title: Sample_50


title: DC1, WT, steady state, rep3

status: Public on Aug 04 2024

type: SRA

city: Paris

first: Despoina

last: Koumantou

address: 16 rue Henri Huchard

country: France

institute: INSERM U1149

library_source: transcriptomic

data_processing:
FastQC using FastQC v0.11.9 tool
Adapter triming using TrimGalore v0.6.2 tool
Alignement on mm10 using STAR v 2.7.6a tool
Assembly: mm10
Supplementary files format and content: excel file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA was extracted using the Single Cell RNA purification kit (Norgen, Cat#51800) according to the manufacturer’s instructions with an additional DNAse treatment on-column
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara).

tag: tissue

value: spleen

tag: cell type

value: type 1 conventional dendritic cells

tag: genotype

value: WT

tag: treatment

value: steady state


title: Sample_53

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The raw short-read sequences  were preprocessed using the Rfastp R/Bioconductor package Rsubread package. The raw short-read sequences  were quality-checked and trimmed to remove adapters and low-quality bases using the Rfastp R/Bioconductor package.
The preprocessed reads were then aligned and mapped to the human genome reference GRCh38 using the Subread aligner algorithm provided by Rsubread R/Bioconductor package. The aligned reads (BAM files) from each sample were employed to calculate gene expression abundance at the whole-genome level using the featureCounts function provided by the Rsubread package.
For metatranscriptomic analysis, the obtained RNA sequencing data were processed using the Biobakery suite of tools: KneadData was used to separate the human and the non-human reads; taxonomic profiling was performed using MetaPhlAn to identify and quantify microbial taxa at species level present in the anal samples.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of the raw counts per sample
Supplementary files format and content: raw_counts.txt

organism: Homo sapiens

source_name: HGSIL

extract_protocol:
Total RNA was isolated from the collected samples using the miRNeasy Tissue/Cells Advanced Kits (Qiagen) following standard manufacturer's protocol. RNA concentration and integrity were measured on a Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA samples with RNA integrity number (RIN) over 7 were considered for RNA sequencing. The RNA samples were processed for directional RNA-seq library construction using the Illumina Total RNA Prep with Ribo-Zero Plus library preparation kit according to the manufacturer's protocol.
We performed  100 nt paired-end sequencing using an Illumina Novaseq 6000 platform and obtained ~80 million clusters per sample with 92% >Q30.

value: HGSIL


title: TG75_G2Depleted_25_N2

city: London

first: Thomas

middle: M.

last: Guerin

address: nw1 1at, 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

library_source: genomic

data_processing:
Micro-C datasets were processed through the Distiller pipeline (https://github.com/open2c/distiller-nf, commit 8aa86e)
Reads were aligned to W303 using bwa 0.17.7 and the resulting maps filtered to remove low-quality alignments (MAPQ<30) and cis alignment pairs within 150 bp
Replicates were analysed independently, and their quality assessed before aggregation into sample-level datasets.
Merged contact matrix are provided in mcool files
Assembly: w303
Supplementary files format and content: mcool files contain the contact probabilities of merged replicates

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Micro-C was performed following published protocols[Costantino, 2020 #1788][Slobadyanyuk, 2022 #1888] with minor modifications. Yeast cultures were crosslinked with 3% formaldehyde for 15 minutes at 30 °C. The reactions were quenched by the addition of 250 mM glycine at 30 °C for 5 minutes with agitation. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 5 minutes and washed twice with water. Cells were then resuspended in Buffer Z (50 mM Tris-HCl pH 7.5, 1M sorbitol, 10 mM β-mercaptoethanol) and spheroplasted by addition of 250 mg/ml Zymolyase (100T) in a 30 °C incubator at 200 rpm for 40 to 60 minutes. Spheroplasts were washed once by 4 °C PBS and then pelleted at 4000 rpm at 4 °C for 10 minutes. Chromatin was further crosslinked by suspending pellets in PBS supplemented with 3 mM disuccinimidyl glutarate (ThermoFisher) and incubated at 30 °C for 40 minutes with gentle shaking before quenching by addition of 400 mM glycine for 5 minutes at 30 °C. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 10 minutes, washed once with ice-cold PBS and stored at −80 °C. Pellets were then treated as described[Costantino, 2020 #1788] until the de-crosslinking step. The De-crosslinking solution was added with an equal volume of phenol-chloroform-isoamyl alcohol (25:24:1), vortexed intensively and centrifuged for 15 minutes at room temperature. The aqueous phase was purified on a ZymoClean column (Zymo Research) according to the manufacturer instructions. Dinucleosome-sized DNA fragments were purified and excised from a 3% NuSieve GTG agarose gel (Lonza) using the Zymoclean Gel DNA Recovery Kit (Zymo).
17 ul of recovered DNA were treated with an end polishing following End-It DNA End-Repair Kit (Lucigen) manufacturer instruction before being diluted in 125 μL of water and added with 150 μL of 2x BW buffer. Biotynilated DNAs were precipitated using 5 μL of Dynabeads™ MyOne™ Streptavidin C1 for 30 minutes at 25 °C on a nutator. Beads were washed twice in 1x TBW buffer at 55 °C and once in 10 mM Tris HCl pH 7.5. Beads were then treated following NEBNext® Ultra™ DNA Library Prep Kit for Illumina® procedure. Briefly, beads were resuspended in 30 μL of End prep master mix and incubated according to the manufacturer instruction, followed by a standard adaptator ligation and USER enzyme digestion protocol. Adaptors were then washed 2 times in 1x TBW at 55 °C followed by one wash in 10 mM Tris pH 7.5. Beads were resuspended in 20 μL of Zymo Elution Buffer and an on-bead PCR was performed (8 to 12 cycles). Two rounds of 0.85X AMPure cleanup were performed. DNA fragments size were assessed on a Tapestation. Library were sequenced using an Illumina NovaSeq 6000 sequencer (100 bp paired). (see Slobodyanyuk et al. 2022 https://doi.org/10.1007/978-1-0716-2497-5_4)

tag: strain

value: MATa URA3::pMET3-scc2-aid::KANMX6 pADH1-OsTIR1-MYC9::ADE2 SMC3-PK3::HIS3MX rat1-1::LEU2


title: Sample_49


title: TG75_G1Depleted_N2


title: TG75_G2Depleted_25_N1


title: 2272_37_N2

value: FY23 background MATa rat1-1 leu2delta1 ura3-52  trp1delta63 SCC1-PK9::TRP1


title: 2272_25_N2


title: Sample_48


title: L.N Ctrl4

city: Tel Aviv

first: Carmit

last: Levy

state: israel

address: kalchekin 35

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

library_source: transcriptomic single cell

data_processing:
FASTQ files were created using CellRanger mkfastq function (v7 10×Genomics)63. Gene counts were obtained by aligning reads to the mm10 genome using CellRanger count function. To remove doublets and poor-quality cells, we excluded cells that: Contained more than 25% mitochondrially-derived transcripts. Contained less than 200 or more than 5,000 genes detected. Contained less than 200 or more than 25,000 detected molecules. The filtering process yielded 33,703 cells. Four samples of lymph nodes from control mice and 3 samples of lymph nodes of UV treated mice were merged and transcript counts were normalized and scaled using the NormalizeData ScaleData functions in Seurat 4.3.264 R package, which normalizes scales, and centers features in the dataset. For principal component analysis (PCA) and clustering, we used a log-transformed expression matrix. Variably expressed genes were used to construct principal components (PCs) and PCs covering the highest variance in the dataset were selected. The selection of these PCs was based on an elbow plot.
Clusters were calculated by the FindClusters function with a resolution between 0.25 and 0.35 and visualized using the t-SNE dimensionality reduction method. The FindClusters function in Seurat was used to identify clusters of cells by a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm. First, we calculated the k-nearest neighbors and constructed the SNN graph. To generate tSNE plots of single cell profiles, we used the Seurat's RunTSNE function
Single-cell gene signature scoring was done as described previously65. Briefly, as an initial step, to remove bias towards highly expressed genes the data was scaled using z-score across each gene. For a given gene signature (list of genes), a cell-specific signature score was computed. Scores were computed by first sorting the normalized scaled gene expression values for each cell followed by summing up the indices (ranks) of the signature genes. The same method was also applied to gene-signatures which includes both up-regulated and down-regulated genes. In this case, two ranking scores were obtained separately, and the down-regulated associated signature score was subtracted from the up-regulated generated signature score. A contour plot which takes into account only those cells that have a signature score above the indicated threshold was added on top of the tSNE space, in order to further emphasize the region of highly scored cells.
Assembly: FASTQ files were created using CellRanger mkfastq function (v7 10×Genomics)63.

source_name: Lymph nodes

growth_protocol: Spleen and lymph node were homogenized in Hank’s balanced salt solution (Gibco) supplemented with 2% FBS and 5 mmol/L EDTA and were isolated through a 70-μm strainer (Corning). Tumors were digested in RPMI 1640 with 2 mg/mL collagenase IV, 2,000 U/mL DNase I (Sigma Aldrich) for 30 minutes at 37 °C and then homogenized and strained through a 70-μm strainer.

extract_protocol:
. Lymph nodes and liver were homogenized, and total RNA was extracted using Trizol (Invitrogen). cDNA was produced using the cDNA SuperMix kit (QuantaBio) and then subjected to qRT-PCR using the Blue SYBR low ROX kit (PCR Biosystems). mRNA levels were normalized to endogenous actinβ. Naïve lymph nodes and liver were used as negative controls. The qRT-PCR primers were mCherry forward, 5'-GAACGGCCACGAGTTCGAGA-3'; mCherry reverse, 5'-CTTGGAGCCGTACATGAACTGAGG-3'; actinβ forward, 5'-CTGTCCCTGTATGCCTCTG-3'; and actinβ reverse, 5'-ATGTCACGCACGATTTCC-3'. For the other genes we used these primers:  36B4 forward, 5'-GATGATCAAAGGGATGTGGC-3' and reverse, 5'-AGCTCGGCAACAGACTCTTC-3'.
10μL of sorted cells were stained with Trypan Blue and counted using a hemocytometer and optical microscope. Cells were then centrifuged at 300 G for 5 min, resuspended into sorting medium at concentration of 1000 cells/ μL. Cells were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 30 Reagent Kits v3 according to manufacturer’s protocol (10× Genomics). The generated single-cell RNA-seq libraries were sequenced using a 75 cycle NextSeq 500 high output V2 kit.

