 μM) for 1 h before LPS stimulation.

value: FHC

value: Fetal Human Colon

value: LPS + Tat (48-60) YVEEL


title: FHC,LPS, 6h

value: LPS induced


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR19.LC78) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC78_B000_2738.AAV.PGK.GFP_BM


title: rheumatoid arthritis fibroblast-like synoviocytes, SiATF6α, Day3, rep2

value: rheumatoid arthritis synovial tissue

value: synoviocytes

value: ATF6{alpha} knockdown


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR3.LC74) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC74_B003_2738.AAV.PGK.GFP_BM


title: Myc.high.Methionine.high_3

description: normalized counts

value: MYC on

value: methionine 200 µM, 24h


title: CUTO28 gDNA


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR19.LC72) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR19LC72_B001_2738.AAV.PGK.GFP_BM


title: CUTO37-ER_SAMPLE3

data_processing:
Novogene utilized STAR software to map reads to the hg19 reference genome by positioning reads according to known exon-intron junctions. Raw reads were filtered to remove the following: reads of sequencing adaptors, reads that contain >10% uncertain nucleotides, and reads where low quality nucleotides (Base Quality < 5) constitute >50% of the read. Further, reads were normalized using the DESeq2 R package.
Assembly: hg19
Supplementary files format and content: ".xls" for Differentially Expressed Genes (DEG) between respective "-ER" or "-CR" and parental cell lines are provided as RNAseq processed data files.

value: CUTO37 (CD74-ROS1)


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR77.LC71) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC71_B000_2738.AAV.PGK.GFP_BM

value: AAV


title: CUTO37-ER_SAMPLE1

value: adenocarcinoma


title: CUTO37-ER_SAMPLE2


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR59.LC64) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC64_B000_2738.AAV.PGK.GFP_BM


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR27.LC61) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR27LC61_B004_2738.AAV.PGK.GFP_BM


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR77.LC65) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR77LC65_B001_2738.AAV.PGK.GFP_BM


title: CUTO37-CR_SAMPLE2


title: CUTO37-CR_SAMPLE3


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR29.LC86) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR29LC86_A001_2733.IDLV.PGK.GFP_BM

value: IDLV


title: CUTO37-CR_SAMPLE1

value: NSCLC


title: CUTO37_SAMPLE3


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR59.LC58) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC58_B001_2738.AAV.PGK.GFP_BM


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR7.LC57) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC57_B000_2738.AAV.PGK.GFP_BM


title: CUTO37_SAMPLE2


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR59.LC82) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC82_B004_2738.AAV.PGK.GFP_BM


title: CUTO37_SAMPLE1


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR77.LC53) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC53_B003_2738.AAV.PGK.GFP_BM


title: CUTO28-CR_SAMPLE3

description: s

value: CUTO28 (TPM3-ROS1)


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR59.LC46) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC46_B003_2738.AAV.PGK.GFP_BM

value: BM


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR7.LC45) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC45_B002_2738.AAV.PGK.GFP_BM


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR3.LC50) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC50_B000_2738.AAV.PGK.GFP_BM


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR17.LC40) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR17LC40_B004_2738.AAV.PGK.GFP_BM


title: CUTO28-ER_SAMPLE2

value: 500nM entrectinib


title: CUTO28-CR_SAMPLE2

value: 500nM crizotinib


title: CUTO28-CR_SAMPLE1


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR91.LC39) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR91LC39_B003_2738.AAV.PGK.GFP_BM


title: CUTO28_SAMPLE3


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR91.LC33) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR91LC33_B004_2738.AAV.PGK.GFP_BM


title: CUTO28-ER_SAMPLE3


title: Exp8 BM on 2738.AAV.PGK.GFP (LTR19.LC60) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC60_B003_2738.AAV.PGK.GFP_BM


title: CUTO28_SAMPLE1


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR31.LC36) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR31LC36_B000_2738.AAV.PGK.GFP_BM


title: UMSCC22B input chip-seq

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

institute: UW Health

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files.  Uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K27ac enrichment over “input” background
deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files and bed peak files

growth_protocol: Human HNSCC cell lines were acquired and characterized as previously described [59]. Briefly, cell lines were cultured in DMEM supplemented with 10% FBS, L-glutamine, sodium pyruvate, nonessential amino acids, vitamins, and 1% penicillin-streptomycin. All cell lines were cultured at 37 °C in an atmosphere of 5% CO2

extract_protocol:
Cells were crosslinked with both 0.75% formaldehyde and glycine. Chromatin was sheared to 300-700 bp using a Diagenode Bioruptor.
DNA were end-repaired, adapter-ligated using NEBNext Ultra II DNA library prep kit from Illumina and sequenced by Illumina HiSeq2000 at SR-50.

value: head and neck squamous cell carcinoma cell line


title: UMSCC6 H3K4me1 chip-seq

tag: chip antibody

value: H3K4me1 Abcam ab8895


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR53.LC37) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR53LC37_B001_2738.AAV.PGK.GFP_BM


title: UMSCC6 input chip-seq (KMT2D HNSCC control)


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR23.LC32) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR23LC32_B003_2738.AAV.PGK.GFP_BM


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR53.LC31) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR53LC31_B002_2738.AAV.PGK.GFP_BM


title: UMSCC11A H3K4me1 chip-seq


title: UMSCC11A input chip-seq


title: UMSCC22B H3K4me1 chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR23.LC26) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR23LC26_B004_2738.AAV.PGK.GFP_BM


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR31.LC30) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR31LC30_B001_2738.AAV.PGK.GFP_BM


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR41.LC29) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR41LC29_B000_2738.AAV.PGK.GFP_BM


title: CUTO28_SAMPLE2


title: PCI24 input chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR53.LC25) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR53LC25_B003_2738.AAV.PGK.GFP_BM


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR31.LC24) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR31LC24_B002_2738.AAV.PGK.GFP_BM


title: MDA886LN input chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR41.LC23) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR41LC23_B001_2738.AAV.PGK.GFP_BM


title: PCI24 H3K4me1 chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR17.LC22) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR17LC22_B000_2738.AAV.PGK.GFP_BM


title: MDA686LN input chip-seq


title: R6_DH_5d_860_hip

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

institute: CNRS

description: Total RNA prepared from mouse hippocampus with 4 groups of 3 samples : WT home cage (HC), R6/1 home cage (HC), WT after probe, R6/1 after probe

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10

source_name: Hippocampus

extract_protocol: RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Hippocampus

tag: Sex

value: male

tag: age

value: 13 weeks

tag: replicate

value: 3rd replicate


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR37.LC19) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR37LC19_B004_2738.AAV.PGK.GFP_BM


title: WT_DH_5d_835_hip

value: Wild-type

value: 2nd replicate


title: WT_DH_5d_844_hip


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR87.LC18) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR87LC18_B003_2738.AAV.PGK.GFP_BM


title: R6_DH_5d_862_hip


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR51.LC17) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR51LC17_B002_2738.AAV.PGK.GFP_BM


title: HN5 input chip-seq


title: JHU029 H3K4me1 chip-seq


title: HN5 H3K4me1 chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR35.LC15) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR35LC15_B000_2738.AAV.PGK.GFP_BM


title: MDA686TU input chip-seq


title: Exp7 PB on NONE (LTR37.LC13) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR37LC13_UThuman_NONE_PB

source_name: Untransduced

value: PB


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR57.LC16) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR57LC16_B001_2738.AAV.PGK.GFP_BM

value: AAV


title: WT_DH_5d_836_hip

value: 1st replicate


title: R6_HC_890_hip


title: MDA886LN H3K4me1 chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR87.LC12) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR87LC12_B004_2738.AAV.PGK.GFP_BM


title: Exp7 PB on NONE (LTR29.LC20) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR29LC20_UThuman_NONE_PB


title: R6_HC_882_hip


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR51.LC11) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR51LC11_B003_2738.AAV.PGK.GFP_BM


title: JHU029 input chip-seq


title: MDA686LN H3K4me1 chip-seq


title: R6_HC_889_hip


title: MDA1586 H3K4me1 chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR57.LC10) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR57LC10_B002_2738.AAV.PGK.GFP_BM


title: WT_HC_878_hip


title: WT_HC_877_hip


title: R6_DH_5d_859_hip


title: HN30 shNT H3K27me3 chip-seq

source_name: HN30 shNT

value: H3K27me3 Abcam ab6002


title: HN30 shNT input chip-seq


title: Exp7 PB on NONE (LTR87.LC6) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR87LC6_UThuman_NONE_PB


