title: BxPC3,noIFNγ, Replicate2, ATAC-seq

city: NEW YORK

first: Xinhe

last: Xue

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

description: Illumina NextSeq 500

tag: cell line


title: WT_S13_2

status: Public on Nov 28 2024

type: SRA

city: Urbana

first: Thomas

last: Gaj

state: IL

address: 1406 W. Green St.

department: Bioengineering

country: USA

institute: University of Illinois Urbana-Champaign

library_source: transcriptomic

data_processing:
Sequenced reads were pseudo-aligned to NCBI’s Annotation Release 109.2020112 (NCBI)  along with the GRCh38 reference genome as the decoy sequence for the Salmon index. Quasi-mapping was then performed  with Salmon (v1.5.2) with additional arguments: --seqBias and –gcBias, which were used to correct for sequence- and GC-specific biases, --numBootstraps=30, which was used to compute bootstrap transcript abundance estimates, and –validateMappings and –recoverOrphans, which were used to improve the accuracy of mappings.
The transcript-levels counts were then read into R (v.4.2.2) and gene-level counts were calculated using the "lengthScaledTPM" method from the tximport package (v1.26.1)
Assembly: GRCm39, NCBI Annotation Release 109.2020112
Supplementary files format and content: McCallister_HEK293T_rawcounts.txt: gene level annotations and counts in tab-delimited text format

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: Cells were maintained in DMEM with 10% FBS and 1% anti-anti at 37 C for 48 hr after transfection, at which point they were harvested.

extract_protocol:
RNA was extracted from HEK293T cells using the PureLink RNA Mini Kit (Invitrogen) and converted to complementary DNA (cDNA) using the iScript cDNA Synthesis Kit (Bio-Rad).
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche).  The libraries were pooled; quantitated by qPCR and sequenced on one S1 lane for 151 cycles from both ends of the fragments on a NovaSeq 6000 with V1.5 sequencing kits.

treatment_protocol: Cells were transfected with plasmids encoding the CRISPR effector protein, with either a C0ORF72-targeting crRNA or a non-targeting crRNA, via transient transfection.

tag: tissue

value: Kidney

value: HEK293T cells

tag: cell type

value: Human embyronic kidney cells

tag: genotype

value: Wild-type

tag: treatment

value: RfxCas13d with crRNA 13


title: Murine skin, Healthy, Day4, Biological replicate 2, Mouse 13

city: Copenhagen

first: Kristian

middle: Kåber

last: Pedersen

address: Bispebjerg Bakke 23

department: Department of Dermatology

country: Denmark

institute: Copenhagen University Hospital – Bispebjerg

data_processing:
The raw reads were cleaned with SOAPnuke version 1.5.2 (RRID:SCR_015025, parameters: -l 15 -q 0.2 -n 0.05).
The reads were mapped to the murine genome (GRCm39, version GCA_000001635.9) with Bowtie 2 version v2.2.5 (RRID:SCR_016368; parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200).
The mapped reads were quantified using RSEM version v1.2.8 (parameters: -p 8 --forward-prob 0 --paired-end). The final result is the processed count matrix. The count matrix include gene counts with decimals because RSEM return probabilistically-weighted read alignments.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

organism: Mus musculus

source_name: Skin

extract_protocol:
Tissue samples were homogenized in TRIzol and RNA isolated with chloroform. Total RNA was harvested using the Nucleospin RNA kit which includes DNAse treatment (Machery-Nagel).
Library preparation was performed using the MGIEasy RNA Directional Library Prep Set, which uses oligo dT primers for mRNA enrichment

treatment_protocol:
To induce basal cell carcinoma in the murine skin we gave the mice Tamoxifen (3 i.p. injections with 300 µg tamoxifen) and treated them with x-ray (1 irradiation, 4 Gy over 2.05 minutes)
Induced skin then received one of the following treatments: no treatment; ablative fractional laser (1 treatment; 5% density, 40 mJ/microbeam, 1 pass); vismodegib (8 treatments, twice daily)

value: Skin

tag: strain

value: Ptch1+/- K14-CreER2 p53fl/fl

tag: time from_treatment

tag: Sex

value: Female

tag: age (days)

tag: disease

tag: tumor state

tag: group

tag: tumor induction

value: No treatment


title: Circular RNA_siSMG6_BeforeIP_biological rep2

type: RNA

city: Daejeon

first: Sung Ho

last: Boo

address: 291, Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The signals were scanned using the Agilent Scanner G2505C

data_processing: Quantification was performed by Feature Extraction Software (Agilent Technology, Palo Alto, CA), and analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA)

source_name: HeLa

label_protocol: The enriched circular RNAs were amplified and transcribed into Cy3 labeled cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (QIAGEN)

growth_protocol: HeLa cells were grown with Dulbecco’s Modified Eagles Medium (Sigma-aldrich) supplemented with 10% (vol/vol) fetal bovine serum (Sigma-aldrich) and 1% (vol/vol) penicillin/streptomycin (Sigma-aldrich)

extract_protocol: Total RNAs associated with CBP80 or eIF4E were extracted using Trizol by manufacturer's recommendations

treatment_protocol: RNA immunoprecipitations were performed using either α-CBP80 or α-eIF4E antibodies.

tag: gender

value: siSMG6 + Before IP


title: Circular RNA_siControl_eIF4EIP_biological rep2

value: siControl + eIF4E IP


title: WT_S13_3


title: Murine skin, BCC, Vismodegib, Day4, Biological replicate 5, Mouse 12

value: Day 4

value: Basal cell carcinoma

value: Early-stage

value: INDUC+VISMO

value: Tamoxifen (3 i.p. injections with 300 µg tamoxifen) + x-ray (1 irradiation, 4 Gy over 2.05 minutes)

tag: time from_tumor_induction_(days)

value: Vismodegib (8 treatments, twice daily)


title: BxPC3,noIFNγ, Replicate1, ATAC-seq

state: New York

description: Illumina NextSeq 500

library_source: genomic

data_processing:
For Illumina data, adaptors were trimmed with trimmomatic (version 0.39) with the options ILLUMINACLIP:Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:24 (Bolger, Lohse and Usadel, 2014). For Ultima data, cram files were converted to fastq using samtools (version 1.9), and trimmed using cutadapt (version 4.0) (Danecek et al., 2021; Martin, 2011).
Reads from both sequencing platforms were aligned to GRCh38 with bowtie2 (version 2.4.4) (Langmead and Salzberg, 2012), deduplicated with picard through gatk MarkDuplicates (version 4.2.5.0), and downsampled to the sample with the lowest reads using samtools, then peaks were called with MACS2 callpeak (version 2.2.7.1) with default parameters (Zhang.,2008).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
ATAC-seq was performed using homemade transposomes with minor modifications that are detailed below (Buenrostro et al.,2013; Picelli et al., 2014)). For each replicate, we trypsinized, washed, and resuspended 250,000 cells in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40, 0.1% tween-20, 0.01% digitonin) and lysed for 10 minutes on ice (Corces et al., 2017). After lysis, 50,000 cells were resuspended in transposase reaction mix (1ul Tn5 (0.5 µM), 4ul 5X TD-TAPS (50mM TAPS-NaOH, 25mM MgCl2, 50% DMF), 5ul dilution buffer (10mM Tris-HCl, pH 7.4, 100mM NaCl, 1mM DTT, 50% glycerol), 2ul 10% Tween, and 8ul PBS) and tagmentation was performed at 37°C for 30 minutes. Next, samples were purified using the Zymo Clean and Concentrate kit.
For the library preparation, DNA was amplified with NEBNext High-Fidelity 2× PCR Master Mix as previously described (Buenrostro et al.,2013). The PCR program was as followed: 72 °C for 5 minutes, 98 °C for 30 seconds, (98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds) x 12 cycles. Samples were sequenced on both Illumina NextSeq 500 and Ultima Genomics platforms.

treatment_protocol: For IFNγ-stimulated conditions, cells were cultured in medium supplemented with 100 IU/mL human IFNγ (BioLegend) for 48 hours.

value: PDAC

value: no treatment


title: Murine skin, BCC, Ablative fractional laser, Day4, Biological replicate 4, Mouse 11

value: INDUC+AFL

value: Ablative fractional laser (1 treatment; 5% density, 40 mJ/microbeam, 1 pass)


title: WT_NTG_3

value: Kidney

value: HEK293T cells

value: Human embyronic kidney cells

value: Wild-type

value: RfxCas13d with NTG crRNA


title: WT_S13_1

value: RfxCas13d with crRNA 13


title: Murine skin, Healthy, Day4, Biological replicate 4, Mouse 15

value: Skin

value: Ptch1+/- K14-CreER2 p53fl/fl

value: Female

value: No treatment


title: HJ-4-2

city: lianyungang

first: Luyao

last: Zhang

address: tongguan

country: China

institute: Jiangsu Ocean University

description: Library name: B2

data_processing:
Raw data quality assessed with FastQC.
Quality trimming using Trimmomatic.
Alignment with HISAT2.
Redundancy and insertion fragment distribution analysis with RSeQC.Uniformity and genome structure distribution analysis with Qualimap.
Gene coverage and sequencing distribution analysis with BEDTools.
Assembly: HISAT2
Supplementary files format and content: The counts matrices provide gene expression counts across different samples. RSEM quantification files contain estimated expression levels for each gene and transcript. Quality control reports from FastQC are also included to visualize and assess the sequencing data quality.

source_name: Colorectal Carcinoma

growth_protocol: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 32µM HJ-4 drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: Colorectal Carcinoma

value: Colorectal cells

value: WT

value: HJ-4, 32 μM, 24 hours


title: Circular RNA_siControl_CBP80IP_biological rep2

value: siControl + CBP80 IP


title: Murine skin, BCC, Day4, Biological replicate 4, Mouse 8

value: Basal cell carcinoma

value: Early-stage

value: INDUC

value: Tamoxifen (3 i.p. injections with 300 µg tamoxifen) + x-ray (1 irradiation, 4 Gy over 2.05 minutes)


title: WT_NTG_2

value: Kidney

value: HEK293T cells

value: Human embyronic kidney cells


title: N2V7_NTG_1

value: Wild-type

value: RfxCas13d-N2V7 with NTG cRNA


title: Circular RNA_siSMG6_eIF4EIP_biological rep1

value: siSMG6 + eIF4E IP


title: Circular RNA_siSMG6_CBP80IP_biological rep1

value: Female

value: siSMG6 + CBP80 IP


title: Circular RNA_siSMG6_eIF4EIP_biological rep2


title: WT_NTG_1

value: RfxCas13d with NTG crRNA


title: Circular RNA_siControl_CBP80IP_biological rep1


title: Linear RNA_siSMG6_BeforeIP_biological rep2

hyb_protocol: Fragmented endlabeled cDNA was hybridized to the Affymetrix arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: After the final wash & staining step, Affymetrix array was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software1.1. The raw .cel file generated through above procedure meant expression intensity data and was used for the next step. Expression data were generated by Transcriptome Analysis Console 4.0.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Transcriptome Analysis Console software was used. Data mining and graphic visualization were performed using ExDEGA (Ebiogen Inc., Korea).