treatment_protocol: For killing assays, mononuclear layers were collected from splenocyte suspensions using Ficol Histopaque®-1077 (Sigma Aldrich), washed by adding 10 mL of RPMI 1640 medium, and centrifuged at 700 xg for 10 minutes at 18 °C. The pellet of spleen mononuclear cells or the pellet of sDLN cells was re-suspended in MACS buffer (0.5% BSA, 2 mM EDTA in PBS). CD8+ T-cells enrichment was conducted using CD8 mouse magnetic MicroBeads (Miltenyi Biotec) according to manufacturer's instructions. CD4+ and CD8+ cells were enriched by negative selection using Pan T-cells Isolation Kit II, mouse (Miltenyi Biotec). CD11b+cells were isolated using magnetic CD11b MicroBeads and column (both from Miltenyi Biotec). Ly6anegative/low T-cells were sorted from spleen mononuclear cells using FACS (BD FACSAria III, BD Biosciences).

value: Lymph nodes

tag: cell line

value: not relevant

value: control


title: 6875_chl1_G1_N2

extract_protocol:
Micro-C was performed following published protocols[Costantino, 2020 #1788][Slobadyanyuk, 2022 #1888] with minor modifications. Yeast cultures were crosslinked with 3% formaldehyde for 15 minutes at 30 °C. The reactions were quenched by the addition of 250 mM glycine at 30 °C for 5 minutes with agitation. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 5 minutes and washed twice with water. Cells were then resuspended in Buffer Z (50 mM Tris-HCl pH 7.5, 1M sorbitol, 10 mM β-mercaptoethanol) and spheroplasted by addition of 250 mg/ml Zymolyase (100T) in a 30 °C incubator at 200 rpm for 40 to 60 minutes. Spheroplasts were washed once by 4 °C PBS and then pelleted at 4000 rpm at 4 °C for 10 minutes. Chromatin was further crosslinked by suspending pellets in PBS supplemented with 3 mM disuccinimidyl glutarate (ThermoFisher) and incubated at 30 °C for 40 minutes with gentle shaking before quenching by addition of 400 mM glycine for 5 minutes at 30 °C. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 10 minutes, washed once with ice-cold PBS and stored at −80 °C. Pellets were then treated as described[Costantino, 2020 #1788] until the de-crosslinking step. The De-crosslinking solution was added with an equal volume of phenol-chloroform-isoamyl alcohol (25:24:1), vortexed intensively and centrifuged for 15 minutes at room temperature. The aqueous phase was purified on a ZymoClean column (Zymo Research) according to the manufacturer instructions. Dinucleosome-sized DNA fragments were purified and excised from a 3% NuSieve GTG agarose gel (Lonza) using the Zymoclean Gel DNA Recovery Kit (Zymo).
17 ul of recovered DNA were treated with an end polishing following End-It DNA End-Repair Kit (Lucigen) manufacturer instruction before being diluted in 125 μL of water and added with 150 μL of 2x BW buffer. Biotynilated DNAs were precipitated using 5 μL of Dynabeads™ MyOne™ Streptavidin C1 for 30 minutes at 25 °C on a nutator. Beads were washed twice in 1x TBW buffer at 55 °C and once in 10 mM Tris HCl pH 7.5. Beads were then treated following NEBNext® Ultra™ DNA Library Prep Kit for Illumina® procedure. Briefly, beads were resuspended in 30 μL of End prep master mix and incubated according to the manufacturer instruction, followed by a standard adaptator ligation and USER enzyme digestion protocol. Adaptors were then washed 2 times in 1x TBW at 55 °C followed by one wash in 10 mM Tris pH 7.5. Beads were resuspended in 20 μL of Zymo Elution Buffer and an on-bead PCR was performed (8 to 12 cycles). Two rounds of 0.85X AMPure cleanup were performed. DNA fragments size were assessed on a Tapestation. Library were sequenced using an Illumina NovaSeq 6000 sequencer (100 bp paired). (see Slobodyanyuk et al. 2022 https://doi.org/10.1007/978-1-0716-2497-5_4)
micro-c

value: MATa pGAL1-10- SICV5,V33 A76::ADE2 chl1 -delta::KlTRP1


title: 2272_25_N1


title: Sample_47


title: L.N Ctrl3


title: L.N Ctrl2


title: rat1-1_37_N2


title: rat1-1_37_N1


title: Sample_46

source_name: LGSIL

value: LGSIL


title: wt_37_N2

value: FY23 background MATa leu2delta1 ura3-52  trp1delta63 SCC1-PK9::TRP1


title: Sample_45


title: wt_37_N1


title: L.N Ctrl1

description: R1-28 R2-90


title: smc1_4E_N2

value: MATa SMC1R53E, R58E, N60E, K63E-PK3::ADE2


title: smc1-4E_N1


title: Sample_44


title: scc3-3E_N1

value: MATa SCC3K423E, K520E, K669E -MYC1::URA3 SMC3-PK3::HPHr


title: TG75_G1Depleted_N1


title: Sample_43


title: scc3-3E_N2


title: L.N UV1

value: UVB


title: 2272_37_N1


title: scc1_aid_Raffinose_N2


title: scc1-aid_Raffinose_N1


title: scc1_aid_Galactose_N2


title: scc1-aid_Galactose_N1


title: scc1_aid_N2


title: Sample_42


title: scc1-aid_N1

value: MATa scc1-aid::KANR pGPD1-OsTIR1::LEU2 SMC3-PK3::HIS3MX


title: Sample_40


title: Treated_G2_N2

value: MATa tor1-1 fpr1-delta::NATR SMC3-PK3::HPHR pGAL1/10-SIC1V5, V33, A76-HA::ADE2 RPL13A-2xFKBP12::TRP1 rpb3-FRB::HIS3MX rpb1-GFP-FRB::HIS3MX RPB1-GFP-FRB::HIS3MX


title: Treated_G1_N2


title: Sample_39


title: Treated_G1_N1


title: Sample_38


title: Treated_G2_N1


title: Control_G2_N2


title: Control_G2_N1


title: Control_G1_N2


title: Control_G1_N1


title: Sample_36


title: Sample_41


title: Python Regius, Cardiomyocytes, 24 hours post feeding control 5

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

country: USA

institute: University of Colorado

description: this is a negative control so It does not have a processed data file

data_processing:
fastq files were adapter and quality trimmedand mapped to the python molurus bitvittatus genome using the Dowell lab ChIP-seq pipeline (GCF_000186305.1_Python_molurus_bivittatus-5.0.2_genomic.fna, Jun 11 2016). The ChIP-seq pipeline runs BBTools BBDuk , fastqc, hisat2 and samtools and was downloaded on Feb 2 ,2021 (https://github.com/Dowell-Lab/ChIP-Flow).
One of the replicates was sequenced on multiple lanes, so the reads from that replicate were merged and sorted via samtools (v 1.8).
HMMRATAC was then used to call peaks.
The regions called by HMMRATAC between the Open state start and the Open state end were used for all subsequent analysis.
The HMMRATAC peaks are the processed data files.
Assembly: Python molurus bivittatus
Supplementary files format and content: Bedgraph
Supplementary files format and content: HMMRATAC Open sorted peak bed file

organism: Python regius

source_name: Heart

growth_protocol: Python regius were housed individually in a climate-controlled animal facility for 6–12 months, at ∼30°C on a 10/14 h light/dark cycle. The snakes were fed whole rats on a biweekly basis and grew to approximately 1,000 – 1,500 g.

extract_protocol:
Approximately 50,000 cardiomyocytes were used for each transposition reaction, and ATAC libraries were isolated using the original omni-ATAC protocol, with modifications specified in the methods section of the paper.
ATAC libraries were constructed using the original omni-ATAC protocol with modifications specified in the methods section of the paper.
ATAC-seq libraries were sequenced at the BioFrontiers next generation sequencing facility on Nextseq V2 high output 75-cycle kits. Libraries were sequenced paired end 2x37 reads with dual 8bp indexes.

treatment_protocol: Pythons were first acclimated to three 28-d feeding cycles. After the final fasting period, pythons were fed rats ∼25% of their body mass. Pythons were euthanized either fasted or 24h post-feeding, and hearts were extracted and perfused for cardiomyocyte isolation

value: Heart

value: cardiomyocyte

value: Fasted 28 Days then Fed, Sacrificed 24 hours later


title: Claustrum_WT_4

city: Stockholm

first: Behzad

last: Yaghmaeian Salmani

state: Solna, Stockholm

address: Department of Cell and Molecular Biology (CMB) Karolinska Institute,, Biomedicum, Solnavägen 9, Solna, Stockholm, P.O. Box 285 SE-171 77 Stockholm, Sweden

department: CMB

country: Sweden

institute: Karolinska Institute

data_processing:
reads were aligned and mapped to reference transcriptome Mus_musculus.GRCm39.cdna.all (release-107) from Ensembl.
Salmon/1.6.0 was used to create an index on the transcriptome
Next, “tximport” package version 1.20.0,  was used to import and summarize the transcript abundances and construct of a transcript-level DESeqDataSet object from Salmon output files.
“tximport” package version 1.20.0 was also used to construct a tx2gene table for linking transcripts to genes using Gencode Mouse Transcript Annotation (GTF file) Release M30 (GRCm39).
DESeq2 package version 1.34.0 was used to construct a DESeqDataSet from the txi object, using sample information and design = ~ condition. Pre-filtering was done by removing transcripts with less than 3 reads across all 8 samples.
Assembly: Mus_musculus.GRCm39.cdna.all (release-107) from Ensembl
Supplementary files format and content: one csv file includes raw counts of mapped reads for all 8 samples.

source_name: CLA cells

extract_protocol:
RNA extraction was performed with Qiagens RNeasy micro RNA kit. 1ng of RNA was used for cDNA and amplified for 15 cycles.
cDNA libraries were made using the protocol Smart-seq2 for sensitive full-length transcriptome profiling in single cells. cDNA libraries were tagmented using home-made Tn5 enzyme and amplified for 11 cycles. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects and Nextera dual indexes (Illumina).