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR23.LC38) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR23LC38_B002_2738.AAV.PGK.GFP_BM


title: HN30 shNT H3K4me3 chip-seq

value: H3K4me3 Abcam  ab8580


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR35.LC9) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR35LC9_B001_2738.AAV.PGK.GFP_BM


title: R6_HC_889

description: Total RNA prepared from mouse striatum 6 groups of 3 samples each included: WT home cage, R6/1 home cage, WT learning, R6/1 learning, WT memory, R6/1 memory

source_name: Striatum

value: Striatum

value: 14 weeks


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR29.LC8) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR29LC8_B000_2738.AAV.PGK.GFP_BM

value: BM


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR51.LC5) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR51LC5_B004_2738.AAV.PGK.GFP_BM


title: HN30 shNT H3K79me2 chip-seq

value: H3K79me2 Abcam ab3594


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR57.LC4) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR57LC4_B003_2738.AAV.PGK.GFP_BM


title: WT_DH_2d_866


title: R6_DH_5d_862


title: MDA1586 input chip-seq (KMT2D HNSCC control)

value: head and neck squamous cell carcinoma cell line


title: R6_DH_5d_860


title: MDA686TU H3K4me1 chip-seq

value: H3K4me1 Abcam ab8895


title: HN30 shNT H3K27ac chip-seq

value: H3K27ac Abcam ab4729


title: HN30 shNT H3K9me3 chip-seq

value: H3K9me3 Abcam ab8898


title: R6_DH_5d_859

value: male


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR35.LC3) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR35LC3_B002_2738.AAV.PGK.GFP_BM


title: WT_DH_5d_844

value: 3rd replicate


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR29.LC2) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR29LC2_B001_2738.AAV.PGK.GFP_BM


title: WT_DH_5d_843

value: Wild-type


title: HN30 shKMT2D input chip-seq

source_name: HN30 shKMT2D


title: HN30 shKMT2D H3K27me3 chip-seq


title: Exp7 BM on 2738.AAV.PGK.GFP (LTR37.LC1) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR37LC1_B000_2738.AAV.PGK.GFP_BM


title: Exp4 BM on AAV-SA-RAG1 (LTR55.LC10) rep 3

description:
AAV_RAG1.tsv
Exp4_LTR55LC10_BM6_AAV-SA-RAG1_BM

source_name: AAV RAG1


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC23) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR3LC23_BM7_AAV-SA-RAG1_BM


title: WT_DH_5d_836


title: Exp3 BM on AAV-SA-RAG1 (LTR27.LC21) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR27LC21_BM1_AAV-SA-RAG1_BM


title: HN30 shKMT2D H3K4me3 chip-seq


title: HN30 shKMT2D H3K27ac chip-seq


title: R6_DH_2d_868

value: 2nd replicate


title: WT_DH_2d_869


title: Exp3 BM on AAV-SA-RAG1 (LTR27.LC17) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR27LC17_BM1_AAV-SA-RAG1_BM


title: Exp3 BM on AAV-SA-RAG1 (LTR27.LC13) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR27LC13_BM1_AAV-SA-RAG1_BM


title: HN30 shKMT2D H3K9me3 chip-seq


title: HN30 shKMT2D H3K4me1 chip-seq


title: R6_DH_2d_867


title: WT_DH_2d_864


title: Exp3 BM on AAV-SA-RAG1 (LTR89.LC9) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR89LC9_BM1_AAV-SA-RAG1_BM


title: R6_HC_887


title: WT RL3000 Input Rep 1

first: Robert

last: Landick

address: 5445 Microbial Science Building 1550 Linden Dr.

department: Biochemistry

institute: University of Wisconsin-Madison

description: Input for WT RL3000 for HNS IP

data_processing:
Paired-end reads were trimmed of adapter sequences using CutAdapt version 2.10 (16) with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT’. Quality trimming was performed using trimmomatic (version 0.39) with parameters " -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15". The reads were aligned to the CFT073 genome (NC_004431.1 for CFT073 or GenBank accession no. U00096.3 for RL3000) using bowtie2 (version 2.4.2) under parameters “--end-to-end --very-sensitive --phred33”. Read coverage per five bp bin was scaled to the median coverage over all bins for each sample. Read coverage was calculated using (deepTools version 3.5.0; (20)) with the parameters ‘--binSize 5 –samFlagInclude 66 –extendReads' for paired end samples and ‘--binSize 5’ for single end samples. Normalization of the coverage based on the input (IP/Input) or log2(IP/input)) was calculated with custom python scripts included in the coverage and norm module of the pipeline. Read quality control was performed using fastqc version 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and multiqc version 1.11.0. RfaH regions were called using macs2 (version 2.27.1) using the parameters ‘–broad’ with the corresponding input used as a control sample.
Assembly: NC_004431.1 for CFT073 and U00963.3 for RL3000.
Supplementary files format and content: bigWig files

organism: Escherichia coli

source_name: NA-bacteria

growth_protocol: Strains were grown aerobically in Niehardt MOPs rich defined media supplemented with 0.2% glucose at 37° C with shaking at 140 RPM.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 minutes at an apparent OD600 ~0.4. After quenching with 500 mM glycine, cells were lysed and chromatin sonicated using a Misonix Ultrasonic Liquid Processor to fragments with a median size of ~200-600 nt in length. H-NS, StpA, RfaH, Beta, and σ70 IPs and input controls were performed with modifications as described in Davis SE et al. 2011. Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide. Methods Enzymol 498:449-71. DNA was quantified with QuBit dsDNA HS assay (ThermoFisher) on a QuBit 3.0 fluorimeter.
DNA sequencing paired-end libraries were prepared using the NEBNext Ultra II DNA library reagents with NEBNext sample purification beads according to the manufacturer’s protocols without size selection. Quality and size ranges of libraries were determined using HS DNA Screentape (Agilent) on a TapeStation 4200 system (Agilent). Libraries were sequenced on Illumina MiSeq or NovaSeq 6000 sequencers.

value: NA-bacteria

value: WT


title: HN30 shNT H3K4me1 chip-seq


title: Exp3 BM on AAV-SA-RAG1 (LTR89.LC1) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR89LC1_BM1_AAV-SA-RAG1_BM

value: AAV


title: R6_HC_882

value: 1st replicate


title: WT RL3000 H-NS Rep 1

description: HNS ChIP in WT RL3000

value: Polyclonal, Harlan, Final bleed, ID R10041, Cat POL001


title: WT_HC_879

value: Striatum


title: Exp3 BM on AAV-SA-RAG1 (LTR77.LC71) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR77LC71_BM7_AAV-SA-RAG1_BM


title: double mutant Δphok/ΔpSok, replicate 5

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

institute: University of Bordeaux

data_processing:
Raw FASTQ files were generated by the sequencing platform.
(1) trimming low-quality 3ʹ ends of reads and discard low quality reads using cutadapt 1.1 and prinseq-lite 0.20.4; reverse reads (R2 reads) were also trimmed of their first seven bases (option “-trim_left 7” in prinseq-lite) because there was a large proportion (>20%) of these reads with undefined bases in this region.
(2) recovering read pairs for which both mates passed the quality filtering steps using cmpfastq and assembling mates into a single sequence by means of PANDAseq 2.9 run with options “-N -o 20 -O 0 -t 0.6 -A simple_bayesian -C empty”.
(3) aligning these assembled reads onto the 486 nucleotides (nts) reference sequence (hok/Sok, hok/ΔpSok, or Δphok/ΔpSok sequence, depending on the sample) by the BWA-MEM algorithm of BWA 0.7.17 run with options “-A 1 -B 4 -O 6 -E 1 -L 10,10”.
(4) extracting mapped sequences of length 486 nts, and showing a single-base substitution compared to the reference using samtools 1.9 and bamtools 2.3.0.
(5) performing statistical analyses of the differential distribution of single-base mutations in the WT and mutant sequences. For substitutions, a “nucleotide-specific” analysis to determine whether particular nucleotides were enriched at specific positions was carried out using Trinity 2.10.0, R 3.5.3, and DESeq2 1.22.2. Mutations were considered as significantly over- or under-represented in the mutant vs the reference sample if the adjusted p-value (padj, corresponding to the False Discovery Rate) was inferior or equal to 5% (padj ≤ 0.05) and the log2 Fold Change was superior or equal to 1 or inferior or equal to −1 (log2 FC ≥ |1|).
Assembly: X05813.1 (positions 84-569)
Supplementary files format and content: Single_Substitutions_stats_length486_V2.xlsx; format: Excel spreadsheet; content: raw sequence counts (for single substitutions)
Supplementary files format and content: Single_Substitutions_differential_analysis_length486_by_sequenceV2.xlsx; format: Excel spreadsheet; content: log2 fold-changes and p-values (analysis of single substitutions by sequence)
Library strategy: DNA-Seq

extract_protocol:
The genomic DNA of bacterial colonies was extracted using the Quick Bacteria Genomic DNA extraction Kit (Nebiotech) following the supplier’s recommendations.
After genomic DNA extraction, the hok/Sok toxin-antitoxin locus was amplified with a specific primer pair generating an amplicon of 486 nt. The primers carried an overhang 5’-tail containing the adaptors for Illumina sequencing. Sequencing of the amplicon libraries was done on a MiSeq instrument in paired-end mode 2 x 300 nt (overlapping reads) at the Bordeaux Transcriptome Genome Platform, Cestas Pierroton, France.


title: double mutant Δphok/ΔpSok, replicate 4


title: WT_HC_878

value: 14 weeks


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC69) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR7LC69_BM1_AAV-SA-RAG1_BM

value: BM


title: HN30 shKMT2D H3K79me2 chip-seq

value: H3K79me2 Abcam ab3594


title: R6_DH_2d_870


title: double mutant Δphok/ΔpSok, replicate 3


title: Exp3 BM on AAV-SA-RAG1 (LTR77.LC67) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR77LC67_BM7_AAV-SA-RAG1_BM


title: WT_HC_877

description: Total RNA prepared from mouse striatum 6 groups of 3 samples each included: WT home cage, R6/1 home cage, WT learning, R6/1 learning, WT memory, R6/1 memory