label_protocol: Total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the doublestranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and endlabeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

value: siSMG6 + Before IP


title: Murine skin, BCC, Ablative fractional laser, Day4, Biological replicate 2, Mouse 7

value: Skin

value: Ptch1+/- K14-CreER2 p53fl/fl

value: Day 4

value: INDUC+AFL

value: Ablative fractional laser (1 treatment; 5% density, 40 mJ/microbeam, 1 pass)


title: Murine skin, BCC, Vismodegib, Day4, Biological replicate 2, Mouse 6

value: Basal cell carcinoma

value: Early-stage

value: INDUC+VISMO

value: Vismodegib (8 treatments, twice daily)


title: Circular RNA_siControl_eIF4EIP_biological rep1

value: siControl + eIF4E IP


title: Murine skin, BCC, Day4, Biological replicate 1, Mouse 3

value: INDUC

value: Tamoxifen (3 i.p. injections with 300 µg tamoxifen) + x-ray (1 irradiation, 4 Gy over 2.05 minutes)

value: No treatment


title: AD5

city: guangzhou

first: yalan

last: wu

address: guangzhou

institute: guang zhou university of China medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform (www.novelbrain.com).
Assembly: mm10
Supplementary files format and content: Supplementary_files

source_name: terminal ileum tissues

extract_protocol:
Tissue samples were processed as follows: First, they were washed with phosphate-buffered saline (PBS) and then minced into small pieces (approximately 1mm3) on ice. Next, they were enzymatically digested using 285 U/mL collagenase I (Worthington), 355 U/mL collagenase II (Worthington), 0.5 U/mL Dispase II (Sigma), and 50 U/mL DNase I (Worthington) for 45 min at 37°C with agitation. After digestion, the samples were sieved through a 70µm cell strainer and then centrifuged at 300g for 5 min. Following the removal of the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse any remaining red blood cells. The cell pellets were then washed with PBS containing 0.04% BSA and re-suspended in the same buffer. The samples were then re-filtered through a 35μm cell strainer to ensure single-cell dissociation. The dissociated single cells were stained with AO/PI to assess cell viability using the Countstar Fluorescence Cell Analyzer.
For the scRNA-Seq libraries, the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA) were used.

value: terminal ileum tissues

tag: disease state

value: atopic dermatitis


title: AD4

description: 10x Genomics


title: Murine skin, BCC, Vismodegib, Day4, Biological replicate 1, Mouse 1

value: Female


title: Murine skin, Healthy, Day4, Biological replicate 5, Mouse 16


title: AD2

description: 10x Genomics


title: Murine skin, BCC, Vismodegib, Day4, Biological replicate 4, Mouse 12


title: AD1

description: 10x Genomics


title: Murine skin, BCC, Ablative fractional laser, Day4, Biological replicate 3, Mouse 11


title: NH5

description: 10x Genomics

value: healthy


title: Linear RNA_siControl_BeforeIP_biological rep1

value: siControl + Before IP


title: Linear RNA_siSMG6_BeforeIP_biological rep1

value: siSMG6 + Before IP


title: Murine skin, BCC, Vismodegib, Day4, Biological replicate 3, Mouse 9

value: Skin

value: Ptch1+/- K14-CreER2 p53fl/fl

value: Day 4


title: NH4

description: 10x Genomics


title: NH3

description: 10x Genomics


title: MeJA treated NtCOI1-silenced leave Replicate 1

city: Qingdao

first: Fuzhu

last: Ju

address: Laoshan District No.11 Forth Longitudinal Keyuan Rd.

institute: Chinese Academy of Agricultural Sciences Institute of Tobacco research

description: Biological replicate 1 of 3.  NtCOI1-silenced  leave, MeJA treated, harvested after 7 days of MeJA treatment.

hyb_protocol: The labeled cDNAs were then hybridized with a 44K tobacco gene expression chip from Agilent Technologies (Santa Clara, USA).

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: CapitalBio Analyzer Software was used for background subtraction and LOWESS normalization.

organism: Nicotiana tabacum

source_name: MeJA treated NtCOI1-silenced leave

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and enzymatic reaction.

growth_protocol: Seeds of NtCOI1-RI and Control tobacco (NtCOI1-RI , NtCOI1-silenced; Control, empty vector transformed) were surface sterilized and sown onto Petri plates containing ½ MS supplemented with 25 μg/mL Hygromycin. The sown seed were germinated at an indoor growth room at 25°C and 14 h light/10 h dark. After 10 days of germination

extract_protocol: Total RNA containing small RNA was extracted by using  the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol.

tag: tag

value: MeJA treated NtCOI1-silenced


title: AD3

description: 10x Genomics


title: MeJA treated NtCOI1-silenced leave Replicate 3

description: Biological replicate 3 of 3.  NtCOI3-silenced  leave, MeJA treated, harvested after several passages.


title: NtCOI1-silenced leave Replicate 3

description: Biological replicate 3 of 3.  NtCOI3-silenced  leave, untreated, harvested after several passages.

source_name: NtCOI1-silenced leave


title: NtCOI1-silenced leave Replicate 1

description: Biological replicate 1 of 3.  NtCOI1-silenced  leave, untreated, harvested after several passages.


title: MeJA treated NtCOI1-silenced leave Replicate 2

description: Biological replicate 2 of 3.  NtCOI2-silenced  leave, MeJA treated, harvested after 7 days of MeJA treatment.


title: Murine skin, BCC, Day4, Biological replicate 3, Mouse 5

value: Basal cell carcinoma

value: Early-stage


title: Linear RNA_siControl_eIF4EIP_biological rep2


title: Linear RNA_siSMG6_eIF4EIP_biological rep2

value: siSMG6 + eIF4E IP


title: NH2

description: 10x Genomics


title: Murine skin, BCC, Day4, Biological replicate 2, Mouse 4


title: MeJA treated control leave Replicate 3

description: Biological replicate 3 of 3.  Control leave, MeJA treated, harvested after 7 days of MeJA treatment.

source_name: MeJA treated control leave

value: MeJA treated control


title: Murine skin, BCC, Ablative fractional laser, Day4, Biological replicate 1, Mouse 2

value: INDUC+AFL

value: Ablative fractional laser (1 treatment; 5% density, 40 mJ/microbeam, 1 pass)


title: NH1

description: 10x Genomics


title: Linear RNA_siControl_BeforeIP_biological rep2


title: Linear RNA_siControl_CBP80IP_biological rep2

value: siControl + CBP80 IP


title: MeJA treated control leave Replicate 1

description: Biological replicate 1 of 3.  Control leave, MeJA treated, harvested after 7 days of MeJA treatment.


title: MeJA treated control leave Replicate 2

description: Biological replicate 2 of 3.  Control leave, MeJA treated, harvested after 7 days of MeJA treatment.


title: Linear RNA_siSMG6_eIF4EIP_biological rep1


title: Reads obtained from sequencing of sample HC20

status: Public on Nov 27 2024

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human stool

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose >Log_di_cutadapt.txt
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 271 --p-trunc-len-r 177 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV.fasta -S bowtie2_SAM_output.txt -f -p 4 2> percentuals_aligned_bowtie2.txt
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
The R scripts are available at https://github.com/LeandroD94/Papers/tree/main/2023_SSc_vs_VEDOSS
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundances of ASVs in each sample and the related taxonomic assignments
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

value: Stool

tag: sample id

tag: condition

value: Healthy

tag: kit dna_extraction

value: QIAmp PowerFecal Pro DNA Kit


title: Linear RNA_siSMG6_CBP80IP_biological rep1

value: Female

value: siSMG6 + CBP80 IP


title: Linear RNA_siSMG6_CBP80IP_biological rep2


title: NtCOI1-silenced leave Replicate 2

description: Biological replicate 2 of 3.  NtCOI2-silenced  leave, untreated, harvested after several passages.


title: Reads obtained from sequencing of sample HC19

tag: tissue


title: Reads obtained from sequencing of sample HC16


title: Reads obtained from sequencing of sample HC18


title: Control leave Replicate 3

description: Biological replicate 3 of 3.  Control leave, untreated, harvested after several passages.

source_name: control leave

value: control


title: Control leave Replicate 2

description: Biological replicate 2 of 3.  Control leave, untreated, harvested after several passages.


title: Reads obtained from sequencing of sample HC15


title: Reads obtained from sequencing of sample HC17


title: Reads obtained from sequencing of sample HC14


title: Linear RNA_siControl_eIF4EIP_biological rep1

tag: treatment

value: siControl + eIF4E IP


title: Reads obtained from sequencing of sample HC13


title: Reads obtained from sequencing of sample HC9


title: Reads obtained from sequencing of sample HC11


title: Reads obtained from sequencing of sample HC10


title: Reads obtained from sequencing of sample HC7


title: Reads obtained from sequencing of sample HC5


title: Reads obtained from sequencing of sample HC6


title: Reads obtained from sequencing of sample HC12


title: Reads obtained from sequencing of sample HC4


title: Reads obtained from sequencing of sample HC3


title: Murine skin, Healthy, Day4, Biological replicate 1, Mouse 10

value: Skin

tag: strain

value: Ptch1+/- K14-CreER2 p53fl/fl

value: No treatment


title: Linear RNA_siControl_CBP80IP_biological rep1


title: Reads obtained from sequencing of sample HC1


title: Reads obtained from sequencing of sample HC2


title: Reads obtained from sequencing of sample SSC11

value: SSc


title: Reads obtained from sequencing of sample SSC10


title: Reads obtained from sequencing of sample SSC7


title: Control leave Replicate 1

description: Biological replicate 1 of 3.  Control leave, untreated, harvested after several passages.