value: CLA cells

value: WT

tag: time

value: 2 months


title: Claustrum_Nurr1_3


title: Python Regius, Cardiomyocytes, 24 hours post feeding replicate 4


title: Sample_35


title: Claustrum_Nurr1_4


title: Python Regius, Cardiomyocytes, 24 hours post feeding replicate 3


title: Python Regius, Cardiomyocytes, 24 hours post feeding control 6


title: Sample_34


title: Claustrum_Nurr1_2


title: Python Regius, Cardiomyocytes, 24 hours post feeding replicate 2


title: Claustrum_WT_3


title: Python Regius, Cardiomyocytes, 24 hours post feeding replicate 1


title: Sample_37


title: Python Regius, Cardiomyocytes, 24 hours post feeding control 4


title: Python Regius, Cardiomyocytes, 28 days fasted control 3

value: Fasted 28 Days


title: Claustrum_WT_2


title: Python Regius, Cardiomyocytes, 28 days fasted control 2


title: Sample_32


title: Sample_31


title: Python Regius, Cardiomyocytes, 28 days fasted replicate 4


title: Python Regius, Cardiomyocytes, 28 days fasted control 1


title: Python Regius, Cardiomyocytes, 28 days fasted replicate 3


title: Sample_30


title: Claustrum_Nurr1_1


title: Sample_29


title: Python Regius, Cardiomyocytes, 28 days fasted replicate 1


title: Python Regius, Cardiomyocytes, 28 days fasted replicate 2


title: Python Regius, Heart, 24 hours post feeding replicate 2

description: 44, tissue mass (mg), RNA concentration 346 ng/ul

data_processing:
fastq files were mapped to to the python GCF_000186305.1_Python_molurus_bivittatus-5.0.2_genomic.fna using the dowell lab RNA-seq pipeline (https://github.com/Dowell-Lab/RNAseq-Flow) which runs fastqc, hisat2 and samtools and was downloaded on Feb  2  2021.
Reads over genes were then counted using featurecounts (subread version 1.6.2) over the GCF_000186305.1_Python_molurus_bivittatus-5.0.2_genomic.Gnomon.gff which was first converted to a gtf via a in house script
deseq2 1.26.0 was then used to create normalized counts
gene symbols were collected from ncbi.datasets.openapi and merged with the normalized counts via the python bivittatus transcript_accessiontranscript_name
All scripts are available at https://github.com/Dowell-Lab/PythonRegius2023Paper
Assembly: Python molurus bivittatus
Supplementary files format and content: normalized couns file for each bidirectional
Supplementary files format and content: This file was made by loading the raw count file into deseq and normalizeing the data

source_name: Ventricle

growth_protocol: Python regius were housed individually in a climate controlled animal facility for 6–12 months, at ∼30°C on a 10/14 h light/dark cycle. The snakes were fed whole rats on a biweekly basis and grew to approximately 1,000 – 1,500 g.

extract_protocol:
RNA was extracted using Tri Reagent (Molecular Research Center) and chloroform phase separation. 1 ug of total RNA was used for sequencing library preparation
Libraries were generated using KAPA HyperPrep mRNA kit (Kapa Biosystems) per the manufacturer's instructions.
RNA-seq libraries were prepared and sequenced by the BioFrontiers next generation sequencing facility using a Nextseq V2 highoutput 75 cycle kit. Libraries were sequenced single end 1x76bp with dual 8bp indexes.

treatment_protocol: Pythons were first acclimated to three 28-d feeding cycles. After the final fasting period, pythons were fed rats ∼25% of their body mass. Pythons were euthanized either fasted or 24h post-feeding, and hearts were snap frozen and stored at −80°C.

value: Ventricle


title: cortex_KO_Rep3

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
Briefly, STAR 2.7.7a (Dobin et al., 2013) was used to align the RNA-seq FASTQ files to the mouse mm10 genome using the parameters of ‘--runThreadN 40 --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --outFilterScoreMinOverLread 0.25 --outFilterMatchNminOverLread 0.25’. A Perl script, which is available at our GitHub repository (https://github.com/Jerry-Zhao/Hs6st2KO2022), was used to quantify the number of RNA-seq reads aligned to the exonic regions of each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each gene
Supplementary files format and content: BigWig files for the visualization of RNA-seq data

source_name: Cerebral cortex

growth_protocol: All mice used in this study were maintained in the C57BL/6 genetic background. Mice were kept on a regular 12-h light/12-h dark cycle. All animal studies, including handling and housing, were carried out in accordance with the National Institutes of Health’s Guide for the Care and Use of Laboratory Animals recommendations and according to the approved Institutional Animal Care and Use Committee (IACUC) protocol of the New York Institute of Technology.

extract_protocol:
RNA was isolated from the brain, spleen, kidney, heart, lung, and liver of 9-week-old WT mice and from the cerebral cortex and hippocampus of 14-week-old male Hs6st2 KO mice and their WT littermates. The Trizol reagent (Invitrogen, #15596026) was used to extract the total RNAs following the manufacturer’s instruction. The Nanodrop spectrometer and the Bioanalyzer (Agilent 2100) using RNA 6000 Nano Chip were used to assess the quality, concentration, and integrity of the isolated RNAs. RNA samples with a RIN value of > 8 were included for the downstream experiments.
RNA-seq libraries were prepared according to the manufacturer instructions. The Stranded Total RNA Library Prep kit (Zymo, #R3003) was used to generate RNA-seq libraries for the cerebral cortex samples, while the Invitrogen™ Collibri™ Stranded RNA Library Prep Kit for Illumina™ Systems (Thermo Fisher Scientific, # A38994096) was used to generate RNA-seq libraries for the hippocampus samples. The 1000 ng of total RNAs were used to prepare the RNA-seq libraries. The Bioanalyzer (Agilent 2100) using DNA 7500 chip was used to assess the quality of the RNA-seq libraries to make sure that the fragment sizes of all libraries were within the range of 300–500 bp. The Illumina NovaSeq sequencer was used to sequence the RNA-seq libraries.

value: Cerebral cortex

tag: developmental stage

value: 14 weeks old

value: Hs6st2 KO

tag: Sex

value: male


title: Sample_28

value: HGSIL


title: cortex_KO_Rep2


title: Spatial_Transciptomics_Mouse_628_LUNG

city: Palermo

first: Claudio

last: Tripodo

address: Corso Tukory 211

department: PROMISE

country: Italy

institute: Univerisity of Palermo

description: Visium Spatial Gene expression for FFPE tissue Sequencing

data_processing:
The raw sequencing data was processed using the 10x Genomics Space Ranger pipeline to produce FASTQ files.
The sequences were mapped to the mm10 genome for gene expression counting using Space Ranger's default parameters.
The gene expression levels of RefSeq coding genes were quantified using Space Ranger's default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducilas of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowers_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots

molecule: polyA RNA

source_name: Lung

extract_protocol:
Tissues underwent decrosslinking and enzymatic permeabilization for the preparation of RNA libraries, followed by the addition of Illumina indexes (i5 and i7) required for sequencing, as outlined in the Visium Spatial Gene Expression for FFPE protocol (10x Genomics Visium, CG000407).
Right-hand side (RHS) and left-hand side (LHS) probes specific to mouse samples from the Mouse Transcriptome Probe Kit (10x PN 2000457 and 2000458) were applied to the Visium slide according to the manufacturer's guidelines. The slide was then incubated at around 50 °C in a Thermocycler for approximately 18 hours.

treatment_protocol: 1x105 4T1 cells were resuspended in PBS and injected in the mammary fat pad of 8-week- old BALB/c mice. After 28 days from the inoculum, mice were sacrificed, and tumors and lungs were collected for histopathologicand spatial transcriptomical analyses.  Four micrometer-thick FFPE sections  were sliced and mounted on a Visium glass slide before undergoing HE staining.

value: Lung

value: BALB/c

value: 1x10^5 4T1 cells were resuspended in PBS and injected in the mammary fat pad of 8-week- old  murine model.


title: Spatial_Transciptomics_Mouse_628_TM

source_name: Breast tumor

value: Breast tumor


title: Sample_27

value: LGSIL


title: Python Regius, Heart, 24 hours post feeding replicate 3

description: 57, tissue mass (mg), RNA concentration 575.2 ng/ul


title: Python Regius, Heart, 24 hours post feeding replicate 1

description: 28, tissue mass (mg), RNA concentration 268 ng/ul


title: cortex_KO_Rep1


title: Python Regius, Heart, 28 days fasted replicate 3

description: 47, tissue mass (mg), RNA concentration 491.5 ng/ul


title: Spatial_Transciptomics_Mouse_627_LUNG


title: cortex_WT_Rep4


title: Spatial_Transciptomics_Mouse_627_TM


title: Claustrum_WT_1


title: Sample_26

source_name: ASCC

value: ASCC


title: Python Regius, Heart, 28 days fasted replicate 2

description: 44, tissue mass (mg), RNA concentration 455 ng/ul


title: Sample_24


title: Sample_25


title: Scc3-3E_Smc3PK_IP_N2

data_processing:
data were aligned using the nf core (v2.0.0) pipeline
Occupancy ratio was calculated as published in: 10.1093/nar/gkv670
Bam files were multiplied by the occupancy ratio using BamCoverage
Bigwig files of the IP are calibrated according to (Hu et a. 2015)
Assembly: w303
Supplementary files format and content: BigWig

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

extract_protocol:
50 OD600 units of Saccharomyces cerevisiae cells were mixed at a 1:5 ratio with Candida glabrata cells in which corresponding cohesin subunits were fused to a Pk epitope tag[Hu, 2015 #1305], and broken in 700 ml Lysis Buffer (50mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium Deoxycholate) supplemented with protease inhibitors by glass bead rupture. The lysate was retrieved by centrifugation for 1 minute at 2000 rpm and the supernatant then removed after centrifugation for 10 minutes at maximum speed in a benchtop centrifuge. The pellet was resuspended in 1 ml lysis buffer and sonicated to reach an average DNA fragment size of 500 bp. Cohesin was precipitated using and a-Pk antibody (clone SV5-Pk1, Bio-Rad) and protein A-coupled Dynabeads for 2 hours. Beads were washed 3 times with Lysis Buffer, 3 times with Lysis Buffer supplemented with 500 mM NaCl and 2 times with Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate). The samples were resuspended in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS including 3 mg/ml proteinase K and 2 mg/ml RNase A) and de-crosslinked overnight at 65 °C. DNA was purified by phenol-chloroform extraction and the aqueous fraction was further cleaned using DNA Clean & Concentrator-5 with Zymo-Spin Columns (Zymo Research).
Libraries were built with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer instruction. Sequencing was performed on an Illumina NovaSeq 6000 (100 bp paired).

value: SCC3-3E SMC3-PK3


title: cortex_WT_Rep3


title: Sample_23


title: cortex_WT_Rep2


title: Scc3-3E_Smc3PK_IN_N1


title: Sample_21


title: cortex_WT_Rep1


title: Sample_22


title: RNA_N_HD7

city: Seattle

first: Ye

last: Zheng

state: WA

address: 1100 Fairview ave N

institute: Fred Hutchinson Cancer Center

data_processing:
Raw RNA sequencing data were aligned using RSEM (v1.3.1)
RNA-seq were normalized by Voom algorithm provided in the Limma (v3.58.1) R package.
Differentially expressed genes were detected using Limma (v3.58.1)
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes expected_count, TPM, FPKM values for each genes

source_name: PBMC

extract_protocol:
RNA was harvested using SMART-Seq v4 Ultra Low Input RNA Kit from Takara with SMART-seq v4 PLUS library kit.
RNA-seq libraries were prepared using SMART-seq v4 PLUS library kit.

