title: WS234 H3K9me3 Rep 1

data_processing:
Nextera adapters were trimmed from sequenced reads with Cutadapt 4.4 (Python 3.9.6).
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.4.4 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Duplicates, non-uniquely aligned reads were marked with Picard (3.1.1) and filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads with greater than 10 Q-score.
Genome coverage was calculated using bamCoverage v3.5.3 (deepTools v3.5.3) with the following parameters: --effectiveGenomeSize 2467481108 --binSize 1 --normalizeUsing 'RPKM' --ignoreForNormalization 'chrM' --extendReads.
Peaks were called using MACS (3.0.0) with parameters: -f BAMPE -g 2805636331 -q 1e-5.
Assembly: GRCh38_hg38
Supplementary files format and content: bigWig, bigBed
Library strategy: CUT&Tag

source_name: Skeletal muscle

growth_protocol: WS234 cells were cultured on 0.1% gelatin-coated plates in LHNC media (4:1 DMEM:Medium 199, 15% BGS (v/v), 0.03 ug/ml Zinc Sulfate, 1.4 ug/ml vitamin B12, 0.055 ug/ml dexamethasone, 2.5 ng/ml HGF, 10 ng/ml FGF, 0.6X penicillin/streptomycin, 20 mM HEPES (pH 7.4)). Cells were collected under proliferating conditions.

extract_protocol:
Tn5-PA tagmented DNA was treated with proteinase K, extracted with phenol chloroform, and precipitated with ethanol.
Extracted DNA was amplified with barcoded i5 and i7 compatible primers
CUT&Tag libraries were sequenced on the Illumina NextSeq 6000 instrument

treatment_protocol: CUT&Tag experiements were performed on 75,000 cells

value: Skeletal muscle

value: muscle progenitor

value: Wildtype

value: proliferative conditions

tag: antibody

value: Rabbit anti-Histone H3 (tri methyl K9) abcam ab8898


title: G-MDSCs,after FACS sorting, 90days, rep5

status: Public on Jun 25 2024

type: SRA

city: Gui Yang

first: MING

last: NI

address: 28 Guiyi St., Yunyan District

department: Department of Hematology

country: China

institute: Affiliated Hospital of Guizhou Medical University,

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set;
The expression level of gene was calculated by RSEM.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes row counts for each sample
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was extracted using Trizol
RNA transcriptome profiles were generated by the Beijing Genomics Institute (BGI) using the DNA Nanoball sequence (DNBSEQ) platform.

tag: tissue

value: Blood


title: ChIPseq of Adn2-FLAG, 2h with methanol, FLAG-IP, rep 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities) were used and read coverage was normalized to 1 million genome mapping reads (RPM).
Assembly: Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized read counts (to 1 mio genome mapping reads per library) for visualization in UCSC or IGV genome browser.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures were grown in standard YES medium (OD = 1, exponential phase) at 30 degrees celsius. At time point 0, cells were diluted to OD = 0.01 and shifted to EMM(187mM NH4Cl) with MeOH or NSF at 30 degrees celsius.

extract_protocol:
Cells were fixed with 1% formaldehyde and lysed by beat-beating. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol and  the IP was performed for 2h at 4°C. ChIPs were decrosslinked overnight at 65°C and cleaned up using AMPure XP beads. For a detailed protocol, see Kuzdere et al, 2022.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.

treatment_protocol: 2h growth at low density (OD=0.01) either with NSF or MeOH as control.

value: S. pombe cell culture

tag: strain

tag: genotype

value: h- leu1-32 ura4-D18 ade6-704 adn2-6xGly-3xFlag::kanMX

tag: treatment

value: MeOH


title: Jurkat, control, rep2

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

data_processing:
ATAC-Seq reads were mapped to the UCSC hg38 genome using bowtie2 vx.1.0 with the parameters --local --very-sensitive-local
Duplicated reads were removed with Picard MarkDuplicates
Peaks were called using macs2 vx.1.z with the parameters --nomodel –nolambda --cutoff-analysis
bigWig files were generated using bamCoverage v1.x.1 with the parameter --normalizeUsing CPM
Assembly: hg38 + HIV inserts
Supplementary files format and content: bigwig, narrowPeak, HIV_construct_inserts_coordinates.csv

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

growth_protocol: Primary T cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), antibiotics, 50 U/mL of human IL-2 and 5,000 Gy-irradiated NK and CD8 T cell depleted PBMCs, in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Genomic DNA was collected, tagmented and purified using the ATAC-Seq Kit (Active Motif)
PCR amplification of tagmented DNA and library preparation were performed using the ATAC-Seq Kit (Active Motif)

treatment_protocol: Cells were stimulated with 0.1 µg/mL of anti-CD3 and anti-CD28 monoclonal antibodies in above culture medium for 1 week (activated conditions) then cultured with 10 ng/mL of human IL-7 for an additional week (resting conditions).

tag: cell line

value: Jurkat


title: ChIPseq of Adn2-FLAG, 2h with methanol, FLAG-IP, rep 1


title: WS234 H3K9me3 Rep 2

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

tag: cell type


title: surface epithelium_GRHL3_rep2

city: Guangzhou

first: Huaxing

last: Huang

address: 7 Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

data_processing:
Reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software (version 0.7.17). Duplicated reads were removed by Picard Markduplicates (version 2.18.16) and only uniquely mapping reads were retained for further analysis. MACS2 (version 2.1.1) was used to call peak.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: surface epithelium

growth_protocol: For surface epithelium differentiation, H1 hESCs were digested into colonies of 100 to 200 μm in diameter and seeded onto Matrigel-coated plates. The next day, mTeSR1 medium was changed to Essential 6 medium supplemented with recombinant human BMP4 (5 ng/ml) and 1 μM RA.

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Thermo Fisher Sci_x0002_entific, 28906) in Dulbecco’s Modified Eagle Medium for 10min at room temperature. Formaldehyde was then quenched with 125 mM glycine (Sigma-Aldrich, 50046) for 5min at room temperature. Cells were lysed in sonication buffer [50 mM Hepes-NaOH (pH 7.5), 500 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100, and 0.1% SDS]. Chromatin was sheared with Covaris M220 focused-ultrasonicator to an average DNA fragment length of 200 to 500base pairs (bp). Chromatin was then diluted in lysis buffer without SDS and immunoprecipitated with primary antibodies overnight at 4°C. The immunocomplexes were captured with Protein A and Protein G magnetic beads (1:1, Invitrogen). After three washes with sonication buffer, two washes with low-salt wash buffer [10 mM tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% Na-deoxycholate], and one wash with TE buffer [10 mM tris-HCl (pH 8.0) and 1 mM EDTA], chromatin was then eluted from beads and de–cross-linked with 1% SDS in TE for 4 hours. After 1-hour digestion at 37°C with proteinase K (Invitrogen) and ribonuclease A (Invitrogen), DNA was purified using the MinElute PCR Purification Kit (QIAGEN)
Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS).

value: surface epithelium


title: surface epithelium_TFAP2C_rep1


title: surface epithelium_TFAP2C_rep2


title: G-MDSCs,after FACS sorting, 28days, rep7


title: WS234 H3K4me1 Rep 2

value: Rabbit anti-Histone H3 (mono methyl K4) abcam ab8895


title: ChIPseq of Adn2-FLAG, 0h, FLAG-IP, rep 3


title: surface epithelium_GATA3_rep2


title: surface epithelium_GRHL3_rep1


title: WS234 H3K4me1 Rep 1


title: ChIPseq of Adn2-FLAG, 0h, FLAG-IP, rep 2


title: G-MDSCs,after FACS sorting, 28days, rep6


title: Total RNAseq after SETDB1 depletion in wt mES cells, replicate 3

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 (STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesIn R1.fastq.gz R2.fastq.gz --readFilesCommand zcat –genomeDir tar2_7_3a_GRCm38.primary_assembly_gencodeM23_spliced_sjdb50  --runThreadN 10 --outFilterType BySJout --outFilterMultimapNmax 10000 --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 10000 --outSAMunmapped Within).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

molecule: total RNA

organism: Mus musculus

source_name: hybrid 129-C57BL/6

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
RNA was collected using Absolutely RNA miniprep kit (Agilent) according to manufacturer's instructions
Libraries were prepared using TruSeq Ilumina total RNA-seq

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 setdb1 (N) 2HA-FKBP12F36V

value: 500nM dTAG13


title: WS234 H3K4me3 Rep 2

value: Rabbit anti-Histone H3 (tri methyl K4) abcam ab8580


title: G-MDSCs,after FACS sorting, 90days, rep4


title: ChIPseq of Adn2-FLAG, 0h, FLAG-IP, rep 1


title: Jurkat, control, rep1

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: ChIPseq of Php3-FLAG, 2h with NSF, input, rep 3

value: h- leu1-32 ura4-D18 ade6-704 php3-6xGly-3xFlag::kanMX

value: NSF


title: ChIPseq of Adn2-FLAG, 2h with NSF, FLAG-IP, rep 2


title: WS234 H3K27ac Rep 2

value: Skeletal muscle

value: muscle progenitor

value: Wildtype

value: proliferative conditions

value: Rabbit anti-Histone H3 (acetyl K27) abcam ab177178


title: G-MDSCs,after FACS sorting, 90days, rep3

value: Blood


title: Total RNAseq after SETDB1 depletion in wt mES cells, replicate 2


title: Total RNAseq after SETDB1 depletion in wt mES cells, replicate 1


title: G-MDSCs,after FACS sorting, 90days, rep2


title: Total RNAseq in untreated wt mES cells, replicate 2

value: DMSO


title: ChIPseq of Php3-FLAG, 2h with NSF, input, rep 1

value: S. pombe cell culture


title: G-MDSCs,after FACS sorting, 28days, rep5


title: ChIPseq of Php3-FLAG, 2h with methanol, input, rep 3

value: MeOH


title: WS234 H3K4me3 Rep 1


title: Total RNAseq in untreated wt mES cells, replicate 1

value: hybrid 129-C57BL/6


title: WS234 H3K27me3 Rep 2

value: Rabbit anti-Tri-Methyl-Histone H3 (Lys27) Cell Signaling 9733


title: WS234 H3K27me3 Rep 1


title: ChIPseq of Php3-FLAG, 2h with methanol, input, rep 2


title: G-MDSCs,after FACS sorting, 28days, rep4


title: G-MDSCs,after FACS sorting, 28days, rep3


title: ChIPseq of Php3-FLAG, 2h with methanol, input, rep 1


title: H3K4me3_Pdgfra_R3

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
Raw reads where processed with bcl2fastq (v 2.19.1)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.12) flags (-b -F4 -q13)
Normalised bigwigs for visualisation was generated with bamCoverage (anaconda2 v 4.4.0) using binsize 5 and RPKM.
Peaks were called using SEACR (https://seacr.fredhutch.org/) for each population with population-specific IgG using the 'stringent' setting
Consensus peaks pr condition was defined as peaks present in at least 2 of 3 biological replicates, and these were combined to generate a counttable for downstream analysis (reads within defined peaks were counted using bedtools, v 2.26.0, coverage).
Assembly: mm10
Supplementary files format and content: bigWig, bed
Library strategy: CUT&Tag