title: Reads obtained from sequencing of sample SSC6


title: Reads obtained from sequencing of sample HC8


title: Reads obtained from sequencing of sample SSC28


title: Reads obtained from sequencing of sample SSC25


title: Reads obtained from sequencing of sample SSC4


title: Reads obtained from sequencing of sample SSC24


title: Reads obtained from sequencing of sample SSC8


title: Reads obtained from sequencing of sample SSC23


title: Reads obtained from sequencing of sample SSC3


title: Reads obtained from sequencing of sample SSC29


title: Reads obtained from sequencing of sample SSC26


title: Reads obtained from sequencing of sample SSC21


title: Reads obtained from sequencing of sample SSC19


title: Reads obtained from sequencing of sample SSC17


title: Reads obtained from sequencing of sample SSC27


title: Reads obtained from sequencing of sample SSC13


title: Reads obtained from sequencing of sample SSC22


title: Reads obtained from sequencing of sample SSC1


title: Reads obtained from sequencing of sample SSC18


title: Reads obtained from sequencing of sample SSC20


title: Reads obtained from sequencing of sample 22V

value: VEDOSS


title: Reads obtained from sequencing of sample SSC30


title: Reads obtained from sequencing of sample 21V


title: Reads obtained from sequencing of sample SSC14


title: Reads obtained from sequencing of sample SSC12


title: Reads obtained from sequencing of sample SSC31


title: Reads obtained from sequencing of sample 19V


title: Reads obtained from sequencing of sample 17V


title: Reads obtained from sequencing of sample 15V


title: Reads obtained from sequencing of sample 12V


title: Reads obtained from sequencing of sample 16V


title: Reads obtained from sequencing of sample 13V


title: Reads obtained from sequencing of sample 14V


title: Reads obtained from sequencing of sample 10V


title: Reads obtained from sequencing of sample SSC16


title: Reads obtained from sequencing of sample 18V


title: Reads obtained from sequencing of sample 11V


title: Reads obtained from sequencing of sample 9V


title: Reads obtained from sequencing of sample 6V


title: Reads obtained from sequencing of sample 7V


title: Reads obtained from sequencing of sample 5V


title: RA2318M_Day6

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

data_processing:
Illumina NextSeq 500 generated BCL files that were converted to FastQ files
FastQ files were demultiplexed using bcl2fastq2
Genomics Workbench was used to filter and trim the fastQ files
miRbase was used to generate miRNA expression count data
Data was normalized to CPM values using TMM normalization
Assembly: NHP gene assmebly in miRbase
Supplementary files format and content: raw count data contains the count data for miRNA

organism: Macaca mulatta

source_name: Serum

extract_protocol:
Blood samples were extracted and centrifuged to obtain serum samples for analysis
TruSeq small RNA Sample Preparation kit was used for library construction

treatment_protocol: Subjects were irradiated and dose measurement were performed by EMXmicro spectrometer

value: Serum

tag: timepoint

tag: radiation dose_gy

value: M

tag: survival

value: Deceased


title: Reads obtained from sequencing of sample 8V


title: Reads obtained from sequencing of sample 4V


title: RA2742F_Day6

value: F


title: RA2116F_Day6


title: RA2475M_Day6


title: RA2685M_Day6


title: RA2694M_Day6


title: RA2689M_Day6


title: RA2816M_Day6


title: RA2596M_Day6

value: Survived


title: RA2598M_Day6


title: RA2592M_Day6


title: RA1938M_Day6


title: RA2691M_Day6


title: RA2709M_Day6


title: RA2700M_Day6


title: RA2265F_Day6


title: RA2597M_Day6


title: RA2021F_Day6


title: RA2257F_Day6


title: RA2743F_Day6


title: RA2267F_Day6


title: RA2705M_Day6


title: RA2284F_Day6


title: RA2118F_Day6


title: RA1547M_Day6


title: RA1782F_Day6


title: RA2445M_Day6


title: RA2733F_Day6


title: RA0521F_Day6


title: RA0529F_Day6


title: RA0724F_Day6


title: RA2576M_Day6


title: RA2580M_Day6


title: RA2743F_Day2


title: RA2475M_Day2


title: RA2318M_Day2


title: RA2745F_Day6


title: RA0456F_Day6


title: RA2116F_Day2


title: RA2742F_Day2


title: KYSE30 cells, shKAT8

city: Zhengzhou

first: Dandan

address: Dongming road

institute: China-US (Henan) hormel cancer insititute

description: Library name: Sample 2

data_processing:
Raw reads were controlled by FASTP to filter out low-quality data,then obtain clean reads. The alignment tool Bowtie2 was used to align the clean reads to the human ribosome database, and the retained unmapped reads were used for subsequent transcriptome data. HISAT2 software was used for reference genome-based alignment analysis
Assembly: Ensembl_release 111
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

growth_protocol: KYSE30 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifined atmosphere with 5% CO2 at 37 ℃

extract_protocol:
RNA was harvested using Trizol. 1ug of total RNA was used for the construction of sequencing libraries
RNA  libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols

tag: cell line

tag: cell type

value: Human esophageal carcinoma

tag: genotype

value: KAT8 knockdown

value: Virus infection


title: RA2685M_Day2


title: KYSE30 cells, SC

description: Library name: Sample 1


title: RA2694M_Day2


title: adult_green_anole_lizard_saccule_snATAC

city: Los Angeles

first: Tuo

last: Shi

state: California

address: 1425 San Pablo St BCC 403

institute: University of Southern California

description: 10x Genomics multiome snATAC library

data_processing:
Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles
Zebrafish sequences were alinged to danRer11 and UMI counts were created using cellranger-atac count v2 (14dpf) or cellranger-arc count v2.0.0 (12mpf). Lizard sequences were aligned to AnoCar2.0v2 and UMI counts were created using cellranger-arc count v2.0.0
Downstream analysis was performed in R using Seurat v5.0.1 and Signac v1.12.0 and in Unix Shell using deepTools
Assembly: danRer11/GRCz11 and AnoCar2.0v2
Supplementary files format and content: .h5 files of filtered barcode feature count matrix for each individual library
Supplementary files format and content: .bigwig files of 14 dpf and 12 mpf zebrafish hair and supporting cell pseudo-bulk ATAC tracks
Supplementary files format and content: .tsv and .tbi files of snATAC fragments required to visualize ATAC coverage in R
Library strategy: snATAC-seq (14dpf zebrafish) and Single Cell Multiome ATAC + Gene Expression (12 mpf zebrafish and adult lizard)

organism: Anolis carolinensis

source_name: inner ear saccule

extract_protocol:
For 14 dpf zebrafish, heads from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf zebrafish, utricle, saccule, and lagena were extracted from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish after brains and otolith crystals were removed. For adult lizard, saccules were extracted from lizard heads and otoconia crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min, followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution (0.25% trypsin (Life Technologies, 15090-046), 1 mM EDTA, and 400 mg/mL Collagenase D (Sigma, 11088882001) in PBS) and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS). Cells were pelleted (376 × g, 5 min, 4 °C) and resuspended in suspension media (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, and 0.05 mg/mL streptomycin (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)) twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence-activated cell sorted (FACS) to isolate live cells that excluded the nuclear stain DAPI
10X Genomics Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1.1 (14 dpf zebrafish) or Single Cell Multiome ATAC + Gene Expression kit (12 mpf zebrafish and adult lizard)

value: inner ear saccule

value: mixed


title: RA2689M_Day2


title: adult_green_anole_lizard_saccule_snRNA

description: 10x Genomics multiome snRNA library

molecule: nuclear RNA


title: RA2816M_Day2


title: RA2598M_Day2


title: B2

city: Bethesda

first: Sichuan

last: Xi

address: Building 10

institute: NCI/NIH

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. The 4 mRNA level files were imported into Agilent GeneSpring Software (version 11.0) for further analysis. lncRNAs and mRNAs that at least 2 out of 4 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for data analysis. Differentially expressed lncRNAs and mRNAs were identified through Fold Change filtering. Pathway Analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show distinguishable lncRNA and mRNA expression profiling among samples.

source_name: SAEC cells exposed to CSC

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: All lung cancer cell lines from The American Type Culture Collection (ATCC; Manassas, VA) were kept in RPMI media supplemented with 10% FBS, 10 mM of glutamic acid, and 1% penicillin/streptomycin (normal media). Primary normal human small airway epithelial cells (SAEC) from Lonza, Inc. (Frederick, MD) were cultured following the vendor’s instructions. The immortalized human bronchial epithelial cells (HBEC) generously offered by John D. Minna (U-T Southwestern, Dallas, TX) were cultivated according to the instructions (30). All cells were routinely checked for mycoplasma using a Sigma kit (Cat. no. MP0025) and confirmed by HLA typing to match their original stocks.

extract_protocol: Total RNA from each sample was quantified using the Nanodrop 1000 and the RNA integrity was assessed by Agilent 2100 Bioanalyzer. About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with Nimblegen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the Nimblegen wash buffer kit. 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

treatment_protocol: Cigarette smoke and drug exposures: After being prepared as previously mentioned ,  cigarette smoke condensates (CSC) generated from Kentucky Reference 1R4F research blend cigarettes (University of Kentucky) were resuspended in DMSO at a stock concentration of 25 mg tar/ml. Cells were grown in 10-cm plates in suitable normal media (NM) containing DMSO or NM containing CSC (0.025mg/ml) for smoke exposure experiments. Daily medium changes included the inclusion of brand-new CSC or DMSO control. Cells were collected for analysis at different times after being subcultured as needed. The DNA demethylating agent, decitabine (MilliporeSigma, St. Louis, MO) was added in the culture medium daily (100nM x 72hrs). Mithramycin was obtained from Sigma. Methysticin (MCE) was obtained from MilliporeSigma, St. Louis, MO. Cells were cultivated in NM containing or lacking mithramycin or methysticin for drug exposure treatments. After changing the media and adding mithramycin or methysticin for 24 hours at the recommended concentrations, the cells were harvested for additional analysis at the designated times. NFkB-P65 siRNA (#6261S /Cell Signaling) was used to deplete NFkB in relative experiments.

value: Wild-type


title: RA2596M_Day2


title: B1

source_name: SAEC cells


title: RA2740F_Day6


title: RA1938M_Day2


title: RA2592M_Day2


title: RA2709M_Day2


title: Aged_limb_1

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Delegación Cuajimalpa de Morelos

address: Av. Vasco de Quiroga 4871

country: Mexico

institute: Universidad Autónoma Metropolitana

data_processing:
Reads were trimmed for adaptor/low quality bases with Trimmomatic v0.39
Raw counts were aligned to the reference genome AmexG_v6.0-DD using STAR v.2.7.9a
Read counts were quantified using featureCounts for R, and the AmexT_v47 transcriptome, accessible at https://www.axolotl-omics.org/assemblies
DESeq2 v.1.32.093 was employed for the differential expression analysis.
Assembly: AmexG_v6.0-DD
Supplementary files format and content: Tab delimited files include raw counts for each sample

organism: Ambystoma mexicanum

source_name: posterior leg

extract_protocol:
The collected tissue was preserved in RNAlater (Invitrogen), at 4°C for a maximum of 24 hrs prior to processing. The RNA was extracted according to the protocol established by Peña-Llopis et al (Peña-Llopis, S. & Brugarolas, J. Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications. Nat. Protoc. 8, 2240–2255)
Libraries were constructed using the SmarterStranded V2 kit (Takara Bio)

treatment_protocol: Amputation of the inferior limbs of the axolotls was performed using a stereoscopic microscope. Samples from five juvenile axolotls, aged 8 months, as well as from two aged axolotls, aged 8 years. 10 days post-amputation, blastema tissues were collected from juvenile axolotls, whereas aged axolotls did not display any development of blastema tissue.