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC65) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR7LC65_BM1_AAV-SA-RAG1_BM


title: double mutant Δphok/ΔpSok, replicate 2


title: Exp3 BM on AAV-SA-RAG1 (LTR89.LC5) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR89LC5_BM1_AAV-SA-RAG1_BM


title: Exp3 BM on AAV-SA-RAG1 (LTR77.LC63) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR77LC63_BM7_AAV-SA-RAG1_BM


title: double mutant Δphok/ΔpSok, replicate 1


title: Exp3 BM on AAV-SA-RAG1 (LTR59.LC59) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR59LC59_BM5_AAV-SA-RAG1_BM


title: mutant hok/ΔpSok, replicate 4


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC61) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR7LC61_BM1_AAV-SA-RAG1_BM


title: mutant hok/ΔpSok, replicate 5


title: mutant hok/ΔpSok, replicate 3


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC58) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR7LC58_BM4_AAV-SA-RAG1_BM


title: mutant hok/ΔpSok, replicate 2


title: mutant hok/ΔpSok, replicate 1


title: Exp3 BM on AAV-SA-RAG1 (LTR59.LC55) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR59LC55_BM5_AAV-SA-RAG1_BM


title: WT_DH_5d_K27ac_rep2

description: ChIP is performed using the striatum of HD R6/1 and control mice at 14 weeks. Striata from different animals are pooled. Samples contain 4 different groups: WT home cage, R6/1 home cage, WT memory, R6/1 memory

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

extract_protocol: ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with Qubit (Invitrogen). ChIP-seq libraries were prepared from 2 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode), according to manufacturer's instructions. Illumina compatible indexes were added through PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt® AMPure® XP beads (Beckman Coulter) to remove unincorporated primers and other reagents. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). Libraries were sequenced on Illumina Hiseq 4000 sequencer as Paired-End 50 base reads following Illumina’s instructions. Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.

treatment_protocol:
Whole tissue: Frozen striata from 4 mice were pooled (sex-matched between HD and WT animals), cut into small fragments, fixed in 1% formaldehyde and incubated for 15 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then homogenized in sonication buffer, and lysates were sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (Millipore) for 1 h at 4°C. Subsequently, samples were incubated overnight at 4°C with antibodies to H3K27ac (Abcam, ab4729), H3K27me3 ()  or 7C2 RNAPII antibody. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3 h at 4°C. Agarose beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.
NeuN sorted: Frozen striata from 4 mice were homogenized in ice-cold PBS supplemented with 1x Protease Inhibitors Cocktail (PIC, cOmplete EDTA free, Roche) and cross-linked in 1% formaldehyde for 15 minutes at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M and tissue was washed using ice-cold PBS. Cells were lysed then in Cell Lysis Buffer (10mM Hepes pH8; 85mM KCl; 0.5% NP-40) and nuclei were were collected after treatment with Nuclear Extraction Buffer (0.5% SDS, 10mM EDTA pH8, 50mM Tris). Purified nuclei were then resuspended in PBTB (PBS 1x, 5% BSA, 0.5% Tween-20) + 1x PIC, 3% Normal Horse Serum (NHS) and stained using α-NeuN antibody (1:1000, Merck Millipore). After washing, nuclei were labelled with α-Ms AF488 antibody (1:1500) and washed with ice-cold PBS. Immunostained nuclei were sorted using BD Aria Fusion flow cytometer, recovered in ice-cold 1x PBS, pelleted and stocked at -80ºC. Nuclei were resuspended in sonication buffer and sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (Millipore) for 1 h at 4°C. Subsequently, samples were incubated overnight at 4°C with antibodies to H3K27ac (Abcam, ab4729) or H3K27me3 (). Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3 h at 4°C. Agarose beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.

value: female

value: H3K27ac: ab4729, Abcam


title: R61_DH_5d_K9ac_rep2

value: H3K9ac:ab4441, Abcam


title: R61_HC_K9ac_rep2


title: R61_DH_5d_K27ac_rep2


title: R61_HC_K27ac_rep2


title: WT_HC_K9ac_rep2


title: wild-type hok/Sok, replicate 5


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC54) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR7LC54_BM4_AAV-SA-RAG1_BM


title: wild-type hok/Sok, replicate 4


title: WT_HC_K27ac_rep2


title: WT_DH_5d_K9ac_rep2


title: R61_DH_5d_Input_rep2

value: No antibody


title: Exp3 BM on AAV-SA-RAG1 (LTR59.LC51) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR59LC51_BM5_AAV-SA-RAG1_BM


title: wild-type hok/Sok, replicate 2


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC50) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR7LC50_BM4_AAV-SA-RAG1_BM


title: wild-type hok/Sok, replicate 3


title: R61_HC_Input_rep2


title: wild-type hok/Sok, replicate 1


title: WT_HC_Input_rep2


title: Exp3 BM on AAV-SA-RAG1 (LTR89.LC47) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR89LC47_BM5_AAV-SA-RAG1_BM


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC49) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR3LC49_BM3_AAV-SA-RAG1_BM


title: R61_DH_5d_H3K9ac_rep1

value: male


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC57) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR3LC57_BM3_AAV-SA-RAG1_BM


title: Exp3 BM on AAV-SA-RAG1 (LTR21.LC46) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR21LC46_BM4_AAV-SA-RAG1_BM


title: WT_DH_5d_H3K9ac_rep1


title: Exp3 BM on AAV-SA-RAG1 (LTR47.LC45) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR47LC45_BM3_AAV-SA-RAG1_BM


title: LMS19_Mlung

city: Seville

first: Juan

last: Diaz-Martin

address: Av Manuel Siurot

country: Spain

institute: IBiS

data_processing:
Base-calling: Illumina Basespace
Generation of read counts: HTG Edgeseq Parser v. 5,2,823,5648
Normalization : R Bioconductor DESeq2 v. 1,28,1
Assembly: hg19
Supplementary files format and content: Table with median transformation normalized counts
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung metastasis

extract_protocol:
Total RNA was prepared from 5µm FFPE tissue sections of microdissected ITF using the Agencourt FormaPure kit (A33341; Beckman Coulter, Indianapolis, IN, USA) and following the manufacturer’s instructions. RNA concentration was determined with Qubit 4 Fluorometer and Qubit® RNA HS Reagent (Thermo Fisher Scientific, Waltham, MA, USA).
HTG EdgeSeq Chemistry was employed to synthetize the RNA-Seq library. Briefly, target capture was performed by hybridizing the mRNA with Nuclease Protection Probes (NPPs). The S1 nuclease was added to the mix, producing a stoichiometric amount of target mRNA/NPP duplexes. This reaction was blocked by enzyme heat denaturation of S1. The samples were randomized before inclusion in the HTG EdgeSeq system to reduce potential biases in the run. Each hybridized sample was used as template to set up PCR reactions with specially designed tags, sharing common sequences that are complementary to both 5’-end and 3’-sequences of the probes, and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode used for sample identification and multiplexing. After PCR amplification, a clean-up procedure was performed using Agencourt AMPure XP (Beckman Coulter). The library was quantified by quantitative PCR, using KAPA Library Quantification (Roche), according to the manufacturer’s instructions. All samples and controls were quantified in triplicate and no template control was included in any run.

value: Lung metastasis

tag: tumor type

value: uterine leiomyosarcoma

tag: tumor area

value: invasive tumor front


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC53) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR3LC53_BM3_AAV-SA-RAG1_BM

tag: tissue


title: Exp3 BM on AAV-SA-RAG1 (LTR89.LC43) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR89LC43_BM5_AAV-SA-RAG1_BM

tag: vector


title: LMS21_Mlung


title: LMS20_Mlung


title: R61_HC_H3K9ac_rep1

value: pooled male and female


title: WT_HC_H3K9ac_rep1

value: Wild-type


title: Exp3 BM on AAV-SA-RAG1 (LTR21.LC42) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR21LC42_BM4_AAV-SA-RAG1_BM

value: AAV

tag: vector id


title: R61_DH_4d_Input2_rep1

value: 1st replicate


title: LMS15_Mlung


title: WT_DH_5d_Input_rep2

value: 2nd replicate


title: LMS07_Mlung


title: sample.mnk3_ut1

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Sequencing of RNA isolated from spheroid lines: Total RNA was extracted using RNeasy Micro Kit (Qiagen) per manufacturer’s instructions. Samples were prepared according to library kit manufacturer’s protocol (Dynal mRNA Direct Invitrogen) and sequencing was conducted on an Illumina HiSeq. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
Gene count tables were processed and analyzed using the DESeq2 package with R 4.1. Prior to differential comparison, genes with fewer than 10 counts among all of the samples were excluded. Differentially expressed genes (DEG) were considered significant when padj<0.05.
Assembly: mm10
Supplementary files format and content: aligned raw count table

source_name: siLP

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Qiagen) per manufacturer’s instructions
. Samples were prepared according to library kit manufacturer’s protocol (SMARTer Low Input RNA Kit, Clontech Takara Bio), indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

value: siLP

value: CCR6+ ILC3

value: Rorc-Cre Odc1-flox


title: sample.mnk3_ut2


title: LMS23_Mlung


title: sample.mnk3_stim_2

value: WT


title: Exp3 BM on AAV-SA-RAG1 (LTR89.LC39) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR89LC39_BM5_AAV-SA-RAG1_BM

value: BM

tag: subject


title: WT_DH_4d_Input2_rep1

value: Striatum

value: 14 weeks


title: WT_HC_879_hip

description: Total RNA prepared from mouse hippocampus with 4 groups of 3 samples : WT home cage (HC), R6/1 home cage (HC), WT after probe, R6/1 after probe