extract_protocol:
nEnd subpopulations were isolated by fluorescence activated cell sorting (FACS) based on OCT4-mCherry and PDGFRA-APC expression (Oct4+, douple positive (DP) and Pdgfra+) using a BD FACSAria III Cell Sorter
Library preparation according to the protocol detailed in Kaya-Okur et al. 2020 (Nature Protocols)

value: nEnd

tag: cut&tag antibody

value: H3K4me3, Diagenode, C15410030

value: no treatment


title: WS234 IgG Rep 2

value: Rabbit IgG Isotype Control ThermoFisher 10500C


title: WS234 IgG Rep 1


title: ChIPseq of Php3-FLAG, 0h, input, rep 3

value: h- leu1-32 ura4-D18 ade6-704 php3-6xGly-3xFlag::kanMX


title: H3K4me3_Pdgfra_R1


title: G-MDSCs,after FACS sorting, 28days, rep2


title: H3K4me3_Pdgfra_R2


title: COG415 cells CMLD12824 replicate 2 RNAseq

city: Boston

first: Marina

last: Volegova

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw Illumina reads from PAR-CLIP and matched total RNA sequencing libraries were collapsed and adapters were trimmed using fastx_collapser from the FASTX Toolkit. Bowtie2 was used to remove rRNA reads, and to align reads to the human genome (GRCh37) for bulk RNA sequencing libraries,  with Cuffdiff v2.2.1 used to extract and merge raw read counts of the biological replicates. For PAR-CLIP libraries, identical reads were collapsed into distinct reads and aligned to the human genome (GRCh37) with Burrows-Wheeler Alignment (BWA) v0.7.17 allowing for up to one edit distance (mismatch, insertion or deletion). The unaligned reads were removed and aligned reads were sorted into a BAM formatted file with Samtools v1.13.
The clusters on the reference genome that eIF4A1 bound to were then identified with the pipeline-provided script that collects reads contiguously covering a section of the reference genome while screening for cross-link conversions. The identified clusters involve at least two distinct read sequences and at least one cross-link conversion. The cluster identification analysis was performed for each individual sample; also replicate consensus was taken into account, such that a cluster is reported only if it is called in both replicates. The false discovery rates (FDRs) of mapping for each sample and replicate consensus were assessed as per the pipeline by aligning the sequence reads to a decoy genome. A filter was applied to retain only those clusters between the length of 20-1000 nucleotides.
Assembly: GRCh37
Supplementary files format and content: GFF files, tab-delimited values files (cuffdiff output)

extract_protocol:
Total RNA was extracted from matched samples using miRNeasy RNA Extraction kit (QIAGEN) according to manufacturer’s instructions.
RNA sequencing libraries prepared with the Illumina TruSeq stranded mRNA kit (Illumina) following the manufacturers’ instructions.

value: Neuroblastoma

value: MYCN-amplified


title: WS234 H3K27ac Rep 1

value: Skeletal muscle

value: muscle progenitor


title: ChIPseq of Php3-FLAG, 2h with NSF, input, rep 2

value: NSF


title: G-MDSCs,after FACS sorting, 90days, rep1


title: Total RNAseq in untreated wt mES cells, replicate 3

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 setdb1 (N) 2HA-FKBP12F36V


title: H3K4me3_Oct4_R4


title: G-MDSCs,after FACS sorting, 28days, rep1

value: Blood


title: ChIPseq of Php3-FLAG, 0h, input, rep 1

value: S. pombe cell culture


title: ChIPseq of Php3-FLAG, 0h, input, rep 2


title: MCF7_E2, bio rep3

first: Sicong

last: Zhang

description: BRD4 binding sites from triplicates of V and E2 were combined and provided as a single BED file.

data_processing:
Pair-end reads were aligned to the human genome (hg38) with decoy sequences using Bowtie2 v2.4.4 with default settings.
Samtools v1.132 was used to generate BAM files for peak calling with MACS3 v3.0.0a63.
ChIP signal was normalized to counts per million reads by deepTools2.0 v3.5.14  with duplicates ignored. Bigwg files were generated with binSize of 10.
Regions overlapping with ENCODE Blacklist regions were excluded from analysis.
ChIP-seq from some batches were analyzed using Galaxy.
Assembly: hg38
Supplementary files format and content: bigwig, bed (BRD4 binding sites from triplicates and BRD4-BD mutant binding sites)

source_name: breast

growth_protocol: To study ER-dependent effect, cells were grown in 15 cm dishes for 3-4 days in phenol red-free DMEM/F-12 supplemented with 5% charcoal-dextran-treated FBS and then treated with 10 nM estrogen for 40 min.

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min. Glycine was then added to quench cross-linking. Chromatin fragments were generated by sonication (Branson sonifier).
ChIP-seq library was prepared with NEBNext Ultra™ II DNA Library Prep with Sample Purification Beads (New England Biolabs)

value: breast

value: breast cancer cells

tag: chip antibody


title: ChIPseq of Hsr1-FLAG, 2h with NSF, input, rep 3

value: h- leu1-32 ura4-D18 ade6-704 hsr1-6xGly-3xFlag::kanMX


title: COG415 cells solvent replicate 2 RNAseq

value: Solvent


title: COG415 cells solvent replicate 1 RNAseq


title: H3K4me3_Oct4_R2

value: nEnd

value: H3K4me3, Diagenode, C15410030


title: MCF7_V, bio rep3

value: ethanol


title: H3K4me3_Oct4_R3

value: no treatment


title: MCF7_E2_input, bio rep3

value: none (input)


title: H3K4me3_Oct4_R1


title: ChIPseq of Hsr1-FLAG, 2h with NSF, input, rep 2


title: ChIPseq of Hsr1-FLAG, 2h with NSF, input, rep 1


title: COG415 cells CMLD12824 replicate 2 PAR-CLIP

library_source: other

data_processing:
*library strategy: PAR-CLIP
Raw Illumina reads from PAR-CLIP and matched total RNA sequencing libraries were collapsed and adapters were trimmed using fastx_collapser from the FASTX Toolkit. Bowtie2 was used to remove rRNA reads, and to align reads to the human genome (GRCh37) for bulk RNA sequencing libraries,  with Cuffdiff v2.2.1 used to extract and merge raw read counts of the biological replicates. For PAR-CLIP libraries, identical reads were collapsed into distinct reads and aligned to the human genome (GRCh37) with Burrows-Wheeler Alignment (BWA) v0.7.17 allowing for up to one edit distance (mismatch, insertion or deletion). The unaligned reads were removed and aligned reads were sorted into a BAM formatted file with Samtools v1.13.
The clusters on the reference genome that eIF4A1 bound to were then identified with the pipeline-provided script that collects reads contiguously covering a section of the reference genome while screening for cross-link conversions. The identified clusters involve at least two distinct read sequences and at least one cross-link conversion. The cluster identification analysis was performed for each individual sample; also replicate consensus was taken into account, such that a cluster is reported only if it is called in both replicates. The false discovery rates (FDRs) of mapping for each sample and replicate consensus were assessed as per the pipeline by aligning the sequence reads to a decoy genome. A filter was applied to retain only those clusters between the length of 20-1000 nucleotides.
Assembly: GRCh37
Supplementary files format and content: GFF files, tab-delimited values files (cuffdiff output)

molecule: other

value: Neuroblastoma

value: MYCN-amplified


title: MCF7_V_input, bio rep3


title: COG415 cells CMLD12824 replicate 1 PAR-CLIP


title: H3K4me3_DP_R3


title: MCF7_E2, bio rep2


title: COG415 cells CMLD12824 replicate 1 RNAseq


title: ChIPseq of Hsr1-FLAG, 2h with methanol, input, rep 3

value: MeOH


title: COG415 cells solvent replicate 2 PAR-CLIP


title: H3K4me3_DP_R2


title: MCF7_V, bio rep2


title: ChIPseq of Hsr1-FLAG, 2h with methanol, input, rep 2


title: H3K4me3_DP_R1


title: MCF7_E2_input, bio rep2


title: COG415 cells solvent replicate 1 PAR-CLIP


title: MOLM13_sgRBBP5_2_Dox_4d_rep2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Doxycycline was treated for 4 days. DMSO or dTAG-13 were treated for 24 hours.

value: leukemia

value: 1µg/mL Doxycycline 4d


title: ChIPseq of Hsr1-FLAG, 2h with methanol, input, rep 1


title: MCF7_V_input, bio rep2


title: ChIPseq of Hsr1-FLAG, 0h, input, rep 3


title: Input of ChIPseq for ADNP2 in wt mES cells, replicate 1

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 (STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesIn R1.fastq.gz R2.fastq.gz --readFilesCommand zcat --genomeDir mm10_hg38Spike_refSTAR --runThreadN 10 --alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix _ --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG --outBAMsortingBinsN 100).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

extract_protocol:
10-20^6 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ahel,Pandey et al. 2024.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F


title: MCF7_NVP2

treatment_protocol: Cells were treated with 250 nM NVP2 for 1 hour prior to E2.

value: breast

value: NVP2, E2


title: MOLM13_sgRBBP5_1_Dox_4d_rep2


title: ChIPseq of Hsr1-FLAG, 0h, input, rep 2

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 hsr1-6xGly-3xFlag::kanMX


title: MCF7_E2_2

treatment_protocol: Cells were treated with DMSO for 1 hour prior to E2.

value: breast cancer cells

value: DMSO, E2


title: MOLM13_sgRBBP5_1_Dox_4d_rep1


title: ChIPseq for ADNP2  in wt mES cells, replicate 1

value: FLAG, Sigma F1804


title: ChIPseq of Hsr1-FLAG, 0h, input, rep 1


title: ChIPseq of Adn2-FLAG, 2h with NSF, input, rep 3

value: h- leu1-32 ura4-D18 ade6-704 adn2-6xGly-3xFlag::kanMX

value: NSF


title: MCF7_Vehicle_2

treatment_protocol: Cells were treated with DMSO for 1 hour prior to ethanol.