value: posterior leg

value: aged


title: RA2745F_Day2


title: Juvenile_limb_8

value: juvenile


title: Aged_limb_2


title: RA2700M_Day2


title: Juvenile_limb_5


title: RA2733F_Day2


title: RA2691M_Day2


title: Juvenile_limb_3


title: Juvenile_limb_6


title: Juvenile_limb_2


title: RA0456F_Day2


title: RA2265F_Day2


title: RA2021F_Day2


title: RA2257F_Day2


title: A1


title: RA2284F_Day2


title: A2


title: Blastema_3

source_name: blastema

value: blastema


title: Blastema_8


title: Blastema_2


title: RA2705M_Day2


title: Blastema_5


title: RA1547M_Day2


title: A549, biol rep 3

city: Vilnius

first: Linas

last: Kunigėnas

address: Santariškių str. 1

country: Lithuania

institute: National Cancer Institute

data_processing:
Sequenced reads were trimmed for the adaptor sequence (AACTGTAGGCACCATCAAT) using Cutadapt 1.15. Sequences that quality score was less than 25 and sequences shorter than 15 nt were excluded.
Trimmed reads were aligned to human genome GRCh38p12 using bowtie2 2.1.0 and end-to-end alignment.
Human genome aligned reads were further aligned to mirbase.org miRNA sequences (release 22.1)  using bowtie2 2.1.0 using parameters --local -N 0 -L 16
miRNA mapped reads were counted and count tables were generated for differential expression analysis using EdgeR package 3.4.2. Data were normalized using TMM method. miRNAs with fold changes >2, FDR<0.05 and reads per million >10 were considered differentialy expressed.
Assembly: GRCh38p12, miRBase v22.1
Supplementary files format and content: tab-delimited text files with raw miRNA counts for each sample

source_name: lung

growth_protocol: Cells were grown as multicellular spheroids (MCS) for 6 days at 37°C and 5% CO2. HBEC cells were grown in Airway Epithelial Cell Basal Medium supplemented with Bronchial Epithelial Cell Growth Kit. NCI-H1299 and NCI-H23 cells were grown in RPMI-1640 Medium containing 10% fetal bovine serum. A549 cells were grown in F-12K medium containing 10% fetal bovine serum. Calu-1 cells were grown in McCoy’s 5a Medium containing 10% fetal bovine serum. All of the media were additionally supplemented with 1% penicillin/streptomycin mix.

extract_protocol:
Total RNA from all cell lines after 6 days of growth was extracted using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Small RNA libraries were prepared using QIAseq miRNA Library Kit (Qiagen) according to the manufacturer’s instructions.

value: lung

value: epithelial cell

value: wt

value: cultured for 6 days as multicellular spheroids


title: RA2576M_Day2

value: Serum

value: M


title: RA2118F_Day2

value: F

value: Survived


title: A549, biol rep 2


title: A549, biol rep 1


title: RA2597M_Day2

value: Deceased


title: Calu-1, biol rep 2


title: Calu-1, biol rep 3


title: Calu-1, biol rep 1


title: RA1782F_Day2


title: RA0521F_Day2


title: H1299, biol rep 2

value: epithelial-like cell


title: RA2445M_Day2


title: Blastema_6


title: H23, biol rep 3


title: H1299, biol rep 3


title: H1299, biol rep 1


title: RA2267F_Day2


title: H23, biol rep 2


title: HBEC3, biol rep 3

source_name: lung; bronchus

value: lung; bronchus


title: RA2580M_Day2


title: RA2740F_Day2


title: HBEC3, biol rep 2


title: RA2318M_Day1


title: H23, biol rep 1


title: HBEC3, biol rep 1


title: RA0724F_Day2


title: RA2475M_Day1


title: RA0529F_Day2


title: RA2116F_Day1


title: RA2742F_Day1


title: RA2685M_Day1


title: RA2689M_Day1


title: RA2598M_Day1


title: RA2733F_Day1


title: RA2694M_Day1


title: RA2745F_Day1


title: RA2743F_Day1


title: RA2816M_Day1


title: DSS anti-PD1 - 5

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Applied Biosystems Clariom S Mouse Arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Colitis tissue

label_protocol: We used the Applied Biosystems GeneChipTM WT PLUS Reagent Kit (catlog n.: 902280) for cDNA synthesis, amplification, cRNA synthesis, second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin according to manufacturer's instructions.

extract_protocol: Tissue samples were blended in RLT buffer and total RNA was isolated using the miRNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: C57BL/6 WT mice were treated with 3% DSS in drinking water and anti-PD1 i.p. to induce colitis (samples P). Some mice were additionally transplanted with ECP treated donor cells (samples E).

value: Wildtype

value: ICI-mediated colitis

value: control

value: Complete colon tissue


title: LDB1_AID_auxin_H3K27ac_rep1

city: Philadelphia

first: Nicholas

last: Aboreden

state: PA

address: 3615 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
Reads were aligned using bowtie2 with default settings, de-duplicated, and filtered for MAPQ>20
bigwig files were generated using deeptools (v3.5.1) bamCoverage (binSize=20, normalizeUsing=BPM). Pol2 bigwig files were normalized using CPM.
Macs2 (v2.2.9.1) was used to identify peaks using matched input and p = 1e-5
Assembly: mm9
Supplementary files format and content: bed:peak calls, bw: tracks of ChIP-seq signals

extract_protocol:
DNA from lysed cells was sonicated using the Bioruptor Pico, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106).
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440).

value: Erythroblast

value: LDB1-AID subline

value: auxin


title: LDB1_AID_auxin_H3K27ac_rep2


title: RA1938M_Day1


title: DSS anti-PD1 - 1


title: DSS anti-PD1 ECP - 5

value: ECP-treated donor cells


title: DSS anti-PD1 - 3


title: DSS anti-PD1 ECP - 4


title: DSS anti-PD1 ECP - 1


title: DSS anti-PD1 ECP - 3


title: RA2709M_Day1


title: DSS anti-PD1 ECP - 2


title: LDB1_AID_untreated_H3K27ac_rep2

value: Untreated


title: CTCF_AID_untreated_LDB1_rep2

value: CTCF-AID subline


title: RA2700M_Day1

value: Serum


title: LDB1_AID_untreated_H3K27ac_rep1


title: CTCF_AID_auxin_LDB1_rep2


title: RA2691M_Day1

value: M


title: RA2021F_Day1

value: F


title: CTCF_AID_auxin_LDB1_rep1


title: CTCF_AID_auxin_CTCF_rep1


title: RA2257F_Day1


title: RA2597M_Day1


title: DSS anti-PD1 - 4


title: RA2265F_Day1


title: DSS anti-PD1 - 2


title: CTCF_AID_auxin_CTCF_rep2


title: 8580 NR TAC

city: Seattle

first: Matthew

last: Walker

address: 850 Republican

institute: University of Washington

description: Library name: 8580

data_processing:
Data analysis–RNA sequencing samples were aligned using Tophat (Trapnell et al, 2009, version 2.0.13). Gene-level read counts were quantified using htseq-count (Anders et al, 2015). Genes expressed above 4 transcripts per million in at least 2 samples were used. In differential expression, a gene to have total normalized reads >10 across all samples. DeSeq (Anders and Huber, 2010) was used for differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: excel normalized read count

source_name: heart

extract_protocol:
Total RNA was extracted from 30 mg of heart tissue using the Qiagen RNeasy kit
RNA sequencing and quality control were performed Beijing Genomics Institute (BGISEQ-500)

value: heart


title: 8578 Vehicle SHAM

description: Library name: 8578


title: RA0456F_Day1

value: Deceased


title: RA2284F_Day1

value: Survived


title: RA2705M_Day1


title: CTCF_AID_untreated_CTCF_rep1


title: LDB1_AID_clone1_rep2

data_processing:
Data processed using the ENCODE3 long RNA-Seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Assembly: mm9
Supplementary files format and content: bw: tracks of RNA-seq signals

extract_protocol:
RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN, 74104). Geneomic DNA was removed using QiAshredder (QIAGEN, 79656) and on-column digestion with RNAse-free DNAse.
Libraries were constructed using the TruSeq Stranded mRNA kit (Illumina, 20020594)


title: LDB1_AID_clone2_rep1


title: RA2267F_Day1


title: 8576 NR SHAM

description: Library name: 8576


title: G1E_ER4_parental_rep1

value: parental


title: G1E_ER4_parental_rep2


title: LDB1_AID_clone2_rep2


title: CTCF_AID_untreated_LDB1_rep1


title: LDB1_late_G1_rep3

description:
LDB1_late_G1_merged_rpm.bw
late_rep3.bw

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
Reads were aligned using bowtie2 with default settings, de-duplicated, and filtered for MAPQ>20
bigwig files were generated using deeptools (v3.5.1) bamCoverage (binSize=20, normalizeUsing=BPM). Pol2 bigwig files were normalized using RPKM.
Macs2 (v2.2.9.1) was used to identify peaks using matched input and p = 1e-5
Assembly: mm9
Supplementary files format and content: bed:peak calls, bw: tracks of ChIP-seq signals

