title: HCC-1395_dz67

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.

growth_protocol: MDA-MB-453 and HCC-1395 cells were maintained in DMEM or RPMI respectively, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Cells were treated overnight with 5µM (R)-9b (dz67)

value: Human breast cancer

value: treatment

value: (R)-9b (dz67) treated


title: mammary tumor 148

status: Public on May 23 2023

type: SRA

city: Davis

first: Michele

last: La Merrill

state: CA

address: 4138 Meyer Hall

department: Department of Environmental Toxicology

country: USA

institute: University of California, Davis

library_source: transcriptomic

data_processing:
Illumina bcl2fastq version 2.20.0.422 was used for base-calling
Data was filtered using HTStream version 1.0.0
Data was aligned using STAR 2.6.1d
Unique molecular identifiers (UMI) processing was done using umitools version 0.5.5
Read counts were conducted using HTSeq version 0.10.0
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized counts per gene per mouse
Supplementary_files_format_and_content: normalized intron counts per gene per mouse

molecule: total RNA

organism: Mus musculus

source_name: mammary tumor

extract_protocol:
Mice were euthanized and tumors were excised and cut in half, with one half flash frozen in liquid nitrogen. Flash-frozen tumors were later pulverized and total RNA was extracted using the Qiagen AllPrep kit (80004).
RNA quality, quantity, and purity (260/280 absorbance ratios) were assessed using a Fragment Analyzer, a Qubit fluorometer, and a Nanoquant plate using an Infinite 200 PRO absorbance reader, respectively. Total RNA was diluted with nuclease free water to a normalized concentration (33.33 ng/uL) and sequenced.

tag: tissue

value: mammary tumor

tag: strain

tag: genotype

tag: treatment

value: Methylparaben


title: inVivo_OP1_lin-_14d_1 mRNA

city: Cambridge

first: Brian

last: Huntly

address: Hills Road

department: Department of Haematology

country: United Kingdom

institute: University of Cambridge

description:
Perturb-seq of mouse cells in vivo
inVivo_OP1_lin-_14d_1.h5
CellAnnotation_invivo.tsv

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 6.1.1).
Sequencing data were aligned to the reference genome with Cell Ranger count
Assembly: GRCm38/mm10 reference genome assembly (GENCODE vM23/Ensembl 98) with BFP and GFP sequences
Supplementary files format and content: h5 matrices: read count matrix with cells / barcodes (columns) and genes (rows); one for each sample
Supplementary files format and content: CellAnnotation: mapping of cell types and other information to barcodes across samples; one for each source (leukemia, in vivo, ex vivo)

growth_protocol: Primary LSKs were isolated from 12-14 weeks-old ROSA26xCas9 mice and grown ex vivo for 36 hours under Stem Cell conditions (DMEM/F12, ITSX 1X, 1 mg/mL PVA 87%, 10 mM Hepes, 100 ng/uL Tpo, 10 ng/uL SCF). Then, 50,000 viable cells were transplanted to irradiated (902 cGy, 1 minute) 12 weeks-old adult B6.SJL-Ptprca Pepcb/BoyJ (CD45.1) mice via tail injection.

extract_protocol:
After two weeks, the transplanted mice were euthanised and bone marrow cells were harvested and stained with BV510 anti Lineage (CD3, CD19, Ter119, CD11b, Gr1) and APC anti c-Kit antibodies. For single-cell RNAseq we FACS-sorted Lineage- and Lineage+/cKit+ fractions and processed each of them in a 10X single-cell RNA-seq partition aimed at a final coverage of 500 single-cells per sgRNA.
Single-cell libraries were generated using the Chromium Next GEM Single-Cell 3’ Reagent Kits v3.1 (Dual Index) using the 10x Genomics manufacturer recommended protocol and targeting 16,000 cells per library.The resulting libraries were quantified using Qbit and qPCR and analysed on a Tape Station. Libraries were sequenced in a NextSeq 1000 or a Novaseq 6000 to a final coverage of 50,000 reads/cell for 3’ Gene Expression libraries and 5,000 reads/cell for CRISPR Feature Barcode libraries.

treatment_protocol: Cas9-LSK cells were transduced with lentiviral vectors expressing sgRNAs against specific CFs.

tag: sort markers

value: lin-

tag: time point

tag: secondary readout

value: CRISPR screen (Perturb-seq)


title: MDA-MB-453_UNT RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: untreated


title: inVivo_OP1_ckit_14d_1 mRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP1_ckit_14d_1.h5
CellAnnotation_invivo.tsv

value: lin+ckit+


title: MDA-MB-453_dz67


title: MDA-MB-453_UNT

library_source: genomic

data_processing:
Raw fastq files were aligned against human genome hg38 assembly using Burrows-Wheeler Alignment tool and then processed using methylQA to generate bed and bigwig files.
The MACS2 peak caller was used to compare the ChIP-Seq signal to a corresponding input control to identify narrow regions of enrichment (peaks) using default parameters.
ChIP-Seq signals and peak locations were further visualized using UCSC Genome Browser.
The top 500-1000 ChIP-Seq peaks were assigned to the nearest genes using the annotatePeaks function from HOMER2, motif binding sites were determined using HOMer2, and GO and pathway enrichment analyses were performed by EnrichR.
Assembly: hg38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

growth_protocol: MDA-MB-453 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degreeC

extract_protocol:
The lysates were immunoprecipitation with pY88-H4 antibodies (2 ug) for overnight.
Ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Roche Sequencing Solutions Inc., Pleasanton, CA). The size and quality of the library was evaluated using the Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA), and the library was quantitated with the Kapa Library Quantification Kit.  Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 40-50 million 75-base paired-end reads (Illumina, Inc., San Diego, CA).  The raw sequence data were aligned using BowTie 2 [1], and the binding sites were identified using the MACS peak-finding software

treatment_protocol: 5x10^7 MDA-MB-453 cells were treated with R-9b (dz67) inhibitor overnight (5 uM) and lysates were prepared by sonication in RLB bufffer.

tag: chip antibody


title: MDA-MB-453_DZ


title: inVivo_NTC_lin-andckit_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_NTC_lin-andckit_14d_1.h5
CellAnnotation_invivo.tsv

value: lin-ckit+


title: inVivo_OP1_ckit_14d_1 gRNA


title: mammary tumor 133


title: Sample_2234-JES-1, Day21

city: Ann Arbor

first: Jennifer

last: Harder

state: MI

address: 1301 Catherine St.

department: Internal Medicine, Division of Nephrology

institute: University of Michigan Medical School

data_processing:
Total RNA from whole wells underwent library preparation using NEBNext Ultra II kit and sequencing using paired end read length of 150 bases on a NovaSeq4000.
RNAseq was performed by the University of Michigan Advanced Genomics Core (https://brcf.medicine.umich.edu/cores/advanced-genomics/).
Fastq files were mapped to ENSEMBL 38.104 using STAR 2.7.8a (PMID: 23104886)
Assembly: Read counts were extracted from the fastq files using HTSeq (version0.11) (PMID: 25260700), voom-transformed (PMID: 24485249) and log-2 transformed.
Supplementary files format and content: ENSEMBL GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Kidney organoid

extract_protocol: Kidney organoids were generated from human embryonic stem cells (UM77-2, NIH registry #0278) according to published protocol (Harder et al., JCI Insight 2019).  Isolated spheroids were collected at day 21, day 25 and day 29, then lysed and RNA extracted.  Library prep and next-generation sequencing of total RNA on a NovaSeq4000 (150 bp, paired end) were carried out in the Advanced Genomics Core at the University of Michigan.

value: Kidney organoid

value: UM77-2 hESC

value: Day 21


title: HCC-1395_UNT


title: CNE2_PS5_ChIP-seq

city: Changsha

first: Honglu

last: Liu

state: Hunan

address: Kaifu district, Xiangya road

department: Xiangya hospital

country: China

institute: Central South University

data_processing:
ChIP-seq raw reads were filtered using trim_galore v0.6.0, aligned to the hg38 genome assembly using Bowtie2 v2.3.5.1 with default parameters.
Duplicate reads were removed using MarkDuplicates from the gatk package v.4.1.4.1.
ChIP-seq and input reads were calculated using bedtools coverage v2.26.0, mapped to the TSS regions (TSSR,–50 to +300 bp relative to TSS) and the gene bodies (TSS +300 bp to +3 kb past the TES) for each annotated RefSeq isoform.
The reads density was normalized by the region length and by the mapped filtered read numbers multiplied by 1 million (rpm/bp).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: nasopharyngeal carcinoma cell

growth_protocol: NPC cell lines were cultured with DMEM/High Glucose medium (Biological Industries) containing 10% FBS (VISTECH, SE100-B), in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Lysates were clarified from sonicated nuclei and RNAPII-DNA complexes were isolated with antibody.
ChIP-seq library was prepared using NEBNext® ChIP-Seq Library Prep Reagent Set (New England Biolab, E7645S). The library was sequenced on Illumina NovaSeq 6000 (Novogene).

treatment_protocol: After 24 hours, cells were irradiated with the indicated X-ray dose at room temperature at 200 cGy/min with a linear accelerator (X-Rad 225, Precision), and cells were harvested at day 2 after IR treatment.

value: anti-RNAPII phospho S5 (Abcam, ab5408)


title: inVivo_NTC_lin-andckit_14d_1 mRNA


title: CNE2-4Gy_PS2_ChIP-seq

value: anti-RNAPII phospho S2 (Abcam, ab5095)

value: treated with 4Gy radiation


title: CNE2_PS2_ChIP-seq


title: mammary tumor 132

value: Vehicle


title: DM_OP0_NM_6d_1 gRNA

description:
Perturb-seq of mouse leukemic model
DM_OP0_NM_6d_1.h5
CellAnnotation_leukemia.tsv

source_name: Npm1c/Flt3ITD leukemia model

value: nomarker


title: mammary tumor 126


title: CNE2-4Gy_PS5_ChIP-seq


title: MDA-MB-453_INPUT

value: Human breast cancer


title: DM_OP0_NM_6d_1 mRNA


title: CNE2-IR_PS2_ChIP-seq


title: CNE2-IR_PS5_ChIP-seq


title: mammary tumor 125

value: Propylparaben


title: CNE2_RNAPII_ChIP-seq

value: anti-RNAPII Ab (Abcam, ab817)


title: CNE2-IR_PS5_PS2_input_ChIP-seq


title: CNE2-IR_RNAPII_ChIP-seq


title: CNE2-IR_RNAPII_input_ChIP-seq


title: ∆sigL-50DPD-1

city: Worcester

first: Christopher

last: Sassetti

state: MA

address: 55 Lake Ave North

institute: University of Massachusetts Chan Medical School

data_processing:
Reads were mapped to the M. tuberculosis H37Rv genome using Burrows-Wheeler Alignment
Read-count normalization and statistical analysis of differentially expressed genes (DEGs) were calculated using DESeq2
Assembly: Genbank accession NC_000962.3
Supplementary files format and content: Tab delimited text file with raw read counts for all samples

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacterial cell

growth_protocol: Standard 7H9 or 50 µM dipyridyl-treated 7H9, grown at 37 degrees shaking for 4 divisions

extract_protocol:
Total RNA extracted using Trizol and Zymo Direct-zol kit, NEB DNase I treatment, cleanup with Zymo Clean and Concentrate Kit
Libraries were prepped using NEB Ultra II Directional RNA Library Prep Kit for Illumina following manufacturers' instructions.

