title: ChIPseq Ikaros 0h Rep2

value: B3 transduced with Ikaros-ERt2


title: RV2_2G, Right ventricle region 2G sample from chambers_2, replicate 1

status: Public on Oct 28 2024

type: SRA

city: Cambridge

first: Stephen

middle: Jordan

last: Fleming

state: MA

address: 415 Main St.

country: USA

institute: Broad Institute

description: 10x Genomics 3' v2 chemistry

library_source: transcriptomic single cell

data_processing:
CellRanger v3.0.2 was used to run cellranger mkfastq in order to generate FASTQ files.
Assembly: rn6
Supplementary files format and content: Creation of the h5 count matrix files for each sample included the following: (1) FASTQ trimming using cutadapt. (2) Cellranger count was used to obtain h5 count matrices using a GTF file from our manuscript (supplementary file rn6.broad.cardiac.3.gtf.gz here). Note that these h5 files have not had CellBender run on them.

molecule: total RNA

organism: Rattus norvegicus

source_name: Right ventricle region 2G

extract_protocol:
17-week-old animals were euthanized between 10am and 12pm using CO2, followed by perfusion with PBS to remove excess blood. Right ventricle, left ventricle and septum were immediately rinsed with ice cold PBS, then minced on ice by sterile razor blade, finally mixed with 4mL of nuclei isolation buffer (NIB). Left atria, right atria, SA node, AV node, aorta (from aortic root to iliac bifurcation), pulmonary vein, and pulmonary artery were immediately frozen in LN2 and stored at -80°C until use. Since AV nodes from rat have an approximate volume of 0.5mm3, we pooled 3-4 rat samples to obtain 1 sample for further processing. The same approach was used for SA node.
Frozen tissues were mounted on OCT and sectioned at 60μm at -20°C using a cryotome (Leica CM 1950). Tissue slices were transferred to 4mL of ice-cold NIB (Hepes 20 mM, Sucrose 0.25M, MgCl2 3mM, KCl 25mM, Igepal-630 0.01%, BSA 0.5%, pH 7.2). All tissue mixtures were dounce homogenized on ice with 10 strokes of a loose fit pestle followed by 10 minutes incubation, followed by 10 strokes of a tight fit pestle and 10 min incubation. Homogenate was transferred to a 15mL conical tube, filled to 8mL with nuclei wash buffer (NWB = NIB without detergent), and centrifuged at 40g x 4’, at 4°C (Beckman Coulter Allegra X-15R swinging bucket centrifuge). Supernatant was filtered through sequential 40μm and 10μm meshes (Pluriselect, Germany) in 50mL conical tube, filtrate topped up to 10mL with NWB and centrifuged at 600g x 5’, at 4°C. Supernatant was discarded and pellet resuspended, transferred to 15mL tube, topped up with 8mL NWB centrifuged (600g x 5’, 4°C). Final pellet was resuspended in 150μL nuclei resuspension buffer (NRB = NWB with 1:80 murine RNAse inhibitor, NEB). All procedures were performed on ice. Nuclei, stained with Trypan blue, were manually counted using a hemocytometer (inCyto.com). 7,000 nuclei input (5,000 calculated recovery) per sample were used for droplet generation and library construction according to the manufacturer's protocol (10x Genomics, single-cell 3-prime V2 chemistry), with minor modifications. First, after emulsion generation, nuclei were incubated on ice for 15 minutes to promote nuclear lysis. Second, the reverse transcription protocol was extended to enable the retention of longer transcripts. Libraries were multiplexed at an average of 4-5 libraries per flow cell. Sequencing was performed on an Illumina Nextseq550 in the Broad Institute’s Genomics Platform (genomics.broadinstitute.org).

treatment_protocol: 17-week-old healthy male Wistar rats

tag: tissue

value: Right ventricle region 2G

tag: individual or_pool

tag: developmental stage

value: 17 week

tag: Sex

value: male

tag: strain

value: Wistar

tag: disease

value: healthy


title: HIV014 colon

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
10X genomics
Seurat_object_scaled_data_integrated.rda

library_source: transcriptomic

data_processing:
single cell RNA seq were processed with 10x Cell Ranger pipeline and downstream analysis was conducted using Seurat
Bulk RNA seq analysis was conducted in R
Assembly: hg19
Supplementary files format and content: RDS object

organism: Homo sapiens

source_name: colon

extract_protocol:
human intestinal biopsies were collected in RPMI and processed fresh to ontain single cell suspension. Biopsies underwent two 20 minute rounds of dissociation to remove the epithelial layer (Dissociation media: 10 ml HBSS (free of calcium and magnesium) EDTA (0.5M, pH 8, Invitrogen) and HEPES (1M, Lonza)) was followed by transfer to 10 ml of digestion solution (containing RPMI, FBS (Corning 35-010-CV), 0.005 g of Type IV collagenase (Sigma-Aldrich, cat # C5138-1G) and DNAase I (Sigma Aldrich Fine Chemicals Biosciences cat # 10104159001)) and incubated for 40min at 37°C using gentle agitation (180 rpm). The digested tissue was then further mechanically broken down by aspirating 10-times with a 10ml syringe by sequentially filtering through a 100-µm and a 40-µm cell strainer and washed with RPMI twice to obtain a single cell suspension of the intestinal lamina propria.
For scRNASeq, Gene expression libraries were prepared as per 10x Genomics protocol. For RNA-seq Gene expression libraries were prepared as per SMART-Seq v4 Ultra Low Input Nextera XT or SureSelect XT RNA Direct v6 protocols

value: colon


title: ChIPseq H3K27ac 30m Rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: genomic

data_processing:
Raw paired-end 41bp sequencing reads were aligned against mouse genome (mm10) using Bowtie2 (v. 2.4.2; Langmead and Salzberg, 2012) with parameters: '--no-mixed --no-discordant'. Picard (v. 2.23.7; https://broadinstitute.github.io/picard/) SortSam and MarkDuplicates were applied for sorting and converting sam files to bam files and duplicated reads were marked. Peak calling was proceeded with MACS2 (v.2.2.7.1) callpeak function (with -f BAMPE -g mm for Ikaros and H3K27ac; with -f BAMPE --broad -g mm for CHD4).
Downsampling for generating bigwig files for Ikaros and CHD4:
We used the IP raw concentration at 2 hours from each ChIPs as the baseline to calculate the size factor (SF) for the downsampling analysis at each time point. The SF at each time point was calculated by dividing the IP raw concentration at time 0 hours or 1 hour by the IP raw concentration at 2 hours. Reads from raw fastq files were randomly selected based on the SF calculated for downsampling by using seqtk (v1.3; https://github.com/lh3/seqtk) with 'seqtk sample -s100 $ori.fastq.gz $sizeFactor - | gzip - > $DS_fastq.gz'. After downsampling the fastq files, we applied the same analytical pipeline described in this section for alignment, sorting, converting to BAM files, and marking duplicated reads. We generated downsampled BigWig files using Deeptools (v. 3.5.0) with the following command: 'bamCoverage -b ChIP.DupMark.bam -p 16 -bl mm10-blacklist_v1.bed --extendReads --effectiveGenomeSize 2652783500 -o ChIP_MarkedDup.bw'.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: Peak files (broad peaks for CHD4; narrow peaks for Ikaros and H3K27ac)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: B3 pre-B cells were maintained in IMDM with 10% heat inactivated FBS and 1x Pen/Strep (Gibco™ 15070063) and 1x L-glutamine (Gibco™ 25030081) between 0.5 – 2 million/ml. The inducible Ikaros-ERt2 construct was introduced in the B3 cell line using retroviral transduction.

extract_protocol:
Cells were fixed at room temperature in 10ml PBS with 1mM DSG (ThermoFisher 20593) for 30 min followed by addition of 1% formaldehyde (ThermoFisher 28908) and incubated for a further 10min. The reaction was quenched with 125mM glycine. Chromatin was digested by sonication or MNase to obtain fragments between 100-300bp. A small aliquot was reserved for the Input sample, and chromatin equivalent to 4 million cells was used per IP. HA-Ikaros-ERt2 ChIP performed using overnight incubation with Pierce magnetic anti-HA beads (Pierce 88836). For H3K27ac (Active Motif 39133) and CHD4 (Abcam ab70469), 4-6 mg of antibodies were incubated with each reaction overnight, followed by 2h of incubating with magnetic Prot A/G Dynabeads (ThermoFisher 10001D, 10003D). Washes were performed for 5 min rotating in the cold room twice with each buffer, Low Salt Buffer, High Salt Buffer, LiCl Buffer and TE. DNA was eluted with 1% SDS and 0.1M NaHCO3. For reverse crosslink, NaCl was added to a final concentration of 0.2M, and samples were incubated at 65°C shaking overnight, following by 2h of RNaseA and 2h of Proteinase K treatment.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645S) was used for all ChIP-seq libraries with PCR amplification of 5-8 cycles. Clean-up was performed with Ampure beads and quantification and quality control of libraries was performed using DNA Qubit and HS DNA Bioanalyser.

treatment_protocol: 500nM of 4-hydroxytamoxifen (Sigma-Aldrich H7904-5MG) was used to induce nuclear translocation of Ikaros for 30m, 1h, or 2h.

tag: cell line

tag: cell type

value: mouse pre-B

tag: genotype

tag: treatment

value: 4-hydroxytamoxifen 30m

tag: chip antibody

value: H3K27ac Active Motif 39133


title: SA2c, Sinoatrial node sample from sa_2, replicate c

description: 10x Genomics 3' v2 chemistry

source_name: Sinoatrial node

value: Sinoatrial node


title: RV1_2G, Right ventricle region 2G sample from chambers_1, replicate 1

description: 10x Genomics 3' v2 chemistry


title: HIV014 ileum

source_name: ileum

value: ileum


title: Vehicle treated M1 biol rep 1

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E 57th street

department: Medicine

institute: University of Chicago

data_processing:
Data was analyzed using Rosalind with a HyperScale architecture developed by ROSALIND, Inc.
Reads were trimmed using catadapt. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel files with raw counts
Supplementary files format and content: excel files with normalized counts

molecule: polyA RNA

source_name: BMDM

growth_protocol: RPMI containing 10% FBS, 10 mM HEPES, and 100 U/ml penicillin/ streptomycin) supplemented with 10 ng/ml M-CSF

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: BMDMs were pre-treated with vehicle (DMSO) or 50 nM ISRIB followed with 10 ng/ml LPS and 25 ng/mL IFN-γ for M1-like polarization in the presence of vehicle or ISRIB.