value: Hippocampus

value: 13 weeks

value: 3rd replicate


title: R61_HC_Input2_rep1

value: No antibody


title: CE39_Mlung

value: Lung metastasis

value: uterine adenocarcinoma

value: invasive tumor front


title: LMS05_Mlung

value: uterine leiomyosarcoma


title: sample.mnk3_stim_1


title: Exp3 BM on AAV-SA-RAG1 (LTR21.LC38) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR21LC38_BM4_AAV-SA-RAG1_BM

value: AAV


title: sample.mnk3_put_stim_2

tag: cell line

value: putrescine + IL23


title: WT_HC_Input2_rep1

value: Wild-type

value: pooled male and female

value: 1st replicate


title: CE38_Mlung


title: Exp3 BM on AAV-SA-RAG1 (LTR47.LC37) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR47LC37_BM3_AAV-SA-RAG1_BM


title: CE30_Mlung


title: sample.mnk3_put_stim_1


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC25) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR7LC25_BM3_AAV-SA-RAG1_BM


title: CE29_Mlung


title: R61_DH_5d_K27ac_rep1

description: ChIP is performed using the striatum of HD R6/1 and control mice at 14 weeks. Striata from different animals are pooled.  Samples contain 4 different groups: WT home cage, R6/1 home cage, WT memory, R6/1 memory

value: female

value: H3K27ac: ab4729, Abcam


title: WT_DH_5d_K27ac_rep1

value: Striatum


title: sample.mnk3_put_2


title: Exp3 BM on AAV-SA-RAG1 (LTR37.LC21) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR37LC21_BM3_AAV-SA-RAG1_BM

value: BM


title: R61_HC_K27ac_rep1

value: 14 weeks


title: CE28_Mlung


title: sample.mnk3_put_1


title: Exp3 BM on AAV-SA-RAG1 (LTR47.LC41) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR47LC41_BM3_AAV-SA-RAG1_BM


title: Exp3 BM on AAV-SA-RAG1 (LTR37.LC17) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR37LC17_BM3_AAV-SA-RAG1_BM


title: CE06_Mlung


title: sample.6.ccr6.ko.2

value: putrescine


title: Exp3 BM on AAV-SA-RAG1 (LTR37.LC13) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR37LC13_BM3_AAV-SA-RAG1_BM


title: WT_HC_K27ac_rep1


title: Syn.Tom_d120-122064

city: Vienna

first: Jaydeep

last: Sidhaye

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
RNA-seq reads were trimmed using trim-galore v0.5.0
Reads were mapped to abundant sequences included in the iGenomes UCSC hg38 reference were removed using bowtie2 v2.3.4.1 alignment (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter sequences were removed)
Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94.
The original reference was filtered using cellranger mkgtf v3.1.0 to select for genes with biotypes (protein_coding, lncRNA, antisense, IG_LV_gene, IG_V_gene, IG_V_pseudogene, IG_D_gene, IG_J_gene, IG_J_pseudogene, IG_C_gene, IG_C_pseudogene, TR_V_gene, TR_V_pseudogene, TR_D_gene, TR_J_gene, TR_J_pseudogene), and by adding marker genes dTomato, EGFP.
Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Brain organoids

extract_protocol: RNA sequencing libraries were generated using 500 ng of RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB). Isolation of mRNA was done using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490). The size of libraries was assessed using NGS HS analysis kit and a fragment analyzer system (Agilent). Library concentrations were quantified with KAPA Kit (Roche) and 75-bp single-read sequencing was performed using the Illumina NextSeq550 platform

value: Brain organoids

value: H9 hESC

tag: cell type

value: Day120 Tomato+

value: WT


title: sample.5.ccr6.ko.1


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC11) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR7LC11_BM5_AAV-SA-RAG1_BM


title: WT_DH_5d_Input_rep1

tag: genotype

value: No antibody


title: sample.2.ccr6.wt.2

tag: treatment

value: untreated


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC10) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR3LC10_BM4_AAV-SA-RAG1_BM

value: AAV


title: R61_HC_Input_rep1


title: sample.1.ccr6.wt.1


title: Sox2.GFP_d120-122062

value: Day 120 EGFP+


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC7) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR7LC7_BM5_AAV-SA-RAG1_BM


title: intrascapular brown adipose tissue, auranofin treated [BAT_AF4]

city: Houston

first: Aaron

middle: R

last: Cox

state: TX

address: 1825 Pressler St

department: Institute of Molecular Medicine

institute: University of Texas Health Science Center at Houston

data_processing:
Original image data file from Illumina NovaSeq 6000 was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Raw reads were filtered by (1) removing reads with adaptor contamination (2) removing reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) and then (3) removing reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
Filtered reads were mapped to the mouse reference genome mm10 using STAR (v2.6.1d) (parameter - mismatch = 2)
Quantification was performed with FeatureCounts (v1.5.0-p3)
Differential expression analysis was performed using the DESeq2 (v1.20.0) R package with padj <= 0.05
clusterProfiler software (v3.8.1) was used for GO, KEGG, and Reactome enrichment analysis (p value < 0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: intrascapular brown adipose tissue

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Plus (Zymo) according to manufacturer's instructions
Library construction was performed using NEBNext Ultra II non-stranded kit (New England BioLabs) according to manufacturer's instructions

value: intrascapular brown adipose tissue

tag: strain

value: wild-type

value: auranofin


title: Exp3 BM on AAV-SA-RAG1 (LTR27.LC9) rep 3

description:
AAV_RAG1.tsv
Exp3_LTR27LC9_BM3_AAV-SA-RAG1_BM

data_processing:
Library strategy: SLiM-PCR, custom amplicon sequencing
FASTQ files processed by RAAVIoli software
Custom software for matrix creation
Genome_build: Hg19 + custom reference AAV genome or IDLV genome
Supplementary_files_format_and_content: Data matrix if integrations (rows) observed in specific samples (columns) and quantified by the number of cells (values).


title: intrascapular brown adipose tissue, auranofin treated [BAT_AF2]


title: WT_HC_Ppp1r1b

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers

data_processing:
Library strategy: 4C-seq
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2)
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata
Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Frozen striata from 4 mice were homogenized in ice-cold PBS supplemented with 1x Protease Inhibitors Cocktail (PIC, cOmplete EDTA free, Roche) and cross-linked in 2% formaldehyde for 15 minutes at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M and tissue was washed using ice-cold PBS. Cells were lysed then in Cell Lysis Buffer (10mM Hepes pH8; 85mM KCl; 0.5% NP-40) and nuclei were were collected after treatment with Nuclear Extraction Buffer (0.5% SDS, 10mM EDTA pH8, 50mM Tris). Nuclei were counted and aliquoted at 5 million nuclei/tube. 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation.
50 ng aliquots of 4C DNA were used as template for PCR with bait-specific primers containing Illumina adapter termini (primer sequences and optimal PCR conditions available on request). PCR reactions were pooled, primers removed by washing with 1.8x AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).

tag: condition

value: Home-cage

value: Wild-type

value: female

tag: restriction enzymes

value: DpnII - Csp6I


title: WT_HC_Input_rep1

value: Striatum

value: 14 weeks

value: 1st replicate

tag: chip antibody


title: DblPos_d120-121574

value: Brain organoids

value: H9 hESC

value: Day 120 double positive


title: WT_HC_Nr4a1

tag: Sex


title: Exp3 BM on AAV-SA-RAG1 (LTR27.LC5) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR27LC5_BM3_AAV-SA-RAG1_BM

extract_protocol:
gDNA was sheared using a Covaris E220 Ultrasonicator (Covaris Inc.), generating fragments with a target size of 1,000 bp.
The fragmented DNA was subjected to end repair, 3’ adenylation and ligation (NEBNext® Ultra™ DNA Library Prep Kit for Illumina, New England Biolabs) to custom linker cassettes (LC) (Integrated DNA Technologies). LC sequences containing 8-nucleotide barcode for sample identification. Ligation products were subjected to 35 cycles of exponential PCR with primers complementary to different regions of the AAV or IDLV genomes and to the LC. For each set of AAV or IDLV specific primers, the procedure was performed in technical replicates (n = 2-3) using 80-100 ng of sheared DNA/each. Next, ten additional PCR cycles were done to include sequences required for sequencing and a second 8-nucleotide DNA barcode. PCR products were quantified by qPCR using the Kapa Biosystems Library Quantification Kit for Illumina, following the manufacturer’s instructions. qPCR was performed in triplicate on each PCR product diluted 10:3, and the concentrations were calculated by plotting the average Ct values against the provided standard curve. The amplification products were sequenced by Illumina Next/Novaseq platforms (Illumina).