value: Bacterial cell

value: deltasigL (delta0736)

value: Standard 7H9 + 50 µM Dipyridyl


title: CNE2_PS5_input_ChIP-seq

value: untreated


title: CNE2_RNAPII_input_ChIP-seq


title: ∆rip1-50DPD-2

value: deltarip1 (delta2869c)


title: CNE2-4Gy_RNAPII_input_ChIP-seq


title: mammary tumor 95

value: mammary tumor


title: mammary tumor 105

value: Methylparaben


title: mammary tumor 115


title: CNE2_PS2_input_ChIP-seq


title: ∆sigL-50DPD-3


title: CNE2-IR_1_RNA-seq

data_processing:
CASAVA1.4
Raw reads were filtered using trim_galore v0.6.0(http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/): trim_galore –paired ${sample}_1.fq.gz ${sample}_2.fq.gz --gzip -o trim
The reads from each RNA-seq sample were then mapped to hg38 genome assembly using STAR v2.7.1a.The key alignment parameters were as follows:“--outFilterMismatchNoverLmax 0.04 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 500 --outMultimapperOrder Random --outSAMmultNmax 1”
Differential expression analysis was performed using the Bioconductor package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

growth_protocol: CNE2 and CNE2-IR were cultured with DMEM/High Glucose medium (Biological Industries) containing 10% FBS (VISTECH, SE100-B), in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
The RNA of the treated cells was extracted by TRIzol (Life Technologies, 87804) according to the manufacturer’s protocol.
Libraries were prepared using mRNA-Seq Sample Preparation Kit (Illumina) and sequenced on an Illumina NovaSeq platform(Novogene).

value: nasopharyngeal carcinoma cell


title: mammary tumor 81


title: ∆sigL-50DPD-2


title: CNE2-4Gy_RNAPII_ChIP-seq


title: ∆rip1-50DPD-1


title: WT-50DPD-3

value: WT


title: CNE2_1_RNA-seq


title: mammary tumor 74


title: mammary tumor 121


title: mammary tumor 62


title: mammary tumor 60


title: WT-50DPD-1


title: CNE2-4Gy_PS5_PS2_input_ChIP-seq


title: ∆sigL-7H9-3

value: Standard 7H9


title: mammary tumor 55


title: CNE2-IR_2_RNA-seq


title: ∆sigL-7H9-2


title: mammary tumor 48


title: mammary tumor 42


title: ∆rip1-7H9-3


title: ∆sigL-7H9-1


title: CNE2_2_RNA-seq


title: WT-50DPD-2


title: ∆rip1-7H9-2


title: Dsim_dcr2_mutant_3seq_replicate1

city: New Yor

first: Jeffrey

last: Vedanayagam

state: NY

address: 1275 York Avenue

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

data_processing:
RNA sequencing analysis. Paired-end RNA-seq reads from wild-type and mutant dcr-2 samples in Dmel and Dsim were mapped to dm6 (FlyBase) and Dsim PacBio assemblies (Chakraborty et al., 2021), respectively using hisat2 aligner (Kim et al., 2015; Pertea et al., 2016).The resulting alignments in SAM format was converted to BAM using SAMtools software (Li et al., 2009) for downstream analyses. Mapping quality and statistics were determined using the bam_stat.py script provided in the RSeQC software (Wang et al., 2012). Transcript abundance was determined using FeatureCounts software from the subread package (Liao et al., 2014), using Dmel gene annotations from FlyBase r6.25. For Dsim, we used both gene annotations from FlyBase and de novo transcript annotation using StringTie software (see details below) (Pertea et al., 2015). As FlyBase gene annotations for Dsim correspond to Dsim r2.02 assembly, we converted the FlyBase assembly annotations to Dsim PacBio coordinates using the UCSC liftover tool implemented in the KentUtils toolkit from UCSC (https://github.com/ENCODE-DCC/kentUtils). We combined FlyBase liftover and de novo annotations in Dsim to determine transcript abundance for RNA-seq analyses. The following description for differential gene expression (DFE) analysis is the same for Dmel and Dsim data. DFE comparing control and dcr-2 mutant data was performed using the DEseq2 package in R (Love et al., 2014). Genes with low read counts and/or high variability among technical or biological replicates can lead to log fold change differences that are not representative of true differences. Therefore, to minimize variance, we used the log fold change (LFC) shrinkage implemented in the DEseq2 package using the ‘normal’ method described in (Love et al., 2014). For visualization of mapped reads, the BAM alignment files were converted to bigwig format using bam2wig.py script from RSeQC (Wang et al., 2012) and the bigwig tracks were visualized on the IGV genome browser (Robinson et al., 2011).
Small RNA sequencing analysis. Adapters were trimmed from small RNA sequences using Cutadapt software (https://github.com/marcelm/cutadapt); then the 5’ and 3’ 4-nt linkers (total 8 bp) were removed using sRNA_linker_removal.sh script described in (Vedanayagam et al., 2021) (https://github.com/Lai-Lab-Sloan-Kettering/Dox_evolution). The adapter and linker removed sequences were then filtered to remove < 15 nt reads. We mapped > 15 nt reads from Dmel and Dsim genotypes to dm6 reference genome assembly and Dsim PacBio assembly, respectively, with Bowtie (Langmead et al., 2009) using the following mapping options: bowtie -q -p 4 -v 3 -k 20 --best –strata. The resulting BAM alignments from bowtie mapping were converted to bigwig for visualization using bam2wig.py script from the RSeQC software (Wang et al., 2012).
In addition to previously annotated transcripts/genes from the FlyBase annotation, we performed de novo annotation of our transcriptome data to identify additional, novel testis-expressed transcripts in D. melanogaster and D. simulans. The novel annotated transcripts were then supplemented with known annotations to make a combined set of 17285 transcripts in D. melanogaster and 15119 transcripts in D. simulans. We employed two independent, genome assembly guided transcript prediction algorithms, Cufflinks (Trapnell et al., 2012) and StringTie (Pertea et al., 2015). For both methods, de novo transcripts were predicted for each RNA-seq dataset, and a merged transcript model was generated encompassing the transcriptome from WT and mutant datasets. hpRNAs were predicted using the scheme shown in Supplementary Figure 2, and visualized using the Integrated Genomics Viewer (IGV) (Thorvaldsdottir et al., 2013). The termini of primary hpRNA transcripts were refined using the 5'-seq and 3'-seq data.
Assembly: For D. melanogaster, we used the dm6 genome assembly (Flybase) and for D. simulans, we used Dsim PacBio genome assembly (Chakraborty et al. 2021)
Supplementary files format and content: The processed data files for IGV visualization are in bigiwg format

organism: Drosophila simulans

source_name: testis

extract_protocol:
For D. melanogaster testis dissections dcr-2 mutant testis were collected from wIR; dcr-2[L811fsx]/dcr-2[R416X] trans-heterozygotes and wIR; dcr-2[R416X]/+ heterozygous flies were used as controls. For D. simulans, we collected testis from dcr2[DsRed]/[white+] trans-heterozygous mutants, and used the parental strain w[XD1] as control. Briefly, testis from 3 days old flies were extracted in TRIzol (Invitrogen) in batches of 10 flies at a time and the testis samples were flash frozen in liquid nitrogen. RNA was extracted from 25-50 testis per genotype.
RNA extraction was performed as described in (Lin et al., 2018), and the quality of RNA samples were assessed with the Agilent Bioanalyzer. RNA samples with RIN >6.5 were used for library preparation using the Illumina TruSeq Total RNA library Prep Kit LT. Briefly, for RNA-seq libraries we used 650 ng of total RNA, and we used the Manufacturer’s protocol except for reducing the number of PCR cycles from 15 as recommended to 8, to minimize artifacts that may arise from PCR amplification. We prepared stranded RNA-seq libraries for D. simulans and unstranded libraries for D. melanogaster as RNA samples were extracted and processed in different time points. Samples were pooled using barcoded adapters provided by the manufacturer and the paired-end sequencing was performed at New York Genome Center using PE75 in the Illumina HiSeq2500 sequencer. We prepared small RNA libraries used ~20 μg total RNA, as previously described in Lin et al. 2018. To the total RNA pool, we added a set of 52 RNA spike-ins, spanning a range of concentrations (QIAseq miRNA Library Spike-In kit #800100). Briefly, small RNAs of size 18- to 29-nt-long small RNAs were purified by preparative PAGE. Next, the 3′ linker (containing four random nucleotides) was ligated overnight using T4 RNA ligase 2, truncated K227Q (NEB), after which the products were recovered by a second PAGE purification. 5′ RNA linkers with four terminal random nucleotides were then ligated to the small RNAs using T4 RNA ligase (NEB) followed by another round of PAGE purification. The cloned small RNAs were then reverse transcribed, PCR amplified and sequenced using P50 single-end sequencing on the Illumina HiSeq 2500 sequencer. We prepared small RNA libraries used ~20 μg total RNA, as previously described in Lin et al. 2018. To the total RNA pool, we added a set of 52 RNA spike-ins, spanning a range of concentrations (QIAseq miRNA Library Spike-In kit #800100). Briefly, small RNAs of size 18- to 29-nt-long small RNAs were purified by preparative PAGE. Next, the 3′ linker (containing four random nucleotides) was ligated overnight using T4 RNA ligase 2, truncated K227Q (NEB), after which the products were recovered by a second PAGE purification. 5′ RNA linkers with four terminal random nucleotides were then ligated to the small RNAs using T4 RNA ligase (NEB) followed by another round of PAGE purification. The cloned small RNAs were then reverse transcribed, PCR amplified and sequenced using P50 single-end sequencing on the Illumina HiSeq 2500 sequencer. To map 5' ends, we used the parallel analysis of RNA 5′ ends from low-input RNA (nanoPARE) strategy (Schon et al., 2018). For Dsim libraries, testis was extracted from <1-week males and total RNA was extracted using TRIzol. cDNA was prepared using Smart-seq2 (Picelli et al., 2013) and tagmented using the Illumina Nextera DNA library preparation kit, purified using the Zymo 5x DNA Clean and Concentrator kit (Zymo Research), and eluted with resuspension buffer. For 5’-end enrichment PCR, the purified reaction was split and amplified either Tn5.1/TSO or Tn5.2/TSO enrichment oligonucleotide primer sets. PCR reaction products with Tn5.1/TSO enrichment oligonucleotide and Tn5.2/TSO enrichment oligonucleotide primer sets were pooled and purified using AMPureXP DNA beads. Final libraries were checked for quality on an Agilent DNA HS Bioanalyzer chip. Libraries with size ranges between 150 and 800 bp were diluted and sequenced to 10–15 million single-end 50-bp reads per sample using a custom sequencing primer (TSO_Seq) and a custom P5/P7 index primer mix on an Illumina HiSeq 2500 instrument. To annotate 3' transcript termini, we used the QuantSeq 3’ mRNA-seq library preparation REV kit for Illumina (Lexogen) with a starting material of 50 ng total RNA from Dmel and Dsim control and dcr-2 mutant samples, according to manufacturer’s instructions. cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with single-end SE 50 mode.
RNA-sequencing was done with the paired-end sequencing mode, while the small RNA sequencing was peformed with the single-end sequencing protocol.