source_name: cell line

value: cell line

value: G1E-ER4 MD-mCherry subline


title: RA2118F_Day1


title: LDB1_AID_clone1_rep1


title: CTCF_AID_untreated_CTCF_rep2


title: RA2576M_Day1


title: 8577 NR SHAM

description: Library name: 8577


title: LDB1_prometaphase_rep3

description:
LDB1_prometaphase_merged_rpm.bw
prometa_rep3.bw


title: 8523 NR SHAM

description: Library name: 8523


title: RA1547M_Day1


title: LDB1_anatelophase_rep3

description:
LDB1_anatelophase_merged_rpm.bw
anatelo_rep3.bw


title: RA1782F_Day1


title: LDB1_early_G1_rep3

description:
LDB1_early_G1_merged_rpm.bw
early_rep3.bw


title: RA2592M_Day1


title: LDB1_late_G1_rep1

description:
LDB1_late_G1_merged_rpm.bw
late_rep1.bw


title: RA2445M_Day1


title: LDB1_mid_G1_rep1

description:
LDB1_mid_G1_merged_rpm.bw
mid_rep1.bw


title: 8520 Vehicle TAC

description: Library name: 8520


title: 8525 Vehicle SHAM

description: Library name: 8525


title: LDB1_early_G1_rep1

description:
LDB1_early_G1_merged_rpm.bw
early_rep1.bw


title: RA0529F_Day1


title: LDB1_anatelophase_rep1

description:
LDB1_anatelophase_merged_rpm.bw
anatelo_rep1.bw


title: 8518 NR TAC

description: Library name: 8518


title: 8519 Vehicle TAC

description: Library name: 8519


title: LDB1_AID_auxin_POL2_rep3

description:
4419.bw
LDB1_AID_auxin_pol2_merged.bw

value: 4 hour auxin


title: LDB1_AID_auxin_POL2_rep2

description:
3351.bw
LDB1_AID_auxin_pol2_merged.bw


title: LDB1_prometaphase_rep1

description:
LDB1_prometaphase_merged_rpm.bw
prometa_rep1.bw


title: RA0521F_Day1


title: LDB1_AID_untreated_POL2_rep3

description:
4418.bw
LDB1_AID_untreated_pol2_merged.bw


title: RA2580M_Day1


title: LDB1_AID_untreated_POL2_rep2

description:
3350.bw
LDB1_AID_untreated_pol2_merged.bw


title: RA0724F_Day1


title: LDB1_AID_auxin_POL2_rep1

description:
3345.bw
LDB1_AID_auxin_pol2_merged.bw


title: LDB1_mid_G1_rep3

description:
LDB1_mid_G1_merged_rpm.bw
mid_rep3.bw


title: 8505 Vehicle TAC

description: Library name: 8505


title: LDB1_AID_untreated_POL2_rep1

description:
3344.bw
LDB1_AID_untreated_pol2_merged.bw


title: 8521 NR TAC

description: Library name: 8521


title: 8504 Vehicle SHAM

description: Library name: 8504


title: SMC3_AID_auxin_input

value: SMC3-AID subline


title: SMC3_AID_untreated_input

value: Erythroblast


title: RA2743F_Preradiation

value: Preradiation


title: RA2740F_Day1


title: SMC3_AID_auxin_LDB1_rep3

description:
SMC3_AID_LDB1_4h_merged.bw
smc3_aid_ldb1_4hr_consensus.bed


title: 8503 NR TAC

description: Library name: 8503


title: RA2318M_Preradiation


title: SMC3_AID_auxin_LDB1_rep2


title: 8502 NR TAC

description: Library name: 8502


title: SMC3_AID_untreated_LDB1_rep1

description:
SMC3_AID_LDB1_0h_merged.bw
smc3_aid_ldb1_0hr_consensus.bed


title: SMC3_AID_untreated_LDB1_rep2


title: RA2475M_Preradiation


title: RA2116F_Preradiation


title: RA2742F_Preradiation


title: PCNB_T11_K3

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

data_processing:
Reads were then mapped onto the Escherichia coli genome (version NC_000913.3, GenBank) with tmap from Torrent suite software (v 5.12.1). Counting was performed with HTSeq-count version 0.11.2 using the « intersection non empty » mode.
For transcriptome analysis on T0 samples, transcripts with fewer than 10 reads on 5 of 6 samples (418 genes) were excluded from the analysis, as well as duplicated genes (45 genes) and overlapping genes for at least 50 bp (60 genes) leading to a working set of 4172 genes. To correct for experimental variations, a TMM (Trimmed Mean of M values) normalization was applied.
For the stabilome experiment to measure genome-wide RNA half-lives, 12 RNA-sequencing data (3 reference T0 samples and 9 time points after addition of rifampicin) were used. Normalization between sequencing data was performed using the first three invariant genes for the 12 sequencing data of each strain (genes with the lowest variance in rank between sequencing data, namely b2621 (ssrA), b2911 (ssrS) and b3760 (aspT)).
Supplementary files format and content: Matrix of read counts for every gene in the stabilome and transcriptome experiments for the 2 strains

organism: Escherichia coli

source_name: strain PCNB, T0 of kinetics 12

growth_protocol: The strains were grown in M9 minimal medium supplemented with 16.7 mM glucose (M9-glucose). All cultures were inoculated from overnight precultures in M9-glucose. Cells were washed twice with NaCl 9 g/L and used to inoculate 1.8 L of M9-glucose at OD600nm= 0.1 in a 2 L Biostat B+ bioreactor. Temperature was automatically regulated at 37°C, pH at 7 by adding HCl 2 N or NaOH 1 M and dissolved oxygen pressure at minimum 30%.

extract_protocol:
Total RNA was extracted with TRI Reagent (Sigma Aldrich) from 12 samples from the three biologically independent kinetics as follows: for MG1655, T0, 0.5, 2 and 4 min for the first kinetic; T0, 1, 2.5 and 5 min for the second kinetic; and T0, 1.5, 3 and 7 min for the third kinetic; for the pcnB mutant, T0, 1, 3 and 7 min for the first kinetic; T0, 0.5, 1.5 and 5 min for the second kinetic; and T0, 2, 4 and 11 min for the third kinetic. DNA contamination was removed with a Turbo DNase treatment (Invitrogen).
Total RNA (1 µg) was ribodepeleted using the riboPOOLs kit (siTOOLs Biotech). 10 ng ribodepleted RNA was further used to construct a sequencing library using the Ion Total RNA-Seq Kit v2 and the Ion Xpres RNA-Seq Barcode Kit (Thermo Fisher Scientific). The library was constructed according to the manufacturer’s protocol. After quality control, 15 pg/µl of each library were amplified by emulsion PCR on the Ion One Touch 2 instrument. Then, 100 base pair [bp] single-end library was sequencing on an Ion GeneStudio S5 system with an Ion 540 Chip was performed by the GeT-BioPuces platform (http://get-biopuces.insa-toulouse.fr/).

treatment_protocol: When OD600nm reached 1.2, samples were collected for transcriptomic analysis; this time point was the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (0.5 g/L) was added to the culture to inhibit the initiation of transcription, and cells were sampled over time, and rapidly frozen in liquid nitrogen. The experiments were repeated three times on independent cultures for each strain. After thawing and centrifugation steps, the cells were suspended in Tris-EDTA buffer and lysed mechanically with glass beads.

value: MG1655 deleted of the pcnB gene


title: SMC3_AID_auxin_LDB1_rep1


title: SMC3_AID_auxin_RAD21_rep3

description:
SMC3_AID_RAD21_4h_merged.bw
smc3_aid_rad21_4hr_consensus.bed


title: PCNB_T7_K1

source_name: strain PCNB, T0 of kinetics 11


title: RA2685M_Preradiation


title: SMC3_AID_auxin_RAD21_rep2


title: SMC3_AID_untreated_RAD21_rep2

description:
SMC3_AID_RAD21_0h_merged.bw
smc3_aid_rad21_0hr_consensus.bed


title: SMC3_AID_auxin_RAD21_rep1


title: SMC3_AID_untreated_RAD21_rep3


title: PCNB_T5_K2

source_name: strain PCNB, T0 of kinetics 10


title: LDB1_AID_auxin_input

value: LDB1-AID subline


title: RA2733F_Preradiation


title: 8501 Vehicle TAC

description: Library name: 8501


title: SMC3_AID_untreated_RAD21_rep1

value: Untreated


title: LDB1_AID_untreated_input


title: PCNB_T4_K3

source_name: strain PCNB, T0 of kinetics 9


title: RA2694M_Preradiation


title: LDB1_AID_auxin_CTCF_rep2


title: PCNB_T3_K1

source_name: strain PCNB, T0 of kinetics 8


title: SMC3_AID_untreated_LDB1_rep3


title: RA2689M_Preradiation


title: LDB1_AID_auxin_CTCF_rep1


title: LDB1_AID_untreated_CTCF_rep2

description:
LDB1_AID_untreated_CTCF_merged_rpm.bw
LDB1_AID_CTCF_untreated_consensus_peaks.bed


title: PCNB_T2_K3

source_name: strain PCNB, T0 of kinetics 7


title: LDB1_AID_untreated_CTCF_rep1


title: PCNB_T1.5_K2

source_name: strain PCNB, T0 of kinetics 6


title: LDB1_AID_auxin_RAD21_rep2


title: RA2598M_Preradiation

source_name: Serum


title: LDB1_AID_auxin_RAD21_rep1


title: PCNB_T1_K1

source_name: strain PCNB, T0 of kinetics 5


title: LDB1_AID_untreated_RAD21_rep1

description:
LDB1_AID_untreated_RAD21_merged_rpm.bw
LDB1_AID_RAD21_untreated_consensus_peaks.bed


title: RA2596M_Preradiation


title: LDB1_AID_auxin_LDB1_rep2

description:
LDB1_AID_auxin_LDB1_merged_rpm.bw
LDB1_AID_LDB1_4h_auxin_consensus.bed


title: RA2745F_Preradiation


title: RA1938M_Preradiation


title: LDB1_AID_untreated_LDB1_rep1

description:
LDB1_AID_untreated_LDB1_merged_rpm.bw
LDB1_AID_LDB1_untreated_consensus_peaks.bed


title: LDB1_AID_untreated_LDB1_rep2


title: PCNB_T0.5_K2

source_name: strain PCNB, T0 of kinetics 4


title: PCNB_T0_K3

source_name: strain PCNB, T0 of kinetics 3


title: LDB1_AID_auxin_YY1_rep2


title: RA2592M_Preradiation


title: LDB1_AID_untreated_YY1_rep2

description:
LDB1_AID_untreated_YY1_merged_rpm.bw
LDB1_AID_YY1_untreated_consensus_peaks.bed


title: LDB1_AID_auxin_YY1_rep1


title: RA2816M_Preradiation


title: PCNB_T0_K1

source_name: strain PCNB, T0 of kinetics 1


title: LDB1_AID_untreated_YY1_rep1


title: PCNB_T0_K2

source_name: strain PCNB, T0 of kinetics 2


title: MG_T7_K3

source_name: strain MG, T7 min of kinetics 3


title: LDB1_AID_MICRO_C_auxin_rep7

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
.mcool files were generated using the distiller pipeline (v3.3)
Loops were identified using cooltools (v0.5.3)
Domains were identivied using rGMAP
Assembly: mm9
Supplementary files format and content: mcool:multi-resolution contact map, bedpe: list of Micro-C  loop coordinates, bed: list of domain coordinates
Library strategy: Micro-C-seq

extract_protocol:
DNA was digested with Mnase and proximity ligated. Ligated DNA was isolated using phenol:chloroform:isoamyl and ethanol precipitation. Dinucleosomes were isolated by gel extraction. Dinucleosomes weree purified with Zymoclean Geel DNA Recovery kit (D4007)
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440).


title: LDB1_AID_untreated_RAD21_rep2


title: RA2709M_Preradiation


title: LDB1_AID_auxin_LDB1_rep1


title: RA2700M_Preradiation


title: LDB1_AID_MICRO_C_auxin_rep6


title: MG_T5_K2

source_name: strain MG, T5 min of kinetics 2


title: LDB1_AID_MICRO_C_auxin_rep5


title: RA2691M_Preradiation


title: RA0456F_Preradiation


title: LDB1_AID_MICRO_C_auxin_rep3


title: LDB1_AID_MICRO_C_auxin_rep8


title: MG_T3_K3

source_name: strain MG, T3 min of kinetics 3


title: LDB1_AID_MICRO_C_auxin_rep4

source_name: cell line


title: MG_T4_K1

source_name: strain MG, T4 min of kinetics 1


title: LDB1_AID_MICRO_C_auxin_rep1


title: RA2596M_Day1


title: LDB1_AID_MICRO_C_auxin_rep2


title: LDB1_AID_MICRO_C_untreated_rep9


title: RA2597M_Preradiation


title: 8516 NR SHAM

description: Library name: 8516

source_name: heart


title: MG_T2.5_K2

source_name: strain MG, T2.5 min of kinetics 2


title: RA2021F_Preradiation


title: LDB1_AID_MICRO_C_auxin_rep9


title: LDB1_AID_MICRO_C_untreated_rep8


title: RA2265F_Preradiation


title: LDB1_AID_MICRO_C_untreated_rep7


title: MG_T2_K1

source_name: strain MG, T2 min of kinetics 1


title: LDB1_AID_MICRO_C_untreated_rep6


title: RA2257F_Preradiation


title: LDB1_AID_MICRO_C_untreated_rep5


title: LDB1_AID_MICRO_C_untreated_rep4


title: MG_T1_K2

source_name: strain MG, T1 min of kinetics 2


title: LDB1_AID_MICRO_C_untreated_rep3


title: MG_T0.5_K1

source_name: strain MG, T0.5 of kinetics 1


title: RA2284F_Preradiation


title: LDB1_AID_MICRO_C_untreated_rep2


title: LDB1_AID_MICRO_C_untreated_rep1


title: MG_T0_K3

source_name: strain MG, T0 of kinetics 3


title: LDB1_AID_TRI_C_auxin_biorep4

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
Capcruncher was used to identify multiway contacts.
Cooler was used to genereate cool files (binned at 5kb).
Assembly: mm9
Supplementary files format and content: cool: contact map for multiway interactions with Myc promoter. All reads in cool file contain one fragment mapping to capture region (Myc promoter), and at least two additional fragments separated by NLAIII recognition site.
Library strategy: Tri-C-seq

extract_protocol:
DNA was digested with NLAIII and proximity ligated. Oligonucleotide capture was performed using a biotinylated probe to enrich for the Myc promoter using KAPA HyperCapture Reagents (Roch, 9075810001).
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440).