value: BMDM

value: mouse macrophage

value: Vehicle (DMSO)


title: ChIPseq H3K27ac 2h Rep2

value: 4-hydroxytamoxifen 2h


title: Vehicle treated M0 biol rep 3


title: wild type sw480 colorectal cancer cell, RIP sequencing

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

country: China

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome.
Mapped reads of IP and input libraries were provided for MACS2(version 2.2.7.1).
HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs. Differential expression analysis was performed using R package edgeR for experimental design without replication while using R package DESeq for experimental design with replication. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Collect enough tissue culture cells, this is comparable to 10000000 cells per RIP. Resuspend final cell pellet with an equal volume of polysome lysis buffer (100 mM KCl, 5 mM MgCl2, 10 mM HEPES (pH 7.2), 0.5% NP40, 1 mM DTT, RNase inhibitors, protease inhibitors)，incubated on ice for 5 minutes and cellular debris was pelleted by 4°C centrifugation at 15,000 x g for 15 minutes. After centrifugation 40μL of supernatant was collected for RNA extraction as input sample. The remaining supernatant was used for immunoprecipitation.100ul protein A/G magnetic beads were washed with NT2 buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2 and 0.05% NP-40) three times. Magnetic beads resuspended in 850 μl of the immunoprecipitation reaction solution (200 units of an RNase inhibitor, 400 μM RVC, 10 μl of 100 mM DTT, 30 μl of 0.5 mM EDTA and 800 μl of cold NT2 buffer). Cleared cell lysates were incubated with immunoprecipitation reaction solution at 4 °C for 4 h on a tube rotator. The beads were then washed with 1 ml of ice-cold NT2 buffer five times.TRIzol was added to input and immunoprecipitation (IP) samples to isolate total RNA. RNA quality control was measured on a Qubit. Sample libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Kit Cat# 63488). Libraries were sequenced on a NoveSeq 6000 (Illumina) .
RNA Immunoprecipitation sequencing

value: colorectal cancer cell

value: wild type sw480


title: HIV026 colon


title: RA8, Right atrium sample from chambers_8, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Right atrium

value: Right atrium


title: Vehicle treated M0 biol rep 1


title: Vehicle treated M0 biol rep 2


title: ChIPseq H3K27ac 1h Rep2

value: B3 transduced with Ikaros-ERt2

value: 4-hydroxytamoxifen 1h


title: RA6_12, Right atrium sample from chambers_6, replicate 1

description: 10x Genomics 3' v2 chemistry

value: 17 week

value: male

value: Wistar


title: RA3, Right atrium sample from chambers_3, replicate 1

description: 10x Genomics 3' v2 chemistry

value: healthy


title: RA2, Right atrium sample from chambers_2, replicate 1

description: 10x Genomics 3' v2 chemistry


title: ChIPseq CHD4 2h Rep2

value: mouse pre-B

value: CHD4 Abcam ab70469


title: METTL1 knocked out colorectal cancer cell, RIP input RNA

value: METTL1 knocked out


title: ChIPseq H3K27ac 0h Rep2

value: H3K27ac Active Motif 39133


title: ChIPseq CHD4 1h Rep2


title: ChIPseq CHD4 30m Rep2

value: 4-hydroxytamoxifen 30m


title: Stim TA, Aged DEX, 4

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using STAR version 2.7.10a for alignment to the mouse genome (GRCm39) and to generate count tables using default settings.
Differential expression analysis of count tables was performed using the default settings of DESeq2 version 1.30.1 (Benjamini-Hochberg FDR correction).
Assembly: NCBI GRCm39
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx). Contains normalized counts generated by DESeq2.

source_name: Skeletal muscle (Tibialis anterior)

growth_protocol: Male C57BL/6 mice were housed in a temperature- (25℃) and light- (12 h light/12 h dark) controlled environment within the vivarium at Florida State University and were provided standard 5001 rodent chow (LabDiet, St. Louis, MO) and water ad libitum until the day of testing. Animals were euthanized by cardiectomy while under deep isoflurane anesthesia.

extract_protocol:
RNA was isolated using Zymo RNA Miniprep kit with on-column Dnase treatment. 300 micrograms of total RNA was used for construction of sequencing libraries.
A cDNA library was prepared for each sample using the the NEBNext PolyA mRNA and Ultra II Directional RNA library kit for Illumina. Libraries were barcoded for multiplexing with NEBNext Multiplex Oligos for Illumina unique dual index Primer Pairs. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). The pooled sample was sequenced, with paired-end, 50 base reads on an Illumina NovaSeq 6000 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

treatment_protocol: At the start of the mouse light cycle, 4-mo-old male mice (Charles River; Young) and 24-25-mo-old male mice (NIA; Aged) were randomized to receive an intraperitoneal (IP) injection of dexamethasone at 2 mg/kg diluted in saline or an IP injection of saline only as a control. The mice were given 2 h recovery after the injection to allow for full activation of the glucocorticoid receptor in the DEX treated group. Mice were then subjected to unilateral high force eccentric contractions by electrical stimulation of the sciatic nerve under deep isoflurane (3%) anesthesia. The left thigh was shaved, two subcutaneous bipolar electrodes straddled the sciatic nerve, and the nerve was stimulated with a ~20 mAmp current at a stimulation frequency of 100 Hz using a constant current stimulator (Model #701C, Aurora Scientific, ON, Canada). Each stimulus consisted of 300 pulses, each 1 ms in duration. The entire protocol consisted of 10 sets of 6 stimuli with each stimulus within a set separated by a 10 s rest period, and each set separated by a 60 s rest period. Following the contractions, all mice received a 500 µL subcutaneous injection of warm saline before returning to their cages. During the recovery, all mice had access to water but not food. Four hours after completing the contractions protocol (6.5 h post-DEX or saline injection), the TA muscles were extracted under deep isoflurane (3%) anesthesia, snap-frozen in liquid nitrogen, and stored at -80°C until analysis.

value: Skeletal muscle (Tibialis anterior)

tag: contractions protocol

value: Stim

tag: age

value: Aged

value: WT

value: Dexamethasone


title: Stim TA, Aged DEX, 5


title: METTL1 knocked out colorectal cancer cell, RIP sequencing

value: colorectal cancer cell


title: wild type sw480 colorectal cancer cell, m7G sequencing

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome.
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A/m1A/m7G/m5C peaks with bed format.
HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A/m1A/m7G/m5C-specific antibody in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.
m6A-seq/m1A-seq/m7G-seq/m5C-seq

value: wild type sw480


title: LV5_2B, Left ventricle region 2B sample from chambers_5, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Left ventricle region 2B

value: Left ventricle region 2B


title: Aorta_2_06072019, Aorta sample from aorta_2, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Aorta

value: Aorta

value: 17 week


title: LV6_2B, Left ventricle region 2B sample from chambers_6, replicate 1

description: 10x Genomics 3' v2 chemistry

value: male

value: Wistar


title: METTL1 knocked out colorectal cancer cell, m7G sequencing


title: ChIPseq Input 30m Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: ChIPseq CHD4 0h Rep2

value: CHD4 Abcam ab70469


title: ChIPseq Input 2h Rep1

value: 4-hydroxytamoxifen 2h


title: Stim TA, Aged DEX, 1


title: liver metastatic colorectal cancer tissue, m5C sequencing

value: liver metastatic colorectal cancer


title: LV3_2B, Left ventricle region 2B sample from chambers_3, replicate 1

description: 10x Genomics 3' v2 chemistry

value: healthy


title: wild type sw480 colorectal cancer cell, RIP input RNA


title: LV7_2B, Left ventricle region 2B sample from chambers_7, replicate 1

description: 10x Genomics 3' v2 chemistry


title: Stim TA, Aged DEX, 2

value: Skeletal muscle (Tibialis anterior)

value: Stim


title: METTL1 knocked out colorectal cancer cell, m7G input RNA

value: METTL1 knocked out


title: LV2_2B, Left ventricle region 2B sample from chambers_2, replicate 1

description: 10x Genomics 3' v2 chemistry


title: Stim TA, Aged DEX, 3

value: Aged

value: WT

value: Dexamethasone


title: liver metastatic colorectal cancer tissue, m5C input RNA


title: wild type sw480 colorectal cancer cell, m7G input RNA

value: colorectal cancer cell

value: wild type sw480


title: Stim TA, Aged DEX, 6


title: LV1_2B, Left ventricle region 2B sample from chambers_1, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 2B

value: 17 week


title: Non-Stim TA, Aged DEX, 4

value: Non-Stim


title: Non-Stim TA, Aged DEX, 6


title: LV4_2B, Left ventricle region 2B sample from chambers_4, replicate 1

description: 10x Genomics 3' v2 chemistry

value: male

value: Wistar


title: ChIPseq Input 0h Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: ChIPseq Input 1h Rep1

value: 4-hydroxytamoxifen 1h


title: Non-Stim TA, Aged DEX, 5


title: SA1b, Sinoatrial node sample from sa_1, replicate b

description: 10x Genomics 3' v2 chemistry

value: Sinoatrial node

value: healthy


title: Non-Stim TA, Aged DEX, 3

value: Skeletal muscle (Tibialis anterior)


title: LV14_3B, Left ventricle region 3B sample from chambers_14, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Left ventricle region 3B

value: Left ventricle region 3B


title: primary colorectal cancer tissue, m5C input RNA

source_name: primary colorectal cancer tissue

value: primary colorectal cancer tissue

value: primary colorectal cancer


title: LV14_2C, Left ventricle region 2C sample from chambers_14, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Left ventricle region 2C

value: Left ventricle region 2C


title: primary colorectal cancer tissue, m5C sequencing


title: ChIPseq Ikaros 2h Rep1

value: 4-hydroxytamoxifen 2h

value: anti-HA Pierce 88836


title: LV14_2A, Left ventricle region 2A sample from chambers_14, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Left ventricle region 2A

value: Left ventricle region 2A


title: liver metastatic colorectal cancer tissue, m7G input RNA

value: liver metastatic colorectal cancer


title: ChIPseq Ikaros 30m Rep1

value: 4-hydroxytamoxifen 30m


title: ChIPseq Ikaros 1h Rep1


title: liver metastatic colorectal cancer tissue, m7G sequencing


title: ChIPseq Ikaros 0h Rep1


title: Non-Stim TA, Aged DEX, 2

value: Non-Stim

value: Aged

value: WT

value: Dexamethasone


title: LV14_1B, Left ventricle region 1B sample from chambers_14, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Left ventricle region 1B