value: testis


title: Dsim_dcr2_mutant_3seq_replicate2


title: ∆rip1-7H9-1


title: Dsim_dcr2_het_3seq_replicate2


title: WT-7H9-3


title: Dsim_dcr2_het_3seq_replicate1


title: WT-7H9-2


title: Dsim_dcr2_sRNA_replicate2


title: WT-7H9-1


title: Dsim_dcr2_sRNA_replicate1


title: mammary tumor 31


title: mammary tumor 32


title: mammary tumor 29


title: mammary tumor 23


title: mammary tumor 38


title: Dsim_wXD1_sRNA_replicate2


title: mammary tumor 22


title: mammary tumor 24


title: 20221012_210180310224_FRE10832A36_12

type: RNA

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

hyb_protocol: As Per Nanostring nCounter System

scan_protocol: As Per Nanostring nCounter System

data_processing: Normalised and Analysed using Nsolver (Nanostring)

source_name: Hidradenitis Suppurativa

label_protocol: As Per Nanostring nCounter System

extract_protocol: Total RNA extraxcted usign Quagen RNEasy

tag: diagnosis

value: Hidradenitis Suppurativa

value: dermal fibroblast

tag: timepoint

tag: disease state

value: Lesional


title: Dsim_wXD1_sRNA_replicate1


title: mammary tumor 18

value: Vehicle


title: mammary tumor 17

value: Propylparaben


title: Dsim_dcr2_replicate2


title: 20221012_210180310224_FRE10832A35_11


title: 20221012_210180310224_FRE10832A33_09


title: Dsim_dcr2_replicate1


title: mammary tumor 9


title: mammary tumor 15


title: Dsim_wXD1_replicate2


title: 20221012_210180310224_FRE10832A34_10


title: Dsim_wXD1_replicate1


title: mammary tumor 2


title: 20221012_210180310224_FRE10832A30_06


title: 20221012_210180310224_FRE10832A29_05


title: AME-d0, male, rep5 (RNA-seq)

city: Kansas City

first: Robert

middle: H.

last: Lane

address: 2401 Gillham Rd

institute: Children's Mercy

data_processing:
Base calling is performed using Illumina’s RTA version 2.5.2.
Quality control check via FastQC, read trimming using Trimmomatic
Sequence alignment using the MapRSeq3 package (using STAR)
read counting using the MapRseq3 package (using featureCounts)
Assembly: mm10

source_name: Liver

extract_protocol:
Ground livers from d0 and d21 male (n = 5) mice were used for total RNA isolation by using a miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions, including an on-column DNase I treatment. RNA was quantified spectrophotometrically. The integrity of RNA was assessed with an Agilent 2100 bioanalyzer in conjunction with the RNA 6000 Nano Kit (Agilent), and a RNA integrity number greater than or equal to nine was used.
RNA libraries were prepared by using 200 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq RNA v2 kit

value: Liver

tag: Sex

value: Male

value: WT, C57BL/6J

value: AME

tag: time


title: 20221012_210180310224_FRE10832A28_04


title: mammary tumor 1


title: PCs, ADT-derived cDNA donor2

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
filtered_feature_bc_matrix_106.h5

library_source: other

data_processing:
cellranger demultiplex and mkfastq
cellranger gene count with GRCh38 library
Assembly: GRCh38
Supplementary files format and content: filtered gene count matrix in h5 generated by cellranger.
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
Ex vivo differentiated B cells/PC at day10, day 13  was removed debris by ficoll gradient and following SEC-seq nanovial loading and secretion incubation. And then CITEseq labeling protocol (CG000149). Sorting loaded viable cells before loading on chromian controller.
10X CG00317 next gem single cell 3' (dual index) with feature barcode technology for surface protein
first antibody: anti IgG-PE, second antibody: TotalSeq™-B0911 anti-phycoerythrin (PE) Antibody

value: PBMC

value: B cells

tag: library type

value: ADT

tag: antibodies/tags


title: PCs, mRNA-derived cDNA donor2

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
filtered_feature_bc_matrix_106.h5

tag: tissue

value: mRNA


title: AME-d0, male, rep2 (RNA-seq)


title: 20220830_210050551023_FRE10832A24_12


title: AME-d0, male, rep3 (RNA-seq)


title: 20220830_210050551023_FRE10832A23_11


title: PCs, ADT-derived cDNA donor1_4

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
filtered_feature_bc_matrix_105.h5

value: TotalSeq™-B0911 anti-phycoerythrin (PE) Antibody


title: Dorsal horn of spinal cord, bone cancer pain, biol rep 2 input

city: Jiaxing

first: Lei

last: Yang

state: Zhejiang

address: 1882 Zhonghuan South Road

institute: Affiliated Hospital of Jiaxing University

description:
RIP-target.log2FC1.P0.05.anno.xls
2-input

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome rn6 using Hisat2 aligner (v2.1.0) under parameters.
Differential ac4C peak were identified using exomePeak R package under parameters.
GO and KEGG analysis were performed using clusterprofile R package (v3.6.0). ac4C-RNA-related genomic features were visualized using Guitar R package (v1.16.0).
Identified ac4C peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters.
The reads mapped the genome were calculated using featureCounts (v1.6.3). Differential gene expression analysis was performed using the DESeq2 R-package.
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Dorsal horn of spinal cord

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).Acetylated RNA immunoprecipitation was performed using Epi TM ac4C immunoprecipitation kit (Epibiotek, R1815).
The library was prepared by Epi TM mini longRNA-seq kit (Epibiotek, E1802).

value: Dorsal horn of spinal cord

value: WT

tag: group

value: total RNA


title: Dorsal horn of spinal cord, bone cancer pain, biol rep 2 IP

description:
RIP-target.log2FC1.P0.05.anno.xls
2-IP

tag: genotype

value: IP RNA


title: Dorsal horn of spinal cord, bone cancer pain, biol rep 1 input

description:
RIP-target.log2FC1.P0.05.anno.xls
1-input


title: AME-d0, male, rep1 (RNA-seq)

tag: treatment


title: AME-d0, male, rep4 (RNA-seq)


title: Con-d0, male, rep5 (RNA-seq)

value: Control


title: 20220830_210050551023_FRE10832A18_06

value: Hidradenitis Suppurativa

value: dermal fibroblast

value: Lesional


title: PCs, ADT-derived cDNA donor1_3


title: Dorsal horn of spinal cord, bone cancer pain, biol rep 1 IP

description:
RIP-target.log2FC1.P0.05.anno.xls
1-IP


title: Con-d0, male, rep4 (RNA-seq)

value: Liver


title: Teratoma 4

type: genomic

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Bead array (850k) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data and bioinformatic analyses were carried out using ‘GenomeStudio’ software (version 2011.1, Methylation Module v1.9) (Illumina).
Data processing and QC according to the in-house analysis pipeline  and calculation beta-values.

label: Cy3 and Cy5

source_name: non-seminoma germ cell tumor, teratoma

label_protocol: The Infinium MethylationEPIC array BeadChip (Illumina, San Diego, CA, USA) was used to analyze DNA methylation profiles. 100 - 500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research, Freiburg. i. B., Germany). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega, Walldorf, Germany) according to manufacturer’s instructions.

value: Teratoma


title: 20220830_210050551023_FRE10832A22_10


title: Yolk-sac tumor 3

source_name: non-seminoma germ cell tumor, yolk-sac tumor

value: Yolk-sac tumor


title: Teratoma 3


title: PCs, mRNA-derived cDNA donor1_3

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
filtered_feature_bc_matrix_105.h5


title: 20220830_210050551023_FRE10832A20_08


title: PCs, ADT-derived cDNA donor0_5

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
filtered_feature_bc_matrix_100.h5


title: Dorsal horn of spinal cord, bone cancer pain, biol rep 3 input

description:
CFA3_peak.xls
CIBP3-input


title: Con-d0, male, rep3 (RNA-seq)

value: Male

value: WT, C57BL/6J


title: STM-rhabdomyosarcoma 5

source_name: STM from germ cell tumor

value: STM-rhabdomyosarcoma


title: Yolk-sac tumor 2


title: 20220830_210050551023_FRE10832A19_07


title: Teratoma 1


title: Yolk-sac tumor 1


title: Teratoma 2


title: STM-adenocarcinoma 4

value: STM-adenocarcinoma


title: PCs, mRNA-derived cDNA donor1_4

value: PBMC

value: B cells

value: mRNA


title: STM-rhabdomyosarcoma 1


title: PCs, ADT-derived cDNA donor0_4

value: ADT

value: TotalSeq™-B0911 anti-phycoerythrin (PE) Antibody


title: STM-adenocarcinoma 5


title: STM-rhabdomyosarcoma 4


title: STM-rhabdomyosarcoma 3


title: 20220830_210050551023_FRE10832A17_05

description: sample failed QC. Processed data not included.


title: Teratoma 5


title: STM-rhabdomyosarcoma 6


title: STM-adenocarcinoma 3


title: Con-d0, male, rep1 (RNA-seq)


title: Dorsal horn of spinal cord, bone cancer painl, biol rep 1 IP

description:
CFA1_peak.xls
CIBP1-IP

value: Dorsal horn of spinal cord

value: WT

value: IP RNA


title: AME-d21, male, rep3 (RNA-seq)

value: AME


title: 20220830_210050551023_FRE10832A16_04

value: Hidradenitis Suppurativa

value: dermal fibroblast

value: Lesional


title: STM-adenocarcinoma 2


title: Dorsal horn of spinal cord, bone cancer pain, biol rep 3 IP

description:
CFA3_peak.xls
CIBP3-IP


title: AME-d21, male, rep2 (RNA-seq)

value: Liver


title: 20220830_210050551023_FRE10832A13_01


title: 20220823_210050771023_FRE10832A8_08


title: Yolk-sac tumor 4

value: Yolk-sac tumor


title: 20220830_210050551023_FRE10832A14_02


title: STM-rhabdomyosarcoma 2


title: STM-adenocarcinoma 1


title: Dorsal horn of spinal cord, normal, biol rep 3 IP

description:
Control3_peak.xls
Control3-IP


title: Dorsal horn of spinal cord, bone cancer painl, biol rep 2 IP

description:
CFA2_peak.xls
CIBP2-IP


title: Con-d0, male, rep2 (RNA-seq)

value: Male

value: WT, C57BL/6J

value: Control


title: yfppos_cdc2_normalizedcounts_rep1

city: Stanford

first: David

last: Seong

state: California

address: 299 Campus Drive

institute: Stanford

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data was analyzed by ROSALIND® with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Normalization, fold changes and p-values were calculated using criteria provided by NanoSTRING ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual

label: not provided

source_name: sorted dendritic cell

label_protocol: standard protocol

growth_protocol: MC38 tumor cells were implanted into C57BL/6J mice and treated with radiationtherapy (20Gy) once the tumor reached 40-100 mm3.

extract_protocol: Cells were washed and resuspended in 1/3 RNeasy Lysis Buffer RLT (Qiagen) at a concentration of 1,000-5,000 cells/μL. Samples were analyzed on the NanoSting nCounter® Mouse NanoString nCounter® Mouse Myeloid Innate Immunity V2 Panel Standard Platform according to the manufacturer’s instructions.