value: auxin


title: RA2705M_Preradiation

source_name: Serum

value: Serum


title: LDB1_AID_TRI_C_auxin_biorep2


title: LDB1_AID_TRI_C_auxin_biorep1


title: MG_T0_K2

source_name: strain MG, T0 of kinetics 2


title: RA2118F_Preradiation


title: RA2267F_Preradiation


title: LDB1_AID_TRI_C_untreated_biorep4


title: RA2576M_Preradiation

value: M


title: LDB1_AID_TRI_C_untreated_biorep3


title: LDB1_AID_TRI_C_untreated_biorep2


title: LDB1_AID_TRI_C_untreated_biorep1


title: MG_T0_K1

source_name: strain MG, T0 of kinetics 1


title: LDB1_late_G1_rep2

description:
LDB1_late_G1_merged_rpm.bw
late_rep2.bw


title: LDB1_mid_G1_rep2

description:
LDB1_mid_G1_merged_rpm.bw
mid_rep2.bw


title: MG_T1.5_K3

source_name: strain MG, T1.5 min of kinetics 3


title: HKDC1 LKO sample 17

city: Chicago

first: MD Wasim

last: Khan

address: 835 S Wolcott

department: Division of Endocrinology, Diabetes & Metabolism, Department of Medicine,

institute: University of Illinois at Chicago

description: Library name: S17

data_processing:
1.Data quality control Use fastp to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads. 2. Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT to construct the index, and compare clean reads to the reference genome. 3. New transcript prediction Use StringTie for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster. 4. Quantification of gene expression levels Use featureCounts to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels.
Assembly: Mus_musculus.GRCm39.109
Supplementary files format and content: raw counts and FPKM for each sample

source_name: liver

extract_protocol:
RNA from liver was extracted by trizol protocol
A total amount of l ug RNAper sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextRUltraTMRNA Library Prep Kit for lluminaR(NEB,USA) following manufacturer 's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads.Fragmentation was carried out using divalent cations under elevated tecmperature in NEBNext First Strand Synthesis Reaction Buffer(5X).First strand cDNA was synthesized using random hexamer primer and M-MuLVReverse Transcriptase(RNase H-).Second strand cDNA synthesis was subsequently performed using DNA Polymerase l and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments，NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.In order to select cDNA fragments of preferentially 250~300 bp in length,the library ragments were purified with AMPure XP system (Beckman Coulter,Beverly,USA).Then 3 ul USER Enzyme (NEB, USA) was used with size-selected,adaptor-ligated cDNAat 37C for 15 min followed by 5 min at 95C before PCR.Then PCR was performed with Phusion HighFidelity DNA polymerase,Universal PCR primers and Index (X)Primer.Atlast,PCR products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: liver

value: HKDC1 LKO

value: western diet 20 weeks


title: HKDC1 LKO sample 18

description: Library name: S18


title: RA1782F_Preradiation

value: F

value: Deceased


title: LDB1_early_G1_rep2

description:
LDB1_early_G1_merged_rpm.bw
early_rep2.bw

value: cell line


title: LDB1_anatelophase_rep2

description:
LDB1_anatelophase_merged_rpm.bw
anatelo_rep2.bw

value: G1E-ER4 MD-mCherry subline


title: RA2445M_Preradiation

value: Survived


title: HKDC1 fl/fl liver Sample 11

description: Library name: S11


title: HKDC1 LKO sample 6

description: Library name: S6

value: HKDC1 fl/fl


title: LDB1_prometaphase_rep2

description:
LDB1_prometaphase_merged_rpm.bw
prometa_rep2.bw

value: Erythroblast


title: HUVEC, BRG1 CUT&RUN, siPVT1, 2

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

data_processing:
Resulting reads were aligned to the GRCh38 genome assembly using Bowtie2 (v2.4.5) (https://doi.org/10.1038/nmeth.1923) with the parameters –local and –very-sensitive.
Mates were fixed with samtools (v1.1.0) (10.1093/gigascience/giab008) fixmate with the parameter –m set, and duplicate alignments were subsequently removed using samtools markdup with the –r flag set. Reads aligning to blacklisted regions as defined by ENCODE were removed using bedtools (2.27.1) (https://doi.org/10.1093/bioinformatics/btq033) intersect with the –v flag set.
Resulting BAM files were indexed using samtools index. Peaks were called using MACS3 (v3.0.0) (https://doi.org/10.1186/gb-2008-9-9-r137) with the parameters –scale-to-small –f BAM and –g hs.
Differential BRG1 CUT&RUN peaks were called using the R package DiffBind (v3.10.1) (10.18129/B9.bioc.DiffBind). Peak counts per replicate were normalized to the proportion of total reads falling within called peaks. Peak counts were then compared between conditions, and peaks with a false discovery rate-adjusted p-value less than 0.05 were considered as being significantly different between conditions.
Peaks were annotated with genomic contexts by using ChromHMM (v1.24) (https://doi.org/10.1038/nprot.2017.124)  to compute chromatin states in HUVECs using ChIP-sequencing data from ENCODE (doi: 10.1093/nar/gkz1062) , which were annotated for functionality based on published literature. CUT&RUN genomic coverage was computed using bamCoverage (v3.5.3) (10.1093/nar/gkw257). Normalized genomic coverage was accomplished by setting the parameter –scale-factor to the appropriate scale based on the fraction of reads in peaks detected by DiffBind.
Assembly: hg38
Supplementary files format and content: BigWig files of genomic coverage per condition normalized by the fraction of reads falling with peak regions (FRiP).
Library strategy: CUT&RUN

source_name: HUVEC

growth_protocol: Pooled human umbilical vein endothelial cells (HUVEC) were purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) and cultured at 37 °C with 5 % CO2 in a humidified incubator.

extract_protocol:
5X volume of binding buffer (20 mM HEPES pH 7.9, 20 mM KCl, 1 mM CaCl2, 1 mM MnCl2) was added to the samples and the pH adjusted with sodium acetate before being transferred to a purification column (ActiveMotif, 58002) and centrifuged at 11,000 xg for 30 sec. The column was then washed with 750 µl wash buffer and dried by centrifugation for 2 min. DNA was eluted with 25 µl elution buffer and the DNA concentration measured with a Qubit 3.0 Fluorometer (Life Technologies).
Samples were brought to 50 µl with 0.1X TE buffer and DNA end preparation performed as instructed but with incubation at 20 °C for 20 min and then 58 °C for 45 min. Adaptor ligation was performed with a 1:10 dilution of adaptor (NEB, E6440S). For DNA purification, 0.9X Volume AMPure XP beads (Beckman Coulter, A63881) was added to the samples and incubated for 5 min at RT. Beads were washed twice with 200 µl 80 % ethanol and DNA eluted with 17 µl 0.1X TE buffer for 2 min at RT. PCR amplification of the eluted DNA was performed as described in the manufacturer’s protocol but with the addition of 2.5 µl Evagreen (20X) for visualization of the amplification curves on an AriaMx Real-time PCR system (Agilent Aria 1.7). The denaturation and annealing/extension steps of the PCR amplification were performed for around 12 cycles and stopped before the curves plateaued. A cleanup of the PCR reaction was performed twice with 1.1X Ampure beads and eluted each time in 33 µl 0.1X TE buffer. DNA concentrations were measured with a Qubit (Thermo Fisher) and size distributions measured on a Bioanalyzer (Agilent).

treatment_protocol: For small interfering RNA (siRNA) treatments, HUVEC (80–90 % confluent) were transfected with GeneTrans II according to the instructions provided by MoBiTec (Göttingen, Germany). A Stealth siRNA was used for siRNA-mediated knockdown of BRG1 (Thermo Fisher Scientific, siRNA ID HSS110006, Cat. No. 1299001). As control, Stealth RNAi™ negative control Med GC (Life technologies) was used. All siRNA experiments were performed for 48 h. 500,000 HUVEC were washed with wash buffer (20 mM HEPES pH 7.9, 150 mM NaCl, 500 nM spermidine, 1X Roche Protein Inhibitor Cocktail) at RT. Cells were resuspended in wash buffer and 10 µl BioMag®Plus Concanavalin A (ConA) beads (Polysciences, 86057-3) were added for 10 min at RT. Beads were separated on a magnetic rack and washed once before being resuspended in 100 µl antibody buffer (wash buffer, 0.25 % Digitonin and 2 mM EDTA) and 1 µl BRG1 antibody (Abcam, ab110641). Beads were incubated with the antibody over night with gentle shaking at 4 °C. The next day, beads were washed twice with 200 µl 0.25 % Digitonin wash buffer and resuspended in Digitonin wash buffer containing 2 µl CUTANA™ pAG-MNase (15-1016, EpiCypher, 15-1016) and incubated on ice for 30 min. Samples were washed twice and then resuspended in 100 µl Digitonin wash buffer containing 2 µl CaCl2 at a final concentration of 100 mM and incubated for 2 h at 4 °C with gentle shaking. 33 µl of 2X “stop solution” (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.25 % Digitonin, 100 µg/ml RNase A, 50 µg/ml Glycoblue) was added to the beads and incubated at 37 °C for 10 min. Samples were placed on a magnetic rack and the supernatant removed and kept for DNA purification.

value: HUVEC


title: HUVEC, BRG1 CUT&RUN, siPVT1, 1


title: HUVEC, BRG1 CUT&RUN, siNEAT1, 3


title: LDB1_AID_TRI_C_auxin_biorep3


title: HUVEC, BRG1 CUT&RUN, siNEAT1, 2


title: HKDC1 fl/fl liver Sample 2

description: Library name: S2


title: RA0724F_Preradiation

value: Preradiation


title: HKDC1 fl/fl liver Sample 1

description: Library name: S1


title: HUVEC, BRG1 CUT&RUN, siNEAT1, 1


title: HUVEC, BRG1 CUT&RUN, siMIR31HG, 3


title: RA0529F_Preradiation


title: HUVEC, BRG1 CUT&RUN, siMIR31HG, 2


title: RA1547M_Preradiation


title: RA2580M_Preradiation


title: HUVEC, BRG1 CUT&RUN, siMIR31HG, 1


title: HUVEC, BRG1 CUT&RUN, siMIR100HG, 3


title: Heart pericytes mouse 4

city: New York

first: William

last: Coetzee

state: United States

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

description: Library name: Sample 9

data_processing:
Alignment to was performed using STAR
Assembly: Mouse mm10 genome
Supplementary files format and content: Further analysis was performed with R, using the DESeq package. We filtered out low expressing genes with fewer than 25 summed raw counts across the 10 samples. This reduced the data complexity and decreased the gene count from 39,395 to 20,685. Putative ion channels and transporters (CTP) were extracted from a list of such genes (Github: BillAC/List-of-Channels-and-Transporters).