value: PBMC

value: CD8 Naive T Cell


title: Scc3-3E_Smc3PK_IP_N1


title: hippocampus_KO_Rep3

source_name: Hippocampus

value: Hippocampus


title: Scc3_Smc3PK_IN_N2

value: SCC3 SMC3-PK3


title: Scc3-3E_Smc3PK_IN_N2


title: RNA_N_HD6


title: Sample_19


title: Python Regius, Heart, 28 days fasted replicate 1

description: 51, tissue mass (mg), RNA concentration 475.7 ng/ul

value: Ventricle

value: Fasted 28 Days


title: RNA_N_HD5


title: Scc3_Smc3PK_IN_N1


title: hippocampus_KO_Rep1

value: 14 weeks old


title: Sample_18


title: hippocampus_WT_Rep4

value: WT


title: Scc3_Smc3PK_IP_N1


title: Sample_33


title: Sample_17


title: RNA_N_HD2


title: HUVEC_JPH203_48hours

type: RNA

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

country: Japan

institute: Kyorin University School of Medicine

description: Gene expression data from HUVEC treated with 100µM JPH203 for 48 hours

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

label: biotin

source_name: HUVEC

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were purchased from Ronza and cultured in EGM-2 complete medium (Ronza).

extract_protocol: total RNA was extracted with TRIzol reagents (Invitrogen) according to manufacturer's protocol.

treatment_protocol: HUVEC were precultured in EGM2 complete media for 24 hours, and then treated with 100µM Captisol or JPH203 (J-Pharma) for 48 hours.

tag: cell

value: HUVEC

tag: stimulation


title: hippocampus_KO_Rep4

value: Hs6st2 KO

value: male


title: Sample_16


title: hippocampus_WT_Rep2


title: Smc1-4E_PK_IP_N2


title: RNA_N_HD1


title: Sample_20


title: RNA_EM_HD7

value: CD8 Effector Memory T Cell


title: hippocampus_WT_Rep3


title: Sample_15


title: hippocampus_WT_Rep1


title: hippocampus_KO_Rep2


title: Sample_14


title: RNA_EM_HD6


title: Sample_13


title: Smc1-4E_PK_IP_N1


title: Smc1-4E_PK_IN_N1


title: Sample_12

value: HGSIL


title: RNA_N_HD3


title: HUVEC_control_48hours

description: Gene expression data from HUVEC treated with 100µM Captisol for 48 hours

value: Captisol


title: Sample_11

value: LGSIL


title: Smc1-4E_PK_IN_N2


title: 4T1 tumor tissue treated with DiI-labeled liposomes

city: Seoul

first: Jeongbin

last: Park

state: Not US or Canada

address: 23, Sinhyeon-ro 38beon-gil, Siheung-si, Gyeonggi-do, 14957, Rep. of KOREA

department: Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University

description: DiI-labeled liposomes were injected intravenously into 4T1-tumor bearing mice.

data_processing:
Raw FASTQ files and H&E images were processed by sample with the Space Ranger v1.1.0
software. The process uses STAR v.2.5.1b (Dobin et al., 2013) for genome alignment, against the Cell
Ranger (mouse mm10 reference package). The process was performed by ‘spaceranger count’
commend.

source_name: 4T1 cells

extract_protocol:
ST library was acquired by several steps: cryo-sectioning, fixation, permeabilization, cDNA synthesis, and RNA sequencing. All the methods were carried out in the way  that 10x Genomics visium protocol recommended. The fresh tissue samples were embedded in OCT  compound (25608-930, VWR, USA). We prepared consecutive tissue slices were used for H&E  staining, spatial transcriptomics library, and fluorescence imaging. The slices were acquired by thin  blades used in cryotome so that the fluorescence pattern affected by gene expression could be  explored thoroughly. The tissue section for ST were placed on Visum slides (both Visium Tissue  Optimization Slides, 1000193, 10X Genomics, USA and Visium Spatial Gene Expression Slides,  1000184, 10X Genomics). The fixation was performed under the recommended protocol using chilled  methanol. cDNA libraries were prepared and were sequenced on a NovaSeq 6000 System S1200  (Illumina, USA) at a sequencing depth up to 250M read-pairs.
10x Genomics visium protocol

value: solid tumor

value: breast cancer

value: Balb/c

value: untreated


title: K562 SF3B1 K666N-DMSO-2-nuclear-smallRNA

status: Public on Aug 05 2024

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: nuclear RNA

data_processing:
All samples were trimmed with Trimmomatic (v0.32) to remove low-quality and short reads and aligned to the human genome hg19 using STAR aligner (v 2.7.9a).
For total RNA and polyA RNA, RSEM (v 1.3.1) was used to obtain expected gene counts against the human gene reference Gencode (v 41). Differential expression was determined using DESeq2 and R (v 4.2.0). A gene was considered detected if the TPM (Transcripts Per Million) >1 in at least two replicates of one sample and significantly changed if the adjusted p-value was < 0.05 and fold change >1.5<−1.5.
Alternative splicing bam files with the Gencode v41 annotation file were used as input for rMATS (v4.1.2). Events with |inclusion level difference| > 0.05, P < 0.05 and FDR < 0.05 were identified as significantly differentially expressed AS events
For small RNAseq reads were aligned against human elements in RepBase (v23.08) with STAR (v2.7.9a), and the unmapped output was then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the Differentially expressed genes per comparison

growth_protocol: K562 cells were cultured in 10% fetal bovine serum and 1% pencillin/streptomycin at early passages (P1-10) and then treated with either vehicle (DMSO) or 200nM selinexor for 24 hours. After 24 hours, RNA was extracted. For the combination treatment RNA sequencing, cells were treated with either vehicle/DMSO, 200nM eltanexor, 1uM venetoclax, 1uM A1331852, 1uM navitoclax, or the combinations of eltanexor+venetoclax, eltanexor+A1331852, and eltanexor+navitoclax for 24 hours.

extract_protocol:
Total RNA for mRNA sequencing was extracted using QIAGEN RNeasy mini kit. To separate nuclear and cytoplasmic fractions, pellet the cells via centrifugation for 5 minutes at 1500RPM and discard the supernatant. The pellet was then resuspended into 300mL of ice cold 0.25x lysis buffer (Tris-Cl pH 8.0, NaCl, MgCl2, Nonidet P-40). The pellet was kept on ice for two minutes and rotate the tube every 45 seconds to ensure proper lysis followed by centrifugation at highest speed at 4°C for two minutes. After centrifugation, the supernatant was carefully removed and placed in a new tube as this was the cytoplasmic fraction. For the remaining nuclear fraction pellet, 500mL of ice-cold PBS was added and centrifuged at 1500RPM for 5 minutes. The QIAGEN RNeasy mini kit was then used for long RNAs and miRNeasy Tissue/Cells Advanced Micro Kit was used for small RNA extraction.
For mRNA sequencing was Poly(A)-selected and the Illumina libraries were prepared using the TruSeq stranded mRNA Library Preparation kit. For the nuclear cytoplasmic mRNAs, ribsomoal RNA depeletion method with the TruSeq stranded Total RNA library was used with 50 million paired end reads. For the nuclear cytoplasmic small RNAs, the size selection step with the Perkin Elmer Next Flex Small RNA library preparation kit on the Illumina sequencing platform with 50 million single end reads.

value: chronic myeloid leukemia cells

value: Vehicle/DMSO


title: Smc1PK_IN_N2


title: RNA_EM_HD5

value: PBMC


title: RNA_EM_HD3


title: db_c_2b

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to  the mouse transcriptome (Ensembl version 94) by using kallisto.
Transcript counts were converted  to gene counts by using tximport.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV of gene counts

source_name: iPSC

extract_protocol:
Total RNA was isolated by using RNeasy kit (Qiagen).
Libraries were prepared by using Illumina's Truseq Stranded mRNA Prep Kit.

tag: group

tag: cell id

value: iPSC


title: RNA_EM_HD2


title: Smc1PK_IP_N2


title: Smc1PK_IN_N1


title: db_c_1b


title: Sample_10


title: db_c_1a


title: Smc1PK_IP_N1


title: RNA_EM_HD1


title: Sample_9

value: ASCC


title: bdb_db7_2


title: RNA_CM_HD7

value: CD8 Central Memory T Cell


title: Scc3_Smc3PK_IP_N2

value: SCC3 SMC3-PK3


title: db_c_2a


title: RNA_CM_HD6


title: G1_Treated_IN_N2

value: MATa tor1-1 fpr1-delta::NATR SMC3-PK3::HPHR pGAL1/10-SIC1V5, V33, A76-HA::ADE2 RPL13A-2xFKBP12::TRP1 rpb3-FRB::HIS3MX rpb1-GFP-FRB::HIS3MX RPB1-GFP-FRB::HIS3MX


title: bdb_db7_1


title: Sample_7


title: bdb_db5_2


title: RNA_CM_HD5


title: G1_Treated_IP_N2


title: G1_Untreated_IN_N2


title: Sample_5


title: RNA_CM_HD2


title: Sample_6


title: adb_db7_2


title: RNA_CM_HD1


title: RNA_CM_HD3


title: G1_Untreated_IP_N2


title: G1_Treated_IP_N1


title: G1_Treated_IN_N1


title: Sample_4


title: Sample_8


title: bdb_db5_1


title: H3K27me3_N_HD7

data_processing:
Raw CUT&RUN sequencing data were aligned using bowtie2 (v2.4.1)
CUT&RUN alignment results were normalized with respect to the e.coli spike-in.
CUT&RUN peaks were called by SEACR (v1.3)
Differential histone enrichment results were detected using Limma (v3.58.1)
Assembly: hg38
Supplementary files format and content: bedgraph files for CUT&RUN samples
Library strategy: CUT&RUN

extract_protocol:
AutoCUT&RUN protocol (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-6qpvre6zblmk/v1) was used.
Library construction follows AutoCUT&RUN protocol (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-6qpvre6zblmk/v1) corresponding procedures.

value: CD8 Naive T Cell


title: G1_Untreated_IN_N1


title: adb_db7_1


title: Sample_3


title: H3K27me3_N_HD6


title: adb_db5_1


title: G1_Untreated_IP_N1


title: adb_db5_2


title: Sample_1


title: H3K27me3_N_HD4


title: bB6_B1_2


title: H3K27me3_N_HD5


title: G2_Treated_IN_N2


title: PLC/PRF/5 Control rep2 [C2]

city: Shanghai

first: Chuan

middle: Yuan

last: Wei

state: Shanghai

address: fenglin road 180

department: Liver cancer institute

country: China

institute: Zhongshan, Fudan

description: EV

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using hisat2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM, raw count values

source_name: Hepatocellular carcinoma

growth_protocol: PLC/PRF/5-ZFP64 and PLC/PRF/5-EV cells were cultured in DMEM media supplemented with 10% FBS, incubated at 37°C in a humidified chamber containing 5% CO2.