value: BM


title: intrascapular brown adipose tissue, auranofin treated [BAT_AF1]


title: R61_DH_5d_Input_rep1

tag: age

value: No antibody


title: Exp3 BM on AAV-SA-RAG1 (LTR7.LC3) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR7LC3_BM5_AAV-SA-RAG1_BM

value: AAV


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC6) rep 2

description:
AAV_RAG1.tsv
Exp3_LTR3LC6_BM4_AAV-SA-RAG1_BM


title: WT_HC_Npas4


title: intrascapular brown adipose tissue, vehicle treated [BAT_V4]

value: vehicle


title: DblPos_d120-122063

value: WT


title: Syn.Tom_d120-121572

value: Day120 Tomato+


title: WT_HC_Jarid1c


title: intrascapular brown adipose tissue, vehicle treated [BAT_V3]

value: intrascapular brown adipose tissue

value: wild-type


title: Exp3 BM on AAV-SA-RAG1 (LTR27.LC1) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR27LC1_BM3_AAV-SA-RAG1_BM


title: Sox2.GFP_d120-121570

value: Day 120 EGFP+


title: WT_HC_Fos

value: Home-cage

value: Wild-type

value: female


title: Exp3 BM on AAV-SA-RAG1 (LTR3.LC2) rep 1

description:
AAV_RAG1.tsv
Exp3_LTR3LC2_BM4_AAV-SA-RAG1_BM


title: DblPos_d120-121571


title: Syn.Tom_d120-121575


title: WT_HC_Egr4

value: Striatum

value: 14 weeks

value: DpnII - Csp6I


title: intrascapular brown adipose tissue, auranofin treated [BAT_AF3]

value: auranofin


title: Syn.Tom_d90-116159

value: Brain organoids

value: H9 hESC

value: Day90 Tomato+


title: Sox2.GFP_d120-121573


title: intrascapular brown adipose tissue, vehicle treated [BAT_V2]


title: WT_DH_Ppp1r1b

value: Double-H


title: intrascapular brown adipose tissue, vehicle treated [BAT_V1]

value: vehicle


title: DblPos_d90-116158

value: Day 90 double positive

value: WT


title: Exp2 BM on AAV-SA-RAG1 (LTR7.LC80) rep 3

description:
AAV_RAG1.tsv
Exp2_LTR7LC80_BM6_AAV-SA-RAG1_BM

value: BM

value: AAV


title: Sox2.GFP_d90-116157

value: Day 90 EGFP+


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC72) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR3LC72_BM1_AAV-SA-RAG1_BM


title: liver, auranofin treated [liv_AF4]

source_name: liver

value: liver

value: wild-type


title: WT_DH_Nr4a1

value: Wild-type

value: female


title: liver, auranofin treated [liv_AF3]


title: WT_DH_Jarid1c

value: Striatum

value: 14 weeks


title: WT_DH_Npas4

value: DpnII - Csp6I


title: WT_DH_Fos


title: Exp1 BM on AAV-SA-RAG1 (LTR51.LC64) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR51LC64_BM1_AAV-SA-RAG1_BM


title: liver, auranofin treated [liv_AF2]

value: auranofin


title: Syn.Tom_d90-116156

value: Brain organoids

value: H9 hESC


title: Exp1 BM on AAV-SA-RAG1 (LTR19.LC62) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR19LC62_BM1_AAV-SA-RAG1_BM


title: Sox2.GFP_d90-116154


title: liver, auranofin treated [liv_AF1]


title: WT_DH_Egr4

value: Double-H


title: Syn.Tom_d60-116153

value: Day 60 Tomato+


title: DblPos_d90-116155

value: Day 90 double positive


title: Exp2 BM on AAV-SA-RAG1 (LTR55.LC82) rep 3

description:
AAV_RAG1.tsv
Exp2_LTR55LC82_BM6_AAV-SA-RAG1_BM


title: Exp2 BM on AAV-SA-RAG1 (LTR55.LC86) rep 2

description:
AAV_RAG1.tsv
Exp2_LTR55LC86_BM6_AAV-SA-RAG1_BM


title: DblPos_d60-116152

value: Day 60 double positive

value: WT


title: R61_HC_Nr4a1

value: Home-cage


title: R61_HC_Ppp1r1b


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC84) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR3LC84_BM1_AAV-SA-RAG1_BM

value: BM

value: AAV


title: liver, vehicle treated [liv_V3]

value: liver

value: wild-type

value: vehicle


title: liver, vehicle treated [liv_V2]


title: Exp1 BM on AAV-SA-RAG1 (LTR47.LC64) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR47LC64_BM1_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR47.LC70) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR47LC70_BM1_AAV-SA-RAG1_BM


title: liver, vehicle treated [liv_V1]


title: R61_HC_Npas4

value: Striatum

value: female


title: Syn.Tom_d90-114334

value: Day90 Tomato+


title: Exp1 BM on AAV-SA-RAG1 (LTR59.LC80) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR59LC80_BM1_AAV-SA-RAG1_BM


title: DblPos_d90-114333


title: R61_HC_Jarid1c

value: 14 weeks

value: DpnII - Csp6I


title: epididymal white adipose tissue, auranofin treated [eWAT_AF4]

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue

value: auranofin


title: Exp1 BM on AAV-SA-RAG1 (LTR51.LC76) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR51LC76_BM1_AAV-SA-RAG1_BM


title: liver, vehicle treated [liv_V4]


title: Sox2.GFP_d90-114332

value: Brain organoids

value: H9 hESC

value: Day 90 EGFP+


title: R61_HC_Fos

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers


title: Exp1 BM on AAV-SA-RAG1 (LTR19.LC74) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR19LC74_BM1_AAV-SA-RAG1_BM


title: Exp2 BM on AAV-SA-RAG1 (LTR55.LC10) rep 1

description:
AAV_RAG1.tsv
Exp2_LTR55LC10_BM6_AAV-SA-RAG1_BM


title: R61_HC_Egr4


title: Syn.Tom_d60-114331

value: Day 60 Tomato+

value: WT


title: Sox2.GFP_d60-116151

value: Day 60 EGFP+


title: epididymal white adipose tissue, auranofin treated [eWAT_AF1]


title: R61_DH_Ppp1r1b

value: Double-H


title: Exp2 BM on AAV-SA-RAG1 (LTR59.LC2) rep 1

description:
AAV_RAG1.tsv
Exp2_LTR59LC2_BM6_AAV-SA-RAG1_BM

value: BM

value: AAV


title: DblPos_d60-114330

value: Day 60 double positive


title: Sox2.GFP_d60-114329


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC92) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR3LC92_BM1_AAV-SA-RAG1_BM


title: epididymal white adipose tissue, vehicle treated [eWAT_V4]

value: wild-type

value: vehicle


title: R61_DH_Npas4

value: Striatum

value: female


title: R61_DH_Nr4a1

value: 14 weeks

value: DpnII - Csp6I


title: Syn.Tom_d60-114328


title: DblPos_d60-114327


title: epididymal white adipose tissue, vehicle treated [eWAT_V2]

value: epididymal white adipose tissue


title: Exp1 BM on AAV-SA-RAG1 (LTR59.LC44) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR59LC44_BM1_AAV-SA-RAG1_BM


title: epididymal white adipose tissue, vehicle treated [eWAT_V1]


title: epididymal white adipose tissue, vehicle treated [eWAT_V3]


title: Sox2.GFP_d60-114326

value: Brain organoids


title: R61_DH_Fos


title: R61_DH_Egr4


title: Exp1 BM on AAV-SA-RAG1 (LTR47.LC94) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR47LC94_BM1_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR51.LC88) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR51LC88_BM1_AAV-SA-RAG1_BM


title: inguinal white adipose tissue, auranofin treated [iWAT_AF4]

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue

value: auranofin


title: DblPos_d40-110960

value: H9 hESC

value: Day 40 double positive


title: epididymal white adipose tissue, auranofin treated [eWAT_AF2]


title: epididymal white adipose tissue, auranofin treated [eWAT_AF3]


title: Exp1 BM on AAV-SA-RAG1 (LTR19.LC86) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR19LC86_BM1_AAV-SA-RAG1_BM


title: DblPos_d40-110959

value: WT


title: Nef6

city: Fuzhou

first: Jun

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: SHR  rat with 10-week Nef (10mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: GCRmm38/mm10(UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: abdominal aorta

extract_protocol:
The abdominal aorta were dissected and  stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by KAPA Library Quantification Kit (KAPA Biosystem, Wilmington, MA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEB Next rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit  (NEB,Ipswich, MA, USA)for Illumina was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: SHR

value: abdominal aorta

value: Neferine

tag: group

value: SHR+Nef


title: Exp1 NONE on AAV-SA-RAG1 (LTR89.LC58) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR89LC58_CloneA_AAV-SA-RAG1_NONE

value: AAV


title: inguinal white adipose tissue, auranofin treated [iWAT_AF3]

value: wild-type


title: Nef5


title: inguinal white adipose tissue, auranofin treated [iWAT_AF2]


title: inguinal white adipose tissue, auranofin treated [iWAT_AF1]


title: DblPos_d40-110958


title: Exp1 NONE on AAV-SA-RAG1 (LTR57.LC52) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR57LC52_CloneA_AAV-SA-RAG1_NONE


title: Nef4


title: Exp1 BM on AAV-SA-RAG1 (LTR7.LC12) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR7LC12_BM7_AAV-SA-RAG1_BM

value: BM


title: inguinal white adipose tissue, vehicle treated [iWAT_V4]

value: vehicle


title: Nef2


title: R61_DH_Jarid1c

value: Striatum

value: Double-H

value: 14 weeks

value: female


title: Syn.Tom_d40-110956

value: Brain organoids

value: Day 40 Tomato+


title: Syn.Tom_d40-110957

value: H9 hESC


title: Exp1 BM on AAV-SA-RAG1 (LTR65.LC10) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR65LC10_BM7_AAV-SA-RAG1_BM