treatment_protocol: Tumors were digested with collogenase and Dnase into a single cell suspension. Cells were stained with primary antibody, enriched with CD45-biotin and anti-biotin beads, and sorted for CD8+ T cells

value: YFP+ cDC2


title: yfpneg_cdc2_normalizedcounts_rep2

value: YFP- cDC2


title: PCs, mRNA-derived cDNA donor0_5

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
filtered_feature_bc_matrix_100.h5

value: PBMC

value: B cells

value: mRNA


title: PCs, mRNA-derived cDNA donor0_4


title: 20220823_210050771023_FRE10832A5_05


title: AME-d21, male, rep1 (RNA-seq)


title: Dorsal horn of spinal cord, normal, biol rep 3 input

description:
Control3_peak.xls
Control3-input

value: Dorsal horn of spinal cord

value: total RNA


title: Dorsal horn of spinal cord, normal, biol rep 2 input

description:
Control2_peak.xls
Control2-input

value: WT


title: 20220823_210050771023_FRE10832A1_01


title: IgG-exvivoMonocytes_rep2

data_processing:
We followed the ChIP-seq nf-core pipeline
ChIP-seq reads were trimmed with default parameters using Trim Galore  v0.6.6 with Cutadapt v3.4
ATAC-seq reads were aligned to the GRCm38/mm10 reference genome assembly using Bowtie version 2.3.4.2 with parameters -X 1000 --no-discordant --no-mixed --very-sensitive
We removed duplicated regions with Picard v2.25.4 and filtered out ENCODE blacklist regions v2.0 and non-interesting chromosomes
We pooled replicates
We pooled replicates and converted the paired BAM files to single-read bed format using function bamToBed from BEDTools v2.27.1
Peaks were called uing MACS v2.2.7.1 with parameters -f BAMPE--keep-dup all
Assembly: GRCm38/mm10
Supplementary files format and content: bamfile, narrowPeak

source_name: Bone-Marrow

growth_protocol: GMPs, Monocytes, MEPs, Erythroblasts and Bcells were freshly sorted from 12-14 week old C57BL6 mice bone marrow in 1X PBS + 0.01% BSA. Ex vivo Monocytes were expanded for 7 days with 20% FBS, 10 ng/ml GM-CSF, SCF, 5 ng/mL G-CSF, IL3, IL6, IL5, Flt3L, 2 ng/mL Tpo and 2 U/mL Epo. Leukaemia cells were expanded for 5 days with 5% FBS, 50 ng/ mL SCF, 10 ng/mL IL3 and IL6

extract_protocol:
Cells were lysed in hypotonic buffer (10 mM NaCl, 0,1% IGEPAL + Prot Inhibitors) and Chromatin was extracted by Sonication (Bioruptor Pico) in 0.5% SDS, 5mM EDTA + Prot Inhibitors. Then, chromatin fragments were extracted using 4 volumes of 25 mM HEPES, 185 mM NaCl, 1.25% Tx-100 + Protease Inhibitors. Next, samples were incubated for 10-12 hours with the relevant antibodies, then captured using 25 uL Magna ChIP Prot A+G and incubating for 2h at 4 ºC. Next, ChIPed DNA was released and reversed crosslinking by 45 min incubation with 2 uL of Proteinase K in ChIP Elution buffer followed by 1-hour incubation at 68 ºC. Finally, the ChIPed DNA was purified with a 2.2X SPRI Cleanup and quantified by Qbit.
ChIP-seq libraries were prepared from 1-10 ng of DNA with NEB Next Ultra II kit, QCed for concentration (Qbit) and size (Tape-Station) and sequenced to 100 million reads per sample.

treatment_protocol: Cells were dual-crosslinked with 3 mM DSG,DMA,EGS for 20 minutes at room temperature followed by 1% Formaldehyde for 5 more minutes. The reaction was quenched by adding Glycine to 125 mM final concentration, then cells were pelleted, washed twice with cold 0.5% BSA/PBS containing 1X Protease Inhibitors and frozen at -80C.

value: Bone-Marrow

tag: strain

value: Exvivo Monocyte

value: Wild-type

value: Expanded with SCF, GM-CSF, Flt3L, IL3, IL6

value: abcam ab171870


title: AME-d21, male, rep4 (RNA-seq)

value: Liver

value: AME


title: Dorsal horn of spinal cord, normal, biol rep 2 IP

description:
Control2_peak.xls
Control2-IP

value: IP RNA


title: yfpneg_cdc2_normalizedcounts_rep1


title: Con-d21, male, rep5 (RNA-seq)

value: Male

value: WT, C57BL/6J

value: Control


title: Dorsal horn of spinal cord, bone cancer painl, biol rep 1 input

description:
CFA1_peak.xls
CIBP1-input


title: Con-d21, male, rep4 (RNA-seq)


title: IgG-exvivoMonocytes_rep1


title: Dorsal horn of spinal cord, normal, biol rep 1 input

description:
Control1_peak.xls
Control1-input


title: Dorsal horn of spinal cord, normal, biol rep 1 IP

description:
Control1_peak.xls
Control1-IP


title: Con-d21, male, rep1 (RNA-seq)


title: Stat5a-exvivoMonocytes

description:
exvivo grown from multipotent LSK progenitors for 7 days in the presence of the cytokines listed under "treatment"
Mye_Stat5a_Cyn1_peaks.narrowPeak

value: Abcam ab32043


title: IgG-DM

value: Leukaemia cell

value: Expanded with SCF, IL3, IL6


title: pdc_normalizedcounts_rep2

value: pDC


title: yfppos_cdc2_normalizedcounts_rep2

value: YFP+ cDC2


title: AME-d0, male, rep5 (RRBS)

data_processing:
Base calling was performed using Illumina’s RTA version 2.7.3.
Quality control check using FastQC, read trimming using TrimGalore
Alignment, CpG methylation rate extracted using Bismark/BWA
Assembly: mm10

extract_protocol:
Ground livers were used for genomic DNA isolation using the DNeasy Blood & Tissue Kit (Qiagen) including RNase treatment. DNA quantity and purity were estimated spectrophotometrically.
RRBS (n=5 for each age) was performed at the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin. RRBS libraries were prepared using 250 ng of genomic DNA, digested with Msp1 (New England Biolabs (NEB), R0106M), and purified using QIAquick Nucleotide Removal Kit (Qiagen, 28004). End-repair A tailing was performed (NEB, M0212L) and TruSeq methylated indexed adaptors (Illumina, 15025064) were ligated with T4 DNA ligase (NEB, M0202L). Size selection was performed with AMPure XP beads (Beckman Coulter, A63882). Bisulfite conversion was performed using EpiTect Plus Bisulfite Kit (Qiagen) as recommended by the manufacturer. Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo Cx HotStart DNA Polymerase (Agilent Technologies, 600414).
Library quantification was performed using Qubit dsDNA HS Assay Kit (Life Technologies, Q32854) and the Bioanalyzer DNA 1000 Kit (Agilent Technologies, 5067-1504). The final libraries from RRBS were prepared for sequencing as per the manufacturer’s instructions in the Illumina cBot and HiSeq Paired end cluster kit v3. Samples were sequenced at 51 bp paired end reads using Illumina HiSeq 2000 with TruSeq SBS sequencing kit v3.


title: cdc1_normalizedcounts_rep2


title: pdc_normalizedcounts_rep1


title: cdc1_normalizedcounts_rep1


title: Stat5a-DM


title: AME-d0, male, rep4 (RRBS)


title: Dmel_dcr2_sRNA_replicate2

organism: Drosophila melanogaster

value: testis


title: Dmel_dcr2_sRNA_replicate1


title: Dmel_dcr2_het_sRNA_replicate1


title: Con-d21, male, rep3 (RNA-seq)


title: Dmel_dcr2_mutant_replicate2


title: Con-d21, male, rep2 (RNA-seq)


title: Kmt2a-exvivoMonocytes_rep2

description: Mye_Kmt2a-merged-sub101786848_peaks.narrowPeak

value: Bone-Marrow

value: Bethyl A300-086A


title: AME-d0, male, rep2 (RRBS)


title: cd11chi_tdc_normalizedcounts_rep1

value: CD11c hi tDC


title: Dmel_dcr2_het_sRNA_replicate2


title: Nfr Liver Young Het Fasted F smp37

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Sample 37

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8) (Andrews, 2017) and the Trim Galore! (v0.6.4) (Krueger, 2015) for Cutadapt (3.4)(Martin, 2011). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score >20 and a remaining length >20-bp. Successful processing was verified by re-running FastQC.
Reads was mapped and quantified to the killifish genome Nfu_20140520 (Reichwald et al., 2015; Valenzano et al., 2015) using STAR 2.7.6a (Dobin et al., 2013)
Genome_build: Nfu_20140520
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Nothobranchius furzeri

source_name: Nfr Liver

growth_protocol: Male or female killifish were either fed ad libidum, or fasted for 24h before liver extraction. All extraction were performed between 9am and 12pm.

extract_protocol:
Samples were disrupted by bead beating in 300μl of TriZol (Sigma) and a single 3mm metal bead (Eldan, BL6693003000) using TissueLyzer LT (QIAGEN, #85600) with a dedicated adaptor (QIAGEN, #69980). Beating was performed twice at 50Hz for 2 minutes. RNA extraction was performed with Direct-zol RNA Purification Kits (Zymo). RNA concentration and quality were determined by using an Agilent 2100 bioanalyser (Agilent Technologies).
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols.  Library concentrations were measured by Qubit (dsDNA HS, Q32854), and quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 500 high output kit V2, 75 cycle single-end (Illumina, 20024906) using a NextSeq 500 machine (Illumina) with ~30 million reads per sample.

treatment_protocol: Livers were quickly removed, flash frozen in liquid nitrogen, and then stored in -80 until RNA extraction (up to 3months)

tag: age

value: 6.5 weeks

value: APRT heterozygous

tag: feeding condition

value: Fasted

value: Female


title: Kmt2a-exvivoMonocytes_rep1

value: Exvivo Monocyte

value: Wild-type

value: Expanded with SCF, GM-CSF, Flt3L, IL3, IL6


title: Dorsal horn of spinal cord, bone cancer painl, biol rep 2 input

description:
CFA2_peak.xls
CIBP2-input

value: Dorsal horn of spinal cord

value: WT

value: total RNA


title: Nfr Liver Young Het Fasted F smp36

description: Sample 36

value: Liver


title: cd11chi_tdc_normalizedcounts_rep2


title: cd11clo_tdc_normalizedcounts_rep2

value: CD11c lo tDC


title: Kmt2a-Monocytes_rep2

value: Monocyte


title: AME-d0, male, rep1 (RRBS)

value: Male

value: WT, C57BL/6J

value: AME


title: AME-d21, male, rep5 (RNA-seq)


title: Dmel_dcr2_mutant_replicate1

value: testis


title: Dmel_dcr2_het_control_replicate2


title: cd11clo_tdc_normalizedcounts_rep1


title: Nfr Liver Young Het Fasted F smp35

description: Sample 35

value: 6.5 weeks


title: Kmt2a-DM_rep1

description:
exvivo grown from multipotent LSK progenitors for 7 days in the presence of the cytokines listed under "treatment"
DM_Kmt2a-merged-sub101786848_peaks.narrowPeak

value: Bone-Marrow

value: Leukaemia cell

value: Expanded with SCF, IL3, IL6

value: Bethyl A300-086A


title: Con-d0, male, rep5 (RRBS)

value: Control


title: AME-d0, male, rep3 (RRBS)


title: Dmel_dcr2_het_control_replicate1


title: Con-d0, male, rep4 (RRBS)


title: Nfr Liver Young Het Fasted F smp34

description: Sample 34

value: APRT heterozygous

value: Fasted

value: Female


title: Con-d0, male, rep3 (RRBS)