value: DMSO, ethanol


title: MOLM13_sgCCR5_255_Dox_4d_rep4


title: Input of ChIPseq for ADNP2 in wt mES cells, replicate 2


title: ATACseq in wt mES cells, replicate 2

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within ).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

extract_protocol:
50k cells per sample were prepared according to the ATAC-seq protocol described in Buenrostro et al, Nature Methods, 2013
Libraries were amplified using NEB Next Ultra II polymerase


title: ChIPseq of Adn2-FLAG, 2h with NSF, input, rep 1


title: MED17-dTAG, clone2, dE

treatment_protocol: MED17-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to E2.

value: dTAG, E2


title: MCF7_input


title: MOLM13_sgAAVS_2_Dox_4d_rep4

value: sgAAVS


title: MOLM13_sgRBBP5_2_Dox_4d_rep1

value: leukemia


title: MED17-dTAG, clone2, dTAG

treatment_protocol: MED17-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to ethanol.

value: dTAG, ethanol


title: ChIPseq of Adn2-FLAG, 2h with methanol, input, rep 3

value: MeOH


title: IgG_Pdgfra

data_processing:
Raw reads where processed with bcl2fastq (v 2.19.1)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.12) flags (-b -F4 -q13)
Normalised bigwigs for visualisation was generated with bamCoverage (anaconda2 v 4.4.0) using binsize 5 and RPKM.
Peaks were called using SEACR (https://seacr.fredhutch.org/) for each population with population-specific IgG using the 'stringent' setting
Consensus peaks pr condition was defined as peaks present in at least 2 of 3 biological replicates, and these were combined to generate a counttable for downstream analysis (reads within defined peaks were counted using bedtools, v 2.26.0, coverage).
Assembly: mm10
Supplementary files format and content: bigWig, bed (except for IgG samples)
Library strategy: CUT&Tag

extract_protocol:
nEnd subpopulations were isolated by fluorescence activated cell sorting (FACS) based on OCT4-mCherry and PDGFRA-APC expression (Oct4+, douple positive (DP) and Pdgfra+) using a BD FACSAria III Cell Sorter
Library preparation according to the protocol detailed in Kaya-Okur et al. 2020 (Nature Protocols)
Cleavage Under Targets & Tagmentation (CUT&Tag)

value: nEnd

value: Rabbit IgG, Abcam, ab171870

value: no treatment


title: ChIPseq of Adn2-FLAG, 2h with methanol, input, rep 2


title: MED17-dTAG, clone2, E2

treatment_protocol: MED17-dTAG cells were treated with DMSO for 2 hours prior to E2.

value: breast


title: MOLM13_sgAAVS_2_Dox_4d_rep3

value: 1µg/mL Doxycycline 4d


title: MED17-dTAG, clone2, Veh

treatment_protocol: MED17-dTAG cells were treated with DMSO for 2 hours prior to ethanol.


title: MOLM13_FKBP-W104A_HA

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

treatment_protocol: Doxycycline were treated for 4 days. DMSO or 500 nM dTAG-13 were treated for 1 h or 24 h before fixation.

value: HA-Tag (Cell Signaling, #3724)


title: ChIPseq for ADNP2 in wt mES cells, replicate 2

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F


title: IgG_DP


title: ATACseq in wt mES cells, replicate 3


title: MOLM13_FKBP-N200_HA


title: ChIPseq of Adn2-FLAG, 0h, input, rep 3

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 adn2-6xGly-3xFlag::kanMX


title: H3K27me3_Pdgfra_R3

value: H3K27me3, Cell Signalling, 9733


title: ChIPseq of Adn2-FLAG, 2h with NSF, input, rep 2

value: NSF


title: MOLM13_FKBP-Emp_HA


title: MED17-dTAG, clone2, dE, ER

value: breast cancer cells

value: ER, Santa Cruz F-10, D-12

value: dTAG, E2


title: ChIPseq of Adn2-FLAG, 0h, input, rep 2


title: MOLM13_sgCCR5_255_Dox_4d_rep3

value: leukemia


title: ATACseq in wt mES cells, replicate 1


title: H3K27me3_Pdgfra_R2

value: nEnd


title: MED17-dTAG, clone2, E2, ER

value: DMSO, E2


title: MOLM13_FKBP-SETD1A_dTAG13_24h_BOD1L

value: 500nM dTAG-13 1h

value: FAM44A/BOD1L1 (Santa Cruz, sc-515761)


title: IgG_Oct4

value: Rabbit IgG, Abcam, ab171870

value: no treatment


title: ChIPseq of Adn2-FLAG, 0h, input, rep 1


title: H3K27me3_Pdgfra_R1


title: MED17-dTAG, clone2, Veh, ER

value: breast

value: DMSO, ethanol


title: MOLM13_FKBP-SETD1A_DMSO_24h_BOD1L

value: DMSO 1h


title: MOLM13_FKBP-BOD1L_dTAG13_24h_H3K4me3

value: H3K4me3 (abcam, ab8580)


title: MED17-dTAG, clone2, input, ER

value: none (input)


title: ChIPseq of Atf1-FLAG, 2h with NSF, FLAG-IP, rep 2

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 atf1-6xGly-3xFlag::kanMX


title: H3K27me3_Oct4_R3

value: H3K27me3, Cell Signalling, 9733


title: ChIPseq of Atf1-FLAG, 2h with NSF, FLAG-IP, rep 3

value: NSF


title: ChIPseq of Adn2-FLAG, 2h with methanol, input, rep 1

value: h- leu1-32 ura4-D18 ade6-704 adn2-6xGly-3xFlag::kanMX

value: MeOH


title: MOLM13_FKBP-BOD1L_DMSO_24h_H3K4me3

value: leukemia


title: MED17-dTAG, clone2, input

value: breast cancer cells


title: ChIPseq of Atf1-FLAG, 2h with NSF, FLAG-IP, rep 1


title: H3K27me3_Oct4_R2

value: nEnd


title: H3K27me3_DP_R3


title: ChIPseq of Atf1-FLAG, 2h with methanol, FLAG-IP, rep 3


title: MED17-dTAG, clone1, DSG, dTAG

treatment_protocol: MED17-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to ethanol. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: dTAG, ethanol


title: MOLM13_sgAAVS_2_Dox_4d_H3K4me3

value: 1µg/mL Doxycycline 4d


title: ChIPseq of Atf1-FLAG, 2h with methanol, FLAG-IP, rep 2


title: MOLM13_sgBOD1L_243_Dox_4d_H3K4me3


title: MED17-dTAG, clone1, DSG, dE

treatment_protocol: MED17-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to E2. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: dTAG, E2


title: MOLM13_sgBOD1L_243_Dox_4d_SETD1A

value: SETD1A (Cell Signaling, #61702)


title: H3K27me3_DP_R2

value: no treatment


title: ChIPseq of Atf1-FLAG, 2h with methanol, FLAG-IP, rep 1


title: MED17-dTAG, clone1, DSG, JE

treatment_protocol: MED17-dTAG cells were treated with 100 nM JQ1 for 2 hours prior to E2.Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: breast

value: DMSO, E2, JQ1


title: MOLM13_sgAAVS_2_Dox_4d_SETD1A


title: MED17-dTAG, clone1, DSG, E2

treatment_protocol: MED17-dTAG cells were treated with DMSO for 2 hours prior to E2. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: DMSO, E2


title: MED17-dTAG, clone1, DSG, dJE

treatment_protocol: MED17-dTAG cells were treated with 100 nM JQ1 and 500 nM dTAG v1 for 2 hours prior to E2. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: dTAG, E2, JQ1


title: ChIPseq of Atf1-FLAG, 0h, FLAG-IP, rep 3

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 atf1-6xGly-3xFlag::kanMX


title: NHBE cells, Cal/04/09 infected, 10 hr timepoint

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger 7.2.0 for demultiplexing, barcode processing, mapping and gene counting
Seurat version 4.3.0 for data processing and statistical analysis
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa, IAV reference genome accession numbers FJ966079-FJ966086
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Normal human bronchial/tracheal epithelial (NHBE) (Lonza Bioscience, CC-2540S) cells, harvested from healthy individuals, were expanded using either Pneumacult-Ex Plus Media (STEMCELL Technologies) and seeded on 6.5mm Transwell 0.4 μm pore polyester inserts (STEMCELL Technologies). Once confluent 2-4 days post-seeding, the ALI cultures were airlifted: apical media was removed to expose cells and basal compartment media was replaced with either Pneumacult-ALI Basal Media (STEMCELL Technologies). Cells were maintained at air-liquid interface (ALI) at 37°C and 5% CO2 in a humidified incubator. Cells were used at 3+ weeks post-ALI.

extract_protocol:
Single cell suspensions were filtered and counted and 10,000 cells per condition were used to generate Gel Bead-in Emulsions (GEMs). The 10X Chromium 3' GEX Capture kit and the 10X Chromium controller were used to generate GEMs and barcoding per manufacturers protocol (10X Genomics, Pleasanton, CA, USA).
Library preparation was performed using the Chromium Single Cell 3' Library Kit.

treatment_protocol: The apical surface of cells was washed with 1X PBS and Influenza A/California/04/2009 (MOI 0.5) in infection media (PBS with Ca/Mg, 1% penicillin-streptomycin, 5% BSA) was added directly to the apical surface and incubated for 1 hr at 37°C. A549 cells were infected alongside the ALI cultures. Unless otherwise noted, flow cytometry phenotyping experiments were performed with MOI 0.5 and multicycle growth experiments were done with MOI 0.1. After 1 hr, the virus inoculum was removed, stored at -80°C, and the apical surface washed with 1X PBS. Cells were incubated at 37°C until harvest

value: Cal/04/09 infected

tag: time point

value: 10 hr timepoint


title: ChIPseq of Atf1-FLAG, 0h, FLAG-IP, rep 2

treatment_protocol: 2h growth at low density (OD=0.01) either with NSF or MeOH as control.


title: H3K27me3_DP_R1

value: H3K27me3, Cell Signalling, 9733


title: H3K27ac_Pdgfra_R3

value: H3K27ac, Abcam, ab4729


title: MED17-dTAG, clone1, DSG, Veh

treatment_protocol: MED17-dTAG cells were treated with DMSO for 2 hours prior to ethanol. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: breast cancer cells

value: DMSO, ethanol


title: H3K27me3_Oct4_R1

value: nEnd


title: ChIPseq of Atf1-FLAG, 0h, FLAG-IP, rep 1


title: MED17-dTAG, clone1, DSG, input

value: none (input)


title: MED17-dTAG, clone1, dJE

treatment_protocol: MED17-dTAG cells were treated with 500 nM JQ1 and 500 nM dTAG v1 for 2 hours prior to E2.