source_name: Heart

extract_protocol:
Following total RNA extraction, RNA-seq was performed at the NYU Langone Medical Center Genome Technology Center (GTC).  Bulk RNA-seq was performed with a NovaSeq 6000 instrument (Illumina). The fastq files were analyzed using the NYU Langone Medical Center’s BigPurple cluster.
SMART-Seq® HT Kit consisting of a one-step cDNA synthesis and amplification, purification and validation of cDNA and library preparation.

value: Heart

value: Isolated pericytes

value: Pericytes

value: Wild-type

tag: batch


title: Heart pericytes mouse 5

description: Library name: Sample 10


title: HUVEC, BRG1 CUT&RUN, siMIR100HG, 2


title: RA0521F_Preradiation

data_processing:
Illumina NextSeq 500 generated BCL files that were converted to FastQ files
FastQ files were demultiplexed using bcl2fastq2
Genomics Workbench was used to filter and trim the fastQ files
miRbase was used to generate miRNA expression count data
Data was normalized to CPM values using TMM normalization
Assembly: NHP gene assmebly in miRbase
Supplementary files format and content: raw count data contains the count data for miRNA

value: Serum

tag: gender


title: HUVEC, BRG1 CUT&RUN, siMIR100HG, 1


title: HUVEC, BRG1 CUT&RUN, siMEG8, 3


title: Heart pericytes mouse 3

description: Library name: Sample 8


title: Heart pericytes mouse 2

description: Library name: Sample 7


title: HUVEC, BRG1 CUT&RUN, siMEG8, 2


title: HUVEC, BRG1 CUT&RUN, siMEG8, 1


title: Heart pericytes mouse 1

description: Library name: Sample 6


title: 15515

type: genomic

city: Newcastle upon Tyne

first: Sarah

last: Rice

address: Central Parkway

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description: Articular cartilage from human foetal femur

hyb_protocol: Genomic DNA was bisulfite converted using the standard protocol for the Illumina methylation EPIC 850k (v1.0) array.

scan_protocol: Scanning was performed as standard with the iScan N0660 (#4498).

data_processing:
R v4.2.2 & minfi
Quantile-normalised Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Genomic DNA methylation profile of articular cartilage from human foetal femur

label_protocol: Illumina

extract_protocol: Genomic DNA was extracted using Qiagen Allprep kit.

tag: Sex

value: female


title: 15507

value: male


title: HUVEC, BRG1 CUT&RUN, siLINC00607, 3


title: 15504


title: Brain pericytes mouse 5

description: Library name: Sample 5

source_name: Brain

value: Brain


title: Brain pericytes mouse 4

description: Library name: Sample 4


title: HUVEC, BRG1 CUT&RUN, siJPX, 3

value: siJPX


title: 15478


title: HUVEC, BRG1 CUT&RUN, siJPX, 1


title: HUVEC, BRG1 CUT&RUN, siRNA control, 3

value: Control siRNA


title: Brain pericytes mouse 3

description: Library name: Sample 3


title: Brain pericytes mouse 2

description: Library name: Sample 2


title: RA2740F_Preradiation

extract_protocol:
Blood samples were extracted and centrifuged to obtain serum samples for analysis
TruSeq small RNA Sample Preparation kit was used for library construction

value: F


title: HUVEC, BRG1 CUT&RUN, siRNA control, 1


title: HUVEC, BRG1 CUT&RUN, siLINC00607, 2


title: HUVEC, BRG1 CUT&RUN, siLINC00607, 1


title: 15479


title: 15472


title: 15512


title: HUVEC, BRG1 CUT&RUN, Untransfected, 3

value: Untransfected


title: Brain pericytes mouse 1

description: Library name: Sample 1


title: 15471


title: HUVEC, BRG1 CUT&RUN, Untransfected, 1


title: HUVEC, BRG1 CUT&RUN, Untransfected, 2


title: 4_CT2A, all-in-one, 72 hrs, offtarget5, rep2

city: Charlestow

first: Lisa

last: Nieland

state: Massachusetts

address: 149 13th street

department: Neurology

institute: Massachusetts General Hospital

description: 300-cycle v2 kit (Illumina)

data_processing:
CRISPR screen was performed using CRISPResso2 analysis (http://www.crispresso2.pinellolab.org). Percentages of Unmodified and Modified reads were used to plot data (CRISPResso2 output: quantification_of_editing_frequency.txt)
mmu-miR21a primer set designed with: https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Fw: TTGACTGCAAACCATGATGCTG-mir21-1-mmu-86584000-fw
Rv: TGCTTTAAACCCTGCCTGAGC-mir21-1-mmu-86584221-rv
amplicon (222bp):
TTGACTGCAAACCATGATGCTgggtaatgtttgaatgaaaacatttgata
tggatggtcagatgaaagataccaaaatgtcagacagcccatcgactgct
gttgccatgagattcaacagtcaacatcagtctgataagctatccgacaa
ggtggtacagccatgcgatgtcacgaccacgacagggggcaagcacgagg
tGCTCAGGCAGGGTTTAAAGCA
sgRNA sequence (without PAM):
GACTGTTGAATCTCATGGCAAC
CRISPR screen was used to check the the top 5 potential murine off-targets of sgRNA3. Mouse genome was amplified with the following primer sets and amplicons designed with: https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Off-target 1; Chr4, location 153280201.
FW: CACTGCCCCAGCTGTAAGAT
RV: CCCTTCATCCACTTTGGCTT
Amplicon (248bp):
CACTGCCCCAGCTGTAAGATcaatctttctccaaagccattgcctctcaa
cagtcttgttacttccagacaattcatgacagggagaaatctgtagctgc
ccctctatccaagaccaccaggcctagtaactcacagggacttggagaac
tctaccaaccaagtctttagtataactgtggcatctcatgacaacagaaa
tggattggtgaaaaatcagcagaaagaaAAGCCAAAGTGGATGAAGGG
Off-target 2; Chr 11, location 112908309.
FW: TAGAAAAGGTCGGCGCTGG
RV: CTCTTGAAGTATGGCCGTGGT
Amplicon (243bp):
TAGAAAAGGTCGGCGCTGGctgctgaaccttatacacccatagtttttaa
cgagaaatagatagcatttactgagctaatgacttgtgcaattaagctct
gatgggctgactataattgccatgaggtttaacagtggggagatgcaggg
ggagatgcagggggagatgcagggagatgcagggggaggatgccaagaca
gttgaccaatcgtgaaggtattACCACGGCCATACTTCAAGAG
Off-target 3; Chr 11, location 119227215.
FW: CCCACACATGGTGATCCGA
RV: GGCCGGCTAAGATTCACCC
Amplicon (247bp):
CCCACACATGGTGATCCGAggctgttaacagacaccgtgattgccaggag
agtcaacagttcccaagaagaacttcctagctatactcaagacattccac
tcaccagaaagctatgggggggggggggggacaaaacaaacaaacagaga
aaaaacccataagtactgctcagctaagagatccatccccagcaaccagc
taagaaccaactctggtaaattcccaatGGGTGAATCTTAGCCGGCC
Off-target 4; Chr 10, location 36314200.
FW: ACAGCCAGGAAATATAGGATCATTC
RV: TTTTGGTGCAGCAGTTGGGT
Amplicon (236bp):
ACAGCCAGGAAATATAGGATCATTCcagattatataattagaattctctt
ttgaagctcatggcaacttaaatacagctagaattttgttttgaatggac
acagggtatgcaaatttatattgcaaaggtaatcaattatgtctgccata
cttgttttaatttattaagtgagttaataaaatcataacagtaaaatgca
ttgcgtgtagtaagtcACCCAACTGCTGCACCAAAA
Off-target 5; Chr 15, location  45517500.
FW: GTGGGGCTCAGATGCAGTAT
RV: TGACTAGGACACACAGCAAATGT
Amplicon (227bp):
GTGGGGCTCAGATGCAGTATacacaaccatctcagataaaataatacaaa
taaaatattaaatagtaaatgaattttaatatacattgaaatatactgga
taactctatatttatttcattgacattgcaaatttacgttgccatgatca
tcaacattgattatgacacacatagattatagcatagtatcttatttttg
aaaaACATTTGCTGTGTGTCCTAGTCA
Library strategy: CRISPR screen

growth_protocol: CT2A cells were cultured in DMEM (10% Fet Bone Serum and 1% penstrep) and maintained in 5% CO2 in 37C

extract_protocol:
1-2-4) genomic DNA was extracted using DNAeasy DNA isolation kit (Qiagen) and quantified using a NanoDrop (Wilmington, DE) ND-1000. 3) genomic DNA was extracted using the adapted TRIzol™ Reagent Experimental protocol for DNA isolation (Invitrogen, 15596026) from FACS sorted mCherryPOS (tumor cells) and mCherryNEG (non-tumor cells) by utilizing the remaining sample post-removal of the aqueous layer of the in Qiazol lysed RNA (Qiagen).
1-2-4) mmu-miR-21a or off-targets were amplified, using the Phusion High Fidelity PCR kit (New England Biolabs), for Next Generation Sequencing (NGS) analysis primers amplified a 222 bp at a Tm of 67°C DNA fragment of the mouse miR-21. The PCR products were purified using the Qiagen PCR purification kit. Next, the PCR products were loaded on a 2% agarose gel (Bio-Research, Worcester, MA), and DNA fragments were resolved by gel electrophoresis. The purified PCR products were sequenced at the MGH CCIB DNA Core and CRISPR efficiency was determined based on CRISPResso2 analysis 3) Genome modified reads were determined by NGS using a two-step PCR-based Illumina library construction method. The first PCR reaction was done with approximately 100 ng of gDNA using Q5 High-fidelity DNA Polymerase (NEB) and the respective primers, with cycling conditions of one cycle at 98 °C for 2 min; 35 cycles of 98 °C for 10 s, 65 °C for 10 s, 72 °C for 20 s; and one cycle of 72°C for 1 min. PCR-1 products were purified using paramagnetic beads at a ratio of 1.8×. Approximately 20 ng of purified PCR-1 product was used as a template for a second PCR (PCR-2) to add Illumina barcodes with adaptor sequences using Q5 (cycling conditions of one cycle at 98°C for 2 min; 10 cycles at 98°C for 10 s, 65°C for 30 s, 72°C 30 s; and one cycle at 72°C for 5 min). PCR-2 products were pooled based on concentrations from capillary electrophoresis (QIAxcel, QIAGEN). Final libraries were quantified by Qubit dsDNA High Sensitivity assay (Thermo Fisher) and sequenced on a MiSeq sequencer using a 300-cycle v2 kit (Illumina). On-target genome editing activities were determined from amplicon sequencing data using CRISPResso2.

treatment_protocol: 1) cells were transfected with lipofectamine 2000 and saCas9:sgRNA 3:1 ratio incubated for 72hrs. 2) cells were transfected with lipofectamine 2000 and 400ng all-in-one plasmid DNA and incubated for 37 hrs, genomic DNA was extracted from cell pellets. 3) mice were implanted with 25,000 CT2A cells and treated intracranially with 2ul AAV8-control or AAV8-CRISPR at day 3 and day 6 post-tumor implantation. Mice were sacked at day 15 post-tumor implantation and brain tissue was FACS sorted for mcherry+ CT2A cells, genomic DNA was extracted immediately after FACS. 4) cells were transfected with lipofectamine 2000 and 400ng all-in-one plasmid DNA and incubated for 37 hrs, genomic DNA was extracted from cell pellets.