title: Nef1


title: Exp1 BM on AAV-SA-RAG1 (LTR19.LC2) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR19LC2_BM7_AAV-SA-RAG1_BM


title: SHR5

description: SHR  rat with 10-week  double distilled water  treatment

value: double distilled water


title: Sox2.GFP_d40-110954

value: Day 40 EGFP+

value: WT


title: inguinal white adipose tissue, vehicle treated [iWAT_V2]

value: inguinal white adipose tissue


title: inguinal white adipose tissue, vehicle treated [iWAT_V3]


title: Syn.Tom_d40-100992


title: Exp1 BM on AAV-SA-RAG1 (LTR77.LC96) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR77LC96_BM5_AAV-SA-RAG1_BM


title: SHR4

value: SHR

value: abdominal aorta


title: inguinal white adipose tissue, vehicle treated [iWAT_V1]


title: Sox2.GFP_d40-100983


title: Exp1 BM on AAV-SA-RAG1 (LTR63.LC94) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR63LC94_BM5_AAV-SA-RAG1_BM

value: AAV


title: Sox2.GFP_d40-100981


title: SHR3


title: SHR2


title: Exp1 BM on AAV-SA-RAG1 (LTR87.LC88) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR87LC88_BM5_AAV-SA-RAG1_BM


title: CD34_T12

city: Hangzhou

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

institute: First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.1.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: heart

extract_protocol:
After collecting the heart of sham or TAC-operated mice hearts, the tissue was minced into fine pieces using a scalpel and transferred into a glass vial with 1.5 ml of cold digestion buffer (Liberase, Roche). The tissues were digested by either using a shaking (100 rpm) 37°C waterbath for 15 min. The obtained cell suspension was gently pipetted up and down (10 x) and transferred onto a 70μm cell strainer placed on top of a 50ml Falcon tube. The tissue was gently rubbed through the strainer using the plunger of a 1ml syringe, after which the strainer was rinsed with 8.5ml of DMEM to obtain a total volume of 10 ml, which was centrifuged for 6 min at 4°C at 300 xg. After the supernatant was removed, non-cardiomyocytes samples pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS, cells were filtered with 40 μm filter and then centrifuged at 300xg for 5 minutes. Cells resuspended in PBS were stained with LIVE/DEAD Fixable Near-IR (APC/Cy7 channel) Dead Cell Stain Kit (Invitrogen; L34975, 1:1000) and Hoechst 33342 (Invitrogen; H3570, 1:1000) for 20 minutes. Unstained cells and cells staining with only 1 fluorochrome prepared concomitantly served as control. After 1 wash in PBS for 5 minutes, cells were resuspended in PBS and then sorted by Flow Cytometer. Nucleated live cells (Hoechst+/APC/Cy7− population) were sorted into PBS with 0.04% BSA for subsequent scRNA-seq. For isolation of single CD34+ cells from the heart, a similar protocol was used as describe above.
RNA libraries were prepared with Chromium™ Single Cell 3′ Reagent Kit v3 chemistry (10× Genomics) according to the manufacturer's protocol.

value: heart

value: CD34+ cells

tag: treatment group

value: 12 weeks after TAC surgery


title: retina u6 barcodes rep2 [scMPPRA]

first: SIQI

last: ZHAO

address: Campus Box 8232 4515 McKinley Ave.

institute: Washington University in St. Louis

description:
Demultiplexed barcodes
retina_pBC_exp_rep2.csv

data_processing:
scRNA-seq data was processed with Cell Ranger 6.0.1; Barcodes were extracted by fuzzy match the 8 bp before and after the barcode region, wrong length barcodes were removed. Barcodes attached to wrong cell barcode determiend by Cell Ranger were removed.
Assembly: mm10
Supplementary files format and content: single-cell RNA-seq processed expression using Cell Ranger is stored in .mtx.gz files. scMPRA barcodes counts per cell are stored in pBC_exp.csv
Library strategy: Massively Parallel Reporter Assay

source_name: Retina

growth_protocol: Retinas from newborn mice were dissected, cultured, and electroporated as described in White et al. For each replicate experiment, three retinas were electroporated with 0.5 μg/μL of the Gnb3 promoter variant library, and co-electroporated with 0.5 μg/μL of a plasmid in which the Rhodopsin promoter drives the dsRED fluorophore. Electroporated retinas were harvested and dissociated as in Murphy et al.42 with modifications as outlined below.

extract_protocol:
For the U6 promoter library construction, we followed Step 4 of the 10x feature barcoding library preparation protocol (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) CG000316 Rev C)
scRNA-seq and scMPRA are extracted using 10X protocol

value: Retina

value: postnatal day 8


title: CD34_T4_BMT

value: Chimeric mice (CD34-CreERT2;Rosa26-tdTomato mice with bone marrow cells from wild-type C57BL/6J mice by BMT(bone marrow transplantation )) heart

value: 4 weeks after TAC surgery


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC86) rep 3

first: Stefano

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

description:
AAV_RAG1.tsv
Exp1_LTR3LC86_BM5_AAV-SA-RAG1_BM

value: BM


title: SHR1


title: Exp1 NONE on AAV-SA-RAG1 (LTR89.LC46) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR89LC46_CloneA_AAV-SA-RAG1_NONE


title: Total_T12

value: total non-cardiomyocytes


title: CD34_T4


title: Exp1 NONE on AAV-SA-RAG1 (LTR57.LC74) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR57LC74_CloneA_AAV-SA-RAG1_NONE


title: WKY5

description: WKY rat with 10-week double distilled water treatment

value: WKY


title: Total_T4


title: WKY4

value: double distilled water


title: WKY3


title: CD34_T0

value: sham group


title: retina single-cell transcriptome rep2 [scRNA-seq]

description: single cell transcriptome

data_processing:
scRNA-seq data was processed with Cell Ranger 6.0.1; Barcodes were extracted by fuzzy match the 8 bp before and after the barcode region, wrong length barcodes were removed. Barcodes attached to wrong cell barcode determiend by Cell Ranger were removed.
Assembly: mm10
Supplementary files format and content: single-cell RNA-seq processed expression using Cell Ranger is stored in .mtx.gz files. scMPRA barcodes counts per cell are stored in pBC_exp.csv

extract_protocol:
The transcriptome is generated using the 10X Dual-Index Set TT expression kit
scRNA-seq and scMPRA are extracted using 10X protocol


title: Total_T0


title: Exp1 BM on AAV-SA-RAG1 (LTR21.LC70) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR21LC70_BM7_AAV-SA-RAG1_BM


title: retina single-cell transcriptome rep1 [scRNA-seq]

description: single cell transcriptome


title: WKY1


title: Exp1 BM on AAV-SA-RAG1 (LTR7.LC82) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR7LC82_BM7_AAV-SA-RAG1_BM


title: retina u6 barcodes rep1 [scMPPRA]

description:
Demultiplexed barcodes
retina_pBC_exp_rep1.csv


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC80) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR3LC80_BM5_AAV-SA-RAG1_BM


title: A30: cGAS-/- BMDC rep3

city: New York

first: Ning

last: Yang

state: NY

institute: MSKCC

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: BMDC

growth_protocol: The bone marrow cells (5 million cells in each 15 cm cell culture dish) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) in the presence of GM-CSF (20 ng/ml, BioLegend, Cat# 576304) for 9-12 days.

extract_protocol:
RNA was harvested using Qiagen Rneasy Mini kit. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with virus at MOI 10 for 6h.

value: bone marrow-derived dendritic cells (BMDCs)

value: cGAS-/-

tag: agent

value: uninfected


title: Exp1 BM on AAV-SA-RAG1 (LTR89.LC88) rep 2

city: Milan

last: Beretta

description:
AAV_RAG1.tsv
Exp1_LTR89LC88_BM5_AAV-SA-RAG1_BM

tag: tissue


title: Exp1 BM on AAV-SA-RAG1 (LTR59.LC72) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR59LC72_BM7_AAV-SA-RAG1_BM

tag: vector


title: retina barcodes rep1 [scMPPRA]

extract_protocol:
To quantify the cBC-rBC pairs, we performed separate PCRs using primers specifically targeting the reporter gene to improve barcode recovery efficiencies. Because the 10x protocol only uses 1/4 of the generated cDNA, we separately amplified the barcodes from another 1/4 of the pellet cleanup. We first used Q5 (New England BioLabs M0515) polymerase to amplify the region containing the cBC-rBC pairs with SCARED P17 and SCARED P18 with 10 cycles. The sample was divided equally into eight PCR reactions, each with 50 μl of total volume to reduce possible jackpotting. The product was then purified with the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L), and eluted with 20 μl of ddH2O. We then added sequencing adapters using an additional two rounds of PCR. The first adapter PCR was performed with SCARED P21 and SCARED PP2 with a total of 10 ng of product from the barcode PCR. Again, we pooled eight PCR reactions, each with 50 μl of total volume and 10 PCR cycles. The PCR product was purified using the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L). For the last PCR, to add the P5 and P7 Illumina adapters, we used the primers SCARED P45, SCARED PP3 with 10ng of product and pooled eight PCR reactions, each with 50 μl of total volume and 10 PCR cycles.
scRNA-seq and scMPRA are extracted using 10X protocol


title: A26: WT BMDC rep2

value: WT


title: Exp1 BM on AAV-SA-RAG1 (LTR77.LC56) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR77LC56_BM5_AAV-SA-RAG1_BM