extract_protocol:
Cell culture medium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PLC/PRF/5 cells was transfeted with ZFP64 overexpressed or control lentivirus

value: PLC/PRF/5 cells

value: Human hepatocellular carcinoma

value: Control lentiviral vector


title: PLC/PRF/5 Control rep3 [C3]

description: EV


title: G2_Treated_IP_N2


title: bB6_A5_2


title: G2_Untreated_IN_N2


title: H3K27me3_EM_HD6

value: CD8 Effector Memory T Cell


title: G2_Untreated_IP_N2


title: H3K27me3_EM_HD7


title: PLC/PRF/5 Control rep1 [C1]

description: EV


title: H3K27me3_EM_HD5


title: Sample_2

extract_protocol:
Total RNA was isolated from the collected samples using the miRNeasy Tissue/Cells Advanced Kits (Qiagen) following standard manufacturer's protocol. RNA concentration and integrity were measured on a Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA samples with RNA integrity number (RIN) over 7 were considered for RNA sequencing. The RNA samples were processed for directional RNA-seq library construction using the Illumina Total RNA Prep with Ribo-Zero Plus library preparation kit according to the manufacturer's protocol.
We performed  100 nt paired-end sequencing using an Illumina Novaseq 6000 platform and obtained ~80 million clusters per sample with 92% >Q30.

value: LGSIL


title: G2_Treated_IN_N1


title: bB6_A5_1


title: aB6_B1_1


title: G2_Treated_IP_N1


title: H3K27me3_EM_HD4


title: PLC/PRF/5 ZFP64-OE rep2 [A2]

value: ZFP64-overexpression lentiviral vector


title: bB6_B1_1


title: aB6_B1_2


title: aB6_A5_1


title: G2_Untreated_IN_N1


title: H3K27me3_CM_HD6


title: H009T

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on HiSeq 3000 platform in a 101-base single-end mode.
Illumina RTA 2.7.7 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffnorm v2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: Lung

value: NSCLC cells

tag: region

value: Tumor region


title: T500

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using hisat2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: HCC tissues of PR patients

extract_protocol:
Tissues were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample group

value: Partial response after anti-PD1 treatment

tag: disease

value: Liver


title: G2_Untreated_IP_N1


title: T480


title: H009N

value: Unaffected lung region


title: PLC/PRF/5 ZFP64-OE rep3 [A3]


title: Untagged_IP

value: w303 WT


title: H3K27me3_CM_HD4

value: PBMC

value: CD8 Central Memory T Cell


title: H008T


title: PLC/PRF/5 ZFP64-OE rep1 [A1]


title: T445


title: T605


title: H3K27me3_CM_HD5


title: H3K4me2_N_HD7


title: T251


title: H3K4me2_N_HD6


title: H008N


title: H007N


title: IGROV1, FHT-1015, ATAC seq, rep 1

city: South San Francisco

first: Karen

last: Gascoigne

state: California

address: 1 DNA way

institute: Genentech

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: Hg38
Supplementary files format and content: BigWig

growth_protocol: RPMI, 10% heat-inactivated fetal bovine serum, 1% L-Glutamine, and 1% Pen/Strep

extract_protocol:
cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter)
Illumina sequencing libraries were prepared on an automated system (Apollo 342, Wafergen Biosystems/Takara).

treatment_protocol: where indicated 72h 1ug/ml doxycycline to induce CAS9 and PAX8 targeted gRNA expression, or 72h 10 uM FHT-1015

value: Ovarian cancer cell


title: IGROV1, FHT-1015, ATAC seq, rep 2


title: H3K4me2_N_HD4

value: CD8 Naive T Cell


title: IGROV1, DMSO, ATAC seq, rep 2

value: DMSO


title: H007T


title: H3K4me2_N_HD5


title: Untagged_Input


title: IGROV1, DMSO, ATAC seq, rep 1


title: H3K4me2_EM_HD7


title: 360

source_name: HCC tissues of PD patients

value: Disease progression after anti-PD1 treatment

value: Human hepatocellular carcinoma


title: MFS-P1-I13 Rep2

city: Houston

first: William

middle: Charles

last: Shropshire

state: TX

address: 1901 East Road

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Raw reads were QC'd with Fastqc and trimmed with bbduk
Trimmed reads were aligned to STAR alignment tool
DESeq2 was used for differential expression analysis; further detail is provided in manuscript
Assembly: NA
Supplementary files format and content: XLSX

organism: Escherichia coli

source_name: Overnight culture

growth_protocol: Overnight cultures were standardized to 0.5 MacFarland in MHB and grown up to 0.5 OD600

extract_protocol:
Three mL of each sample was treated with RNAprotect (QIAGEN) following manufacturer’s instructions, and pellets were stored at 80°C until each sample and respective replicate was ready for RNA extraction. RNA was extracted using the QIAGEN RNeasy Mini Kit using manufacturer’s instructions.
Illumina Nextera

treatment_protocol: 1X ETP MIC (0.06 ug/mL) exposed daily populations were treated with 0.03 ug/mL ETP whereas passage controls had no ETP exposure

value: microfluidic passaging

value: WT

value: 0.03 ug/mL ETP


title: H3K4me2_EM_HD6

value: CD8 Effector Memory T Cell


title: MFS-passControl-I13 Rep 3

value: No ETP


title: IGROV1, plus dox, ATAC seq, rep 1

value: 72h 1ug/ml doxycycline to induce CAS9 and PAX8 targeted gRNA expression


title: 358


title: 342

value: Partial response after anti-PD1 treatment


title: H3K4me2_EM_HD5


title: 343

value: Liver


title: MFS-P1-I13 Rep1


title: IGROV1, plus dox, ATAC seq, rep 2


title: 355


title: MFS-passControl-I13 Rep2


title: 338


title: MFS-passControl-I13 Rep1


title: IGROV1, minus dox, ATAC seq, rep 2


title: H3K4me2_EM_HD4


title: 337


title: IGROV1, minus dox, ATAC seq, rep 1


title: H3K4me2_CM_HD7


title: 335


title: HOS cells, Argimol B 3

city: 杨浦区

first: Yi-Ping

last: Luo

state: 上海

address: 杨浦区中原路

department: Orthopedics

institute: Department of Orthopedics, Shanghai Tenth People's Hospital, Tongji University School of Medicine

data_processing:
Use the cutadapt software to remove the linker sequence in the original off-machine data;
Use the Trimmomatic software to remove low-quality sequences to obtain clean data;
Use the Fastqc software to count the amount of clean data, the ratio of q20 and q30;
Use the HISAT software to compare the clean data to the reference genome;
Use String tie to splice reads into transcripts and analyze gene expression levels;
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Osteosarcoma

extract_protocol:
RNA was harvested using trizol
KAPA Stranded mRNA-Seq Kit was used for cDNA library construction.

value: Osteosarcoma

value: HOS

value: Osteosarcoma cells

value: Agrimol B


title: H3K4me2_CM_HD6

value: PBMC

value: CD8 Central Memory T Cell


title: 334


title: FTP-P1-D2 Rep3

value: flask transfer passaging


title: HOS cells, Argimol B 2


title: FTP-P1-D2 Rep2


title: H3K4me2_CM_HD5


title: 333

value: Disease progression after anti-PD1 treatment


title: H3K4me2_CM_HD4


title: 332

value: Human hepatocellular carcinoma


title: HOS cells, Control 3


title: HOS cells, Argimol B 1


title: PLC-input

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.05 as cutoff
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using Deeptools(3.5.0)

source_name: HCC

growth_protocol: PLC/PRF/5 cell was cultured in DMEM supplemented with 5% FBS, incubated at 37°C in a humidified chamber containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and ZFP64-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (TruSeq® chip DNA LT Sample Prep Kit), including performing end repair, adenylating 3' ends, ligating adapters and enriching DNA Fragments. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: PLC/PRF/5 cells was transfeted with ZFP64 overexpressed lentivirus

value: PLC/PRF/5 cells

value: Human liver cancer cells

tag: genotype/variation

value: ZFP64 overexpression

tag: chip antibody

value: none (input)


title: FTP-passControl-D2 Rep3

tag: cell type

value: WT

value: No ETP


title: FTP-passControl-D2 Rep2

tag: genotype


title: FTP-passControl-D2 Rep1

tag: treatment


title: 327

tag: tissue


title: PLC-Flag

tag: cell line

value: Flag


title: genomic DNA from LSD1 MUT sample 4-2

status: Public on Aug 03 2024

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: mESCs from LSD1 MUT mice

hyb_protocol: Samples were bisulfite converted using EZ DNA Methylation-Gold™ Kit (Zymo Research, CA, USA) following the manufacturer’s protocol with modifications for Illumina Infinium Methylation Assay.

scan_protocol: Infinium Mouse Methylation BeadChip (Illumina) arrays were used to profile genome wide DNA methylation. This platform interrogates over 285,000 methylation sites per sample at single-nucleotide resolution. Samples were hybridized in the array following the manufacturer’s instructions.

data_processing: The DNA methylation status of the studied samples was obtained using the Infinium Mouse Methylation BeadChip Array (~285,000 methylation sites). Raw signal intensities were preprocessed and analyzed using SeSAMe (v1.14.2). DNA methylation beta values were obtained from raw IDAT files using the openSesame pipeline within R statistical environment (v4.0.3). Briefly, this pipeline includes a data preprocessing procedure consisting of strain-specific masking for mouse methylation array probes, followed by masking of non-uniquely mapped probes (poor design), channel inference for Infinium I probes, non-linear dye bias correction, detection p-value masking (P > 0.05) using the pOOBAH algorithm and background subtraction using the noob method.

label: Cy5 and Cy3

source_name: High molecular weight DNA

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA from fresh-frozen mESCs samples was extracted and purified using DNeasy Blood and Tissue Kit (Qiagen GmbH, Hilden, Germany) according to manufacturer’s instructions. Purified genomic DNA was quantified with Qubit (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions.