title: ChIPseq of Atf1-FLAG, 2h with NSF, input, rep 3

value: NSF


title: H3K27ac_Pdgfra_R1


title: NHBE cells, mock infected, 10 hr timepoint

description: 10x Genomics

value: mock infected


title: H3K27ac_Oct4_R3

value: no treatment


title: GJRET GEX

city: Wuhan

first: jian

last: guan

state: China

address: Aier eye hospital,Wuhan

institute: wuhan aier eye hospital

description: 10x Genomics

data_processing:
The offline data was analyzed using CellRanger (3.1.0), the official software provided by 10x Genomics. Reads produced from the 5′ gene expression profiling were aligned to the GRCh38 genome first. Then, low-quality genes and cells were filtered out, retaining genes that were expressed in at least 10 cells. To further remove potential doublets, cells were filtered based on the number of genes and the percentage of mitochondrial genes.
Rapid SBS Kit V2 2x100bp kit (Illumina)
10X single-cell application
CellRanger (3.1.0)
Seurat
Assembly: GRCH38
Supplementary files format and content: .fastq.gz,Tab-separated values files and matrix files

source_name: eye ball

extract_protocol:
The digestive enzyme system was prepared as follows: A clean Miltenyi Biotec C tube was taken and filled with 2.3mL of buffer X, 62.5µL of digestive enzyme P, 25µL of buffer Y, and 100µL of digestive enzyme D. Then, 12.5µL of digestive enzyme A (prepared and dosed according to the instructions of the Multi Tissue Dissociation Kit 2) was added to the C tube along with the cut cornea and limbal tissue.
To ensure proper safety measures, all experimental procedures were performed in a P3-level laboratory. Single-cell lysis and RNA first-strand synthesis were conducted using the 10X Chromium Single Cell 5′ Library & Gel Bead Kit as per the manufacturer's protocol. Subsequently, all samples were heated to 85°C for 5 minutes to denature the viruses. RNA samples were wiped with 80% EtOH thrice and then transferred to a sealed plastic box for transportation30,31.   The RNA and VDJ library preparation followed the protocol provided by the Chromium Single Cell V(D)J Reagent Kits (10X Genomics) in a P2 laboratory. The libraries were then quantified using Qubit 3.0 (Thermo Fisher), Fragment Analyzer, and qPCR. Finally, sequencing was performed using the Hiseq 2500 platform running the Rapid SBS Kit V2 2x100bp kit (Illumina) with a 26x91 pair-end reading mode32,33. Sequencing depths of 10,000 read pairs per cell and 5,000 read pairs per cell were aimed for the mRNA library and VDJ libraries, respectively (Table S3). Sequencing results were available within two days.

value: corneal cells

value: eye ball

tag: age


title: GJRET

description:
10x Genomics
V(D)J-seq


title: H3K27ac_Oct4_R2


title: ChIPseq of Atf1-FLAG, 2h with NSF, input, rep 1


title: MED17-dTAG, clone1, dTAG

value: breast

value: dTAG, ethanol


title: GJREB

description:
10x Genomics
V(D)J-seq


title: MED17-dTAG, clone1, dE

value: dTAG, E2


title: GJLET

description:
10x Genomics
V(D)J-seq


title: ChIPseq of Atf1-FLAG, 2h with NSF, input, rep 2

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 atf1-6xGly-3xFlag::kanMX


title: MED17-dTAG, clone1, JE

treatment_protocol: MED17-dTAG cells were treated with 500 nM JQ1 for 2 hours prior to E2.

value: DMSO, E2, JQ1


title: H3K27ac_Oct4_R1


title: ChIPseq of Atf1-FLAG, 2h with methanol, input, rep 3

value: MeOH


title: H3K27ac_Pdgfra_R2

value: H3K27ac, Abcam, ab4729


title: H3K27ac_DP_R3


title: GJLEB

description:
10x Genomics
V(D)J-seq


title: MED17-dTAG, clone1, E2

value: breast cancer cells

value: DMSO, E2


title: ChIPseq of Atf1-FLAG, 2h with methanol, input, rep 2


title: H3K27ac_DP_R2

value: nEnd


title: MED17-dTAG, clone1, Veh

value: DMSO, ethanol


title: H929, shPPP1R15Bv2, replicate 3

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
H929 treated with shPPP1R15B construct 2, replicate 3
H929.scPPP1R15Bv2-3

data_processing:
Paired-end reads were aligned to hg38 genome using STAR v2.5.3a
transcripts quantification  using RSEM v1.3 (Li 2011) based on Gencode v35 annotation
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: 90% RPMI + 10% FBS + 1% 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Scramble shRNA vs PPP1R15B-shRNA1 and 2


title: ChIPseq of Atf1-FLAG, 2h with methanol, input, rep 1


title: H929, shPPP1R15Bv2, replicate 2

description:
H929 treated with shPPP1R15B construct 2, replicate 2
H929.scPPP1R15Bv2-2


title: H3K27ac_DP_R1


title: ChIPseq of Atf1-FLAG, 0h, input, rep 3


title: MED17-dTAG, clone1, input

value: none (input)


title: 4BD_dBET6+E2

treatment_protocol: BRD4-BD mutant cells were treated with doxycycline at 100 ng/ml overnight. Next day, cells were treated with 500 nM dBET6 for 2 hours prior to E2. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: FLAG, Sigma F1804

value: Dox, dBET6, E2


title: H929, shPPP1R15Bv2, replicate 1

description:
H929 treated with shPPP1R15B construct 2, replicate 1
H929.scPPP1R15Bv2-1


title: H3K9me3_Pdgfra_R3

value: H3K9me3, Upstate, 7442

value: no treatment


title: 4BD_dBET6

treatment_protocol: BRD4-BD mutant cells were treated with doxycycline at 100 ng/ml overnight. Next day, cells were treated with 500 nM dBET6 for 2 hours prior to ethanol. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: breast

value: Dox, dBET6, ethanol


title: H929, shPPP1R15Bv1, replicate 3

description:
H929 treated with shPPP1R15B construct 1, replicate 3
H929.scPPP1R15Bv1-3


title: H929, shPPP1R15Bv1, replicate 2

description:
H929 treated with shPPP1R15B construct 1, replicate 2
H929.scPPP1R15Bv1-2


title: ChIPseq of Atf1-FLAG, 0h, input, rep 1


title: H3K9me3_Pdgfra_R1


title: ChIPseq of Atf1-FLAG, 0h, input, rep 2


title: H3K9me3_Pdgfra_R2


title: H929, shPPP1R15Bv1, replicate 1

description:
H929 treated with shPPP1R15B construct 1, replicate 1
H929.scPPP1R15Bv1-1


title: H3K9me3_Oct4_R3


title: H3K9me3_Oct4_R2


title: 9464D_KO_IGG_REP2

city: Badalona

first: David

last: Corujo

address: Ctra de Can Ruti, Camí de les Escoles

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Paired end reads were adapter and quality trimmed with trimgalore using --stringency 3
Reads were aligned using Bowtie2 (Langmead, et al 2009 PMID: 19261174) to the mm10 mouse genome assembly with the following options: --very-sensitive --no-discordant --no-mixed -X 700 –dovetail
The resulting alignment bam files were filtered to retain only concordant proper pair alignments using samtools sam flag 0x2 and minimum mapping quality score of 30
Coverage signal profiles in bigwig format were generated using the bamCoverage function from deepTools (Ramírez et al., 2014 PMID: 24799436) with a Counts-Per-Million per-sample normalization using a bin of 100bp, ignoring ChrM for normalization
Epic2 (Stovner et al., 2019 PMID: 30923821) was used to perform peak calling in the form of broad domain detection on the filtered aligned reads using the KO samples as background, a bin size of 2000bp and the following options: --guess-bampe -kd -fdr 0.00001 –gaps-allowed 5. Problematic regions from the ENCODE blacklist were substracted and domains with a 75% overlap with a blacklisted region were excluded (Amemiya et al., 2009 PMID: 31249361).
Assembly: mm10
Supplementary files format and content: .bw, BigWig files with signal coverage profiles
Supplementary files format and content: .bed, regions called as peaks by epic2
Library strategy: CUT&RUN

source_name: Brain

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 using IMDM (Thermo Scientific) supplemented with 10% heat-inactivated FBS and 1% Penicillin-Streptomycin (Thermo Scientific).

extract_protocol:
CUT&RUN reactions were performed as described in Meers et al., 2019 (PMID: 31232687) following the “Standard CUT&RUN” protocol. Briefly, freshly harvested 1M 9464D cells were bound to concanavalin-A paramagnetic beads (Epicypher), then split equally, resuspended in antibody binding buffer and incubated overnight with either home-made macroH2A1 antibodies (described in Buschbeck et al., 2009 PMID: 19734898. and Douet et al., 2017 PMID: 28283545) and an IgG non-targeting control (Abcam ab46540). Both antibodies were diluted 1:100 in the binding reaction. Samples were then washed and bound with pA/G-MNase (Epicypher), chromatin digestion started by addition of CaCl2 and stopped after 30min with STOP buffer containing chelating agents. Samples were then incubated for 30min at 37oC to release CUT&RUN fragments, incubated 1h at 50oC with proteinase K and purified using ChIP DNA Clean & Concentrator (Zymo Research).
Sequencing libraries were prepared with the KAPA HyperPrep kit (Roche) and NEXTflex DNA barcodes for Illumina (Bioo Scientific)

treatment_protocol: Murine NB cell line 9464D was transfected with ribonucleoprotein (RNP) complexes containing gene-specific crRNA, tracrRNA, and a recombinant Cas9 protein (all from IDT) using an optimized electroporation program.

value: Brain

value: 9464D cell

value: Mouse neuroblastoma cell line

value: H2afy CRISPR KO


title: 4BD_Veh

description: BRD4-BD muant binding sites from V and E2 were combined and provided as a single BED file.

treatment_protocol: BRD4-BD mutant cells were treated with doxycycline at 100 ng/ml overnight. Next day, cells were treated with DMSO for 2 hours prior to ethanol. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: Dox, DMSO, ethanol


title: 9464D_KO_MH2A1_REP2


title: 4BD_E2

treatment_protocol: BRD4-BD mutant cells were treated with doxycycline at 100 ng/ml overnight. Next day, cells were treated with DMSO for 2 hours prior to E2. Cells were treated with 1 mM DSG for 30 min and then with 1% formaldehyde for 10 min at room temperature.