value: AAV

tag: vector id


title: A27: WT BMDC rep3


title: WKY2

value: abdominal aorta


title: Sample_31DI

city: Indianapolis

first: Kunal

last: Gupta

state: IN

address: 355 W 16th St

institute: Indiana Universitty

data_processing:
NextSeq reads were trimmed using fastp (version 0.20.1) with parameters “-l 17 --detect_adapter_for_pe -g -p”
The resulting reads were mapped against GRCm39 using HISAT2 (version 2.2.1) with parameters “--rna-strandness F“
Read counts for each gene were created using featureCounts from the Subread package (version 1.6.4) with the parameters “-O -M --primary -p --largestOverlap -s 2 -B” and Gencode M28 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.32.0) in R/Bioconductor (R version 4.1.1)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample

source_name: Ipsilateral dentate gyrus

extract_protocol:
Samples were prepared for extraction using the standard protocol for lipid-rich samples described in the QIAsymphony RNA Handbook (issued November 2020).  Tissue disruption and homogenization was carried out using a Qiagen Tissuelyser II.  RNA extraction was performed using a QIAsymphony SP (protocol: RNA_CT_800_V7, kit: QIAsymphony RNA Kit (192), catalog no. 931636).  RNA was eluted into 100 µL of RNase-free water and analyzed using an Agilent 4200 TapeStation.
Libraries were prepared by Illumina TruSeq Stranded mRNA Library Preparation Kit protocol (catalog no. 20020595).  The libraries were analyzed by Agilent 4200 TapeStation, and pooled.  The pooled libraries were loaded on a NextSeq 500/550 High Output v2.5 run with a 75-cycle sequencing module (catalog no. 20024906) to generate paired-end reads.  The demultiplexing of the reads was performed with bcl2fastq version 2.20.0

value: Ipsilateral dentate gyrus

value: Saline

tag: time

value: Day 14


title: Sample_40DI

value: Kainate


title: Sample_39DC

source_name: Contralateral dentate gyrus

value: Contralateral dentate gyrus


title: Sample_39DI


title: Sample_31DC


title: A25: WT BMDC rep1


title: Exp1 BM on AAV-SA-RAG1 (LTR19.LC50) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR19LC50_BM5_AAV-SA-RAG1_BM

tag: subject


title: Sample_40DC


title: Exp1 NONE on AAV-SA-RAG1 (LTR89.LC44) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR89LC44_CloneA_AAV-SA-RAG1_NONE


title: Exp1 BM on AAV-SA-RAG1 (LTR29.LC64) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR29LC64_BM7_AAV-SA-RAG1_BM


title: A24: cGAS-/- BMDC+MVAΔE5R rep3

tag: cell type


title: A29: cGAS-/- BMDC rep2

tag: genotype


title: A28: cGAS-/- BMDC rep1


title: Exp1 NONE on AAV-SA-RAG1 (LTR57.LC28) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR57LC28_CloneA_AAV-SA-RAG1_NONE


title: Sample_14DC

tag: treatment


title: A23: cGAS-/- BMDC+MVAΔE5R rep2

tag: strain


title: Exp1 BM on AAV-SA-RAG1 (LTR77.LC36) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR77LC36_BM7_AAV-SA-RAG1_BM


title: Sample_28DI


title: A22: cGAS-/- BMDC+MVAΔE5R rep1


title: Exp1 BM on AAV-SA-RAG1 (LTR65.LC34) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR65LC34_BM7_AAV-SA-RAG1_BM


title: 195_2_3: Rescue MCF7  + EtOH

type: RNA

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

institute: ANSES

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Tecan MS200 Scanner (NimbleGen MS 200 [Tiff converted by Agilent Tiff4FE tool]) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Tiff converted by Agilent Tiff4FE tool using default parameters (protocol GE1_1105_Oct12 and Grid:072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Rescue MCF7  + EtOH

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF-7 were seeded in red DMEM 10% SVF and then maintained for 72h in phenol red free DMEM with 2% of SVF to maximize E2 stimulation.

extract_protocol: RNA was prepared using the RNAeasy column purification (Qiagen, Hilden, Germany), following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop technology, Cambridge, UK) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the overall RNA integrity numbers (RIN) were between 9.8 and 10.

treatment_protocol: MCF7 were treated with 8h of either EtOH (control) or 10nm of E2 (17beta-estradiol). Hypoxic MCF7 were treated with 200µM with Cobalt chloride (CoCl2). Rescue cells were obtained from MCF7 cultured for 1 month with CoCl2 (200µM) and then cultured 1 month in CoCl2 free media. (M : control MCF7 + EtOH / ME : control MCF7 + E2 / H : hypoxic MCF7 + EtOH / HE : Hypoxic MCF7 + E2 / R : Rescue MCF7  + EtOH / RE : Rescue MCF7  + E2)

tag: cell line

value: MCF-7 Rescue


title: 196_1_1: Rescue MCF7  + E2

source_name: Rescue MCF7  + E2

value: MCF-7 Rescue + E2


title: 196_1_2: Rescue MCF7  + EtOH


title: A21: cGAS-/- BMDC+MVA rep3

value: MVA


title: 194_1_3: Rescue MCF7  + E2


title: 195_2_1: Rescue MCF7  + E2


title: 196_2_4: Rescue MCF7  + E2


title: A19: cGAS-/- BMDC+MVA rep1


title: A20: cGAS-/- BMDC+MVA rep2


title: Sample_24DI


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC26) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR3LC26_BM7_AAV-SA-RAG1_BM

source_name: AAV RAG1

value: BM


title: Exp1 BM on AAV-SA-RAG1 (LTR7.LC24) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR7LC24_BM5_AAV-SA-RAG1_BM


title: 195_1_2: Rescue MCF7  + EtOH


title: Sample_24DC


title: Sample_14DI


title: 196_1_3: Control MCF7 + E2

source_name: Control MCF7 + E2

value: MCF-7 Control + E2


title: 194_2_4: Rescue MCF7  + EtOH


title: 195_2_4: Control MCF7 + E2


title: A18: WT BMDC+MVAΔE5R rep3


title: Sample_36DI


title: 195_1_1: Control MCF7 + E2


title: 194_2_2: Control MCF7 + E2


title: Exp1 BM on AAV-SA-RAG1 (LTR63.LC22) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR63LC22_BM5_AAV-SA-RAG1_BM


title: Sample_36DC


title: Exp1 BM on AAV-SA-RAG1 (LTR51.LC28) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR51LC28_BM7_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR87.LC16) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR87LC16_BM5_AAV-SA-RAG1_BM


title: A17: WT BMDC+MVAΔE5R rep2


title: Sample_28DC


title: A16: WT BMDC+MVAΔE5R rep1


title: Sample_27DI


title: 196_2_2: Control MCF7 + EtOH

source_name: Control MCF7 + EtOH

value: MCF-7 Control


title: Sample_27DC


title: Sample_34DI

value: Day 7


title: Exp1 BM on AAV-SA-RAG1 (LTR19.LC14) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR19LC14_BM5_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC96) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR3LC96_BM4_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR21.LC94) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR21LC94_BM4_AAV-SA-RAG1_BM


title: A14: WT BMDC+MVA rep2

value: bone marrow-derived dendritic cells (BMDCs)


title: Exp1 BM on AAV-SA-RAG1 (LTR27.LC92) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR27LC92_BM4_AAV-SA-RAG1_BM


title: Sample_34DC


title: Sample_20DI


title: 195_1_3: Control MCF7 + EtOH


title: A13: WT BMDC+MVA rep1


title: Exp1 BM on AAV-SA-RAG1 (LTR29.LC88) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR29LC88_BM4_AAV-SA-RAG1_BM


title: S106foxo_switch_gut_4

city: LONDON

first: MengJia

last: Li

state: Please Select

address: flat38 midhopse house, midhope street

country: United Kingdom

institute: University College London

data_processing:
Read quality assessed with FastQC
Aligned to D. melanogaster genome by HiSAT2, sorted by Samtools
Counted with featurecounts
Analysed with DESeq2
Genome_build: dmel 6.19
Supplementary_files_format_and_content: processedData_foxo_switch_RNA.xlsx: Excel file containing read counts for genes analysed in gut and fat body.

organism: Drosophila melanogaster

source_name: Adult female gut

growth_protocol: Flies reared on 10% yeast, 5% sucrose

extract_protocol:
Gut and fat body dissection, Trizol-chloroform extraction, NextFlex Poly(A) beads (PerkinElmer NOVA-512981) for polyA enrichment.
NextFlex Rapid Directional qRNAseq v2 reagents, (barcode sets C and D, PerkinElmer NOVA-5130-14 and NOVA-5130-15 )  and 16 cycles of PCR.

treatment_protocol: Mated 48h, separated from males, fed 200 µM RU486 for 21 days, and switch to control food for 7 days.