value: Left ventricle region 1B

value: 17 week

value: male

value: Wistar


title: Non-Stim TA, Aged DEX, 1

value: Skeletal muscle (Tibialis anterior)


title: primary colorectal cancer tissue, m7G sequencing

value: primary colorectal cancer tissue


title: ChIPseq H3K27ac 2h Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2

value: H3K27ac Active Motif 39133


title: Stim TA, Aged Vehicle, 6

value: Stim

value: Vehicle


title: LV13_2C, Left ventricle region 2C sample from chambers_13, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 2C

value: healthy


title: LV13_2A, Left ventricle region 2A sample from chambers_13, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 2A


title: Stim TA, Aged Vehicle, 4

value: Aged


title: ChIPseq H3K27ac 30m Rep1

value: 4-hydroxytamoxifen 30m


title: LV13_3B, Left ventricle region 3B sample from chambers_13, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 3B


title: LV13_1B, Left ventricle region 1B sample from chambers_13, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 1B


title: primary colorectal cancer tissue, m7G input RNA

value: primary colorectal cancer


title: Stim TA, Aged Vehicle, 2

value: WT


title: liver metastatic colorectal cancer tissue, m1A input RNA

value: liver metastatic colorectal cancer


title: Stim TA, Aged Vehicle, 3

value: Skeletal muscle (Tibialis anterior)


title: LV11_3B, Left ventricle region 3B sample from chambers_11, replicate 1

description: 10x Genomics 3' v2 chemistry

value: 17 week

value: male

value: Wistar


title: Stim TA, Aged Vehicle, 5


title: liver metastatic colorectal cancer tissue, m1A sequencing


title: primary colorectal cancer tissue, m1A input RNA

value: primary colorectal cancer tissue


title: Stim TA, Aged Vehicle, 1

value: Stim


title: ChIPseq CHD4 0h Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2

value: CHD4 Abcam ab70469


title: LV11_1B, Left ventricle region 1B sample from chambers_11, replicate 1

description: 10x Genomics 3' v2 chemistry

value: healthy


title: primary colorectal cancer tissue, m1A sequencing


title: ChIPseq H3K27ac 0h Rep1

value: H3K27ac Active Motif 39133


title: ChIPseq CHD4 30m Rep1

value: 4-hydroxytamoxifen 30m


title: ChIPseq CHD4 2h Rep1

value: 4-hydroxytamoxifen 2h


title: primary colorectal cancer tissue, m6A input RNA


title: RNAseq 30min Rep2

data_processing:
Sequence data was processed using RTA version 2.4.11 under NextSeq500, with default filter and quality settings for basecalling. The reads were demultiplexed with CASAVA 2.17 (allowing 0 mismatches).
Paired-end 75bp sequencing reads were aligned against mouse genome (GRCm38) with nextflow nfcore/rnaseq:1.3 using star as aligner.
Gene based read counts were obtained using featureCounts function from Rsubread Bioconductor package and intronic reads were also included in the gene level quantification.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw gene counts for each samples

molecule: nuclear RNA

extract_protocol:
Subcellular fractionation and isolation of chromatin bound nascent RNAs was adapted from Nesterova et al 2019. Briefly, cell nuclei were isolated in lysis buffer with a sucrose cushion. Nuclei were then lysed in a urea buffer, and the insoluble pellet containing the chromatin fraction and associated nascent RNAs was purified using the Zymo Direct-zol RNA Miniprep Kit (R2051).
Library prep was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S) using the rRNA depletion (E6310L) workflow

treatment_protocol: 500nM of 4-hydroxytamoxifen (Sigma-Aldrich H7904-5MG) was used to induce nuclear translocation of Ikaros.


title: Non-Stim TA, Aged Vehicle, 2

value: Non-Stim

value: Aged

value: Vehicle


title: Mechanistic elucidation of human pancreatic acinar development_Tag

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

country: Japan

institute: Kyoto University

description: Tag

data_processing:
After adapter trimming and quanity filtering, base composition of sequencing data was analyzed by FastQC-v0.11.9.
Adapter trimming of sequencing data was performed by using Cutadapt 3.4.
Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.15.0.
Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.8.
Associated cDNA reads were mapped to reference RNA (build GRCh38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 2 -N 1 --very-sensitive-local –norc –seed 656565 –reorder.
Cell barcode information of each read were added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted by using mawk.
Resulted count data was converted to genes x cells matrix file and inflection threshold of the knee-plot was detected by using DropletUtils package in R version 4.1.2 (2021-11-01).
Background beads by using emptyDrops formula in DropletUtils package were further estimated.
Assembly: GRCh38 releases-101
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample
Supplementary files format and content: seq_Supplemantary Sheet.xlsx: contains tag-specific metadata

source_name: Mechanistic elucidation of human pancreatic acinar development using single cell transcriptome analysis on a human iPSC differentiation model_Tag

extract_protocol: Pooled single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacture’s instructions. 20000 cells were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow for cDNA and/or hashtag library amplification (Shichino S., bioRxiv, 2021). 150 ng of amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.

value: cell line

value: Induced pluripotent stem cells

value: WT

value: pancreatic differentiation


title: liver metastatic colorectal cancer tissue, m6A sequencing

value: liver metastatic colorectal cancer


title: RNAseq 30min Rep1


title: ChIPseq CHD4 1h Rep1

value: 4-hydroxytamoxifen 1h


title: ChIPseq H3K27ac 1h Rep1


title: LA6, Left atrium sample from chambers_6, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Left atrium

value: Left atrium

value: 17 week

value: male

value: Wistar


title: Non-Stim TA, Aged Vehicle, 6

value: Skeletal muscle (Tibialis anterior)


title: RNAseq 6hr Rep2

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: Non-Stim TA, Aged Vehicle, 4


title: Aorta7, Aorta sample from aorta_7, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Aorta

value: healthy


title: LV11_2A, Left ventricle region 2A sample from chambers_11, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 2A


title: liver metastatic colorectal cancer tissue, m6A input RNA


title: Pre-treatment ER+/HER2− metastatic breast cancer A01014

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCh38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (v35)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Breast cancer

extract_protocol:
Total RNA was extracted from tissue using an NucleoSpin RNA kit (MACHEREY-NAGEL, Düren, Germany)
Illumina TruSeq Stranded mRNA kit

value: Breast cancer

value: metastatic breast cancer

value: PR


title: Non-Stim TA, Aged Vehicle, 5

value: Non-Stim

value: Aged

value: WT

value: Vehicle


title: RNAseq 24hr Rep1


title: RNAseq 21hr Rep2


title: AV2d, Atrioventricular node sample from av_2, replicate d

description: 10x Genomics 3' v2 chemistry

source_name: Atrioventricular node

value: Atrioventricular node


title: primary colorectal cancer tissue, m6A sequencing

value: primary colorectal cancer tissue

value: primary colorectal cancer


title: LV11_2C, Left ventricle region 2C sample from chambers_11, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left ventricle region 2C

value: 17 week

value: male

value: Wistar


title: RNAseq 6hr Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: Non-Stim TA, Aged Vehicle, 3

value: Skeletal muscle (Tibialis anterior)


title: LA8, Left atrium sample from chambers_8, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Left atrium

value: healthy


title: LA3, Left atrium sample from chambers_3, replicate 1

description: 10x Genomics 3' v2 chemistry


title: RNAseq 2hr Rep2


title: Mechanistic elucidation of human pancreatic acinar development_cDNA

description: cDNA

source_name: Mechanistic elucidation of human pancreatic acinar development using single cell transcriptome analysis on a human iPSC differentiation model_cDNA

value: cell line

value: Induced pluripotent stem cells

value: pancreatic differentiation


title: LA2, Left atrium sample from chambers_2, replicate 1

description: 10x Genomics 3' v2 chemistry


title: Pre-treatment ER+/HER2− metastatic breast cancer A01015

value: Breast cancer

value: metastatic breast cancer

value: SD


title: Stim TA, Young DEX, 6

value: Stim

value: Young

value: WT

value: Dexamethasone


title: Stim TA, Young DEX, 5


title: Stim TA, Young DEX, 4


title: Aorta5, Aorta sample from aorta_5, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Aorta

value: 17 week

value: male


title: Non-Stim TA, Aged Vehicle, 1

value: Non-Stim

value: Aged

value: Vehicle


title: Pre-treatment ER+/HER2− metastatic breast cancer A01013


title: RNAseq 21hr Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: RNAseq 24hr Rep2


title: Pre-treatment ER+/HER2− metastatic breast cancer A01011

value: PR


title: RNAseq 18hr Rep1


title: Pre-treatment ER+/HER2− metastatic breast cancer A01004


title: Stim TA, Young DEX, 3

value: Skeletal muscle (Tibialis anterior)


title: AV2c, Atrioventricular node sample from av_2, replicate c

description: 10x Genomics 3' v2 chemistry

value: Atrioventricular node

value: Wistar

value: healthy


title: AV1b, Atrioventricular node sample from av_1, replicate b

description: 10x Genomics 3' v2 chemistry


title: RNAseq 18hr Rep2


title: Pre-treatment ER+/HER2− metastatic breast cancer A01008

value: Breast cancer

value: metastatic breast cancer

value: PD


title: Stim TA, Young DEX, 2

value: Stim

value: Young

value: WT

value: Dexamethasone


title: AV2b, Atrioventricular node sample from av_2, replicate b

description: 10x Genomics 3' v2 chemistry

value: 17 week

value: male


title: Non-Stim TA, Young DEX, 6

value: Non-Stim


title: Pre-treatment ER+/HER2− metastatic breast cancer A01007


title: Stim TA, Young DEX, 1


title: Pre-treatment ER+/HER2− metastatic breast cancer A01006

value: SD


title: RNAseq 2hr Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: AV1d, Atrioventricular node sample from av_1, replicate d

description: 10x Genomics 3' v2 chemistry


title: Pre-treatment ER+/HER2− metastatic breast cancer A01005


title: Non-Stim TA, Young DEX, 5

value: Skeletal muscle (Tibialis anterior)


title: AV1c, Atrioventricular node sample from av_1, replicate c

description: 10x Genomics 3' v2 chemistry

value: Atrioventricular node


title: Non-Stim TA, Young DEX, 1


title: Non-Stim TA, Young DEX, 3


title: Non-Stim TA, Young DEX, 4


title: AV2a, Atrioventricular node sample from av_2, replicate a

description: 10x Genomics 3' v2 chemistry

value: Wistar


title: Pre-treatment ER+/HER2− metastatic breast cancer A01003

value: PR


title: RNAseq 15hr Rep2


title: AV1a, Atrioventricular node sample from av_1, replicate a

description: 10x Genomics 3' v2 chemistry

value: healthy


title: RNAseq 1hr Rep2


title: Pre-treatment ER+/HER2− metastatic breast cancer A01002

value: Breast cancer

value: metastatic breast cancer


title: RVSMC, H4K5ac_SIANK2

city: Beijing

first: Hao

last: Wu

address: Xueyuan Road 38

institute: Peking University

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program
Reads distributions (from bigwig) across peaks are presented as an average plot (average of reads signals across all peaks). The deeptools tool is used for this analysis.
Assembly: Galaxy_UCSC_Rat
Supplementary files format and content: bigWig, peaks
Library strategy: CUT&Tag

source_name: primary vascular smooth muscle cell

extract_protocol:
VSMCs were collected, incubated, and bound to concanavalin A-coated magnetic beads. Then, VSMCs were resuspended, incubated with normal IgG, H3K23ac, H3K27ac, or H4K5ac antibodies overnight at 4 °C, and then incubated with secondary antibodies. The samples were incubated with pA/G-Tnp for transposition. After tagmentation, DNA was isolated, amplified, and purified to construct a library.
CUT&Tag was performed with a Hyperactive Universal CUT&Tag Assay Kit for Illumina (pA/G-Tnp) (TD903-01, Vazyme Biotech) according to the manufacturer’s instructions.