value: Dox, DMSO, E2


title: 4BD_input

value: breast cancer cells


title: H929, shCram, replicate 3

description:
H929 treated with shCram, replicate 3
H929.scScram-3

value: shScram


title: 9464D_CTRL_MH2A1_REP2

value: Control


title: H3K9me3_Oct4_R1

value: nEnd


title: H929, shCram, replicate 2

description:
H929 treated with shCram, replicate 2
H929.scScram-2


title: 9464D_CTRL_IGG_REP2


title: MCF7_JE

treatment_protocol: Cells were treated with 500 nM JQ1 (+) for 2 hours prior to E2.


title: H3K9me3_DP_R3


title: H929, shCram, replicate 1

description:
H929 treated with shCram, replicate 1
H929.scScram-1


title: H3K9me3_DP_R2


title: MCF7_JQ1

treatment_protocol: Cells were treated with 500 nM JQ1 (+) for 2 hours prior to ethanol.

value: JQ1 (+), ethanol


title: 9464D_KO_IGG_REP1


title: MCF7_Vehicle

treatment_protocol: Cells were treated with 500 nM JQ1 (-) for 2 hours prior to ethanol.

value: JQ1 (-), ethanol


title: M6_TRIM9_mRNA

city: Gainesville

first: Lu

last: Li

state: Florida

address: 2033 Mowry Rd

institute: University of Florida

description: polyA RNA

data_processing:
For miRNA abundance analysis, we extracted the miRNA sequence from 21nt to 26nt, and counted the abundance of miRNA of different lengths using a custom script. For miRNA isoform analysis, we first classified miRNAs based on their first 18 nt from the 5¢ end, and then calculated the total isoforms using a custom script. The differential expression levels of each miRNA abundance or miRNA kind number were finished through the Deseq2 package (version 1.20.0) of R. For miRNA tailing analysis, we calculate the total abundance of miRNA 3¢ with or without tailing, and miRNA tailing does not exceed four nucleotides.
The adaptors were removed by Cutadapt software (version 3.4), and then the clean FASTQ file was mapped to the human genome (hg38) by STAR software, and the parameters were STAR --genomeDir genome.index --readFilesIn fastq1 fastq2 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif –outFileNamePrefix output_file. Further, we use stringtie software (version 2.1.3) to estimate transcript abundances and generate read coverage tables for Ballgown, the parameters are stringtie BAM_file -G GTF_file -A output.tab -e -B -o output.gtf. Ballgown (version 2.24.0) were used to perform various statistical analyses for differential expression, in which low-expressed transcripts were filtered out. The cumulative fraction curve (CFC) were drawn by matplotlib (version 3.4.1).
Genome_build: hg38
Supplementary_files_format_and_content: miRNA abundance, miRNA isoform kind number, mRNA abundance

source_name: mRNA, TRIM9 TDMD transfection

growth_protocol: HEK293T cell were cultured in Dulbecco modified Eagle medium (DMEM; Sigma-Aldrich).

extract_protocol:
Total RNA was extracted by the Trizol reagent (Invitrogen) 48 hours post transfection according to the manufacturer’s protocol.
Small RNAs (18-40 nt) from BCL2L11 or TRIM9 trigger expressed 293T cells were sequenced by Novogene, using the NEBNext small RNA library preparation protocol and illumina sequencing. PolyA-RNAs from BCL2L11 or TRIM9 trigger expressed 293T cells were enriched by Poly-dT and sequenced by Novogene using a custom protocol.

treatment_protocol: HEK293T cells were transfected with polyethylenimine (PEI) MAX 40K (Polysciences) or lipofectamine 3000 (Invitrogenaccording to the manufacturer’s protocols. Briefly, 5×105 cells/well were seeded in 6-well plates for 24 hr. For 293T cells, 2 μg GFP-TDMD plasmid was transfected in each well with 8 μg PEI in 250 μl Opti-MEM (Gibco), or 5 µL of lipofectamine 3000 and 5 µL of P3000 reagent in 250 μl Opti-MEM for 293T cells.  Greater than 90% transfection efficiency was achieved as estimated by microscopic evaluation of GFP expression at 48 hours.

tag: transfection


title: MCF7_E2

treatment_protocol: Cells were treated with 500 nM JQ1 (-) for 2 hours prior to E2.


title: 9464D_CTRL_IGG_REP1


title: H3K9me3_DP_R1


title: MCF7_JE_input

value: none (input)


title: M5_BCL2L11_mRNA

description: polyA RNA

source_name: mRNA, BCL2L11 TDMD transfection


title: 9464D_CTRL_MH2A1_REP1


title: 9464D_KO_MH2A1_REP1


title: MCF7_JQ1_input


title: H3K4me1_Pdgfra_R1

value: H3K4me1, Abcam, ab8895


title: H3K4me1_Pdgfra_R3

value: no treatment


title: H3K4me1_Pdgfra_R2


title: 3.glp-1

first: Jiehui

last: Chen

address: 320 Longwood Ave

institute: Boston Children’s Hospital

data_processing:
For data analysis, reference genome sequences and gene annotation were downloaded from ENSEMBL (Caenorhabditis_elegans.WBcel235). Raw data were pre-processed by Fastp (v0.12.1)(Chen et al., 2018) with default parameters. Cleaned data were then aligned to the reference genome via software Hisat2 (v2.1.0)(Kim et al., 2015). FeatureCounts (v1.5.3)(Liao et al., 2014) was used to count the reads mapped to each gene.
The Differentially Expressed Genes (DEGs) were calculated by Deseq2 (v1.26.0)(Love et al., 2014) with padj < 0.01 and Foldchange >2. Enrichment analysis of genes was carried out by Metascape (https://metascape.org/) with default parameters(Zhou et al., 2019).
To discover motifs in the promoters of up-regulated or down-regulated genes, start codons’ positions of these genes were extracted and executed findMotifsGenome.pl of HOMER(v4.11)(Heinz et al., 2010) with ‘-size -600,+50 -len 8’. AnnotatePeaks.pl of HOMER was used to find individual motif occurences in these promoters.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Caenorhabditis elegans

source_name: somatic gonad

growth_protocol: Synchronized worms were grown on NGM plates with standard techniques at 25°C until day 1 of adulthood.

extract_protocol:
Reverse transcription was performed using SuperScript II reverse transcriptase (Invitrogen). cDNA was further PCR-amplified with KAPA HiFi HotStart ReadyMix (KAPA Biosystems) for 18 cycles.
Uncontaminated samples were subjected to automated single-cell RNA-Seq library construction based on a Bravo robot station (Cui et al., 2019).

treatment_protocol: Worms expressing DTC-specific mCherry were anesthetized in levamisole. Gonads were dissected with an insulin needle. Dissected gonads were digested in 20 mg/ml pronase. On an Olympus IX73 microscope, DTCs were isolated from gonad by an insulin needle and picked by a broken microinjection needle (Harvard Apparatus) mounted on an Eppendorf TransferMan 4r.

value: somatic gonad

value: distal tip cells

tag: time

value: Day 1 Worms


title: 4.glp-1


title: M1_GFP_mRNA

description: polyA RNA

source_name: mRNA, GFP control  transfection

value: GFP


title: H3K4me1_Oct4_R3


title: MCF7_Vehicle_input

value: breast


title: H3K4me1_Oct4_R2


title: S6_TRIM9_sRNA

description: small RNA

source_name: sRNA, TRIM9 TDMD transfection


title: 2.glp-1


title: M2_BCL2L11_mRNA

description: polyA RNA


title: PV-A-3 hour3

city: 长春

first: 金涛

last: 茹

state: 中国

address: 吉林省长春市解放大路理化楼

department: 新能源与环境

institute: 吉林大学

data_processing:
It includes quality control, alignment, quantification, differential significance analysis, functional enrichment and gene structure analysis
Supplementary files format and content: tab-delimited text file includes raw counts, fpkm for each Sample

organism: Pseudomonas veronii

source_name: bacteria

extract_protocol:
RNA is extracted from cells using standard extraction methods, followed by an Agilent 2100 bioanalyzer for precise measurement of RNA integrity and total RNA.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: bacteria