value: mouse glioma

value: wild-type

value: all-in-one

tag: endpoint

value: 72 hours


title: 15444


title: HUVEC, BRG1 CUT&RUN, siJPX, 2

value: HUVEC


title: 4_CT2A, all-in-one, 72 hrs, offtarget5, rep1

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A, all-in-one, 72 hrs, offtarget4, rep2

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A, all-in-one, 72 hrs, offtarget4, rep1

description: 300-cycle v2 kit (Illumina)


title: E0del/+_LV_3

city: Boston

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: 1665_LV

data_processing:
Fastq files were aligned using STAR and counts files were generated. Downstream analysis was done using DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data includes feature counts and bam file, which are both generated from STAR aligner.

molecule: polyA RNA

source_name: LV

extract_protocol:
RNA was extracted from mouse tissue using simple TRIzol method.
Libraries were constructed using Illumina's Nextera XT DNA Library Preparation Kit. Before libraries were constructed two rounds of poly-A selection were performed on total RNA before double stranded cDNA was synthesized. This cDNA was used as the templated for the library construction.

value: LV


title: E0del/+_SkM_3

description: Library name: 1665_SkM

source_name: SkM

value: SkM


title: WT_SkM_2

description: Library name: 1663_SkM

value: WT


title: 15400


title: HUVEC, BRG1 CUT&RUN, siRNA control, 2


title: E0del/+_SkM_2

description: Library name: 1662_SkM


title: 4_CT2A, all-in-one, 72 hrs, offtarget2, rep2

description: 300-cycle v2 kit (Illumina)


title: WT_LV_2

description: Library name: 1663_LV


title: 15429


title: 4_CT2A, all-in-one, 72 hrs, offtarget3, rep1

description: 300-cycle v2 kit (Illumina)


title: 15398


title: 4_CT2A, all-in-one, 72 hrs, offtarget2, rep1

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A, all-in-one, 72 hrs, offtarget1, rep2

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A, all-in-one, 72 hrs, offtarget3, rep2

description: 300-cycle v2 kit (Illumina)


title: WT_SkM_1

description: Library name: 1661_SkM


title: 15467


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget3, rep2

description: 300-cycle v2 kit (Illumina)

value: non-transfected


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget4, rep1

description: 300-cycle v2 kit (Illumina)


title: 15417


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget4, rep2

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget5, rep1

description: 300-cycle v2 kit (Illumina)


title: 15442


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget3, rep1

description: 300-cycle v2 kit (Illumina)


title: 15396


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget2, rep2

description: 300-cycle v2 kit (Illumina)


title: 15393


title: E0del/+_LV_1

description: Library name: 1660_LV


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget2, rep1

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A, all-in-one, 72 hrs, offtarget1, rep1

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget5, rep2

description: 300-cycle v2 kit (Illumina)


title: E0del/+_LV_2

description: Library name: 1662_LV


title: 15386


title: WT_LV_1

description: Library name: 1661_LV


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget1, rep2

description: 300-cycle v2 kit (Illumina)


title: 4_CT2A wildtype, nonedited control, 72 hrs, offtarget1, rep1

description: 300-cycle v2 kit (Illumina)


title: 15380


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep8

description: 300-cycle v2 kit (Illumina)

source_name: Tumor implanted brain tissue

value: Tumor implanted brain tissue

tag: time of_treatment

value: day 3 and day 6 post-tumor implant

value: Day 15 post-tumor implant


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep7

description: 300-cycle v2 kit (Illumina)


title: scRNA-seq of Mus musculus: Lupus nephritis receiving MSCs treatment group

city: Nanjing

first: Qixiang

last: Zhang

address: Tongjiaxiang #24, Nanjing, Jiangsu Province, China

institute: China Pharmaceutical University

data_processing:
The software uses the STAR aligner to map the sequencing reads to a reference genome. This step ensures that each read is correctly associated with its corresponding gene.
After alignment, Cell Ranger counts the number of unique molecular identifiers (UMIs) for each gene in every cell. This counting generates a gene-cell matrix, which is crucial for further analyses like clustering and differential expression.
Assembly: mm10
Supplementary files format and content: Cellranger matrix

source_name: Glomerular

extract_protocol:
Mouse kidneys were initially processed for glomerular extraction via enzymatic digestion. In brief, minced kidneys were subjected to digestion with collagenase V (1 mg/mL in TESCA buffer), followed by gradient centrifugation and differential adhesion techniques to predominantly isolate glomeruli. The isolated glomeruli were then dissociated into single cells69. Approximately 8,000 cells were captured and subjected to barcoding of released RNA through reverse transcription within individual Gel Bead-In-Emulsions (GEMs). Reverse transcription was conducted using an S1000TM Touch Thermal Cycler (Bio-Rad) at 53°C for 45 minutes, followed by 85°C for 5 minutes, and then held at 4°C. The resulting cDNA was amplified, and its quality was evaluated using an Agilent 4200, with procedures executed by CapitalBio Technology, Beijing.
Raw sequencing data were processed using the Cell Ranger software (10x Genomics, v1.1.0) for FASTQ file generation and alignment. For data filtration and unsupervised clustering, the gene expression matrix from Cell Ranger was utilized for downstream analysis in R (v4.2.1). Normalization, dimensionality reduction, and cell clustering were conducted using Seurat (R package, v4.2.0). The selection criteria for cells were established based on prior studies, considering the median gene count and mitochondrial gene percentage in samples. Cells with fewer than 200 or more than 3,000 genes (indicative of potential doublets), a mitochondrial gene percentage exceeding 10%, or a ribosomal gene percentage over 5% were excluded. In addition, DoubletFinder (v 2.0.3) was employed to identify and eliminate doublets within each dataset.

value: Glomerular


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep6

description: 300-cycle v2 kit (Illumina)


title: E0del/+_SkM_1

description: Library name: 1660_SkM


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep5

description: 300-cycle v2 kit (Illumina)


title: scRNA-seq of Mus musculus: Control Blank

value: Control Blank


title: scRNA-seq of Mus musculus: Model Group

value: Model Group


title: 15367

value: male


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep4

description: 300-cycle v2 kit (Illumina)


title: 15366


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep2

description: 300-cycle v2 kit (Illumina)


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep1

description: 300-cycle v2 kit (Illumina)


title: 3_mousebrain, CT2Amcherry+, AAV8-CRISPR, day 15, rep3

description: 300-cycle v2 kit (Illumina)


title: 344_2

city: Köln

first: Jens

middle: C

last: Brüning

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

institute: Max Planck Institute for Metabolism Research

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse reference genome GRCm38 and counted using cellranger (version 7.0.0; 10x Genomics).
Ambient RNA molecules were removed from cellranger raw count matrix files with cellbender:remove-background (v0.3). Filtered count matrices were analyzed in R with Seurat (v4.3.0). Nuclei with at least 1000 detectable genes were retained. Genes expressed in at least 10 nuclei were retained. ScDblFinder (v1.15.4) with standard parameters was run on individual 10x lanes to remove doublets. The count data were normalized with NormalizeData and scaled with ScaleData function. Genes were then defined as variable using FindVariableFeatures and used as input into PCA with RunPCA. The top 30 PC were retained and used for further dimensionality reduction using RunUMAP and clustered using a resolution of 0.8 with FindClusters.
To perform cell-type specific quality control, the nuclei were split into two broad categories, neuronal and nonneuronal, using CellAnnotatorR(v) based on the expression of neuronal marker gene Rbfox3 or Snap25 and the absence of nonneuronal markers. Neuronal data was further filtered by removing nuclei with UMI in the first and 99th percentile. Library complexity was calculated by dividing the log of the total genes detected per nuclei by the log of the total UMI per nuclei. Nuclei in the first percentile of this metric were removed. Add_Mito_Ribo_Seurat was used to identify and remove nuclei with >1% mitochondria and ribosomal genes. We finally removed outliers by isOutlier with nmads=5 run on individual 10x lanes from the package SingleCellExperiment70. After all quality control, a total of 23664 neurons remained. Neuronal cell types were labeled by projecting labels from a previously published data set (GSE166649) using Seurat FindtransferAnchors and TransferData function.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated files for barcodes(cells), genes and matrix file for processed counts corresponding to the data set used in the analysis. Matrix contains data in format genes x cells. Comma-separated metadata file with annotations from processing pipeline. barcodes correspond to first column of metadata file.

source_name: hindbrain

extract_protocol:
After decapitation, the brain was removed, and the DVCs were isolated from the brainstem under a surgical microscope. A 1 mm coronal section of the hindbrain from bregma -7.0 to -8.0 mm was cut with a razor blade. From the coronal section, a 1.4 mm square containing the DVC was snap-frozen. Samples from the same experimental condition were pooled (n = 5 mice per sample) and nuclei were extracted. Sorting of 2n nuclei was performed by flow cytometry using a BD FACSAria IIIu Influx cell sorter (BD Biosciences). The gating was set according to size and granularity using FSC and SSC to capture singlets and remove debris. To detect DraQ5-positive nuclei fluorescence was set at 647 nm and 670 nm. Each sample was sorted into separate tubes, each with a total of 20,000 nuclei per 40 µl.
Sequencing libraries were generated using 10x Genomics Chromium Single-Cell 3′ Reagent kit according to the standardized protocol. Paired-end sequencing was performed using an Illumina NovaSeq 6000.

treatment_protocol: All experiments were performed in adult C57BL/6 diet-induced obesity mice with an of age 24 weeks. Mice were housed in solid bottom cages with environmental enrichment at 22°C (± 2°C) in 55% (± 10%) humidity and a 12-hour light/dark cycle (light: 6:00 to 18:00). Mice were s.c. injected with vehicle or 325 nmol/kg EB1002 2 hours prior to euthanasia. Samples from the same experimental condition were pooled together (n = 5 mice/group) for a total of 3 samples per condition.

value: hindbrain

value: Agonist


title: 15365

value: female


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep7

description: 300-cycle v2 kit (Illumina)

value: mouse glioma

value: wild-type


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep8

description: 300-cycle v2 kit (Illumina)


title: 344_1

description: 10x Genomics


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep6

description: 300-cycle v2 kit (Illumina)


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep5

description: 300-cycle v2 kit (Illumina)


title: Veh_3

description: 10x Genomics

value: Veh


title: 15357


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep4

description: 300-cycle v2 kit (Illumina)


title: 15354


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep3

description: 300-cycle v2 kit (Illumina)


title: 15370


title: 15350


title: Veh_2

description: 10x Genomics


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep2

description: 300-cycle v2 kit (Illumina)


title: Veh_1

description: 10x Genomics


title: 2_CT2A, all-in-one, 72 hrs, rep4

description: 300-cycle v2 kit (Illumina)

value: all-in-one

value: 72 hours