value: primary vascular smooth muscle cell


title: RNAseq 15hr Rep1


title: RVSMC, H4K5ac_SIANK1


title: Pre-treatment ER+/HER2− metastatic breast cancer A01001


title: RNAseq 12hr Rep2


title: Non-Stim TA, Young DEX, 2

value: Young


title: Stim TA, Young Vehicle, 4

value: Stim

value: WT

value: Vehicle


title: Diff LUHMES, TG, YY1_C4

city: Dallas

first: Peter

middle: M

last: Douglas

state: Tx

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

data_processing:
FASTQ files of the raw sequencing results were then uploaded to Galaxy and trimmed using TRIMMOMATIC 0.38.1 and the following command: ILLUMINACLIP:/usr/local/share/ trimmomatic-0.38-1/adapters/TruSeq2-PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25. Trimmed reads were then mapped to human genome hg38 using Bowtie2 and the following command: bowtie2 –local --very-fast-local --no-unal -hg38 --no-mixed --no-discordant -I 10 -X 500. Alignment BAM files were then sorted and merged with their duplicate using Samtools. Bigwig coverage files were then generated using bamCoverage (deeptools71 3.5.1) and normalized to each other using counts per million.
Assembly: Homo Sapiens (hg38)
Supplementary files format and content: CPM normalized coverages are provided as BIGWIG files
Library strategy: CUT&RUN

source_name: LUHMES

growth_protocol: LUHMES cells were differentiated using standard DIFF media for 6 days.

extract_protocol:
Differentiated LUHMES cells were treated with 10 nM TG or DMSO and collected 24 hours later. Cells were lifted via trypsinization, and triplicate conditions were mixed and counted. All following steps were done in duplicate where each duplicate was a pool of 3 separate replicates. Per sample 100,000 cells were aliquoted and washed two times using 1x wash buffer (+ spermidine and protease inhibitor cocktail). Cells were then immobilized with concanavalin A beads and incubated overnight at 4ºC with the primary antibody at a 1:50 dilution for both anti-H3K4me3 (Cell Signaling Technology C42D8) and anti-YY1 (Cell Signaling Technology D5D9Z).
The following day, pAG-MNase mixture was added and incubated at 4ºC for 1 hour. After 3 washes with digitonin wash buffer cells were cooled on ice for 5 minutes and pAG-MNase was activated with cold calcium chloride and incubated at 4ºC for 30-minute. 1x stop buffer was added and diffused DNA-samples were purified using DNA spin columns. Input samples were prepared via sonication using 6x 15 seconds pulses with 30 seconds pauses. Input fragment size of ~300-400 bp was confirmed using agarose gel electrophoresis. Enriched DNA samples were then submitted for library prep and paired-end sequencing done by Novogene (Sacramento, CA).
Novogene library prep for CUT&RUN/ChIP-seq

treatment_protocol: Cells were treated with DMSO or 10 nM thapsigargin for 30 minutes and collected 24 hours later.

value: LUHMES

value: Neurons

tag: target

value: Yin Yang 1 (YY1)

tag: antibody

value: TG

tag: biological replicate

value: Biol rep 2


title: RNAseq 12hr Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: AVN3_b, Atrioventricular node sample from av_3, replicate b

description: 10x Genomics 3' v2 chemistry

value: Atrioventricular node

value: 17 week

value: male

value: Wistar


title: RNAseq 0hr Rep2


title: Diff LUHMES, TG, YY1_C3

value: Biol rep 1


title: Stim TA, Young Vehicle, 6

value: Skeletal muscle (Tibialis anterior)


title: RVSMC, H4K5ac_NC2

value: primary vascular smooth muscle cell


title: Stim TA, Young Vehicle, 5

value: Stim

value: Young


title: Diff LUHMES, TG, H3K4me3_B4

value: WT


title: RNAseq 1hr Rep1


title: Stim TA, Young Vehicle, 2

value: Vehicle


title: ATACseq 30min Rep2

data_processing:
Paired-end 76 bp ATAC-seq sequencing were proceeded using RTA version 2.4.11 under NextSeq500, with default filter and quality settings for basecalling. The reads were demultiplexed with bcl2fastq 2.20.0, allowing 0 mismatches.
After demultiplexing, raw reads were processed with Nextflow nf-core/atacseq:1.0.0 (Ewels et al., 2020) with parameters: '--genome GRCm38 -profile conda' using bwa (v0.7.17; Li and Durbin, 2009) aligner.
Processed BAM files from this pipeline was taken forward to perform downstream analysis. ATACshift mode of deeptools (v. 2.3.5; Ramírez et al., 2016) alignmentSieve function was used to shift the reads with parameters: '--minFragmentLength 0 --maxFragmentLength 120' for Nucleosome Free Region (NFR – fragment length less than 120 bp). The filtered bam files were further processed with deeptools alignmentSieve function with parameters: '--ATACshift --minFragmentLength 180' for Nucleosome Bound Region (NBR – fragment length more than 180 bp).
We used the NFR bin for the downstream analysis. Peak calling was proceeded with MACS2 (v2.1.2) callpeak function with parameters: '-f BAMPE -g mm' (Zhang et al., 2008). Consensus peaks throughout different time points were defined by using nf-core/atacseq.
Peaks overlapped with the black list mm10 v1 (Amemiya et al., 2019; ENCODE Project Consortium, 2012) were removed from downstream analysis.
BigWig files were generated based on BAM files from the nucleosome free regions (NFR). Scale factors for each BAM file were calculated beforehand using the formula 1000000 divided by the number of mapped reads obtained from the Samtools (v.1.9; Danecek et al., 2021) flagstat function. genomeCoverageBed function from Bedtools (v2.27.1; Quinlan and Hall, 2010) was applied with command: 'genomeCoverageBed -ibam $outDir/${SAMPLE}.mLb.ss.sorted.NFR.bam  -bg -scale $SCALE_FACTOR -pc | sort -k1,1 -k2,2n > $outDir/bigwig_gcov/${SAMPLE}.mLb.ss.sorted.NFR.bedGraph'. Followed by deploying bedGraphToBigWig (Kent et al., 2010) with the following command: 'bedGraphToBigWig $outDir/bigwig_gcov/${SAMPLE}.mLb.ss.sorted.NFR.bedGraph $gsizes $outDir/bigwig_gcov/${SAMPLE}.mLb.ss.sorted.NFR.bigWig'
Assembly: GRCm38
Supplementary files format and content: bigwig
Supplementary files format and content: peakfile

growth_protocol: B3 pre-B cells were maintained in IMDM with 10% heat inactivated FBS and 1x Pen/Strep (Gibco™ 15070063) and 1x L-glutamine (Gibco™ 25030081) between 0.5 – 2 million/ml.

extract_protocol:
ATAC-seq was performed based on the omni-ATAC protocol. Briefly, for each sample 50 000 cells were lysed (10mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween, 0.01% Digitonin), and nuclei were tagmented with 3 ul of Ilumina Tn5 enzyme (Illumina, catalog # 15027865) in TD Buffer with 0.01% Tween and 0.01% Digitonin for 30 minutes at 37°C.
DNA was purified using the Zymo DNA Clean and Concentrator and libraries were generated with 7 cycles of PCR with index primers described in the original Buenrostro et al. ATAC-seq protocol. Clean-up was performed with Ampure beads and quantification and quality control of libraries was performed using DNA Qubit and HS DNA Bioanalyser.

treatment_protocol: 500nM of 4-hydroxytamoxifen (Sigma-Aldrich H7904-5MG) was used to induce nuclear translocation of Ikaros for 30 minutes, 1 h, and 2h

value: 4-hydroxytamoxifen 30m


title: Stim TA, Young Vehicle, 3


title: Diff LUHMES, TG, H3K4me3_B3

value: LUHMES

value: Neurons


title: RVSMC, H4K5ac_NC1


title: RNAseq 0hr Rep1


title: RVSMC, H3K27ac_SIANK1


title: AVN3_a, Atrioventricular node sample from av_3, replicate a

description: 10x Genomics 3' v2 chemistry

value: healthy


title: ATACseq 30min Rep1

value: mouse pre-B


title: RVSMC, H3K27ac_SIANK2


title: Diff LUHMES, DMSO, H3K4me3_B2

value: DMSO

value: Biol rep 2


title: Stim TA, Young Vehicle, 1


title: ATACseq 2hr Rep2

value: B3 transduced with Ikaros-ERt2

value: 4-hydroxytamoxifen 2h


title: Diff LUHMES, DMSO, YY1_C2

value: Yin Yang 1 (YY1)


title: Non-Stim TA, Young Vehicle, 6

value: Non-Stim


title: RVSMC, H3K27ac_NC1


title: Diff LUHMES, DMSO, YY1_C1

value: Biol rep 1


title: RVSMC, H3K27ac_NC2

value: primary vascular smooth muscle cell


title: ATACseq 2hr Rep1


title: Diff LUHMES, DMSO, H3K4me3_B1


title: Non-Stim TA, Young Vehicle, 4

value: Skeletal muscle (Tibialis anterior)