title: Kmt2a-Bcell

value: GMP

value: Wild-type


title: Kmt2a-Monocytes_rep1


title: Kmt2a-Ery


title: Con-d0, male, rep2 (RRBS)

value: Liver


title: Nfr Liver Young WT Fasted F smp30

description: Sample 30

value: WT


title: Kmt2a-MEP


title: Con-d0, male, rep1 (RRBS)

value: Male


title: Nfr Liver Old Het Fasted F smp24

description: Sample 24

value: 15 weeks


title: Nfr Liver Young WT Fasted F smp29

description: Sample 29


title: Kmt2d-DM_rep2

description: DM_Kmt2d-merged-sub146746296_peaks.narrowPeak

value: Sigma HPA035977


title: Kmt2a-GMP


title: Kmt2d-DM_rep1


title: Nfr Liver Old Het Fasted F smp23

description: Sample 23


title: AME-d21, male, rep4 (RRBS)

value: WT, C57BL/6J

value: AME


title: AME-d21, male, rep5 (RRBS)


title: AME-d21, male, rep3 (RRBS)


title: Kmt2d-exvivoMonocytes_rep3

description:
exvivo grown from multipotent LSK progenitors for 7 days in the presence of the cytokines listed under "treatment"
Mye_Kmt2d-merged-sub146746296_peaks.narrowPeak

value: Bone-Marrow

value: Exvivo Monocyte

value: Expanded with SCF, GM-CSF, Flt3L, IL3, IL6


title: Nfr Liver Old Het Fasted F smp22

description: Sample 22


title: AME-d21, male, rep2 (RRBS)


title: Nfr Liver Old Het Fasted F smp21

description: Sample 21


title: Kmt2d-exvivoMonocytes_rep2


title: AME-d21, male, rep1 (RRBS)


title: Kmt2a-DM_rep2

value: Leukaemia cell

value: Expanded with SCF, IL3, IL6

value: Bethyl A300-086A


title: Kmt2d-exvivoMonocytes_rep1


title: Nfr Liver Old WT Fasted F smp17

description: Sample 17

value: Fasted


title: Hybrid Motor neuron, Hybrid1, rep1

first: Hunter

last: Fraser

address: 327 Campus Drive

institute: Stanford University

description:
RNA30_MN_Hyb1_total; RNA30_MN_Hyb1_human; RNA30_MN_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro6 with STAR version 2.7.6a
Remove duplicate reads with Picard 2.23.8 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Assembly: Human: GRCh38; Chimpanzee: PanTro6
Supplementary files format and content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts)
Supplementary files format and content: matrix text files are provided for samples mapped on both the human and chimpanzee genomes

organism:
Pan troglodytes
Homo sapiens

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina) & Illumina Stranded mRNA Prep (Illumina)

tag: cell line

value: Motor neuron


title: Hybrid Motor neuron, Hybrid2, rep2

description:
RNA31_MN_Hyb2_total; RNA31_MN_Hyb2_human; RNA31_MN_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

tag: cell type


title: Nfr Liver Young WT Fasted F smp28

description: Sample 28

value: 6.5 weeks

value: Female


title: Kmt2d-Monocytes_rep2

value: Monocyte

value: Wild-type

tag: chip antibody


title: Con-d21, male, rep5 (RRBS)

value: Liver

value: Male

value: Control


title: Nfr Liver Old WT Fasted F smp15

description: Sample 15

value: 15 weeks

value: WT


title: Con-d21, male, rep4 (RRBS)

value: WT, C57BL/6J


title: Hybrid Skeletal myocyte, Hybrid2, rep3

description:
RNA33_SKM_Hyb2_total; RNA33_SKM_Hyb2_human; RNA33_SKM_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Skeletal myocyte


title: Nfr Liver Old WT Fasted F smp16

description: Sample 16


title: Hybrid Retinal pigment epithelium, Hybrid2, rep2

description:
RNA29_RPE_Hyb2_total; RNA29_RPE_Hyb2_human; RNA29_RPE_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Retinal pigment epithelium


title: Con-d21, male, rep3 (RRBS)


title: Mi-2β KO-3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from Chd4-/- B16F10 mouse melanoma cells.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.58.0), using R version 3.5.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label: biotin

source_name: B16F10 mouse melanoma cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Mi-2β-knockout and non-target control B16F10 cell lines were cultured in complete DMEM media (10% FBS and 100U/ml of Penicillin-Streptomycin).

extract_protocol: Total RNA was extracted from Mi-2β knockout and control B16F10 cells with the RNeasy Mini Kit (74104) (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

treatment_protocol: Mi-2β-knockout and non-target control B16F10 cell lines were treated with IFN-γ (10ng/mL) for 24 hours in complete DMEM media.


title: Kmt2d-Monocytes_rep1

value: Bone-Marrow

value: Sigma HPA035977


title: Mi-2β KO-2


title: Kmt2d-Bcell

value: GMP


title: Hybrid Motor neuron, Hybrid1, rep2

description:
RNA32_MN_Hyb1_total; RNA32_MN_Hyb1_human;RNA32_MN_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Mi-2β KO-1


title: Nfr Liver Young Het Fasted M smp41

description: Sample 41

value: APRT heterozygous

value: Fasted


title: Con-d21, male, rep2 (RRBS)


title: Control-1

description: Gene expression data from Chd4+/+ B16F10 mouse melanoma cells.


title: Kmt2d-Ery_rep2


title: Nfr Liver Young Het Fasted M smp40

description: Sample 40

value: 6.5 weeks


title: Con-d21, male, rep1 (RRBS)


title: Kmt2d-Ery_rep1


title: Nfr Liver Young Het Fasted M smp39

description: Sample 39


title: Control-2


title: Kmt2d-MEP


title: Hybrid Pancreatic progenitor, Hybrid2, rep2

description:
RNA25_PP_Hyb2_total; RNA25_PP_Hyb2_human; RNA25_PP_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Pancreatic progenitor


title: Hybrid Retinal pigment epithelium, Hybrid2, rep1

description:
RNA28_RPE_Hyb2_total; RNA28_RPE_Hyb2_human; RNA28_RPE_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Hybrid Hepatocyte progenitor, Hybrid2, rep2

description:
RNA23_HP_Hyb2_total; RNA23_HP_Hyb2_human; RNA23_HP_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Hepatocyte progenitor


title: Hybrid Hepatocyte progenitor, Hybrid1, rep2

description:
RNA22_HP_Hyb1_total; RNA22_HP_Hyb1_human; RNA22_HP_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Hybrid Retinal pigment epithelium, Hybrid1, rep2

description:
RNA27_RPE_Hyb1_total; RNA27_RPE_Hyb1_human; RNA27_RPE_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Nfr Liver Old Het Fasted M smp27

description: Sample 27


title: Nfr Liver Young WT Fasted M smp33

description: Sample 33


title: Nfr Liver Young WT Fasted M smp31

description: Sample 31


title: Nfr Liver Young Het Fasted M smp38

description: Sample 38


title: Hybrid Skeletal myocyte, Hybrid2, rep2

description:
RNA21_SKM_Hyb2_total; RNA21_SKM_Hyb2_human; RNA21_SKM_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Nfr Liver Young WT Fasted M smp32

description: Sample 32


title: Nfr Liver Old Het Fasted M smp26

description: Sample 26


title: Brd9-DM_rep2

description: DM_Brd9-merged-sub37618974_peaks.narrowPeak

value: Leukaemia cell

value: Expanded with SCF, IL3, IL6

value: Abcam ab137245


title: Brd9-DM_rep1


title: Kmt2d-GMP

value: Wild-type


title: Hybrid Skeletal myocyte, Hybrid1, rep2

description:
RNA20_SKM_Hyb1_total; RNA20_SKM_Hyb1_human; RNA20_SKM_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Control-3


title: Brd9-exvivoMonocytes

description:
exvivo grown from multipotent LSK progenitors for 7 days in the presence of the cytokines listed under "treatment"
Mye_Brd9-abcam-sub37618974_140421_peaks.narrowPeak

value: Exvivo Monocyte

value: Expanded with SCF, GM-CSF, Flt3L, IL3, IL6


title: Hybrid Cardiomyocte, Hybrid2, rep2

description:
RNA19_CM_Hyb2_total; RNA19_CM_Hyb2_human; RNA19_CM_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Cardiomyocyte


title: Hybrid Pancreatic progenitor, Hybrid1, rep2

description:
RNA24_PP_Hyb1_total; RNA24_PP_Hyb1_human; RNA24_PP_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Brd9-Monocytes_rep2

value: Monocyte


title: Nfr Liver Old Het Fasted M smp25

description: Sample 25

value: Liver

value: 15 weeks

value: Male


title: Brd9-Monocytes_rep1

value: Bone-Marrow


title: Hybrid Retinal pigment epithelium, Hybrid1, rep1

description:
RNA26_RPE_Hyb1_total; RNA26_RPE_Hyb1_human; RNA26_RPE_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Retinal pigment epithelium


title: Brd9-Bcell

value: GMP


title: Nfr Liver Old WT Fasted M smp20

description: Sample 20

value: WT

value: Fasted


title: MDA-pc3, T10, TIC, Rep1

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description: T10 Timepoint Replicate 1

hyb_protocol: hybing was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

scan_protocol: scanning was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

data_processing: The raw intensity data extracted from the CEL files were normalized and log transformed.

source_name: Breast

label_protocol: labeling was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

growth_protocol: Cells were collected as describled in the manuscript Hanover et al.

extract_protocol: genomic DNA was extracted as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

treatment_protocol: cell were treated as described in the manuscript Hanover et al.

value: mock-transfected with pcDNA3 expression vector


title: Brd9-Ery_rep2


title: Hybrid Cardiomyocte, Hybrid1, rep2

description:
RNA17_CM_Hyb1_total; RNA17_CM_Hyb1_human; RNA17_CM_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: ChIP CLOCK:BMAL1 rep1

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

institute: LMU Munich

data_processing:
RTA software von Illumina, version ist 1.18.66.3
sequenced reads were demultiplexed and trimmed using JE Demultiplexer
Demultiplexed reads were aligned to the dm6 genome using bowtie 2 version 2.2.9. with settings: -p 24 --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant  -X 400
filtering and sorting was done using samtools 1.9 with -q 10.
genomic tracks were made by Homer 4.9 and normalized to the negative control or the input.
replicates were summarized by subsampling them to the same read counts and summarizing them
peaks were called using findPeaks form Homer 4.9  with settings: -style factor -size 150 -F 8 -L 2
Assembly: dm6
Supplementary files format and content: .bw files

source_name: BG-3 cells

growth_protocol: purified genomic DNA from bg-3 cells was assembled to chromatin for 5h.

extract_protocol:
DNA was purified using Phenol-Chloroform Extraction.
libraries were made using the NEB library Kit for Illumina

treatment_protocol: Respective Proteins were added to the chromatin and bound for 30 min. samples were crosslinked and partially digested by Mnase.