value: Aniline degradation


title: M4_GFP_mRNA

description: polyA RNA


title: S5_BCL2L11_sRNA

description: small RNA

source_name: sRNA, BCL2L11 TDMD transfection


title: H3K4me1_Oct4_R1


title: MCF7_E2_input


title: PV-A-1 hour3

address: 吉林省长春市解放大路理化楼


title: M3_TRIM9_mRNA

description: polyA RNA


title: H3K4me1_DP_R3


title: PV-A-2 hour3

address: 吉林省长春市解放大路理化楼


title: 3.WT


title: S4_GFP_sRNA

description: small RNA

source_name: sRNA, GFP control  transfection


title: 4.WT


title: S3_TRIM9_sRNA

description: small RNA


title: PV-3 hour0

address: 吉林省长春市解放大路理化楼


title: S2_BCL2L11_sRNA

description: small RNA


title: PV-2 hour0

address: 吉林省长春市解放大路理化楼


title: H3K4me1_DP_R2


title: H3K4me1_DP_R1


title: CCS, scRNAseq

city: Ottawa

first: Kyoung-Han

last: Kim

state: Ontario

address: 40 Ruskin Street

country: Canada

institute: University of Ottawa Heart Institute

description: 10x Genomics

data_processing:
Following 10x scRNA-sequencing of samples, reads were aligned using CellRanger (v3.1.0) and the mm10-3.0.0 reference transcriptome annotation file. Sequences and annotations for tdTomato and Cre were manually added to the fasta and gtf file, respectively, using cellranger mkref. A total of 10,407 cells were sequenced, with a mean of 35,041 reads per cell and a median of 3,055 genes detected per cell. Demultiplexing was performed using Python according to the unique MULTI-seq barcodes given to each P1, P2, and P4 sample prior to pooling. Downstream bioinformatic analysis was performed using the Seurat package (v4.0.0). Briefly, the quality assessment of data led to the inclusion of cells with >2,000 and <5,500 detected genes, and percentages of mitochondrial genes of >5% and <25%. Additional biological filtering was applied based on markers of common cell types known to exist in the heart. For instance, 1.03% of all cells (72 out of 6927 cells) that lacked expression of cardiomyocyte genes (Myh6, Myh7, Tnnt2, Tnni1, Ryr2) but expressed markers of fibroblasts (Postn, Col1a1, Col1a2, Col3a1) or smooth muscle cells (Cald1, Emilin1, Hexim1, Tagln and Fabp4), were excluded from downstream analysis. Following pre-processing of the data, feature counts were normalized by log-transformation. The top 5,000 features were identified using “vst” as the selection method. Normalized counts for these variable genes were scaled and mitochondrial gene counts and the number of UMIs were regressed out. Linear dimensional reduction was performed using principal component analysis (PCA).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
P1, P2, and P4 neonatal cardiomyocytes were isolated by enzymatic digestion with 0.075% Collagenase II/Dispase. Isolated cardiomyocytes were suspended in culture medium (DMEM/F-12 with 10% FBS + 1% P/S) were filtered using a 100 uL cell strainer (VWR, 10199-658), then transferred to separate polypropylene tubes (Falcon). Cells were incubated with SytoxTM Blue dead cell stain (Thermofisher, S34857, 1:2000) prior to Fluorescence Activated Cell Sorting (FACS). Gating was done for size and granularity, then for Sytox-based viability, and finally for tdTomato-based identification of conduction cells. Approximately 0.1-0.2% of total viable cardiomyocytes were tdTomato-positive cells for all P1, P2, and P4 cells.   MULTI-seq reagents were generously provided by the developers, and multiplexing of P1, P2, and P4 cells was conducted following the developer’s protocols. In brief, following separate FACS sorting of P1, P2, and P4 CCS cells into culture medium (DMEM/F-12 with 10% FBS + 1% P/S ), cells were pelleted and washed using centrifugation (250 x g, 5 min, 4C) and 1x PBS.  Lipid-modified oligonucleotide anchor mix and unique barcodes were added to each sample at final concentrations of 200 nM. Cells were resuspended by gentle pipetting and were incubated at 4C for 10 min, ensuring to periodically mix by gently tapping. Then, a co-anchor lipid-modified oligonucleotide was added to each sample (final concentration of 200 nM), and cells were incubated at 4C for 5 min. Cells were then pelleted using centrifugation (250 x g, 5 min, 4C) and resuspended in PBS containing 1% BSA to quench residual barcodes. P1, P2, and P4 cells were then pooled into a single tube and subjected to viability assessments and cell counting prior to 10x Genomics scRNA-seq library generation using the Single Cell 3’ v3 kit.
Before library generation, P1, P2, P4 cells were barcoded using MULTI-seq reagents. Then P1, P2, and P4 cells were pooled and library generation was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
scRNA-seq + MULTI-Seq

value: Cardiac cells

value: Heart

value: Postnatal day 1, 2, 4


title: PV-1 hour0

address: 吉林省长春市解放大路理化楼


title: Mtb infected CPT2 knockdown macrophages 4 days post infection_rep3

status: Public on Jun 24 2024

city: Ithaca

first: Nelson

middle: Victor

last: Simwela

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

description:
CPT2_3
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt

data_processing:
STAR-2.7.10b
Reads were mapped to GRCm39 and ASM19595v2 using STAR. Raw read counts were obtained from mapped reads using HTSeq count
Raw and normalised reads were analyzed using DESeq2
Assembly: mm10, ASM19595v2
Supplementary files format and content: txt files for both raw and normalised counts

organism:
Mycobacterium tuberculosis
Mus musculus

source_name: Bone marrow macrophages

extract_protocol:
RNA was extracted using TRIZOL, total RNA from the aqueous phase was purified using the Zymo RNA clean and concentrator kit
Barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit after ribosomal rRNA depletion using the QIAseq FastSelect pan-bacterial and H/M/R kits

value: Bone marrow macrophages

value: CPT2 knockdown

value: Mtb infected - 4 days


title: S1_GFP_sRNA

description: small RNA


title: Mtb infected CPT2 knockdown macrophages 4 days post infection_rep1

description:
CPT2_1
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: Mtb infected FATP1 knockdown macrophages 4 days post infection_rep1

description:
FATP1_1
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt

value: FATP1 knockdown


title: Mtb infected FATP1 knockdown macrophages 4 days post infection_rep3

description:
FATP1_3
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: Mtb infected CPT2 knockdown macrophages 4 days post infection_rep2

description:
CPT2_2
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: 1.glp-1


title: Mtb infected PLIN2 knockdown macrophages 4 days post infection_rep2

description:
PLIN2_2
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt

value: PLIN2 knockdown


title: 1.WT


title: Mtb infected PLIN2 knockdown macrophages 4 days post infection_rep3

description:
PLIN2_3
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: 2.WT


title: Mtb infected PLIN2 knockdown macrophages 4 days post infection_rep1

description:
PLIN2_1
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_rep2

description:
SC_2
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt

value: Scramble (WT)


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_rep3

description:
SC_3
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: Coho salmon, fin, 48h post sea lice exposure

city: Midlothian

first: Sarah

last: Salisbury

address: Easter Bush Campus

country: United Kingdom

institute: The Roslin Institute, University of Edinburgh

description: Sample 28

data_processing:
Genome indexing and library mapping was performed with STAR (version 2.7.10a).
Assembly: We appended the mitochondrial genome from the ENSEMBL V2 Atlantic salmon genome (Salmo_salar.ICSASG_v2.dna_rm.toplevel.fa.gz, v2, release 105, masked genome, assembly ID: GCA_000233375.4) to the ENSEMBL V3 Atlantic salmon genome (Salmo_salar.Ssal_v3.1.dna_rm.toplevel.fa.gz, v3.1, release 106, masked genome, assembly ID: GCA_905237065.2) for both the .gff and .fna files prior to indexing. For coho salmon, we appended this species’ mitochondrial genome (version NC_009263.1, NCBI) to the ENSEMBL V2 coho salmon genome (Oncorhynchus_kisutch.Okis_V2.dna_rm.toplevel.fa.gz, v2, release 106, masked genome, assembly ID: GCA_002021735.2) for both the .gff and .fna files prior to indexing.
Supplementary files format and content: Tab-separated values file for barcodes
Supplementary files format and content: Tab-separated values file for features
Supplementary files format and content: Matrix file

molecule: nuclear RNA

organism: Oncorhynchus kisutch

source_name: pelvic fin

extract_protocol:
Nuclei were extracted in accordance with Ruiz Daniels et al. (2023) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484441/). In brief, approximately 45 mg tissue samples were cut with scissors in 1 mL of TST buffer for 10 minutes on ice before being filtered through a 40 µm Falcon™ cell strainer (Thermo Fisher Scientific, catalog no. 08-771-2). A further 1 mL of TST and 3 mL of 1X PBS + BSA buffer were added to each sample before centrifuging at 4°C for 5 minutes at 500 g. Samples were resuspended in 1 mL 1X ST buffer filtered again through a 40 µm cell strainer, stained with Hoechst 33342 Solution (Thermo Fisher Scientific, catalog no. 62249) and then nuclei integrity was visually assessed using a fluorescent microscope. A disposable flow haemocytometer (C-Chip Neubauer Improved (100 µm depth), NanoEnTek, catalog no. DHC-N01) was then used to estimate nuclei counts.
Samples were processed with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (10X Genomics) using the protocol outlined in the User Guide (CG000315 Rev C). Samples were diluted with nuclease-free water to a target concentration that would recover approximately 7000 nuclei in the final library. Samples were then loaded on the Chromium Controller for nuclei droplet formation. After subsequent nuclei and UMI barcoding and reverse transcription, resulting cDNA was then amplified, fragmented, and indexed with Truseq adapters and Illumina sample indexes.

value: pelvic fin

value: 48h post sea lice exposure


title: Coho salmon, fin, 12h post sea lice exposure

description: Sample 45

value: 12h post sea lice exposure


title: Coho salmon, fin, 60h post sea lice exposure

description: Sample 10

value: 60h post sea lice exposure


title: Coho salmon, fin, 36h post sea lice exposure

description: Sample 9

value: 36h post sea lice exposure


title: Coho salmon, skin, 36h post sea lice exposure

description: Sample 37

source_name: skin

value: skin


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_rep1

description:
SC_1
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: Coho salmon, skin, 24h post sea lice exposure

description: Sample 33

value: 24h post sea lice exposure


title: Coho salmon, skin, control

description: Sample 25

value: control


title: Coho salmon, skin, 48h post sea lice exposure

description: Sample 34


title: Mtb infected FATP1 knockdown macrophages 4 days post infection_rep2

description:
FATP1_2
Lipids raw counts_Mouse.txt, Lipids norm counts_Mouse.txt
Lipids raw counts_Mtb.txt, Lipids norm counts_Mtb.txt


title: Coho salmon, skin, 12h post sea lice exposure

description: Sample 24


title: Coho salmon, fin, 24h post sea lice exposure

description: Sample 16


title: SNAP280_1, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 1

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

data_processing:
Raw reads were filtered for low quality reads using BBDuk (BBtools, Joint Genome Institute)
Reads were aligned to the Phaseolus vulgaris genome using HISAT2 (Kim et al. 2019).
Gene-level counts were obtained using featureCounts (Liao et al. 2014)
Assembly: Phaseolus vulgaris downloaded from Phytozome ("Phaseolus vulgaris v2.1, DOE-JGI and USDA-NIFA, http://phytozome.jgi.doe.gov/")
Supplementary files format and content: tab delimited file contains raw counts for each sample

organism: Phaseolus vulgaris

source_name: Whole seedling

growth_protocol: Seeds were sown in 27.8 × 53.3 cm flats containing fine quartz sand. Thirty seeds of each cultivar were planted 1 cm deep. Flats were kept at 26 °C and watered regularly to maintain soil moisture. Whole seedlings were harvested when the cotyledons had fully emerged. Seedlings were flash-frozen in liquid nitrogen immediately after harvest.

extract_protocol:
E.Z.N.A.® Plant RNA Kit
Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: All cultivars were under the same conditions. Intrinsic difference due to genotype status were investigated.