title: ATACseq 1hr Rep2

value: 4-hydroxytamoxifen 1h


title: Diff LUHMES, TG, input_A3

value: WT

value: Input

value: TG


title: RVSMC, H3K23ac_SIANK2


title: ATACseq 1hr Rep1


title: Non-Stim TA, Young Vehicle, 3

value: Young

value: Vehicle


title: RVSMC, H3K23ac_SIANK1


title: Non-Stim TA, Young Vehicle, 2


title: RVSMC, H3K23ac_NC2


title: Diff LUHMES, DMSO, input_A1

value: LUHMES

value: Neurons


title: Non-Stim TA, Young Vehicle, 1


title: ATACseq 0hr Rep2

value: mouse pre-B


title: ATACseq 0hr Rep1


title: Diff LUHMES, TG, input_A4

value: Biol rep 2


title: RVSMC, siRNA_ANK2

data_processing:
Analysis of differential expression genes (DEGs) was performed using the DESeq2 software.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mRatBN7.2
Supplementary files format and content: txt

extract_protocol:
Total RNA of VSMCs was isolated using the GeneJet RNA Purification Kit (K0732, Thermo Scientific) and 1.3 μg RNA was used to generate a cDNA library
RNA libraries for RNA-seq were prepared using RNA Library Prep Kit for Illumina following munufacturer‘s protocols


title: S1D6_H3K4me3_rep2,CUT&Tag

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

data_processing:
*library strategy: Cut&Tag
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was calculated using MACS2 while peak calling.
Assembly: hg19
Supplementary files format and content: .bw file containing merged signal intensity of each sample

source_name: induced from hADSC

extract_protocol:
Approximately 1 x 10^5 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol. Briefly, harvest fresh cultures and count 1 x 10^5 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4C. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 ℃ for 1 h and then performed DNA extraction with DNA extraction beads.
For extracted DNA, combinate i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and Illumina sequencing.

value: induced from hADSC


title: Diff LUHMES, TG, 24hr, rep3

data_processing:
raw reads were trimmed and mapped using CLC genomics workbench (v23) default settings. CLC was also used for statistical analysis to idenify DEGs and generate expression browsers.
Assembly: Homo Sapiens (hg38)
Supplementary files format and content: Excel file containing RPKMs and statistical tests

extract_protocol:
RNA was extracted with the Invitrogen Purelink RNA kit using Trizol
mRNA library preparation (poly A enrichment)

tag: time point

value: 24 hours

value: Biol rep 3


title: Non-Stim TA, Young Vehicle, 5

tag: tissue

value: Non-Stim


title: Diff LUHMES, TG, 24hr, rep4

value: Biol rep 4


title: RVSMC, H3K23ac_NC1

value: primary vascular smooth muscle cell


title: S1D6_H3K4me3_rep1,CUT&Tag


title: RVSMC, siRNA_ANK3


title: S1D6_H3K4me1_rep2,CUT&Tag


title: Diff LUHMES, TG, 24hr, rep1

value: Biol rep 1


title: RVSMC, siRNA_ANK1


title: LFDxC_XX_-+_3

city: Munich

first: Tim

last: Hasenbein

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University Munich

data_processing:
Paired-end RNA-seq data of spleen samples were aligned using STAR. Reads characterized by intron sizes exceeding 100000, multimappers, and alignments containing non-canonical junctions were removed prior to subsequent analysis. Uniquely aligned reads were quantified using htseq-count and the –stranded reverse flag.
Assembly: mm10
Supplementary files format and content: Text file including the raw read counts for each sample

source_name: Spleen

extract_protocol:
Spleens were harvested from 6-week-old F1 hybrid mice (BL6 x CAST) and snap-frozen in liquid nitrogen. The GentleMACS Dissociator (program RNA_02_01) was used to homogenize tissues in 1 ml TRIzol per 50-100 mg sample. RNA isolation was conducted as described in the manufacturer's instructions (Invitrogen, TRIzol Reagent, Cat. #15596018) using 1 ml of the sample solution.
RNA-seq libraries were constructed with 100 ng of RNA and Illumina's Stranded mRNA Prep Ligation Kit. The Agilent TapeStation System was used to assess the concentration and fragment length of the libraries. Sequencing was performed using a NovaSeq6000 50bp paired-end sequencing.

value: Spleen

value: 6 weeks

value: F


title: Diff LUHMES, DMSO, input_A2

value: WT

value: Input

value: DMSO


title: RVSMC, Negative_control3


title: Diff LUHMES, DMSO, 24hr, rep4

value: LUHMES


title: LFDxC_XX_++_3


title: LFDxC_XX_-+_2


title: S1D6_H3K27me3_rep1,CUT&Tag


title: Diff LUHMES, DMSO, 24hr, rep2

value: Neurons


title: LFDxC_XX_-+_1


title: RVSMC, Negative_control1


title: S1D6_H3K27ac_rep2,CUT&Tag


title: Diff LUHMES, TG, 24hr, rep2

value: TG


title: Diff LUHMES, DMSO, 24hr, rep1


title: GNPTAB KO Clone E4 4

city: Greenwood

first: Heather

last: Flanagan-Steet

state: South Carolina

address: 113 Gregor Mendel Cir.

department: J.C. Self Research Institute

institute: Greenwood Genetic Center

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCh38
Supplementary files format and content: csv text file contains raw gene hit counts for each sample

source_name: Daoy

growth_protocol: All cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% FBS, Pen/Strep, 2mM L-glutamine in humidified CO2 incubator

extract_protocol:
Cells were washed twice with ice cold PBS buffer, scraped and collected in 1.5 mL TRIzol reagent (Thermo), and flash frozen in liquid nitrogen. Frozen samples were shipped on dry ice to Azenta Life Sciences to complete RNA extraction, library extraction, and sequencing.
Libraries for RNA-seq were generated by Azenta Life Sciences. In short, mRNA was selected through poly-A enrichment, fragmented, and randomly primed. First and second strand cDNA synthesis was performed, followed by end repair, 5' phosphorylation, and dA-tailing. Finally, adapters were ligated and enriched via PCR prior to sequencing.

treatment_protocol: The GNPTAB knockout cell clones were generated by Synthego (Redwood City, California USA) using DAOY medulloblastoma cells using a single guide RNA (CACGTAGAGCCCATACCTGT).  Two cell clones (labeled D3 and E4) were identified following Sanger sequencing and shown to bear compound heterozygous alterations in GNPTAB, with clone D3 carrying multiple deletions (-2/-2/-1 bp)[934-935delCC + 933-934delTC + 933delT], while clone E4 harbors a single-nucleotide insertion and a single nucleotide deletion (-1/+1 bp) [934delC + 933_934insN]

value: Daoy

value: GNPTAB-KO


title: Diff LUHMES, TG, 6hr, rep4

value: 6 hours


title: LFDxC_XX_++_1


title: S1D6_H3K4me1_rep1,CUT&Tag

value: induced from hADSC


title: GNPTAB KO Clone E4 2


title: S1D6_H3K27ac_rep1,CUT&Tag


title: HTO

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: 10X genomics

data_processing:
Viable cells were identified onthe basis of library size andcomplexity,whereas cells with >20% oftranscripts derived from mitochondria were excluded from further analysis.After mitochondrial and doublet cleanup, raw count matrix was normalized using scran. The Louvain algorithm with k = 30 was used to perform unbiased clustering and Euclidean distance was used as the metric to construct the nearest neighbor graph81. Normalized data was next imputed using MAGIC.
Assembly: mm10
Supplementary files format and content: 2637_Organs_NK_Fasted_IGO_12068_25_dense.csv contains raw cell-gene count matrix
Supplementary files format and content: tag-list.csv contains information regarding treatment groups and their associated HTOs
Supplementary files format and content: final-classification.tsv.gz contains HTO-cell information

source_name: Spleen, Tumor, Bone Marrow

extract_protocol:
Bone marrow was flushed using PBS + 2% FCS, then subjcted to red blood cell lysis before sorting. Spleen tissue was passed through 100uM strainers in PBS + 2% FCS, then subjcted to red blood cell lysis before sorting.Tumor tissues were digested in DNase I  and Collagenase 4 at 37C for 30 minutes then passed through a 100uM strainer before sorting. Cell sorting was performed on Aria II cytometers (BDBiosciences). NK cells were defined as Lineage- NK1.1+ CD49b+.
Upon cell sorting and HTO staining, NK cells from each condition were mixed at equal ratios, washed once with PBS containing 1% BSA to a final concentration of 700-1,300 cells per ul. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Around 15,000 cells were targeted. Samples were multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO) following previously published protocol79. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using seqc (https://github.com/dpeerlab/seqc).

treatment_protocol: Mice were injected subcutaneously with MC38 cells and subjected to either ad libitum diet or cyclic fasting diet (see Method) until the endpoint of experiment at which point tissue of interest were harvested and NK cells were isolated from the indicated tissues. Please refer to tag_list.csv for treatment group and associated HTO.

value: Spleen, Tumor, Bone Marrow

value: NK cells

value: 12 weeks


title: S1D6-WA-2_H3K4me3_rep2,CUT&Tag


title: S1D6-WA-2_H3K4me3_rep1,CUT&Tag


title: aortic smooth muscle cells library2, HTO

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
HTO
E12_filtered_feature_bc_matrix.tar.gz
E12_molecule_info.h5