value: BG-3 cells

tag: ip target

value: anti Spy Tag

tag: factors added


title: MDA-pc3, T10, TIC, Rep2

description: T10 Timepoint Replicate 2

tag: timepoint


title: Hybrid Motor neuron, Hybrid2, rep1

description:
RNA18_MN_Hyb2_total; RNA18_MN_Hyb2_human; RNA18_MN_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Motor neuron


title: Nfr Liver Old WT Fasted M smp19

description: Sample 19

tag: Sex


title: ChIP CLOCK:BMAL1 rep2


title: Brd9-Ery_rep1

value: Wild-type

value: Abcam ab137245


title: ChIP MYC:MAX rep 2


title: Nfr Liver Old WT Fasted M smp18

description: Sample 18


title: Hybrid Pancreatic progenitor, Hybrid2, rep1

description:
RNA16_PP_Hyb2_total; RNA16_PP_Hyb2_human; RNA16_PP_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Pancreatic progenitor


title: Brd9-MEP_rep3


title: MDA-pc3, T0, Pre, TIC, Rep1

description: T0 Timepoint Replicate 1


title: MDA-pc3, T0, Pre, TIC, Rep2

description: T0 Timepoint Replicate 2


title: MDA-B6-M, T10, TIC, Rep2

description: T10 Timepoint Replicate 2

value: stably transfected with pcDNA3 expression vector encoding Myc-tagged EPHB6


title: Hybrid Pancreatic progenitor, Hybrid1, rep1

description:
RNA15_PP_Hyb1_total; RNA15_PP_Hyb1_human; RNA15_PP_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: MDA-B6-M, T0, Pre, TIC, Rep2

description: T0 Timepoint Replicate 2


title: Nfr Liver Young Het Full M smp55

description: Sample 55

value: 6.5 weeks

value: APRT heterozygous

value: Fully-Fed


title: MDA-B6-M, T0, Pre, TIC, Rep1

description: T0 Timepoint Replicate 1


title: ChIP MYC:MAX rep 1


title: MDA-B6-M, T10, TIC, Rep1

description: T10 Timepoint Replicate 1


title: Nfr Liver Young Het Full M smp54

description: Sample 54

value: Liver

value: Male


title: Brd9-MEP_rep2

value: Bone-Marrow


title: Hybrid Hepatocyte progenitor, Hybrid2, rep1

description:
RNA12_HP_Hyb2_total; RNA12_HP_Hyb2_human; RNA12_HP_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Hepatocyte progenitor


title: chip negative control rep3


title: Brd9-MEP_rep1

value: GMP


title: Hybrid Hepatocyte progenitor, Hybrid1, rep1

description:
RNA11_HP_Hyb1_total; RNA11_HP_Hyb1_human; RNA11_HP_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: chip negative control rep2


title: Hybrid Skeletal myocyte, Hybrid2, rep1

description:
RNA8_SKM_Hyb2_total; RNA8_SKM_Hyb2_human; RNA8_SKM_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Skeletal myocyte


title: chip negative control rep1


title: Hybrid Skeletal myocyte, Hybrid1, rep1

description:
RNA7_SKM_Hyb1_total; RNA7_SKM_Hyb1_human; RNA7_SKM_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Nfr Liver Young WT Full M smp47

description: Sample 47

value: WT


title: Nfr Liver Young Het Full M smp52

description: Sample 52


title: Brd9-GMP_rep1


title: Nfr Muscle Young Het Fasted F Sample 37

description: matrix_expression_RNAseq_star2301_2_fasted.csv

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8) (Andrews, 2017) and the Trim Galore! (v0.6.4) (Krueger, 2015) for Cutadapt (3.4)(Martin, 2011). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score >20 and a remaining length >20-bp. Successful processing was verified by re-running FastQC.
Reads was mapped and quantified to the killifish genome Nfu_20140520 (Reichwald et al., 2015; Valenzano et al., 2015) using STAR 2.7.6a (Dobin et al., 2013)
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, the sample number corresponding to the file name of the same sample.

source_name: Muscle

growth_protocol: Male or female killifish were either fed ad libidum, or fasted for 24h before muscle extraction. All extraction were performed between 9am and 12pm.

extract_protocol:
Samples were disrupted by bead beating in 300μl of TriZol (Sigma) and a single 3mm metal bead (Eldan, BL6693003000) using TissueLyzer LT (QIAGEN, #85600) with a dedicated adaptor (QIAGEN, #69980). Beating was performed twice at 50Hz for 2 minutes. RNA extraction was performed with Direct-zol RNA Purification Kits (Zymo). RNA concentration and quality were determined by using an Agilent 2100 bioanalyser (Agilent Technologies).
Library preparation was performed using KAPA Stranded mRNA-Seq Kit (ROCHE-07962193001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS, Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 2000 P3, 50 cycle, 70 bp single-end (Illumina, 20046810) with ~35 million reads per sample.

treatment_protocol: Muscles were quickly removed, flash frozen in liquid nitrogen, and then stored in -80 until RNA extraction (up to 3months)

value: Muscle

value: Female

value: Fasted


title: Nfr Liver Young Het Full M smp53

description: Sample 53


title: Nfr Liver Young WT Full M smp46

description: Sample 46


title: Nfr Muscle Young Het Fasted F Sample 36


title: Smarcb1-DM_rep1

description:
exvivo grown from multipotent LSK progenitors for 7 days in the presence of the cytokines listed under "treatment"
DM_Smarcb1-merged-sub173331792_peaks.narrowPeak

value: Exvivo Monocyte

value: Wild-type

value: Expanded with SCF, GM-CSF, Flt3L, IL3, IL6

value: Cell Signalling 91735


title: Hybrid Cardiomyocte, Hybrid2, rep1

description:
RNA4_CM_Hyb2_total; RNA4_CM_Hyb2_human; RNA4_CM_Hyb2_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt

value: Cardiomyocyte


title: Hybrid Cardiomyocte, Hybrid1, rep1

description:
RNA3_CM_Hyb1_total; RNA3_CM_Hyb1_human; RNA3_CM_Hyb1_chimp
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_GRCh38.txt
RNAseq_ASE_CM_HP_MN_PP_SKM_RPE_PanTro6.txt


title: Nfr Liver Young WT Full M smp45

description: Sample 45

value: 6.5 weeks


title: Nfr Muscle Young Het Fasted F Sample 34

value: APRT heterozygous


title: Nfr Liver Old Het Full M smp13

description: Sample 13

value: Liver

value: 15 weeks

value: Fully-Fed


title: Brd9-GMP_rep2

value: Bone-Marrow

value: Abcam ab137245


title: Smarcb1-exvivoMonocytes_rep2

description:
exvivo grown from multipotent LSK progenitors for 7 days in the presence of the cytokines listed under "treatment"
Mye_Smarcb1-merged-sub173331792_peaks.narrowPeak


title: Nfr Muscle Young WT Fasted F Sample 30


title: Smarcb1-exvivoMonocytes_rep3


title: Smarcb1-exvivoMonocytes_rep1


title: Nfr Liver Old Het Full M smp12

description: Sample 12

value: Male


title: Hybrid Motor neuron, Hybrid2

description:
ATAC36_MN_Hyb2_total; ATAC36_MN_Hyb2_human; ATAC36_MN_Hyb2_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro6 with bowtie2
Remove duplicate reads with Picard 2.23.8 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Call peaks with MACS2 and count allele specific and total reads in peaks
Assembly: Human: GRCh38; Chimpanzee: PanTro6
Supplementary files format and content: Counts matrix with total and allele-specific raw read counts (rows are peaks, there are 3 columns per sample: total, human and chimpanzee read counts)
Supplementary files format and content: matrix text files are provided for samples mapped on both the human and chimpanzee genomes

extract_protocol:
Omni-ATAC protocol
Illumina Tagment DNA TDE1 Enzyme and Buffer Kits

value: Motor neuron


title: Nfr Liver Old Het Full M smp11

description: Sample 11


title: Smarcb1-Monocytes_rep2

value: Monocyte


title: Hybrid Motor neuron, Hybrid1

description:
ATAC35_MN_Hyb1_total; ATAC35_MN_Hyb1_human; ATAC35_MN_Hyb1_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt


title: Hybrid Pancreatic progenitor, Hybrid2

description:
ATAC20_PP_Hyb2_total; ATAC20_PP_Hyb2_human; ATAC20_PP_Hyb2_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt

value: Pancreatic progenitor


title: Smarcb1-DM_rep2

description: DM_Smarcb1-merged-sub173331792_peaks.narrowPeak

value: Leukaemia cell

value: Expanded with SCF, IL3, IL6


title: Hybrid Pancreatic progenitor, Hybrid1

description:
ATAC19_PP_Hyb1_total; ATAC19_PP_Hyb1_human; ATAC19_PP_Hyb1_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt


title: Hybrid Hepatocyte progenitor, Hybrid2

description:
ATAC16_HP_Hyb2_total; ATAC16_HP_Hyb2_human; ATAC16_HP_Hyb2_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt

value: Hepatocyte progenitor


title: Nfr Muscle Young WT Fasted F Sample 28

value: Muscle

value: Female

value: WT

value: Fasted


title: Nfr Liver Old WT Full M smp6

description: Sample 6


title: Nfr Muscle Old Het Fasted F Sample 24

value: APRT heterozygous


title: Hybrid Skeletal myocyte, Hybrid1

description:
ATAC11_SKM_Hyb1_total; ATAC11_SKM_Hyb1_human; ATAC11_SKM_Hyb1_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt

value: Skeletal myocyte


title: Smarcb1-Monocytes_rep1

value: Wild-type

value: Cell Signalling 91735


title: Smarcb1-Ery

value: Bone-Marrow

value: GMP


title: Smarcb1-MEP


title: Nfr Liver Old Het Full M smp14

description: Sample 14

value: Liver

value: 15 weeks

value: Fully-Fed

value: Male


title: Nfr Muscle Young Het Fasted F Sample 35


title: Nfr Muscle Old Het Fasted F Sample 23


title: Hybrid Cardiomyocte, Hybrid2

description:
ATAC8_CM_Hyb2_total; ATAC8_CM_Hyb2_human; ATAC8_CM_Hyb2_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt

value: Cardiomyocyte


title: Nfr Muscle Old Het Fasted F Sample 22


title: Nfr Liver Old WT Full M smp4

description: Sample 4


title: Nfr Muscle Old Het Fasted F Sample 21


title: Nfr Muscle Young WT Fasted F Sample 29


title: Nfr Muscle Old WT Fasted F Sample 17


title: Hybrid Cardiomyocte, Hybrid1

description:
ATAC7_CM_Hyb1_total; ATAC7_CM_Hyb1_human; ATAC7_CM_Hyb1_chimp
ATACseq_ASCA_CM_HP_MN_PP_SKM_GRCh38.txt
ATACseq_ASCA_CM_HP_MN_PP_SKM_PanTro6.txt


title: LSK-Mye_Smarcd2_rep1_batch3

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-Smarcd2_ATAC6-merged_peaks.broadPeak

data_processing:
We followed the ATAC-seq nf-core pipeline
ATAC-seq reads were trimmed with default parameters using Trim Galore  v0.6.6 with Cutadapt v3.4
ATAC-seq reads were aligned to the GRCm38/mm10 reference genome assembly using Bowtie version 2.3.4.2 with parameters -X 1000 --no-discordant --no-mixed --very-sensitive
we removed duplicated regions with Picard v2.25.4 and filtered out ENCODE blacklist regions v2.0 and non-interesting chromosomes
We removed Tn5 adaptors with alignmentSieve v3.5.1
We pooled replicates and converted the paired BAM files to single-read bed format using function bamToBed from BEDTools v2.27.1
Peaks were called uing MACS v2.2.7.1 with parameters –broad -f BED --keep-dup all --nomodel --shift -75 --extsize 150
Assembly: GRCm38/mm10
Supplementary files format and content: bamfile, broadPeak