tag: condition

value: LSD1 MUT

tag: time


title: genomic DNA from LSD1 WT sample 4

description: mESCs from LSD1 WT mice

value: LSD1 WT


title: genomic DNA from LSD1 MUT sample 4-1

description: mESCs from LSD1 MUT mice


title: genomic DNA from WT sample 4

description: mESCs from WT mice


title: genomic DNA from LSD1 MUT sample 3

description: mESCs from LSD1 MUT mice


title: HOS cells, Control 1

value: Osteosarcoma

value: HOS


title: genomic DNA from LSD1 WT sample 3

description: mESCs from LSD1 WT mice


title: FTP-P1-D2 Rep1

value: 0.03 ug/mL ETP


title: genomic DNA from LSD1 KO sample 3

description: mESCs from LSD1 KO mice

value: LSD1 KO


title: genomic DNA from WT sample 2

description: mESCs from WT mice


title: genomic DNA from LSD1 WT sample 2

description: mESCs from LSD1 WT mice


title: genomic DNA from LSD1 KO sample 2

description: mESCs from LSD1 KO mice


title: genomic DNA from LSD1 MUT sample 2

description: mESCs from LSD1 MUT mice


title: genomic DNA from LSD1 WT sample 1

description: mESCs from LSD1 WT mice


title: genomic DNA from WT sample 1

description: mESCs from WT mice


title: genomic DNA from LSD1 KO sample 1

description: mESCs from LSD1 KO mice


title: HOS cells, Control 2

value: Osteosarcoma cells


title: MS10

city: Halle (Saale)

first: Marcus

last: Bauer

address: Magdeburger Str.

department: Institute of Pathology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description: Genewiz (Azenta)

data_processing:
Adapters were trimmed using trimmomatic and quality checked using FastQC.
Reads were mapped to the human reference genome (GRCh38/hg38) using the splice aware aligner STAR (v2.7.9a)
Read counts for NCBI Gene/Refseq annotation were determined using featureCounts (v2.0.0)
Differentially expressed genes were determined using DESeq2 based on raw counts and a negative binomial distribution
Data were normalized using DESeq2 and log-transformed (rlog).
Assembly: hg38
Supplementary files format and content: tab delimited txt file include raw counts for each sample (raw_counts.txt)
Supplementary files format and content: tab delimited txt file include log2 transformed normalized counts adding a pseudocount of 1 (DESeq2) for each sample (log2_normalized_counts_1.txt)

source_name: myeloid sarcoma

growth_protocol: FFPE tissue

extract_protocol:
Total RNA was isolated with Maxwell RSC RNA FFPE Kit (Promega, USA) according to the manufacturer’s instructions.
Illumina TruSeq Stranded mRNA Library Prep

treatment_protocol: Four to five 10 μm thick tissue slides were prepared.

value: myeloid sarcoma

value: myeloid cells

tag: hla-i

value: low


title: MS11

description: Genewiz (Azenta)

value: high


title: MS7

description: Genewiz (Azenta)


title: MS14

description: Genewiz (Azenta)


title: genomic DNA from LSD1 KO sample 4

description: mESCs from LSD1 KO mice


title: MS9

description: Genewiz (Azenta)


title: MS6

description: Genewiz (Azenta)


title: MS2

description: Genewiz (Azenta)


title: MS4

description: Genewiz (Azenta)


title: genomic DNA from WT sample 3

description: mESCs from WT mice


title: MS5

description: Genewiz (Azenta)


title: ET

city: beijing

first: xiaowei

last: tang

state: beijing

address: xuyuanlu 38

institute: 北医

data_processing:
The Seekoul Tools pipeline was utilized to process the reads and generate the transcript expression matrix. Initially, the cell barcodes and Unique Molecular Identifier (UMI) sequences were extracted based on a defined pattern that localized the barcode, linker, and UMI within each read. The extracted barcodes were corrected using a whitelist, and the corrected barcode, along with the UMI, were placed in the header of their respective reads. Next, the reads were aligned to the reference genomes using STAR 2.5.1b. Subsequently, reads containing barcode and UMI information were assigned to the transcriptome using featureCounts from the Subread package 1.6.4, with the default parameters except for "-s 1-fracOverlap 0.5". This step resulted in a raw UMI count matrix based on barcodes and transcripts, similar to the raw_feature_bc_matrix output of Cell Ranger.
Assembly: hg38
Supplementary files format and content: Table-seprarated values files and matrix files

source_name: female breast tumor tissue

extract_protocol:
Freshly collected tissue samples were immediately washed with RPMI1640 medium (Gibco, Life Technologies) and dissociated using a Multi-tissue dissociation kit 2 (Miltenyi 130-095-929). The addition of DNase was dependent on the viscosity of the homogenate. Subsequently, cell counts and viability were determined using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent, following the removal of erythrocytes (Miltenyi 130-094-183). The decision to perform debris and dead cell removal was made based on experimental requirements (Miltenyi 130-109-398/130-090-101). Finally, the freshly isolated cells were again washed twice with medium and resuspended at a concentration of 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin (BSA) (Thermo Fisher Scientific).
Single-cell RNA-Seq libraries were prepared using the SeekOne® MM Single Cell 3' library preparation kit (SeekGene Catalog No.). Briefly, an appropriate number of cells were loaded into the flow channel of the SeekOne® MM chip, which contained 170,000 microwells, and allowed to settle in the microwells by gravity. After removing unsettled cells, Cell Barcoded Magnetic Beads (CBBs) was pipetted into the flow channel and also allowed to settle in the microwells with the assistance of a magnetic field. Next, excess CBBs were removed, and the cells in the MM chip were lysed to release RNA, which was captured by the CBB in the same microwell. Subsequently, all CBBs were collected, and reverse transcription was performed at 37°C for 30 minutes to label the cDNA with the cell barcode on the beads. Exonuclease I treatment was then carried out to remove unused primers on the CBBs. Following that, the barcoded cDNA on the CBBs was hybridized with a random primer that had the 2 SeqPrimer sequence on the 5' end and could extend to form the second strand DNA with the cell barcode on the 3' end. The resulting second strand DNA was denatured off the CBBs, purified, and amplified in a PCR reaction. The amplified cDNA product was subsequently purified to remove unwanted fragments and added to full-length sequencing adapters and sample indices by indexed PCR. The indexed sequencing libraries were cleaned up with SPRI beads, quantified using quantitative PCR (KAPA Biosystems KK4824), and then sequenced on the Illumina NovaSeq 6000 platform with PE150 read length or the DNBSEQ-T7 platform with PE150 read length.

value: female breast tumor tissue


title: FT


title: EN

source_name: female breast normal tissue

value: female breast normal tissue


title: GT


title: DT


title: BN2


title: Cox15_CBD1 [AS2949]

city: Barcelona

first: Emma

last: Puighermanal

address: Passatge de la Independència 30 2-3

institute: Autonomous University of Barcelona

data_processing:
RNAseq reads were mapped against the human reference genome (GRCh38) with STAR/2.7.8a using ENCODE parameters. Genes were quantified with RSEM/1.3.0 with default parameters using gencode.v42. Only genes with >1 cpm in at least 12 samples were retained for analysis. Differential expression was performed with limma1 using the voom1 transformation of the counts. Genes with FDR<5% were considered significant. Functional enrichment was performed with g:profiler1 and gene set enrichment analysis with fgsea1 with a pre-ranked list of genes by the limma moderated t statistic.
Assembly: GRCh38
Supplementary files format and content: TSV
Supplementary files format and content: Raw counts

source_name: Human dermal fibroblats (neonate)

growth_protocol: Primary mutant and control skin fibroblasts were grown in high-glucose DMEM  supplemented with 10% (v/v) fetal bovine serum  and 1% (v/v) Pen/Strep  in an incubator at 37°C with a humidified atmosphere at 5% CO2.

extract_protocol:
Total cellular RNA was extracted using the RNeasy Mini Kit (Qiagen, #74106) according to manufacturer’s instructions, followed by DNAse (RNase-Free DNase Set, Qiagen, #79254) treatment.
The RNAseq library was prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following the manufacturer´s protocol. The sequencing was performed on NovaSeq 6000 (Illumina) with a read length of 2x51bp.

treatment_protocol: Cells were treated with 5 µM CBD for 24h. CBD stock solution was prepared in DMSO with a final concentration of 0.1% (v/v) DMSO in cell culture.

value: Human dermal fibroblats (neonate)

value: Primary skin fibroblasts

value: CBD (5 µM)


title: Cox15_CBD2 [AS2950]


title: BT


title: Cox15_CBD3 [AS2951]


title: Ndusf4_CBD2 [AR1266]

value: Ndufs4 c.350 + 5G > A


title: Cox15_Veh3 [AR1270]

value: Vehicle


title: Cox15_Veh2 [AR1269]


title: Cox15_Veh1 [AR1268]


title: Ndusf4_CBD3 [AR1267]


title: Ndusf4_Veh1 [AR1262]


title: Ndusf4_CBD1 [AR1265]


title: Ndusf4_Veh3 [AR1264]


title: MS1

description: Genewiz (Azenta)


title: CT_Old_CBD3 [AR1261]

value: WT


title: CT_Old_CBD2 [AR1260]


title: Ndusf4_Veh2 [AR1263]


title: CT_Old_Veh_1 [AR1256]


title: BN1


title: CT_Old_Veh_2 [AR1257]


title: CT_Old_Veh_3 [AR1258]


title: CT_Old_CBD1 [AR1259]


title: CT_New_CBD1 [AR1253]


title: CT_New_CBD3 [AR1255]


title: CT_New_CBD2 [AR1254]


title: CT_New_Veh1 [AR1250]


title: CT_New_Veh2 [AR1251]


title: A549 cells, ORF6 overexpression, rep 3

city: Fuzhou

first: Song

last: Wang

state: Fujian

address: Cangshan District

institute: Fujian Agriculture and Forestry University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
Based on the hypergeometric distribution, GO6, KEGG7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: A549 cells overexpressing ORF6 or control cells were maintained in Dulbecco’s modified Eagle’s medium(DMEM) containing 10% fetal bovine serum (FBS) supplemented with penicillin (100U/ml) and streptomycin (100μg /ml) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit following manufacture's protocols.

treatment_protocol: A549 cells overexpressing ORF6 or control cells were infected with PR8 virus for 12 h.

value: human alveolar epithelium cells

value: ORF6 overexpression

value: PR8 virus infection


title: A549 cells, ORF6 overexpression, rep 1


title: A549 cells, control, rep 3


title: A549 cells, control, rep 2


title: A549 cells, control, rep 1


title: A549 cells, PR8 infection, Ribo-Seq, rep 3

library_source: other

data_processing:
After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.
Raw data of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing  reads with 5’ adapter, without 3’ adapter or insert sequence, with more than 10% N, with more than 50% nucleotides with Qphred<=20, with ploy A/T/G/C, with rRNA and tRNA.
Ribo-seq used TopHat2(2.0.12) for genome mapping.
Assembly: homo_sapiens_Ensembl_97
Supplementary files format and content: tab-delimited text files include gene count and ribo FPKM values for each Sample.