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.3.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: other

source_name: Aorta

extract_protocol:
B6.Ldlr-/- SMMHC CreERT2Rosafl-mT-stop-fl-mG mice were each i.p. injected with 1 mg Tamoxifen (solved in peanut oil) per day for 5 consecutive days. In this reporter strain, the red fluorescent protein tomato is ubiquitously expressed at baseline and switches to enhanced green fluorescent protein (GFP+) in all cells that have undergone estrogen receptor-dependent Cre-mediated recombination as well as their progeny. 5 days after the last injection, mice were fed a HFD for 3 months and treated with an irrelevant isotype control antibody (250 µg rat IgG2b anti-Phyt1, clone AFRC Mac51, i.p. once weekly) or an CD8+ T cell depleting antibody (250 µg anti-CD8 antibody , clone YTS156.7.7, i.p. once weekly) for 1 month before sacrifice. After euthanasia, arteries were flushed with PBS, aortas were harvested and aortas were separately processed. Aortas were minced and digested for 45 min at 37°C in RPMI-1640 containing 4 U/ml liberase, 60 U/ml hyaluronidase and 120 U/ml DNase I10. Digested aortas were passed through a 70 µm cell strainer to obtain single cell suspension. Each sample was labeled with a specific hashtag antibody (Hashtag #8-11: isotype treated control, Hashtag 12-15: CD8+ T cell depleted, final concentration 1:50, Biolegend) by incubation for 25 min at 4°C. After washing the cells twice, control and CD8+ T cell depleted samples were each pooled and stained with Dapi (dilution 1:1000). Total viable GFP+ cells were sorted in PBS containing 0.04 % BSA using FACS Aria III (BD Bioscience) with a 100 µm nozzle. For each group 15,000 cells were loaded into the 10x Genomics Chromium at a concentration of 1000 cells/µl and cell sequencing was performed as described above.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Aorta

value: viable cells

value: CD8+ T cell depletion


title: Diff LUHMES, TG, 6hr, rep3

value: Biol rep 3


title: GNPTAB KO Clone E4 3


title: aortic smooth muscle cells library2, GEX

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
E12_filtered_feature_bc_matrix.tar.gz
E12_molecule_info.h5


title: RVSMC, Negative_control2

value: primary vascular smooth muscle cell


title: GNPTAB KO Clone E4 1


title: Diff LUHMES, DMSO, 24hr, rep3

value: WT

value: 24 hours


title: Diff LUHMES, TG, 6hr, rep2

value: LUHMES

value: Biol rep 2


title: NK_Tissues_Tumor_Fasting

description:
NK_AdLib_versus_CFD
10X genomics


title: aortic smooth muscle cells library1, HTO

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
HTO
E11_filtered_feature_bc_matrix.tar.gz
E11_molecule_info.h5

value: isotype treatment


title: Diff LUHMES, TG, 6hr, rep1

value: Neurons

value: TG

value: Biol rep 1


title: GNPTAB KO Clone D3 4

value: Daoy

value: GNPTAB-KO


title: S1D6-WA-2_H3K4me1_rep1,CUT&Tag

value: induced from hADSC


title: aortic smooth muscle cells library1, GEX

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
E11_filtered_feature_bc_matrix.tar.gz
E11_molecule_info.h5


title: GNPTAB KO Clone D3 3


title: Diff LUHMES, DMSO, 6hr, rep4

value: 6 hours

value: DMSO

value: Biol rep 4


title: S1D6-WA-2_H3K27me3_rep2,CUT&Tag


title: GNPTAB KO Clone D3 1


title: Diff LUHMES, DMSO, 6hr, rep2


title: Parental Daoy 4


title: WT-ALF-1

city: Changsha

first: Yan

last: Huang

address: Xiangya road

institute: Xiangya hospital

description: 10x Genomics

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28bp for read 1 and 91bp for read2).
Raw scRNA-seq data were analyzed using Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) . Transcripts were aligned to the 10X pre-built mouse reference (refdata-gex-mm10-2020-A) .
Assembly: mm10
Supplementary files format and content: Tab-separeted values files and matrix files

source_name: liver

extract_protocol:
For the quality check and counting of single cell suspension, the cell survival rate is generally above 85%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. The system is operated on the machine. GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection.
The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA.

value: liver

value: hepatic parenchymal and non-parenchymal cells

value: D-galactosamine + LPS


title: WT-NC-1

description: 10x Genomics

value: WT

value: PBS


title: Diff LUHMES, DMSO, 6hr, rep1

value: LUHMES


title: Parental Daoy 3


title: S1D6-WA-2_H3K4me1_rep2,CUT&Tag


title: Diff LUHMES, DMSO, 6hr, rep3

value: Biol rep 3


title: S1D6-WA-2_H3K27ac_rep1,CUT&Tag


title: S1D6-WA-2_H3K27me3_rep1,CUT&Tag


title: S1D4_H3K4me3_rep2,CUT&Tag


title: S1D6-WA-2_H3K27ac_rep2,CUT&Tag


title: PL-ALF-2

description: 10x Genomics

value: Pkm myeloid selective knockout


title: WT-NC-2

description: 10x Genomics


title: Diff LUHMES, TG, 3hr, rep3

value: Neurons

value: 3 hours


title: Parental Daoy 2


title: Diff LUHMES, TG, 3hr, rep2

value: TG

value: Biol rep 2


title: WT-ALF-2

description: 10x Genomics


title: S1D4_H3K4me1_rep2,CUT&Tag


title: PL-NC-2

description: 10x Genomics


title: Random intron library, bulk RNA, rep5

first: Emma

middle: Joanna Katharina

last: Kowal

email: emmajkkowal@gmail.com, ejkk@mit.edu

address: 21 St Mary Road Apt 2

department: Biology

institute: MIT

description: amplicon generated by gene-specific RT-PCR

data_processing:
Fastq files were analyzed with custom python scripts to extract sample id, reporter gene, barcode and splicing status of each read and summed to totals per sample per barcode. Reads were filtered to those with an exact or close match to expected sample, reporter, and barcode sequences, and otherwise discarded.
Assembly: N/A
Supplementary files format and content: tab-delimited text file includes raw read counts for spliced GFP, unspliced GFP, and dTomato, for each barcode and each bulk RNA sample
Supplementary files format and content: tab-delimited text file includes raw read counts for spliced GFP, unspliced GFP, and dTomato, for each barcode and each iterative FACS RNA sample
Supplementary files format and content: excel spreadsheet includes raw read counts for both replicates of polyU validation library, as well as intron and barcode sequences

source_name: HEK293T A2

growth_protocol: HEK293T A2 HILO-RMCE cells were grown in DMEM, with high glucose and pyruvate, supplemented with 10% fetal bovine serum and 10% penicillin/streptomycin. Cells were passaged 1:10 every 2-3 days by washing with PBS and treated with 0.25% Trypsin following standard procedures.

extract_protocol:
Total RNA was extracted from the pooled cells using Zymo Quick RNA Miniprep kits. For each RNA-seq sample, 2µg RNA extracted from the pooled random intron library was treated with Turbo DNase (Thermo) to remove any residual genomic DNA before further processing. We removed DNase using Zymo RNA clean & concentrate kit.
The amplicon library was constructed via gene-specific RT using SuperScript IV (Thermo) and two primers, complementary to the GFP and dTomato N-termini, respectively, in order to generate cDNA of the two reporter gene 5ʹUTRs only. After first strand synthesis we treated the samples with RNase cocktail (Thermo) to avoid interference with downstream PCR. The cDNA was amplified with 16 cycles of PCR using Q5 polymerase (NEB) and custom sample-specific indexing primers. The PCR product was purified by a double-sided SPRI purification, first removing genomic DNA with 0.55x volumes of beads and then adding 85µL beads for a final 1.4x volume.

treatment_protocol: The intron reporter cassettes were integrated by following authors’ recommendations: briefly, we first plated 1.5×105 cells per well on a 12-well plate coated with 0.1mg/mL Poly-d -Lysine. After culturing the cells for 24 hours in antibiotic-free media, the cells in each well were co-transfected using Lipofectamine 2000 with 500 ng of a reporter plasmid plus 0.5% wt/wt Cre recombinase vector pEM784 (Khandelia et al., 2011), and allowed them 24–48 hours before selection with 4–8µg/mL Puromycin for two weeks to ensure genomic integration. Cells were monitored throughout for surviving colony formation and wells were split and pooled before becoming overconfluent.

value: HEK293T A2

value: library integrated via recombinase-mediated cassette exchange


title: Diff LUHMES, TG, 3hr, rep1

value: Biol rep 1


title: S1D4_H3K4me1_rep1,CUT&Tag

value: induced from hADSC


title: GNPTAB KO Clone D3 2

value: Daoy

value: GNPTAB-KO


title: Diff LUHMES, DMSO, 3hr, rep4

value: DMSO

value: Biol rep 4


title: LFDxCast_TKO

description: 10x Genomics

data_processing:
Demultiplexing, alignment, and read count quantification of the raw sequencing data were performed using the cellranger multi pipeline (Cell Ranger 6.1.2 toolkit, 10x Genomics).
Processing of sample matrices was done using R and the Seurat 4.1.1 package
Allelic ratios of single cells and pseudobulk were calculated using the Allelome.PRO pipeline
Assembly: mm10
Supplementary files format and content: Excel (.xlsx) sheet reporting the calculated allelic ratios from pseudobulk for TKO and WT

source_name: adult spleen

extract_protocol:
Spleens were isolated on ice and homogenized between two glass slides. The single-cell suspension was filtered through 70 µm and 30 µm strainers and incubated with Fc-block for 15 min. Then cells were stained with Zombie Green (Viability, BioLegend) and a TER-119-PE antibody (Erythrocytes, ThermoFisher). After staining, cells were incubated with Cell Multiplexing Oligos (CMO, 10X) to add a specific barcode to each sample, allowing the pooling of all four samples in one 10X reaction. The Zombie Green-negative and TER-119-negative population were FACS-sorted and counted.
Single-cell library was generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing (10X).

value: adult spleen

value: 6 weeks

value: F


title: Random intron library, bulk RNA, rep3


title: PL-NC-1

description: 10x Genomics

value: liver

value: hepatic parenchymal and non-parenchymal cells

value: PBS


title: S1D4_H3K27me3_rep2,CUT&Tag


title: Random intron library, bulk RNA, rep4


title: Diff LUHMES, DMSO, 3hr, rep3

value: LUHMES

value: Neurons

value: WT

value: 3 hours

value: Biol rep 3


title: LFDxCast_WT

description: 10x Genomics


title: Diff LUHMES, DMSO, 3hr, rep2

value: Biol rep 2


title: MGPP3 cells, Volasertib resistant 3

first: Athanassios

last: Dovas

address: 1130St Nicholas Avenue

institute: Columbia University

data_processing:
Element AVITI sequencer with a 75-cycle high-output kit
The RNA-Seq data were aligned to the mm10 genome and RefSeq transcriptome annotation using Kallisto
Normalized data were generated using DEseq2 package in R
Assembly: mm10
Supplementary files format and content: tab delimited txt file contains raw counts for each sample

source_name: brain

extract_protocol:
RNA was extracted using RNAqueous phenol-free RNA isolation kit
Libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina from New England Biolabs (E7420S) according to the manufacturer’s protocol.