value: Whole seedling

value: Romano 118/SnAP280


title: SNAP280_4, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 4


title: SNAP353_4, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 4

value: Top Crop/SnAP353


title: SNAP280_2, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 2


title: SNAP353_2, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 2


title: SNAP280_3, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 3


title: SNAP353_1, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 1


title: SNAP353_3, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 3


title: SNAP279_3, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 3

value: Roma II/SnAP279


title: SNAP279_1, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 1


title: SNAP255_3, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 3


title: SNAP255_4, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 4


title: Coho salmon, fin,  control

description: Sample 44


title: Coho salmon, skin, 60h post sea lice exposure

description: Sample 41


title: SNAP255_2, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 2


title: SNAP227_4, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 4


title: SNAP227_3, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 3


title: SNAP255_1, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 1


title: SNAP227_2, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 2


title: SNAP190_4, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 4

value: Kentucky Wonder Pole /SnAP190


title: SNAP190_2, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 2


title: SNAP190_3, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 3


title: SNAP190_1, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 1


title: SNAP153_3, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 3

value: Golden Gate Wax /SnAP153


title: SNAP279_4, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 4


title: SNAP153_2, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 2


title: SNAP095_4, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 4


title: SNAP056_3, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 3

value: Bush Romano 350 /SnAP056


title: SNAP279_2, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 2


title: SNAP095_2, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 2


title: SNAP095_3, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 3


title: SNAP046_4, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 4


title: SNAP056_4, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 4


title: SNAP153_1, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 1


title: SNAP056_2, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 2


title: SNAP046_3, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 3


title: SNAP045_3, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 3


title: SNAP045_4, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 4


title: SNAP046_2, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 2


title: SNAP045_2, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 2


title: SNAP006_4, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 4


title: SNAP046_1, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 1


title: SNAP006_3, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 3


title: SNAP045_1, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 1


title: Optimization2;RPE1;opCas12a;T21C

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

address: 1050 Boyles Street

institute: NCI/NIH

data_processing:
demultiplexing
mapping to library with bowtie 1 and extract read count for each gRNA in the library
Assembly: hg18
Supplementary files format and content: read counts of the mapped sequencing data in the format of txt.
Library strategy: CRISPR

source_name: cell line

extract_protocol:
Genomic DNA was extracted from the cell pellets collected at the start (T0) and end time points using the Wizard Genomic DNA Purification Kit (Promega #A1120).
First, the lentiviral integrated hgRNA expression cassettes were amplified from genomic (g)DNA equivalent of ~ 100-fold library coverage using NEBNext Ultra II Q5 Master Mix (New England Biolabs #M0544X). Individual 50 µL PCR reactions containing 3.5 μg gDNA were performed using PCR1_Hybrid_Outer_F2 and PCR1_Hybrid_Outer_R1 primers for the optimization and exon deletion screens and primers A265 and PCR1_BE_Rev for the base editor screens, respectively (see Table S3). After pooling the individual PCR-1 reactions, a fraction was purified using a PCR purification column and used as template for PCR-2, in which each sample was barcoded with unique i5 and i7 index primer combinations. The resulting PCR-2  products were resolved on a 2% agarose gel using SYBR Safe DNA stain (ThermoFisher Scientific #S33102). The desired band was excised and subjected to gel extraction (ThermoFisher Scientific #K0691). Quantification of the extracted libraries was conducted using the Qubit dsDNA HS assay (ThermoFisher Scientific #Q32851) and Tape Station (Agilent #5067-5582 and #5067-5583). The quantified and validated sequencing libraries were pooled, and paired-end sequencing was performed on either an Illumina NextSeq 500 or a NovaSeq 6000 platform.

value: cell line

value: retinal pigment epithelial cells

value: lenti virus infected


title: Optimization2;RPE1;Cas12a_Ultra;T21C


title: SNAP006_1, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 1


title: Optimization2;RPE1;Cas12a_Ultra;T21B


title: Optimization2;RPE1;opCas12a;T21A


title: SNAP006_2, Marker S02_34499796 Status: "AA", Phenotype: "sensitive", Replicated 2


title: SNAP095_1, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 1


title: Optimization2;RPE1;opCas12a;T21B


title: Optimization2;HAP1;Cas12a_Ultra;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-35

value: wild type


title: Optimization2;HAP1;Cas12a_Ultra;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-33


title: Optimization2;RPE1;Cas12a_Ultra;T0


title: Optimization2;HAP1;opCas12a;T15C

value: chronic myelogenous leukemia (CML) cell line KBM-32


title: Optimization2;HAP1;opCas12a;T15A

value: chronic myelogenous leukemia (CML) cell line KBM-30


title: SNAP056_1, Marker S02_34499796 Status: "GG", Phenotype: "tolerant", Replicated 1


title: Optimization2;HAP1;Cas12a_Ultra;T15B

value: chronic myelogenous leukemia (CML) cell line KBM-34


title: Optimization2;RPE1;opCas12a;T0


title: Optimization2;HAP1;opCas12a;T15B

value: chronic myelogenous leukemia (CML) cell line KBM-31


title: Optimization2;HAP1;Cas12a_Ultra;T0

value: chronic myelogenous leukemia (CML) cell line KBM-29


title: Exon deletion; Plasmid

value: chronic myelogenous leukemia (CML) cell line KBM-7


title: Base editor; evoCDA1; T18B

value: chronic myelogenous leukemia (CML) cell line KBM-14


title: Base editor; evoCDA1; T0

value: chronic myelogenous leukemia (CML) cell line KBM-12


title: Optimization2;HAP1;opCas12a;T0

value: chronic myelogenous leukemia (CML) cell line KBM-28


title: Base editor; evoCDA1; T18C

value: chronic myelogenous leukemia (CML) cell line KBM-15


title: Base editor; ABE8e; T18C

value: chronic myelogenous leukemia (CML) cell line KBM-11


title: Optimization2;RPE1;Cas12a_Ultra;T21A

value: cell line


title: Base editor; evoCDA1; T18A

value: chronic myelogenous leukemia (CML) cell line KBM-13


title: Base editor; ABE8e; T18B

value: chronic myelogenous leukemia (CML) cell line KBM-10

value: lenti virus infected


title: Base editor; BEACON2; T18C

value: wild type


title: Base editor; BEACON2; T18A


title: Base editor; BEACON2; T18B


title: Base editor; APOBEC1; T18B


title: Base editor; APOBEC1; T18C


title: Base editor; APOBEC1; T18A

value: chronic myelogenous leukemia (CML) cell line KBM-9


title: Base editor; APOBEC1; T0

value: chronic myelogenous leukemia (CML) cell line KBM-8


title: Liver, K27, rep1 [D1]

city: Beijing

first: Juntao

last: Bie

address: Xueyuan road 38

institute: Peking university

data_processing:
1. Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
2. Comparative analysis: The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
3. Quantification of gene expression levels: Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
The formula is shown as follow: $$FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * TranscriptLength(kb)}}$$
4. Differential expression analysis:  For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg?s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 found by DESeq2 were assigned as differentially expressed. For the samples without biological replicates: Differential expression analysis of two samples was performed using the edgeR. The Pvalue < 0.01 & Fold Change ≥1.5  was set as the threshold for significantly differential expression.
Assembly: Mus_musculus.GRCm38_release95.genome.fa
Supplementary files format and content: The expression level (fpkm) of all differentially expressed genes

source_name: Liver

extract_protocol:
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer. The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: DOX + K27


title: Liver, DOX, rep1 [B1]

value: DOX


title: Liver, K35, rep3 [C3]

value: DOX + K35


title: Liver, K35, rep2 [C2]


title: Liver, vehicle, rep1 [A1]

value: vehicle


title: Base editor; ABE8e; T0


title: Liver, vehicle, rep3 [A3]


title: 19882X1 P14 Lung ILC2 pIC #2

city: Salt Lake Ciy

first: Anna

last: Beaudin

state: Utah

address: 2001 Circle of Hope Drive

department: Hematology/HCI

institute: University of Utah

data_processing:
Fastq files were aligned to the refdata-gex-mm10-2020-A mouse reference dataset from 10X genomics using cellranger count version 7.0.1 to create quality control metrics, Loupe Browser files and filtered gene barcode matrices.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices in h5 format

source_name: lung

growth_protocol: Mice were born and housed in the Univeristy of Utah Comparitive Medicine Center (CMC) SPF animal facility in accordance with the guidelines estabilshed by the IACUC.

extract_protocol:
Cells were sorted using an Aria III (BD Bioscience) into ice-cold sort media (1X PBS + 5mM EDTA + 10% BSC), media swapped in 0.4% BSA in PBS.
Sorted cells were processed on the same day through the Next GEM Single Cell 3' Gene Expression Library Prep v3.1 with UDI (10X Genomics) per the manufacturer’s protocol.

treatment_protocol: Postnatal day (P)14 wild-type C57BL/6 mouse lungs from prenatal (Embyonic day 14.5) saline or poly(I:C) (20mg/Kg) were used to prepare single cell suspensions using the lung dissociation kit (Miltenyi) and gentleMACS Octo dissocitor with heating (Miltenyi). ST2+Thy1.2+ double positive cells were enriched using streptavidin microbeads (Miltenyi) and sorted as Lin-CD45+IL7ra+Th1.2+ST2+.

value: lung


title: Base editor; ABE8e; T18A


title: Liver, K27, rep3 [D3]


title: 19649X2 P14 Lung ILC2 Saline #2

value: saline


title: 19735X1 P14 Lung ILC2 pIC #1


title: Liver, DOX, rep2 [B2]


title: 19649X1 P14 Lung ILC2 Saline #1


title: Base editor; BEACON2; T0

value: chronic myelogenous leukemia (CML) cell line KBM-12


title: Liver, K35, rep1 [C1]


title: Liver, DOX, rep3 [B3]


title: MNF-OKS-4#

city: Hangzhou

first: Chengchen

last: Zhao

state: Zhejiang

address: Dunyu Road No.600, Xihu District

institute: Westlake University

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4)  and then mapped to the mm10 reference genome with HISAT2 (v2.2.1) , and StringTie (v2.2.1)  was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads).
Assembly: mm10
Supplementary files format and content: expression matrix(FPKM)

source_name: Cell

extract_protocol:
RNA was harvested using FreeZol reagent (Vazyme),1 µg of RNA was used for sequencing libraries construction
Liarbries were constructed by VAHTS mRNA-seq v3 Library Prep Kit for Illumina (NR611, Vazyme)

value: Cell

value: iPSC


title: Library 1: Sm22Cre(-)Wnk1(lox/lox) aortas, GEX

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Pre-processing of sequencing results to generate count matrices was performed using the 10x genomics Cell Ranger pipeline, aligning to the mm10 genome build and Ensembl 93 annotations.
Data was analyzed with Seurat v3.1.1 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output directories as .tar.gz archives, including barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Aorta