growth_protocol: Cas9-LSK progenitors were sorted and grown in Lineage Priming Medium (DMEM/F12 100 ng/ml Tpo, 10 ng/ml SCF, 1 ng/ml Flt3L, 1 mg/mL PVA 87%, ITSX 1X, 10 mM Hepes) or Myeloid differentiaton media (20% FBS, 10 ng/ml GM-CSF, SCF, 5 ng/mL G-CSF, IL3, IL6, IL5, Flt3L, 2 ng/mL Tpo and 2 U/mL Epo)

extract_protocol:
Cells expressing sgRNAs (BFP+) were FACS sorted in 1X PBS + 0.05% BSA, pelleted and permeabilized in 1X TD buffer containing 2 ul Tn5 enzyme (Illumina), 0.01% Digtonin in DMSO, 0.1% Tween 20, 0.1% IGEPAL in Molecular Biology Grade water
Omni-ATAC protocol: Tagmentation was performed at 37 ºC for 30 minutes with agitation at 1000 rpm, then stopped by adding EDTA 5 mM final concentration. Next, 2 uL of Proteinase K were added and the samples were incubated for 30 minutes at 40 ºC. Genomic DNA was purified with a 2X SPRI cleanup and tagmented sites were PCR-amplified with 25 uL Kappa HIFI 2X and 2.5 uL of 10 uM P5-i5-read1 and P7-i7-Read2 primers. The PCR cycling conditions are: 5 min at 72 ºC, 10 x [2 min at 98 ºC, 20 s at 98 ºC, 30s at 60 ºC, 1 minute at 72 ºC] 3 min at 72 ºC. Amplified ATAC-seq libraries were purified with a 1.6X SPRI Cleanup, quantified using the Qubit dsDNA high sensitivity assay kit, and then analysed on a Tape Station 4000. ATAC-seq libraries were sequenced at 50 million reads on a NextSeq 1000.

treatment_protocol: Cas9-LSK cells were transduced with lentiviral vectors expressing sgRNAs against specific CFs

value: Lin- c-kit+ Sca1+

value: Cas9-GFP Smarcd2-KO

value: Ex vivo grown:Flt3L, GM-CSF, IL3, IL6


title: LSK-Mye_Smarcd2_rep2_batch3


title: LSK-Mye_Kmt2d_rep1_batch3

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-Kmt2d_ATAC6_1_peaks.broadPeak

value: Cas9-GFP Kmt2d-KO


title: Nfr Liver Old WT Full M smp5

description: Sample 5

value: WT


title: Nfr Muscle Old WT Fasted F Sample 16

value: Muscle

value: Female

value: Fasted


title: EDL_caput epi_rep3

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
NovaSeq6000 (Illumina) using 101 bp single-ended mode
sequence reads were mapped onto mouse reference genome (mm10) using TopHat ver. 2.1.1
Fragments Per Kilobase of exon per Million mapped reads (RPKM) values for each gene were calculated using Cufflinks ver. 2.2.1
Assembly: mm10
Supplementary files format and content: A Microsoft Excel file including FPKM values for each Sample

source_name: caput epididymis

extract_protocol:
RNA was harvested using RNeasy (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

value: Wild-type

value: caput epididymis

value: efferent duct ligation


title: W/Wv_caput epi_rep2

value: W/Wv

value: no treatment


title: W/Wv_caput epi_rep1


title: EDL_caput epi_rep2


title: G1_Sir2_FLAG_FLOP_rep1

city: Los Angeles

first: Meghan

middle: V

last: Petrie

address: 1050 Childs Way

institute: University of Southern California

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filtered reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup.
Binning: Sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: Binned.bed files.

organism: Saccharomyces cerevisiae

growth_protocol: ~100 mL of cells were grown per sample and harvested at OD ~ 1.0 in YEPD at 23 °C.

extract_protocol:
Chromatin was cross-linked with formaldehyde solution (1 % final concentration) for 15min. After quenching cells were lysed by bead-beating with FastPrep and chromatin sonicated using a S2 sonicator (Covaris). Then PCI extraction and ethanol precipitation.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: At OD ~0.5 when noted alpha-factor was added and cells were grown for an additional ~3.5hr to achieve G1 arrest.

value: alpha-factor

value: anti-FLAG M2 (Sigma F1804)


title: G1_MCM4_HA_HOP_rep2

value: anti-HA (12CA5)


title: G1_Sir2_FLAG_FLOP_rep2


title: G1_MCM4_HA_HOP_rep3


title: W/Wv_caput epi_rep3


title: G1_Sir2_FLAG_FLOP_rep3


title: EDL_caput epi_rep1


title: Nfr Muscle Old WT Fasted F Sample 15


title: Nfr Muscle Young Het Fasted M Sample 41

value: Male

value: APRT heterozygous


title: LSK-Mye_Brd9_rep1_batch3

city: Cambridge

first: Brian

last: Huntly

address: Hills Road

institute: University of Cambridge

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-Brd9_ATAC6-merged_peaks.broadPeak

value: Bone-Marrow

value: Lin- c-kit+ Sca1+

value: Cas9-GFP Brd9-KO


title: Nfr Muscle Young Het Fasted M Sample 40

description: matrix_expression_RNAseq_star2301_2_fasted.csv


title: Smarcb1-GMP

value: GMP

value: Cell Signalling 91735


title: Wild-type_caput epi_rep3


title: G1_MCM4_HA_HOP_rep1


title: LSK-Mye_NTC_rep2_batch3

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-NTC_ATAC6-merged_peaks.broadPeak

value: Cas9-GFP Wild-type

value: Ex vivo grown:Flt3L, GM-CSF, IL3, IL6


title: Wild-type_caput epi_rep2

value: Wild-type


title: Nfr Muscle Young Het Fasted M Sample 38

value: Muscle

value: Fasted


title: G1_ORC1_HA_HOP_rep3


title: LSK-Mye_Rcor1_rep2_batch2

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-Rcor1_ATAC5-merged_peaks.broadPeak

value: Cas9-GFP Rcor1-KO


title: G1_ORC1_HA_HOP_rep2


title: LSK-Mye_Brd9_rep2_batch3


title: Wild-type_caput epi_rep1

value: caput epididymis

value: no treatment


title: LSK-Mye_Rcor1_rep1_batch2


title: LSK-Mye_NTC_rep2_batch2

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-NTC0005_ATAC5-merged_peaks.broadPeak


title: G1_ORC1_HA_HOP_rep1

value: alpha-factor


title: Nfr Muscle Young Het Fasted M Sample 39


title: Nfr Muscle Young WT Fasted M Sample 32

value: WT


title: Nfr Muscle Old Het Fasted M Sample 26

value: Male


title: LSK-Mye_WDR82_rep2_batch1

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-WDR82_ATAC-merged_peaks.broadPeak

value: Cas9-GFP WDR82-KO


title: LSK-Mye_NTC_rep1_batch2

value: Bone-Marrow


title: LSK-Mye_NTC_rep1_batch3

value: Lin- c-kit+ Sca1+


title: LSK-Mye_WDR82_rep1_batch1


title: G1_HOP_rep1

value: TRP-HOP

value: anti-HA (12CA5)


title: G1_HOP_rep3


title: G1_Fkh1_MYC_MOP_rep3

value: anti-Myc (9E10)


title: Nfr Muscle Young WT Fasted M Sample 31


title: G1_Fkh1_MYC_MOP_rep2


title: LSK-Mye_NTC_rep2_batch1

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
Mye-NTC_ATAC-merged_peaks.broadPeak

value: Cas9-GFP Wild-type


title: Nfr Muscle Old WT Fasted M Sample 20


title: LSK-Mye_NTC_rep1_batch1

value: Ex vivo grown:Flt3L, GM-CSF, IL3, IL6


title: G1_Fkh1_MYC_MOP_rep1


title: Nfr Muscle Old WT Fasted M Sample 19


title: Wild-type, caput epi, rep3

value: Wild-type


title: Adgrg2-KO, caput epi, rep2


title: Adgrg2-KO, caput epi, rep1


title: Adgrg2-KO, caput epi, rep3


title: Wild-type, caput epi, rep1


title: bioMBD2a-mutMBD_r2

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

description: ChIP

data_processing:
Reads were trimmed using trim_galore v0.6.6
Trimmed reads were aligned to the mm9 mouse genome using Bowtie directly executed from the R package QuasR with standard alignment parameters allowing up to 2 mismatches and excluding multi-mappers.
Coordinates of unique reads that map only once to the mouse genome were converted to WIG format for visualisation using qExportWig() with standard parameters in QuasR.
Assembly: mm9
Supplementary files format and content: wig track format: read coverage per consecutive 100bp windows

source_name: Mouse Embryonic Stem Cells

growth_protocol: ES cells were were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Biotin ChIP: For cross-linking and chromatin extraction, cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in presence of 1.2M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.2% SDS and 300 mM NaCl for 2 hours on ice. Crosslinked chromatin was subjected to sonication in a Bioruptor Pico instrument (Diagenode) and diluted with equal volumes of 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate after successful sonication. ProteinA-dynabeads pre-cleared 150-250 µg chromatin were incubated with 40 µl blocked (1% CFSG, 100ng tRNA) Streptavidin-M280 magnetic beads over night at 4°C. Beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation.
ChIP-seq library using NEBNext ChIP-seq Library Prep Master Mix set for Illumina (NEB E6240)

value: embryonic stem cells


title: G1_HOP_rep2


title: LSK-LinPriming_Setdb1_rep2_batch5

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Setdb1_ATAC5-merged_peaks.broadPeak

value: Cas9-GFP Setdb1-KO

value: Ex vivo grown:SCF, Flt3L, Tpo.


title: bioMBD2a-mutMBD_r1

description: ChIP


title: Nfr Muscle Old Het Fasted M Sample 27

value: Muscle

value: APRT heterozygous

value: Fasted


title: Nfr Muscle Old Het Fasted M Sample 25


title: Wild-type, caput epi, rep2

value: caput epididymis


title: G1_MOP_rep3

value: ADE-MOP

value: alpha-factor


title: G1_MOP_rep2


title: Nfr Muscle Old WT Fasted M Sample 18

value: Male

value: WT


title: LSK-LinPriming_Rcor1_rep1_batch5

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Rcor1_ATAC5-merged_peaks.broadPeak

value: Bone-Marrow

value: Lin- c-kit+ Sca1+

value: Cas9-GFP Rcor1-KO


title: LSK-LinPriming_Setdb1_rep1_batch5


title: bioMBD2a-delGR_r1

description: ChIP


title: bioMBD2a-delGR_r2

description: ChIP


title: LSK-LinPriming_Rcor1_rep2_batch5


title: G1_MOP_rep1

value: anti-Myc (9E10)


title: bioMBD2a-fulllength_r2

description: ChIP


title: G1_Fkh1_FLAG_FLOPv2x2_rep3

value: anti-FLAG M2 (Sigma F1804)


title: LSK-LinPriming_Rbbp4_rep2_batch5

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Rbbp4_ATAC5-merged_peaks.broadPeak

value: Cas9-GFP Rbbp4-KO


title: bioMBD2a-fulllength_r1

description: ChIP

value: embryonic stem cells


title: DM_Test2_NM_6d_1 gRNA

description:
Perturb-seq of mouse leukemic model
DM_Test2_NM_6d_1.h5
CellAnnotation_leukemia.tsv