value: brain

value: proneural glioma

value: Volasertib


title: S1D4_H3K27ac_rep2,CUT&Tag

value: induced from hADSC


title: Random intron library, bulk RNA, rep1

value: HEK293T A2

value: library integrated via recombinase-mediated cassette exchange


title: PL-ALF-1

description: 10x Genomics

value: Pkm myeloid selective knockout

value: D-galactosamine + LPS


title: S1D4_H3K27me3_rep1,CUT&Tag


title: S1D4_H3K4me3_rep1,CUT&Tag


title: Diff LUHMES, DMSO, 3hr, rep1

value: DMSO

value: Biol rep 1


title: S1D4_H3K27ac_rep1,CUT&Tag


title: Random intron library, bulk RNA, rep2


title: HNSCC-KP_Batch1_UH24

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

description: human patient tongue squamous cell carcinoma, fresh frozen

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into Fastq format
The space ranger count function was used to align reads to the human genome (hg38) and with the microscopic slide image, to generate barcode/UMI counts, feature spot matrices, cluster data, and for gene expression analysis
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: Tab-separated values;Extracted Visium barcodes
Supplementary files format and content: features.tsv.gz: tab-separated values; Genomic features / genes
Supplementary files format and content: matrix.mtx.gz: MatrixMarket; Raw counts matrix
Supplementary files format and content: aggregation.csv: Aggregated copy of input
Supplementary files format and content: aggr_tissue_positions.csv: Aggregated tissue positions list
Supplementary files format and content: filtered_feature_bc_matrix.h5: combined file for barcodes, genomic features and raw count matrix

source_name: human tounge squamous cell carcinoma

extract_protocol:
Permeabilization was optimized according to the manufacturers’ instructions and a 10 min time was selected tocapturedPolyadenylated RNAson the ST arrays.
Polyadenylated RNAs captured on the ST arrays were resuspended in 1.2 ml of 0.1 N HCl for 5 min and reverse transcribed at 53°C for 45 min, followed by second-strand synthesis at 65°C for 5 min. After library preparation, samples were sequenced on a Novaseq 600 (Illumina).
Spatial transcriptomics

value: human tounge squamous cell carcinoma


title: MGPP3 cells, Volasertib resistant 2


title: R1-EdU-16hr-xMNase.rep2

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Paired-end reads were trimmed for adaptor sequence using cutadapt v4.3 with parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -n 2 -m 35 -q 30 –pairfilter = any
Trimed reads were mapped to mm10 using Bowtie2 v2.5.1  with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal.
Duplicates were marked using picard MarkDuplicates v2.27.5 with default parameters and removed using samtools view v1.17  with parameters: -f 2 -F 1024 -q 10.
Unique pair-end reads in bam format was converted to bed format grouped according to fragment length using a custom python script.
Mouse genome was segmented in to non-overlapping 100 kb bins. Then, within each genomic bin, fragment from each fragment length group were counted by annotateBed from bedtools v2.30.0. Fragment length groups used includes 50-80 bp, 80-90 bp, 90-100 bp, 100-110 bp, 110-120 bp, 120-130 bp, 130-140 bp, 140-150 bp, 150-160 bp, 160-250 bp or 50-140bp, 140-250bp. Then when a fragment length break point (X bp) is chosen, nucleosome wrapping score (NRS) is computed as the relative deviation between the number (a) of fragments within X~250 bp and the number (b) of fragments within 50~X bp, expressed as NRS(X) = (a-b)/(a+b). Then the genome-wide NRS was transformed as z-score to derive genome-wide nucleosome wrapping index (NRI).
Assembly: mm10
Supplementary files format and content: bigwig files of nucleosome wrapping index

source_name: Inner cell mass

growth_protocol: Mouse ES cells (R1) were cultured in the medium with 80% DMEM (EmbryoMax, SLM-220-B), 15% FBS (Hyclone, SH30070.03), Nonessential amino acids (EmbryoMax, TMS-001-C), 2-Mercaptoethanol (EmbryoMax, ES-007-E), L-glutamine (EmbryoMax, TMS-002-C), Nucleosides (EmbryoMax, ES-008-D), Pen/Strep (EmbryoMax, TMS-AB-2C) and 1000U/ml leukemia inhibitory factor (LIF) (ESGRO, ESG1107) in standard incubator with 5% CO2 at 37 °C.

extract_protocol:
Cell pellet of ~1x10^7 cells was resuspended in 1 mL nuclei extraction buffer (10 Mm Hepes, PH 7.5; 300 mM NaCl; 3 mM MgCl2; 0.5% IGEPAL CA-630; 0.1% SDS) with EDTA-free protease inhibitor cocktail (Roch, 05892791001) and incubate on ice for min. Then cell pellet was washed once with buffer A (10 mM Tris, PH 7.5; 10 KCl; 60 mM NaCl; 3 mM MgCl2) with EDTA-free protease inhibitor cocktail.
Chromatin was crosslink reversed by heating at 65 °C for 6 hours, and DNA were extracted using a standard phenol-chloroform extraction procedure. For paired-end sequencing, libraries without size selection were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L).
Illumina libraries were sequenced on a DNBSEQ-T7 (MGI) platform with PE150 model.

treatment_protocol: For wrapping-seq, mouse ES cells plated for about 48 hours were directly crosslinked with 1% formaldehyde in PBS for 10 min at room temperature, then quenched by 125 mM glycine, and scraped off from the dish with a cell scraper. Then the cells were washed with cold PBS for twice and the cell pellet were stored at -80 °C.

value: Inner cell mass

value: embryonic stem cell

value: wild type

value: EdU


title: MGPP3 cells, Volasertib resistant 1


title: S1D2_H3K4me3_rep2,CUT&Tag


title: R1-EdU-16hr-xMNase.rep1


title: HNSCC-KP_Batch1_UH22


title: MGPP3 cells, Alisertib resistant 3

value: Alisertib


title: HNSCC-KP_Batch1_UH21


title: R1-non-lable-xMNase.rep2


title: S1D2_H3K4me1_rep1,CUT&Tag


title: HNSCC-KP_Batch1_UH20


title: mESC.RT-S4.rep2

data_processing:
Paired-end reads were trimmed for adaptor sequence using cutadapt v4.3 with parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -n 2 -m 35 -q 30 –pairfilter = any
Trimed reads were mapped to mm10 using Bowtie2 v2.5.1  with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal.
Duplicates were marked using picard MarkDuplicates v2.27.5 with default parameters and removed using samtools view v1.17  with parameters: -f 2 -F 1024 -q 10.
Unique pair-end reads in bam format was converted to bed format grouped according to fragment length using a custom python script.
Mouse genome was segmented in to non-overlapping 100 kb bins. Then, within each genomic bin, fragment from each fragment length group were counted by annotateBed from bedtools v2.30.0. Fragment length groups used includes 50-80 bp, 80-90 bp, 90-100 bp, 100-110 bp, 110-120 bp, 120-130 bp, 130-140 bp, 140-150 bp, 150-160 bp, 160-250 bp or 50-140bp, 140-250bp. Then when a fragment length break point (X bp) is chosen, nucleosome wrapping score (NRS) is computed as the relative deviation between the number (a) of fragments within X~250 bp and the number (b) of fragments within 50~X bp, expressed as NRS(X) = (a-b)/(a+b). Then the genome-wide NRS was transformed as z-score to derive genome-wide nucleosome wrapping index (NRI).
Assembly: mm10
Supplementary files format and content: bedgraphs of Nucleosome wrapping score and nucleosome wrapping index, or replication timing
Supplementary files format and content: bed of nucleosome wrapping domains and RT domains


title: MGPP3 cells, Alisertib resistant 2


title: S1D2_H3K27me3_rep2,CUT&Tag


title: MGPP3 cells, Alisertib resistant 1


title: MGPP3 cells, Ispinesib resistant 3

value: Ispinesib


title: mESC.RT-S4.rep1


title: R1-non-lable-xMNase.rep1


title: HNSCC-KP_Batch1_UH19


title: mESC.RT-S3.rep2


title: HNSCC-KP_Batch1_UH17


title: HNSCC-KP_Batch1_UH12


title: S1D2_H3K27me3_rep1,CUT&Tag


title: MGPP3 cells, Ispinesib resistant 2

value: brain


title: S1D2_H3K27ac_rep2,CUT&Tag


title: mESC.RT-S3.rep1


title: MGPP3 cells, Ispinesib resistant 1

value: proneural glioma


title: HNSCC-KP_Batch1_UH8


title: S1D2_H3K4me3_rep1,CUT&Tag


title: S1D2_H3K27ac_rep1,CUT&Tag


title: MGPP3 cells, naïve 3

value: control


title: mESC.RT-S2.rep2


title: Islet non-ECs 3

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

description: 10X Chromium v3 scRNAseq FASTQ

data_processing:
Single feature counts were generated using Cellranger-7.0.0 with the count function
Assembly: GRCh38-2020-A
Supplementary files format and content: Filtered feature barcode matrix

source_name: Islet non-ECs 3

growth_protocol: Islet and acinar fractions were isolated by clinical islet isolation protocol. Both tissues were cultured in RPMI1640-based serum-free medium for 3-6 hours before treatment.

extract_protocol:
10X Chromium v3 library preparation
sinlge-cell RNAseq paired-end sequencing

treatment_protocol: Single cells were dissociated from whole islets with dispase/collagenase digestion, and the endothelial cells were sorted based on CD31/VECad staining.

tag: time points

value: Donor 3

tag: source

value: negative fraction cells


title: mESC.RT-S2.rep1


title: MGPP3 cells, naïve 2


title: mESC.RT-S1.rep2


title: Islet ECs 3.2

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Islet ECs 3

value: CD31+CD45- cells


title: Islet ECs 3.1

description: 10X Chromium v3 scRNAseq FASTQ


title: MGPP3 cells, naïve 1


title: S1D1_H3K4me1_rep2,CUT&Tag

value: induced from hADSC


title: S1D1_H3K4me3_rep1,CUT&Tag


title: mESC.RT-S1.rep1


title: Acinar non-ECs 3

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Acinar non-ECs 3


title: chase.60min.tpl.pull.down.rep1

value: Triptolide


title: S1D1_H3K27me3_rep2,CUT&Tag


title: S1D1_H3K4me1_rep1,CUT&Tag


title: chase.60min.tpl.input.rep1


title: Acinar ECs 3

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Acinar ECs 3


title: BC01014 - post

type: RNA

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the purified target/probe complexes are eluted out the beads and immobilized on the cartridge for data collection.

data_processing: none provided

label: Nanostring

source_name: ER+/HER2− metastatic breast cancer

extract_protocol: Total RNA was extracted from the formalin-fixed paraffin-embedded (FFPE) specimens of primary tumors by using Qiagen’s miRNeasy FFPE Kit (Qiagen, Valencia, CA, USA).