molecule: other

growth_protocol: A549 cells were maintained in Dulbecco’s modified Eagle’s medium(DMEM) containing 10% fetal bovine serum (FBS) supplemented with penicillin (100U/ml) and streptomycin (100μg /ml) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Sample was treated with specific lysis buffer with cycloheximide (50mg/mL) to acquire the lysate.
To digest the RNA other than ribosome-protected fragments (RPFs), cell lysate was treated with unspecific endoribonuclease RNase I. Isolation of monosomes was performed by size-exclusion chromatography with MicroSpin S-400 HR columns. Following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. The RNA samples were then treated with rRNA depletion kit（Qiagen） to deplete the samples of as much rRNA contamination as possible before PAGE purification of the relatively short (20~38 nt) RPFs. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR.

treatment_protocol: A549 cells were infected with PR8 virus for 12 h.


title: A549 cells, PR8 infection, Ribo-Seq, rep 2


title: A549 cells, PR8 infection, Ribo-Seq, rep 1


title: A549 cells, Mock, Ribo-Seq, rep 3

value: Mock treatment


title: A549 cells, Mock, Ribo-Seq, rep 1


title: A549 cells, Mock, Ribo-Seq, rep 2


title: A549 cells, PR8 infection, rep 2

data_processing:
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-v2.0.5  and paired-end clean reads were mapped to the reference genome.
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. And then FPKM was calculated.It normalizes for both sequencing depth and genome size.
(For samples with biological replicates, edgeR_3.24.3 (lncRNA), DESeq2_R-3.1.2(circRNA)) Differential expression analysis of two conditions/groups (at least two biological replicates per condition/group) was performed using the edgeR.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 <0.05 were assigned as differentially expressed ones.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered as significantly enriched GO functions of gene set. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: homo_sapiens_Ensembl_97
Supplementary files format and content: tab-delimited text files include genes readcount and transcripts readcount for each Sample.

extract_protocol:
RNA was harvested using Trizol reagent.
A total of 1 µg total RNA per sample was used as input material for the lncRNA library preparation. Strand-specific 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


title: A549 cells, Mock, rep 2


title: A549 cells, Mock, rep 3


title: CT_New_Veh3 [AR1252]


title: A549 cells, PR8 infection, rep 1


title: A549 cells, Mock, rep 1


title: RM td TOMATO 30A SWIRLER BASE RETA DAY 3

city: Melbourne

first: Jacky

middle: Yisheng

last: Li

state: Victoria

address: 50 Flemington Rd

department: Cellular Biology

country: Australia

institute: MCRI

data_processing:
For single cell data, sequenced reads were mapped to the GrCh38 whole human genome with cell ranger software using the default parameters.
Assembly: hg38
Supplementary files format and content: Features and barcodes and count matrix for single cell data (feature.tsv, barcodes.tsv, matrix.mtx).

source_name: RM td TOMATO

growth_protocol: iPSC from two independently generated lines were differentiated in Swirling EB cultures to hematopoietic cells over a 14 day period, through sequential stages of mesoderm induction, HOXA patterning, endothelial specification, and endothelial to hematopoietic transition. After 14 days differentiation, blood cells shed into the medium (termed supernatant cells) were harvested as were cells disaggregated from the remaining swirling EB structures (termed swirler base). These samples were analysed separately.

extract_protocol:
Single cell suspensions for each sample were harvested and used for single cell droplet generation, RNA extraction and library preparation in a Chromium controller according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Selected samples were treated with the retinoic acid precursor retinyl acetate (2µM RETA) added at day 3 of differentiation for two days and removed at day 5, or replenished every two days. In these latter samples, RETA was removed at day 11, day 13 or day 14.

value: RM td TOMATO

value: IPSC induced stromal and endothelial cell

value: 30A RETA DAY 3


title: RM td TOMATO 3B5A SWIRLER BASE NO RETA

value: 3B5A NO RETA


title: RM td TOMATO 30A SWIRLER BASE NO RETA

value: 30A NO RETA


title: RM td TOMATO 30A SUPERNATANT RETA DAY 3-14

value: IPSC induced blood cell

value: 30A RETA DAY 3-14


title: RM td TOMATO 3B5A SWIRLER BASE RETA DAY 3

value: 3B5A RETA DAY 3


title: A549 cells, ORF6 overexpression, rep 2


title: RM td TOMATO 3B5A SWIRLER BASE RETA DAY 3-14

value: 3B5A RETA DAY 3-14


title: RM td TOMATO 30A SUPERNATANT RETA DAY 3


title: RM td TOMATO 3B5A SUPERNATANT RETA DAY 3-14


title: RM td TOMATO 3B5A SUPERNATANT NO RETA


title: RM td TOMATO 30A SUPERNATANT NO RETA


title: RM td TOMATO 3B5A SUPERNATANT RETA DAY 3


title: PB BFP 30A SWIRLER BASE RETA DAY 3-13

source_name: PB BFP

value: PB BFP

value: 30A RETA DAY 3-13


title: PB BFP 30A SWIRLER BASE RETA DAY 3-11

value: 30A RETA DAY 3-11


title: PB BFP 3B5A SWIRLER BASE RETA DAY 3-11

value: 3B5A RETA DAY 3-11


title: A549 cells, PR8 infection, rep 3

value: human alveolar epithelium cells


title: PB BFP 30A SWIRLER BASE RETA DAY 3


title: H3K27me3_CM_HD7

source_name: PBMC

extract_protocol:
AutoCUT&RUN protocol (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-6qpvre6zblmk/v1) was used.
Library construction follows AutoCUT&RUN protocol (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-6qpvre6zblmk/v1) corresponding procedures.

value: PBMC

value: CD8 Central Memory T Cell


title: PB BFP 3B5A SWIRLER BASE RETA DAY 3-13

value: 3B5A RETA DAY 3-13


title: PB BFP 30A SUPERNATANT RETA DAY 3-13


title: PB BFP 30A SWIRLER BASE NO RETA


title: PB BFP 30A SUPERNATANT RETA DAY 3-11


title: CT26 xenografts, MCB-294, scRNAseq

city: 上海市

first: 新婷

last: 夏

state: 上海市

address: 东川路500号

department: 生命科学学院

institute: 华东师范大学

data_processing:
Reads were processed using the Cell Ranger (v5.0.1) pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, versionGRCm38, using the STAR algorithm.
Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes.
Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v4.1.1) R toolkit for quality control and downstream analysis of our single cell RNA seq data. All functions were run with default parameters, unless specified otherwise.
Assembly: mm10
Supplementary files format and content: matrix files

growth_protocol: Mice were housed in an animal facility with a 12-hour day/night light cycle, temperature maintained at 25°C and humidity at 60%. Mice were maintained under pathogen-free conditions, with food and water were provided ad libitum.

extract_protocol:
Tissues were transported in In sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no.25200-072) and 10 ug/mL lDNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues, and then tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min. We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40um nylon cell strainer and red blood cells were removed by 1 X Red Blood Cell Lysis Solution (ThermoFisher, Cat. no. 00-4333-57). Dissociated cells were washed with 1 x DPBS containing 2% FBS. Cells were stained with 0.4% Trypanblue (ThermoFisher,Cat.no.14190144) to check the viability on Countess® II Automated Cell Counter (ThermoFisher). The sample was then sent to Majorbio Bio-pharm Technology Co.,Ltd (Shanghai) for testing.
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10×beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹv3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip(Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The sequencing libraries were performed on DNBSEQ-T7 platform (PE150) using DNBSEQ-T7RS Reagent Kit (FCLPE150) version 3.0. The sequencing and bioinformatic analysis were performed on platform of Majorbio Co.,Ltd (Shanghai,China).

treatment_protocol: CT26 xenograft mouse model were MCB-294 or MCB-36(Bid, 30 mg/kg or 60 mg/kg respectively) treated, followed by harvest for scRNAseq.

tag: Sex

value: male

tag: age

value: 6-8 weeks

tag: strain

value: MCB-294, 2days, bid


title: CT26 xenografts, vehicle, scRNAseq

value: Vehicle, 2 days, bid


title: CT26 xenografts, MCB-36, scRNAseq

value: MCB-36, 2days, bid


title: PB BFP 3B5A SWIRLER BASE NO RETA

value: IPSC induced stromal and endothelial cell

value: 3B5A NO RETA


title: PB BFP 30A SUPERNATANT NO RETA

value: IPSC induced blood cell

value: 30A NO RETA


title: cSAM-Setdb1 sg1, bio rep 3

city: Tokyo

first: Yu-Hsuan

last: Chang

address: 4-6-1 Shirokanedai, Minato-ku

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to the mouse reference genome (mm10) using Rsubread (v2.4.3). Raw counts were obtained from read alignments using refGene for gene counts or RepeatMasker annotation for transposable elements, and then further transferred to CPM using edgeR (v3.32.1). After filtering out low-expression genes with CPM < 1, all CPM values were performed with log2 transformed for further analysis.
Assembly: mm10
Supplementary files format and content: csv files include CPM values for each Sample

source_name: mouse bone marrow cells transformed by SETBP1 and ASXL1 mutations

growth_protocol: Mouse cSAM cells were cultured in RPMI-1640 medium, 10% FBS (Biosera), 1 ng/ml mouse interleukin-3 (IL-3, R&D systems), and 1% penicillin-streptomycin.

extract_protocol:
Total RNA of 2 x10^6 cultured Setdb1-depleted or non-targeting control cSAM cells in each sample was extracted by RNeasy Mini Kit (QIAGEN).
rRNA depletion stranded Library. Ribosomal RNA was removed by RNase H. After RNA fragmentation, cDNA was synthesized by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP. Following end repair, add A and adaptor ligation, the DNA fragments were amplified by PCR.

value: cSAM

value: Setdb1 knockout


title: cSAM-Setdb1 sg1, bio rep 1

value: mouse bone marrow cells transformed by SETBP1 and ASXL1 mutations


title: hiPSC40_EV

city: Milano

first: Valeria

last: Peli

address: via Francesco Sforza, 35

institute: IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano

description: EV isolated from hiPSC conditioned medium; E8 medium for EV collection

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Raw data worksheet reports Agilent Feature Extraction file. CircRNA Expression Profiling Data data reports data after processing.

source_name: Extracellular vesicles derived from human induced pluripotent stem cells from human cord blood mesenchymal stem cells

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: StemMACS medium for hiPSC culture maintenance; E8 medium for hiPSC-derived EVs collection.

extract_protocol: Trizol RNA extraction. Total RNA from each sample was quantified using the NanoDrop ND-1000. Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: hiPSCs steady state; EVs isolated from 24h hiPSC conditioned medium via ultracentrifugation.