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 6.1.1).
Sequencing data were aligned to the reference genome with Cell Ranger count
Assembly: GRCm38/mm10 reference genome assembly (GENCODE vM23/Ensembl 98) with BFP and GFP sequences
Supplementary files format and content: h5 matrices: read count matrix with cells / barcodes (columns) and genes (rows); one for each sample
Supplementary files format and content: CellAnnotation: mapping of cell types and other information to barcodes across samples; one for each source (leukemia, in vivo, ex vivo)

source_name: Npm1c/Flt3ITD leukemia model

extract_protocol:
After two weeks, the transplanted mice were euthanised and bone marrow cells were harvested and stained with BV510 anti Lineage (CD3, CD19, Ter119, CD11b, Gr1) and APC anti c-Kit antibodies. For single-cell RNAseq we FACS-sorted Lineage- and Lineage+/cKit+ fractions and processed each of them in a 10X single-cell RNA-seq partition aimed at a final coverage of 500 single-cells per sgRNA.
Single-cell libraries were generated using the Chromium Next GEM Single-Cell 3’ Reagent Kits v3.1 (Dual Index) using the 10x Genomics manufacturer recommended protocol and targeting 16,000 cells per library.The resulting libraries were quantified using Qbit and qPCR and analysed on a Tape Station. Libraries were sequenced in a NextSeq 1000 or a Novaseq 6000 to a final coverage of 50,000 reads/cell for 3’ Gene Expression libraries and 5,000 reads/cell for CRISPR Feature Barcode libraries.

tag: sort markers

value: nomarker

tag: time point

tag: secondary readout

value: CRISPR screen (Perturb-seq)


title: DM_Test2_NM_6d_1 mRNA


title: LSK-LinPriming_Chd4_rep2_batch5

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Chd4_ATAC5-merged_peaks.broadPeak

tag: tissue

value: Cas9-GFP Chd4-KO

value: Ex vivo grown:SCF, Flt3L, Tpo.


title: G1_FLOPv2x2_rep3


title: DM_Test1_NM_6d_1 gRNA

description:
Perturb-seq of mouse leukemic model
DM_Test1_NM_6d_1.h5
CellAnnotation_leukemia.tsv


title: G1_Fkh1_FLAG_FLOPv2x2_rep2


title: G1_FLOPv2x2_rep2


title: DM_Test1_NM_6d_1 mRNA


title: G1_Fkh1_FLAG_FLOPv2x2_rep1


title: LSK-LinPriming_Chd4_rep1_batch5


title: G1_FLOPv2x2_rep1


title: fkh1_dbm_MYC_rep3


title: LSK-LinPriming_NTC_rep1_batch5

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-NTC0005_ATAC5-merged_peaks.broadPeak

value: Cas9-GFP Wild-type


title: LSK-LinPriming_NTC_rep2_batch5


title: DM_OP5_NM_6d_1 mRNA

description:
Perturb-seq of mouse leukemic model
DM_OP5_NM_6d_1.h5
CellAnnotation_leukemia.tsv


title: DM_OP5_NM_6d_1 gRNA


title: DM_OP4_NM_6d_1 gRNA

description:
Perturb-seq of mouse leukemic model
DM_OP4_NM_6d_1.h5
CellAnnotation_leukemia.tsv


title: fkh1_dbm_MYC_rep2


title: LSK-LinPriming_Smarcd1_rep1_batch4

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Smarcd1_ATAC4-merged_peaks.broadPeak

value: Cas9-GFP Smarcd1-KO


title: DM_OP4_NM_6d_1 mRNA


title: fkh1_dbm_MYC_rep1


title: LSK-LinPriming_NTC_rep2_batch4

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-NTC_ATAC4-merged_peaks.broadPeak


title: LSK-LinPriming_NTC_rep1_batch4


title: LSK-LinPriming_Smarcd1_rep2_batch4


title: fkh1_dbm_FLAG_rep3


title: DM_OP3_NM_6d_1 mRNA

description:
Perturb-seq of mouse leukemic model
DM_OP3_NM_6d_1.h5
CellAnnotation_leukemia.tsv


title: LSK-LinPriming_Hdac3_rep2_batch3

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Hdac3_ATAC3-merged_peaks.broadPeak

value: Cas9-GFP Hdac3-KO


title: fkh1_dbm_FLAG_rep2


title: DM_OP3_NM_6d_1 gRNA


title: fkh1_dbm_FLAG_rep1


title: DM_OP2_NM_6d_3 mRNA

description:
Perturb-seq of mouse leukemic model
DM_OP2_NM_6d_3.h5
CellAnnotation_leukemia.tsv


title: DM_OP2_NM_6d_2 gRNA

description:
Perturb-seq of mouse leukemic model
DM_OP2_NM_6d_2.h5
CellAnnotation_leukemia.tsv


title: DM_OP2_NM_6d_3 gRNA


title: Fkh1_MYC_rep3


title: LSK-LinPriming_Smarcd2_rep2_batch2

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Smarcd2_ATAC2-merged_peaks.broadPeak

value: Cas9-GFP Smarcd2-KO


title: LSK-LinPriming_NTC_rep1_batch3

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-WT_ATAC3-merged_peaks.broadPeak


title: LSK-LinPriming_NTC_rep2_batch3


title: Fkh1_FLAG_rep2


title: DM_OP2_NM_6d_2 mRNA


title: DM_OP2_NM_6d_1 mRNA

description:
Perturb-seq of mouse leukemic model
DM_OP2_NM_6d_1.h5
CellAnnotation_leukemia.tsv


title: LSK-LinPriming_Hdac3_rep1_batch3


title: Fkh1_FLAG_rep3


title: DM_OP2_NM_6d_1 gRNA


title: Fkh1_FLAG_rep1


title: LSK-LinPriming_Kmt2d_rep1_batch2

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Kmt2d_ATAC2-merged_peaks.broadPeak

value: Cas9-GFP Kmt2d-KO


title: LSK-LinPriming_Kmt2d_rep2_batch2


title: LSK-LinPriming_Brd9_rep2_batch2

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Brd9_ATAC2-merged_peaks.broadPeak

value: Cas9-GFP Brd9-KO


title: Fkh1_MYC_MOP_rep3


title: DM_OP1_NM_6d_2 mRNA

description:
Perturb-seq of mouse leukemic model
DM_OP1_NM_6d_2.h5
CellAnnotation_leukemia.tsv


title: LSK-LinPriming_Brd9_rep1_batch2

value: Bone-Marrow


title: Fkh1_MYC_MOP_rep2


title: Fkh1_MYC_MOP_rep1


title: Fkh1_MYC_rep2


title: LSK-LinPriming_Smarcd2_rep1_batch2

value: Lin- c-kit+ Sca1+


title: Fkh1_MYC_rep1


title: LSK-LinPriming_NTC_rep2_batch2

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-NTC_ATAC2-merged_peaks.broadPeak


title: DM_OP1_NM_6d_1 mRNA

description:
Perturb-seq of mouse leukemic model
DM_OP1_NM_6d_1.h5
CellAnnotation_leukemia.tsv


title: Nfr Muscle Young WT Fasted M Sample 33

description: matrix_expression_RNAseq_star2301_2_fasted.csv

value: Muscle

value: Male

value: WT

value: Fasted


title: LSK-LinPriming_NTC_rep1_batch2


title: Fkh1_FLAG_FLOPv2x2_rep3

value: anti-FLAG M2 (Sigma F1804)


title: Fkh1_FLAG_FLOPv2x2_rep2


title: Fkh1_FLAG_FLOPv2x2_rep1


title: LSK-LinPriming_WDR82_rep1_batch1

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-WDR82_ATAC-merged_peaks.broadPeak

value: Cas9-GFP WDR82-KO


title: DM_CITEseq-2_NA_NM_1 mRNA

description:
CITE-seq of mouse leukemic model
DM_CITEseq-2_NA_NM_1.h5
CellAnnotation_leukemia.tsv

value: nomarker

value: Antibodies (CITE-seq)


title: DM_OP1_NM_6d_2 gRNA

value: CRISPR screen (Perturb-seq)


title: HOP_rep3

value: TRP-HOP


title: LSK-LinPriming_NTC_rep2_batch1

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-NTC_ATAC-merged_peaks.broadPeak

value: Cas9-GFP Wild-type

value: Ex vivo grown:SCF, Flt3L, Tpo.


title: DM_CITEseq-1_NA_NM_1 gRNA

description:
CITE-seq of mouse leukemic model
DM_CITEseq-1_NA_NM_1.h5
CellAnnotation_leukemia.tsv


title: DM_CITEseq-1_NA_NM_1 mRNA


title: WT_r3

data_processing:
reads were trimmed using trim_galore using standard parameters
reads were aligned to the mouse genome mm9 annotation using STAR with following parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000
counts per gene were obtained in R using quasr::qCount() with the following parameters: reportLevel="gene", orientation="opposite", based on gencode.mouse.v1.annotation.gtf
differential gene expression was calculated using edgeR in R
Assembly: mm9
Supplementary files format and content: gene matrix containing raw counts per gene (rows) for each sample (columns)

source_name: Neuronal progenitor

extract_protocol: not provided

value: ES-derived neural progenitor cells

value: wild type


title: LSK-LinPriming_NTC_rep1_batch1


title: HOP_rep2


title: HOP_rep1


title: WT_r2


title: DM_OP1_NM_6d_1 gRNA


title: MOP_rep2

value: ADE-MOP

value: anti-Myc (9E10)


title: WT_r1


title: MOP_rep3


title: MBD3KO_r3


title: DM_CITEseq-2_NA_NM_1 gRNA


title: MBD3KO_r2


title: LSK-LinPriming_WDR82_rep2_batch1

value: Bone-Marrow

value: Lin- c-kit+ Sca1+


title: FLOPv2x2_rep3


title: MBD3KO_r1


title: MBD2t_r2

value: Mbd3-KO + Mbd2t


title: FLOPv2x2_rep1


title: FLOPv2x2_rep2


title: MBD3dMBD_r3

value: Mbd3-KO + Mbd3a_delMBD


title: Untag_HA_rep3

value: WT


title: Untag_HA_rep2


title: Untag_HA_rep1


title: MBD3dMBD_r2


title: MOP_rep1


title: Untag_MYC_rep3


title: MBD3dMBD_r1


title: Untag_MYC_rep2


title: pCCL4-ex

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

description: liver carcinoma cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C prewarmed GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (3micron) with the the Agilent Scan Control Version A.8.5.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation, median shift) was done in Rstudio following Agilent's standardized method.

source_name: explanted primary carcinoma cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: liver carcinoma cell lines were maintained at 5% CO2 and 37°C

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: IFNγ treated primary carcinoma cell lines (pCCL-IFNγ) were treated with 20ng/ml Interferon-γ for 20 hours, primary carcinoma cell lines (pCCL) and explanted primary carcinoma cell lines (pCCL-ex) remained untreated

value: liver carcinoma cell line

value: HBsAg+, Trp53 -/-

value: pCCL-ex


title: MBD2t_r3


title: pCCL3-ex

description: liver carcinoma cell line


title: LSK-LinPriming_Rbbp4_rep1_batch5

description:
Cas9-LSK progenitors were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors
LSK-Rbbp4_ATAC5-merged_peaks.broadPeak

value: Cas9-GFP Rbbp4-KO


title: pCCL2-ex

description: liver carcinoma cell line


title: MBD2t_r1


title: MBD2aR181C_r3

value: Mbd3-KO + Mbd2a_R181C


title: Untag_MYC_rep1


title: pCCL1-ex

description: liver carcinoma cell line