tag: group

value: Post-treatment


title: S1D1_H3K27me3_rep1,CUT&Tag


title: Islet ECs 2

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Islet ECs 2

value: Donor 2


title: chase.60min.dmso.pull.down.rep1

value: DMSO


title: S1D1_H3K4me3_rep2,CUT&Tag

source_name: induced from hADSC


title: BC01003 - post


title: S1D1_H3K27ac_rep2,CUT&Tag


title: chase.60min.dmso.input.rep1

value: Inner cell mass


title: Acinar non-ECs 2

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Acinar non-ECs 2


title: Acinar ECs 2

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Acinar ECs 2


title: 0618CiPS_H3K4me3_rep2,CUT&Tag

value: human chemically induced pluripotent stem cells


title: S1D1_H3K27ac_rep1,CUT&Tag


title: S1D2_H3K4me1_rep2,CUT&Tag


title: nascent.tpl.pull.down.rep1

value: embryonic stem cell

value: wild type


title: nascent.tpl.input.rep1


title: Islet non-ECs 1

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Islet non-ECs 1

value: Donor 1


title: 0618CiPS_H3K4me3_rep1,CUT&Tag


title: BC01001 - post


title: BC01011 - post


title: BC01007 - post


title: nascent.dmso.pull.down.rep1


title: Islet non-ECs 2

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Islet non-ECs 2


title: BC01019 - pre

value: Pre-treatment


title: 0618CiPS_H3K4me1_rep2,CUT&Tag


title: BC01015 - pre


title: Islet ECs 1

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Islet ECs 1


title: BC01014 - pre


title: BC01013 - pre


title: nascent.dmso.input.rep1


title: Acinar non-ECs 1

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Acinar non-ECs 1


title: 0618CiPS_H3K4me1_rep1,CUT&Tag


title: cellcycle.S.sonication

description: cellcycle.S.sonication


title: BC01004 - pre


title: S1D6_H3K27me3_rep2,CUT&Tag


title: cellcycle.S.MNase

description: cellcycle.S.MNase


title: Deep Sample_22

city: Daegu

first: Taehee

last: Jo

address: 1035 Dalgubeol daero

department: Department of Plastic and Reconstructive Surgery

country: South Korea

institute: Keimyung University Dongsan Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level. Gene expression estimation was performed by RSEM v.1.3.1
Read count and FPKM(Fragment per Kilobase of transcript per Million mapped reads) were calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts, RPKM and FPKM values for each Sample.

source_name: deep subcutaneous adipose tissue (DSAT)

extract_protocol:
The tissues were then homogenized with appropriate volume of Trizol reagent (Invitrogen, USA) in independent bead containing safe lock tubes. After Trizol/chloroform extraction, the aqueous phase was mixed with 100% EtOH, and then loaded onto RNeasy column (Qiagen, USA). The RNA extraction process was continued according to the manufacturer’s protocol.
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, USA)

tag: gender

value: female

value: deep subcutaneous adipose tissue (DSAT)


title: 0618CiPS_H3K27me3_rep1,CUT&Tag


title: Deep Sample_21


title: cellcycle.G2M.sonication


title: 0618CiPS_H3K27me3_rep2,CUT&Tag


title: Deep Sample_20


title: BC01002 - pre


title: cellcycle.G2M.MNase


title: cellcycle.G1.sonication


title: 0618CiPS_H3K27ac_rep1,CUT&Tag


title: cellcycle.G1.MNase


title: 0618CiPS_H3K27ac_rep2,CUT&Tag


title: LFDxC_XX_++_2

source_name: Spleen

value: Spleen

tag: strain

value: 6 weeks

tag: Sex

value: F


title: 0618ADSC_H3K4me3_rep2,CUT&Tag

source_name: Adipose tissue

value: Adipose tissue

tag: cell line

tag: cell type

value: adult human adipose derived mesenchymal stromal cells


title: Deep Sample_18


title: 0618ADSC_H3K4me3_rep1,CUT&Tag


title: MNase.50min

source_name: Inner cell mass

tag: genotype


title: Acinar ECs 1

description: 10X Chromium v3 scRNAseq FASTQ

source_name: Acinar ECs 1

value: CD31+CD45- cells


title: 0618ADSC_H3K4me1_rep2,CUT&Tag


title: MNase.40min


title: Hep 3B-CMTM4-control-3

city: Nanning

first: Xuefeng

last: Guo

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road

department: 1.	Department of Epidemiology and Health Statistics

institute: Xuefeng Guo

description: Hep 3B, Control, Y9662-3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Hep 3B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA .

growth_protocol: Hep3B cells were grown in DMEM medium (Invitrogen) containing 10% FBS and incubated at 37℃ in a humidified CO2 incubator.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

treatment_protocol: shRNAs were transfected into Hep3B cells with Lipofectamine 3000 (Invitrogen) according to the instructions of the manufacturer.

value: Hep 3B

value: Control


title: Deep Sample_19


title: Superficial Sample_16

source_name: superficial adipose tissue (SSAT)

value: superficial adipose tissue (SSAT)


title: Hep 3B-CMTM4-control-2

description: Hep 3B, Control, Y9662-2


title: Superficial Sample_15


title: Hep 3B-CMTM4-KD-3

description: Hep 3B, CMTM4 KO, Y9663-3

value: CMTM4 Knockdown


title: Hep 3B-CMTM4-control-1

description: Hep 3B, Control, Y9662-1


title: MNase.30min

value: Inner cell mass


title: Hep 3B-CMTM4-KD-2

description: Hep 3B, CMTM4 KO, Y9663-2


title: 0618ADSC_H3K4me1_rep1,CUT&Tag

data_processing:
*library strategy: Cut&Tag
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was calculated using MACS2 while peak calling.
Assembly: hg19
Supplementary files format and content: .bw file containing merged signal intensity of each sample


title: MNase.20min

value: embryonic stem cell


title: 0618ADSC_H3K27me3_rep2,CUT&Tag


title: Superficial Sample_14


title: 0618ADSC_H3K27me3_rep1,CUT&Tag


title: Diff LUHMES, TG, 3hr, rep4

data_processing:
raw reads were trimmed and mapped using CLC genomics workbench (v23) default settings. CLC was also used for statistical analysis to idenify DEGs and generate expression browsers.
Assembly: Homo Sapiens (hg38)
Supplementary files format and content: Excel file containing RPKMs and statistical tests

source_name: LUHMES

value: LUHMES

value: Neurons

value: WT

value: 3 hours

tag: treatment

value: TG

value: Biol rep 4


title: Replicate 1 Control

city: Heidelberg

first: Stefan

last: Peidli

state: BW

address: Meyerhofstraße 1

department: Genome Biology

institute: European Molecular Biology Laboratory

description: NanoDan Control Input Rep1

data_processing:
Reads were trimmed using trim_galore (v0.6.10, DOI:10.5281/zenodo.7598955) with settings for illumina reads, removing 10bp from both the 5’ and 3’ ends of all reads, and requiring a minimal read length of 36bp.
Trimmed reads were then aligned to the Drosophila Melanogaster genome using a precompiled bowtie index (BDGP6) and bowtie2 (v2.5.4, DOI:10.1038/nmeth.1923) while allowing for maximum single mismatches.
Resulting alignment files were filtered for uniquely mapped reads, converted to bam, sorted, and indexed using samtools (v1.20, DOI:10.1093/bioinformatics/btp352).
We used MACS2 (v2.2.9.1, DOI:10.1101/496521) for peak calling while filtering out peaks with FDR>0.05. Peaks were then annotated with CHIPseeker (v1.38.0, DOI:10.1093/bioinformatics/btv145) and a genome annotation file from Ensembl (index BDGP6.46.110).
Additionally, a GATC signal was obtained by binning the genome into consecutive GATC sites using a custom python script and a GFF of sites obtained from damidseq_pipeline doi:10.1093/bioinformatics/btv386, then calculating fold-changes of the NanoDam Cph signal with respect to the control for each replicate respectively.
Tracks were plotted using pyGenomeTracks do:10.1038/s41467-017-02525-w, di: 10.1093/bioinformatics/btaa692. The entire workflow was implemented using snakemake (v8.14.0, DI: 10.12688/f1000research.29032.1).
Assembly: BDGP6
Supplementary files format and content: SAMPLE_ID.bw contains read coverage converted to bigwig file for plotting in IGV
Supplementary files format and content: SAMPLE_ID_peaks.broadPeak contains broad peaks called by MACS2
Supplementary files format and content: SAMPLE_ID_peaks.xls also contains broad peaks called by MACS2
Supplementary files format and content: SAMPLE_ID_vs_CONTROL_ID_peaks.broadPeak and similar files contain MACS2 peaks with the respective control samples as a contrast
Library strategy: NanoDam

organism: Drosophila melanogaster

source_name: intestine

growth_protocol: To perform Cph NanoDam in the intestine, we crossed a CphYFP; UAS-NanoDam line with esgTS. As control, we crossed UAS-NanoDam line with esgTS. Flies were reared at 18°C. Adult flies aged between 3-5 days were shifted to 29°C for 17hrs.

extract_protocol:
30 Midguts where dissected in ice-cold PBS, taking care to remove Malpighian tubules, hindgut and proventriculus and samples were frozen in -80°C. DNA was extracted from dissected midgut and methylated fragments were isolated with DpnI and DpnII digestion.
Methylated fragments were then amplified with PCR and sonicated in order to generate libraries suitable for sequencing. Sequencing was performed using single end 86 bp reads with a using a Nextseq 550 at the Deep Sequencing Facility, BioQuant, Heidelberg University.

value: intestine

value: UAS-NanoDam x esgTS

tag: replicate

value: biol rep 1

value: control


title: Replicate 2 Control

description: NanoDan Control Input Rep2

value: biol rep 2


title: Deep Sample_17

value: female

tag: age

value: deep subcutaneous adipose tissue (DSAT)


title: Superficial Sample_12

value: superficial adipose tissue (SSAT)


title: 0618ADSC_H3K27ac_rep2,CUT&Tag

extract_protocol:
Approximately 1 x 10^5 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol. Briefly, harvest fresh cultures and count 1 x 10^5 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4C. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 ℃ for 1 h and then performed DNA extraction with DNA extraction beads.
For extracted DNA, combinate i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and Illumina sequencing.

value: Adipose tissue

value: adult human adipose derived mesenchymal stromal cells


title: Superficial Sample_13