extract_protocol:
Mice under isoflurane anesthesia received an i.v. injection of 2µg anti-CD45.2-APC to label circulating leukocytes 5 minutes before sacrifice (cervical dislocation under isoflurane anesthesia). Mice were perfused with cold PBS and aortas were collected from Sm22Cre-Wnk1lox/lox (n=3) and Sm22Cre+Wnk1lox/lox (n=4) animals. Aortas were minced and digested for 1 hour at 37°C in RPMI containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) for 1 hour at 37°C with agitation, washed in PBS/1% FCS and passed through a 70µm cell strainer to generate aortic cell suspensions. Cells were incubated for 20’ at 37°C with 0.1µM Calcein-AM (BioLegend #425201) in PBS 1%FCS. Cells were subsequently incubated for 5 minutes with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10µg/ml), and labeled with 1:300 anti-Ter119 PE-Cy7 (BioLegend 116221) and 1:1000 Fixable Viability Dye eFluor™ 780 (ThermoFisher #65-0865-14, 1:1000). Cells from each aorta were washed and labelled with Multi-Seq oligos for sample multiplexing in PBS without FCS, washed, and cells from each genotype were pooled (Sm22Cre-Wnk1lox/lox pool of n=3 aortic cell suspensions; Sm22Cre+Wnk1lox/lox pool of n=4 aortic cell suspensions). After washing, viable Calcein-AM+Ter119-CD45.2-APC- cells were sorted using a BD FACS Aria III with a 100µm nozzle. Sorted cells were washed twice with PBS+0.04% ultrapure BSA, resuspended, counted with Trypan blue (final concentration 800 cells/µl, viability >90%) and loaded in the 10x Genomics Chromium with the aim to capture 10,000 cells per library using volumes according to 10x Genomics recommendations. Libraries were sequenced using Illumina NovaSeq6000 with a S1 flow cell.
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.
MULTI-seq library: amplification was performed at 95°C for 5’ followed by nine cycles at 98°C for 15’’; 60°C for 30’’; 72°C for 30’’ and final elongation 72°C for 1’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 and RPI2 primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ SI-PCR primer as i5 primer (Illumina) was used for MULTI-seq library amplification.
Following the final bead purification, both libraries were pooled as 90% mRNA library, 10%  MULTI-seq library before sequencing.
OTHER: MULTI-seq (sample multiplexing for single-cell RNA sequencing using lipid-tagged indices)

value: Aorta

value: not applicable

value: Total viable cells

value: various


title: Library 2: Sm22Cre(+)Wnk1(lox/lox) aortas, MULTIseq

description:
MultiSeq barcode
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Multiplexing Capture


title: MNF-OKS-3#

value: cell line


title: Library 1: Sm22Cre(-)Wnk1(lox/lox) aortas, MULTIseq


title: Library 2: Sm22Cre(+)Wnk1(lox/lox) aortas, GEX


title: MNF-70NO-2#


title: Liver, K27, rep2 [D2]


title: TTF-OKS-3#


title: MNF-70NO-1#


title: Liver, vehicle, rep2 [A2]


title: TTF-OKS-1#


title: TTF

value: TTF

value: mouse tail tip fibroblasts


title: TTF-70NO-3#


title: Nanog

data_processing:
CUT&Tag library construction was performed using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202). In brief, around 10000 living cells per sample were obtained and mixed with activated Concanavalin A beads, followed by sequentially incubated with primary and secondary antibodies. The beads were then washed and resuspended in pA(G)-Tn5 buffer supplemented with 10 mM MgCl2 for DNA tagmentation. Next, DNA fragments were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and PCR amplified. After purified by VAHTS DNA Clean Beads (Vazyme, N411), libraries were subjected to Illumina Novaseq instruments for sequencing. Antibodies against Nanog (Abcam, ab214549, 1:50), H3K4me (Abcam, ab313500, 1:50), H3K27ac (Abcam, ab4729, 1:50), flag (Sigma, F1804, 1:50), and Smarca4 (Cell Signaling Technology, 52251, 1:50) were used in this study.
The CUT&Tag reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5). SAMtools (v1.16.1) was used to remove the repetitive, low sequencing quality (mapq<30) and the mitochondrial DNA mapped reads in the total mapped reads. The value were further compressed into a binary format for downstream analysis and data visualization. Replicates were merged using samtools merge and then peak calling was performed using MACS (v1.4.2) with parameters as follows: -g mm --keep-dup 1 --nomodel --shiftsize 25. The signals were normalized to one million reads for each sample. Promoters were defined as regions ± 2 kb around transcription start sites (TSSs) of genes.
Assembly: mm10
Supplementary files format and content: BigWig, Peaks&Summits bed

extract_protocol:
DNA was harvested using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901), 100000 cells per sample was used for sequencing libraries construction
Liarbries were constructed by Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).

value: MEF

value: mouse embryonic fibroblast

value: Flag


title: TTF-OKS-2#


title: TTF-70NO-2#


title: NanogBiD


title: TTF-70NO-4#


title: Oct4


title: Nr5a2BiD


title: Sox2BiD


title: Sox2


title: Oct4BiD


title: MNF-OKS-1#


title: A Study on COL6 in periodontitis_1-day post inflammation_Col6a2-KO replicate 2

city: Bethesda

first: Taishi

last: Komori

state: Maryland

address: 30 CONVENT DR RM 125

institute: NIH

description: 10x Genomics

data_processing:
Reads were mapped using the 10X Genomics mm10-2020-A reference transcriptome supplemented with some common mouse mouse transgenes.
Libraries were processed using Cell Ranger version 7.1.0
Secondary analysis was performed using Seurat's R package
Assembly: mm10
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format

source_name: PDL

extract_protocol:
Maxillae were dissected 1 day and 3 days after ligature placement. After dissection, gingival tissue was carefully removed using a scalpel under a stereomicroscope. Subsequently, the 1st, 2nd and 3rd molars were extracted from ligature side and collected into 1X PBS in a petri dish. The teeth were washed three times in 1X PBS prior to Liberase digestion (Roche, CA, USA) that was used to liberate cells from the the PDL. Liberase powder was reconstituted with 0.25% trypsin to a final concentration of 500ug/ml. The teeth were incubated in 2 ml digestion buffer for 90 min at 37°C with shaking.  After digestion, cells were centrifuged at 1500 rpm for 5 min at 4°C. The pellet was resuspended in culture medium (10% FBS α-MEM) and passed through a 70-μm cell strainer (Fisher Scientific) and then subjected to single-cell analysis.
Single-cell RNA sequencing was performed using 10X Genomics Chromium instruments.

value: PDL

value: 11 weeks

value: Ligature-induced periodontitis model


title: A Study on COL6 in periodontitis_3-day post inflammation_Col6a2-KO replicate 1

description: 10x Genomics


title: A Study on COL6 in periodontitis_3-day post inflammation_WT replicate 1

description: 10x Genomics

value: Wild Type


title: scRNA-seqforKLF5WTmouseprostateMouse2

city: Shenzhen

first: Jin-Tang

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd

department: Human Cell Biology and Genetics

institute: Southern University of Science and Technology

data_processing:
Cell Ranger toolkit (v6.0.2) were used to perform de-multiplexing and alignment to the mm10 transcriptome. Default parameters were used to trim the adaptor sequence and remove the low quality reads. The raw output data were processed with the Seurat package (v4.3.0) in R software (v4.1.3) for each individual sample. Further quality control were used to filter cells to those with fewer than 20% mitochondrial RNA content, fewer than 5% red blood cell content, more than 200 unique molecular identifiers (UMI) counts, fewer than 10,000 UMI counts and more than 1000 total number of molecules detected within a cell.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Prostate

extract_protocol:
The single cell suspension was prepared by 5 mg/mL Collagenase Type II digestion and TrypLE dissociation, and then filtered using 40 μm cell strainers. The cells were washed with DPBS (0.04% BSA) for three times and resuscitated to a concentration of 700 ~ 1200 cells/ μL (viability > 85%).
ScRNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) according to the manufacturer’s instructions.
For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumina) to generate 150 bp paired-end reads.

value: Prostate

value: PB-Cre;Pten-/-


title: scRNA-seqforKLF5WTmouseprostateMouse1


title: scRNA-seqforKLF5KRmouseprostateMouse1


title: scRNA-seqforKLF5KRmouseprostateMouse2


title: A Study on COL6 in periodontitis_1-day post inflammation_WT replicate 2

description: 10x Genomics


title: WT_LD_HCM_3

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

data_processing:
Trimmed reads were mapped against the mouse reference (mm39 UCSC) using HiSat2 (v 2.1.0) with parameters --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.10)
Mapped reads were summarized using featureCounts (v 2.0.0) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCm39.105)
Assembly: mm39
Supplementary files format and content: Comma-separated text file containing raw count values for each sample

source_name: murine keratinocytes

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Library preparation (Poly(A) tail RNA selection) and strand-specific RNA sequencing (total RNA amount ≥ 2 µg) was performed by LC Sciences (Houston, USA).

treatment_protocol: Cells grown in high calcium medium (= HCM) for 24h (= LD)

value: murine keratinocytes


title: WT_LD_LCM_1

treatment_protocol: Cells grown in low calcium medium (= LCM) for 24h (= LD)


title: WT_LD_LCM_3


title: WT_LD_HCM_1


title: Nr5a2

value: Cell


title: WT_HD_HCM_2

treatment_protocol: Cells grown in high calcium medium (= HCM) for 72h (= HD)


title: KO_LD_LCM_3


title: KO_LD_LCM_2


title: WT_HD_HCM_1


title: WT_HD_LCM_2

treatment_protocol: Cells grown in low calcium medium (= LCM) for 72h (= HD)


title: WT_HD_HCM_3


title: KO_LD_LCM_1


title: WT_HD_LCM_1


title: KO_HD_LCM_3


title: KO_HD_LCM_2


title: KO_LD_HCM_1


title: WT_LD_LCM_2


title: WT_LD_HCM_2


title: KO_HD_HCM_3


title: MNF

value: MNF

value: mouse neonatal fibroblasts


title: KO_HD_HCM_2


title: KO_HD_HCM_1


title: KO_HD_LCM_1


title: GFP_LD_HCM_3

value: GFP-PKP4-tagged Pkp4-knockout


title: GFP_LD_LCM_3


title: GFP_HD_LCM_3


title: GFP_LD_HCM_1


title: GFP_LD_LCM_1


title: GFP_LD_HCM_2


title: GFP_HD_LCM_2


title: WT_HD_LCM_3


title: KO_LD_HCM_3


title: GFP_HD_HCM_3


title: KO_LD_HCM_2


title: GFP_HD_LCM_1


title: GFP_HD_HCM_1


title: GFP_HD_HCM_2