value: female

value: 30 days

tag: induction

value: RU486+ 3weeks, then RU- 1 week


title: 194_2_1: Control MCF7 + EtOH


title: 194_1_4: Control MCF7 + EtOH


title: Sample_20DC


title: 196_1_4: Hypoxic MCF7 + E2

source_name: Hypoxic MCF7 + E2

value: MCF-7 Hypoxic + E2


title: S106foxo_switch_gut_3


title: Exp1 BM on AAV-SA-RAG1 (LTR77.LC86) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR77LC86_BM4_AAV-SA-RAG1_BM

value: AAV


title: A15: WT BMDC+MVA rep3

value: WT


title: 196_2_3: Hypoxic MCF7 + E2


title: S106foxo_switch_gut_2


title: Exp1 BM on AAV-SA-RAG1 (LTR59.LC84) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR59LC84_BM3_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR47.LC82) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR47LC82_BM3_AAV-SA-RAG1_BM


title: Sample_21DI

value: Ipsilateral dentate gyrus


title: S106foxo_switch_gut_1


title: Exp1 BM on AAV-SA-RAG1 (LTR7.LC80) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR7LC80_BM3_AAV-SA-RAG1_BM


title: S106foxo_control_gut_4


title: Sample_21DC

value: Kainate


title: 195_2_2: Hypoxic MCF7 + E2


title: Exp1 BM on AAV-SA-RAG1 (LTR37.LC76) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR37LC76_BM3_AAV-SA-RAG1_BM


title: 194_1_2: Hypoxic MCF7 + E2


title: S106foxo_control_gut_3


title: Sample_33DI

value: Saline


title: Exp1 BM on AAV-SA-RAG1 (LTR27.LC74) rep 3

description:
AAV_RAG1.tsv
Exp1_LTR27LC74_BM3_AAV-SA-RAG1_BM


title: Hv_MtNSP2ox_+P+N_rep3

city: Cambridge

first: Darius

last: Zarrabian

address: 93 Lawrence Weaver Rd

department: Plant Sciences

institute: Crop Science Centre, University of Cambridge

data_processing:
Quality control was conducted with FastQC software
Resultant raw fastq data were mapped to the M. truncatula reference genome version 4.0 or the H. vulgare cv. Golden Promise reference genome with STAR software
The raw count values were calculated with featureCounts in R package Rsubread
Assembly: Mt4.0v1, Hordeum vulgare cv. Golden  Promise
Supplementary files format and content: tab separated files with raw count values

organism: Hordeum vulgare

source_name: whole root

extract_protocol:
H. vulgare total RNA was extracted using the Spectrum™ Plant Total RNA kit (SigmaAldrich) and M. truncatula total RNA was isolated with the RNeasy PlantMini Kit (Qiagen),  following the manufacturer’s instructions.
Poly A enrichment

value: whole root

value: Golden Promise cultivar transformed with pOsUBI3:MtNSP2-FLAG

value: +P+N

value: 21 days


title: 196_2_1: Hypoxic MCF7 + EtOH

source_name: Hypoxic MCF7 + EtOH

value: MCF-7 Hypoxic


title: Sample_35DI


title: S106foxo_control_gut_2


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC60) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR3LC60_BM4_AAV-SA-RAG1_BM

value: BM


title: Sample_35DC

value: Contralateral dentate gyrus

value: Day 7


title: Exp1 BM on AAV-SA-RAG1 (LTR21.LC58) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR21LC58_BM4_AAV-SA-RAG1_BM


title: 195_1_4: Hypoxic MCF7 + EtOH


title: Hv_MtNSP2ox_+P+N_rep2


title: S106foxo_control_gut_1

value: female


title: S106foxo_control_gut_5

value: 30 days


title: Sample_89DC


title: 194_1_1: Hypoxic MCF7 + EtOH


title: WT_switch_gut_5

value: RU486+ 3weeks, then RU- 1 week


title: Exp1 BM on AAV-SA-RAG1 (LTR29.LC52) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR29LC52_BM4_AAV-SA-RAG1_BM


title: Sample_89DI


title: Hv_MtNSP1ox_+P+N_rep3

value: Golden Promise cultivar transformed with pZmUBI:MtNSP1-FLAG


title: Sample_33DC


title: Exp1 BM on AAV-SA-RAG1 (LTR77.LC50) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR77LC50_BM4_AAV-SA-RAG1_BM

value: AAV


title: 194_2_3: Hypoxic MCF7 + EtOH


title: Hv_MtNSP1ox_+P+N_rep2


title: Sample_26DC


title: Hv_MtNSP1ox_+P+N_rep1


title: Exp1 BM on AAV-SA-RAG1 (LTR59.LC48) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR59LC48_BM3_AAV-SA-RAG1_BM


title: WT_switch_gut_2


title: Exp1 BM on AAV-SA-RAG1 (LTR47.LC46) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR47LC46_BM3_AAV-SA-RAG1_BM


title: Sample_23DI


title: Hv_nsp2_-P-N_rep3

value: nsp2-1 mutant in Golden Promise background

value: -P-N


title: Hv_MtNSP2ox_+P+N_rep1


title: Sample_23DC

value: Kainate


title: WT_switch_gut_1


title: WT_switch_gut_4


title: Exp1 BM on AAV-SA-RAG1 (LTR37.LC40) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR37LC40_BM3_AAV-SA-RAG1_BM


title: Exp1 BM on AAV-SA-RAG1 (LTR3.LC24) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR3LC24_BM4_AAV-SA-RAG1_BM


title: Sample_41DC

value: Saline

value: Day 3


title: Exp1 BM on AAV-SA-RAG1 (LTR7.LC44) rep 2

description:
AAV_RAG1.tsv
Exp1_LTR7LC44_BM3_AAV-SA-RAG1_BM


title: Hv_nsp2_-P-N_rep2

value: whole root


title: Hv_nsp2_-P-N_rep1


title: WT_control_gut_5


title: Sample_41DI

value: Ipsilateral dentate gyrus


title: WT_control_gut_3


title: Hv_nsp2_-P+N_rep3

value: -P+N

value: 21 days


title: Sample_26DI


title: Sample_18DI


title: WT_control_gut_2


title: WT_control_gut_1


title: Sample_18DC


title: Hv_nsp2_-P+N_rep2


title: Exp1 BM on AAV-SA-RAG1 (LTR29.LC16) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR29LC16_BM4_AAV-SA-RAG1_BM

value: BM


title: Hv_nsp2_-P+N_rep1


title: S106foxo_switch_fb_4

source_name: Adult female Fat body


title: Exp1 BM on AAV-SA-RAG1 (LTR77.LC14) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR77LC14_BM4_AAV-SA-RAG1_BM


title: Hv_nsp2_+P-N_rep3

value: +P-N


title: S106foxo_switch_fb_3


title: Sample_42DI


title: Sample_42DC

value: Contralateral dentate gyrus


title: S106foxo_switch_fb_2

value: female


title: Exp1 BM on AAV-SA-RAG1 (LTR59.LC12) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR59LC12_BM3_AAV-SA-RAG1_BM


title: Hv_nsp2_+P-N_rep2


title: Exp1 BM on AAV-SA-RAG1 (LTR47.LC10) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR47LC10_BM3_AAV-SA-RAG1_BM


title: Sample_44DI


title: Exp1 BM on AAV-SA-RAG1 (LTR21.LC22) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR21LC22_BM4_AAV-SA-RAG1_BM


title: Hv_nsp2_+P-N_rep1


title: S106foxo_switch_fb_1

value: 30 days


title: Exp1 BM on AAV-SA-RAG1 (LTR7.LC8) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR7LC8_BM3_AAV-SA-RAG1_BM


title: Sample_44DC


title: Hv_nsp2_+P+N_rep3

value: +P+N


title: S106foxo_control_fb_4


title: Exp1 BM on AAV-SA-RAG1 (LTR37.LC4) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR37LC4_BM3_AAV-SA-RAG1_BM


title: Hv_nsp2_+P+N_rep2


title: S106foxo_control_fb_3


title: Exp1 BM on AAV-SA-RAG1 (LTR27.LC2) rep 1

description:
AAV_RAG1.tsv
Exp1_LTR27LC2_BM3_AAV-SA-RAG1_BM


title: Sample_37DI


title: Hv_nsp2_+P+N_rep1


title: Follow-up HN30 sFollow-up HNT – rep 3

first: Scot

institute: UW Health

data_processing:
raw reads were aligned to the hg19 genome using STAR v2.7.2b and quality checked using FastQC v0.11.8
Counts were generated using featureCounts from subread v1.6.3 80
Downstream normalization and differential expression analysis were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample. Samples as columns, genes as rows.

extract_protocol:
RNA extraction was performed using an RNeasy Mini Kit per manufacturer’s instructions (Qiagen). Isolation of mRNA was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module
libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs). Library quality was checked on an Agilent TapeStation 4150 and quantified by Qubit 2000 fluorometer (Invitrogen). Libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq6000 SP runs with paired-end 100-bp reads at the The Advanced Technology Genomics Core (ATGC) at MD Anderson Cancer Center.

treatment_protocol: Human KMT2D knockdown experiments were performed in the HN30 cell line using KMT2D-specific shRNAs described previously (Maitituoheti et al., 2020).

value: head and neck squamous cell carcinoma cell line

tag: status

value: Non-targeting control


title: Sample_29DI


title: Hv_nsp1_-P-N_rep3

value: nsp1-1 mutant in Golden Promise background


title: Follow-up HN30 sFollow-up HNT – rep 2


title: S106foxo_control_fb_1

tag: Sex


title: Hv_nsp1_-P-N_rep2

value: -P-N


title: WT_switch_fb_4

tag: age

value: RU486+ 3weeks, then RU- 1 week


title: Sample_30DI

value: Kainate


title: Follow-up HN30 sFollow-up HNT – rep 1


title: WT_switch_fb_3


title: Hv_nsp1_-P-N_rep1