value: Extracellular vesicles derived from hiPSC

value: Male


title: cSAM-Setdb1 sg1, bio rep 2


title: PB BFP 3B5A SUPERNATANT RETA DAY 3-13

value: PB BFP


title: CT26 xenografts, MCB-36, CD45+ scRNAseq

data_processing:
Reads were processed using the Cell Ranger (v5.0.1) pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, versionGRCm38, using the STAR algorithm.
Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes.
Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v4.1.1) R toolkit for quality control and downstream analysis of our single cell RNA seq data. All functions were run with default parameters, unless specified otherwise.
Assembly: mm10
Supplementary files format and content: Matrix files

extract_protocol:
Tumor xenografts were mechanically and enzymatically (10 U/mL collagenase I, 400 U/mL collagenase IV, and 100 μg/mL DNase I in FBS-free RPMI-1640 medium) digested to obtain a single-cell suspension. Intratumoral CD45+T cells were isolated using BD FACSAriaIII and resuspended in PBS containing 0.04% BSA.
Cells were counted and cell density was adjusted to that recommended for 10x Genomics Chromium single-cell 3’ v3 processing and library preparation. Sequencing was performed on an Illumina platform (NovaSeq 6000), by GENERGY BIO (Shanghai, China), at a sequencing depth of about 90,000 reads per single cell. Sequencing data in a bcl file were converted to FASTQ format using Illumina bcl2fastq2 Conversion Software v2.20 and were subjected to quality control by FastQCv0.11.9.

treatment_protocol: CT26 xenograft mouse model were treatment with MCB-294 (30 mg/kg, BID, IP ) or MCB-36 ( 60 mg/kg, BID, IP) for 2 days, followed by harvest for sorting cd45+ cells

tag: cell population


title: cSAM-control, bio rep 3

value: WT


title: Total pituitary cells from one P4 female Prop1 df/df mouse

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

state: New York

address: 101 Nicolls Road

institute: Stony Brook University

description: ScRNAseq RNA libraries were prepared from one P4 female Prop1+/+ pituitary gland and one P4 female Prop1df/df pituitary gland from the same litter.

data_processing:
Samples were demultiplexed with Cellranger Single Cell Software Suite 3.1.0
Binary sequence alignment maps were converted into the loom format using velocyto.py (La Manno et al. 2018), which were then analyzed in R using the ‘Seurat’ 3.1.2 package (Butler et al. 2018; Stuart et al. 2019).
Core Seurat functions were used to read in loom files, integrate samples, generate uniform manifold approximation and projection (UMAP) plots, calculate clusters, perform differential gene expression analyses, and generate plots of expression data.
Assembly: fastq files aligned to a modified University of California Santa Cruz mm10 (GRCm38) reference genome containing amended annotation for the Prop1 3’ untranslated region (Cheung et al. 2018b) and the Eyfp sequence (https://www.ncbi.nlm.nih.gov/nuccore/LC171744.1, positions 2933-3640).
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)
Supplementary files format and content: loom format matrix created by velocyto.py

source_name: 1 female

extract_protocol:
Pituitary tissue was dissected and dispersed using an enzymatic mix of collagenase, trypsin, and DNaseI for 4 hrs and dispersed cells prepared for scRNAseq library preparation. Dispersed cells were resuspended in HBSS/0.4%BSA.
Single-cell RNA libraries were prepared by the University of Michigan’s Advanced Genomics Core under a standardized pipeline on the 10x Genomics Chromium platform and controller, following manufacturer’s instructions for Single Cell 3’ v3 reagents, and sequenced on the NovaSeq6000 platform with an S4 chip.  From our previous description in Cheung et al., 2018 Endocrinology: Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting post-GEM reverse transcription product was cleaned up using DynaBeads MyOne silane beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA) cleaned and quantified, and then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by KAPA quantitative PCR for Illumina adapters (Roche, Pleasanton, CA) and size was determined by Agilent TapeStation D1000 tapes. Read 1 primer sequences were added to the molecules during GEM incubation. P5, P7, and sample index and read 2 primer sequences were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. Libraries were generated with unique sample indices for each sample.

value: pituitary

value: female

value: total pituitary cells

value: Prop1 df/df


title: hiPSC40

description: StemMACS culture medium; accession number GSE144629

source_name: Human induced pluripotent stem cells from human cord blood mesenchymal stem cells

value: hiPSC


title: PB BFP 3B5A SWIRLER BASE RETA DAY 3

value: 3B5A RETA DAY 3


title: CT26 xenografts, MCB-294, CD45+ scRNAseq

value: male

value: 6-8 weeks

value: MCB-294, 2days, bid


title: cSAM-CRISPR/Cas9 screens

data_processing:
Readcounts after sequencing deconvolution were normalized to reads per million. The number of sgRNAs with > 50 reads was determined from raw readcounts, to determine % recovery of the library in each sample. Readcounts were then log2 transformed, and a log2 fold change from the plasmid DNA (pDNA) for each sample was calculated per sgRNA (Table S1). Low readcount sgRNAs (those that fell below 2 standard deviations under the mean in the pDNA sample) were removed from the data before any analysis. STARS analyses were performed on the log2 fold changes, as previously described69. In STARS, the probability mass function of a binomial distribution was used to calculate a gene score from the sgRNA log2 fold changes, if at least 2 sgRNAs falls in the top 1% of all sgRNAs for an experiment. Permutation testing was then used to generate the null distribution, allowing for the calculation of p-values and FDRs per gene. Depleted or enriched hits were called for genes with an FDR < 0.25.
Assembly: mm10
Supplementary files format and content: lognorm.txt file includes a log normalization of sgRNA for each sample
Supplementary files format and content: LFCData.txt file includes a log2 fold change from the genomic DNA normalized to input control for each sample calculated per sgRNA

growth_protocol: In vitro culture: mouse cSAM cells were cultured in RPMI-1640 medium, 10% FBS (Biosera), 1 ng/ml mouse interleukin-3 (IL-3, R&D systems), and 1% penicillin-streptomycin. In vivo sample: cSAM cells were collected from spleens of C57BL/6 mice.

extract_protocol:
DNA was extracted from each sample using the Blood and Cell Culture DNA Maxi kit (QIAGEN) according to the manufacturer’s instructions. 120 µg of purified gDNA was sent to the Broad Institute for Next Generation Sequencing and deconvolution.
PCR was then used to selectively amplify the sgRNA region and determination of sgRNA abundance was performed by Illumina sequencing.


title: CT26 xenografts, vehicle, CD45+ scRNAseq

value: Vehicle, 2 days, bid


title: PB BFP 30A SUPERNATANT RETA DAY 3

value: IPSC induced blood cell

value: 30A RETA DAY 3


title: cSAM-control, bio rep 2

value: mouse bone marrow cells transformed by SETBP1 and ASXL1 mutations

value: cSAM


title: PB BFP 3B5A SUPERNATANT RETA DAY 3-11

value: 3B5A RETA DAY 3-11


title: PB BFP 3B5A SUPERNATANT RETA DAY 3

value: PB BFP


title: E13.5 eyecups, DKO (Six3F/F;Six6-/-;a-Cre), scRNAseq

city: The Bronx

first: Alexander

last: Ferrena

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: 10x Genomics

data_processing:
Sequencing reads were mapped to the mouse reference genome mm10 (3.0.0) using CellRanger (3.1.0).
Assembly: mouse reference genome mm10/3.0.0
Supplementary files format and content: count matrices output by CellRanger in the tab-separated text format

source_name: eyecups containing retina, lens, and blood

extract_protocol:
We followed instructions provided by 10x Chromium. Briefly, micro-dissected eye cups were dissociated into single cells using activated Papain (Worthington Biochemical) and then harvested in DPBS containing 0.04% BSA for cell capture using the 10x Chromium fluid device, targeting 10,000 cells for each sample.
10x Genomics Single Cell 3’ kit (version 3)


title: cSAM-Setdb1 sg1-H3K9me3 ChIP

data_processing:
Reads for H3K9me3 were trimmed using Trim galore! (Galaxy v.0.6.7) to remove adaptor sequences on Galaxy platform. The trimmed reads were aligned to mm10 and dm6 by Bowtie267 (Galaxy v.2.4.2) with the parameters N1-L25-X2000-no-mixed-no-discordant. Low-quality reads and PCR duplicates were filtered using functions of Filter SAM or BAM, output SAM or BAM (Galaxy v1.8), and RmDup (Galaxy v2.0.1). For analysis of scaled data, read counts were first normalized by computing the numbers of reads per kilobase of bin per million of reads (RPKM). Normalized bigwig files were then generated using the bamCoverage function of deepTools64 (Galaxy v3.3.2) and the signal was normalized between KO and control groups using dm6 reads. Peak Calling was performed using FindPeaks function of HOMER package with -style histone parameter. CPM values were calculated at a set of merged H3K9me3 peaks that were identified in Setdb1-KO or control cells. Requirements to identify peaks with H3K9me3 loss included, (1) twofold more signal in control versus Setdb1-KO cells (2) a minimum CPM of 0.07 in control cells (3) a maximum CPM of 0.07 in Setdb1-KO cells. Threshold value 0.07 was determined by density curve of H3K9me330. Heatmaps were generated by using plotHeatmap function of deepTools.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
All samples were carried out using SimpleChIP® Enzymatic Chromatin IP Kit (CST, 9003) following the manufacturer’s instructions. 10^7 cultured cSAM cells per sample were fixed with 1% formaldehyde and then quenched with glycine. After washing and cell lysis, the chromatin was fragmented with 1 µl of micrococcal nuclease (MNase) at 37oC for 20 min and nuclei were completely lysed by sonication. The 10 µg of chromatin in each reaction was incubated with 10 µl of anti-H3K9me3 monoclonal antibody (CST, #13969) overnight at 4oC with rotation.  50 ng of spike-in chromatin (active motif, 53083) and 2 μg of spike-in antibody (active motif, 61686) were added to each ChIP reaction. Immunoprecipitation was performed with protein G magnetic beads. Following elution, reverse-crosslinks, and purification, DNA was used for further sequencing.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

value: Setdb1 knockout

tag: antibody


title: PB BFP 3B5A SUPERNATANT NO RETA

value: 3B5A NO RETA


title: Total pituitary cells from one P4 female Prop1 +/+ mouse

value: pituitary

value: female

value: Prop1 +/+


title: E13.5 eyecups, control (Six3+/-;Six6+/-), scRNAseq

description: 10x Genomics

value: eyecups containing retina, lens, and blood


title: cSAM-control sg-H3K9me3 ChIP

value: WT

value: anti-H3K9me3 monoclonal antibody (CST, #13969)