title: Osrdr6-meiBS-seq rep-2

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

description:
processed data file:
CpGw100s50diff.csv
CHGw100s50diff.csv
CHHw100s50diff.csv
r6_2.Clean

data_processing:
Low quality reads and adapter sequences in the raw data were removed using Cutadapt (Martin, 2011). tRNAs (http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), rRNAs (Rice Genome Annotation MSU7.0), and snoRNAs and snRNAs (https://www.arb-silva.de/no_cache/download/archive/release_132/Exports/) were also removed. Clean reads were mapped to the rice genome to identify small RNA clusters using the default parameters of Shortstack (Axtell, 2013), a phased score of ~30 or more indicates a well-phased siRNAs locous (phased locous). Annotation and distribution analysis of small RNAs were performed using deepTools2 (Ramirez et al., 2016) and BEDtools (Quinlan and Hall, 2010). Sequence logos were created by Weblogo (Crooks et al., 2004). For differential expression analysis of small RNA clusters, the regions of clusters identified in all three replicates of wild type or Osrdr6-mei were kept and normalized reads count (Count Per Million, CPM) of the clusters were calculated. We used Student's t test to perform statistical inference in identification of the differentially expressed small RNAs with multiple comparison correction using R (FDR less than 0.05).
Low quality reads and adapter sequences in the raw data were removed using Cutadapt (Martin, 2011). Clean reads were mapped to the rice genome using the default parameters of Hisat2 (Kim et al., 2015). Feature Counts (Liao et al., 2014) and DESeq2 (Love et al., 2014)were used to identify differentially expressed genes based on the criteria: q-value≤0.01 and log2 Fold Change≥1.
We used bismark software (Krueger and Andrews, 2011) to mapped bisulfite sequencing data to rice reference genome with default parameters and methylKit (Akalin et al., 2012) to identify differentially methylated regions (window size=100bp, step size=50bp, meth.diff=25, qvalue=0.01).
Genome_build: Rice Genome Annotation MSU7.0
Supplementary_files_format_and_content: Processed data were stored in excel files and cvs files.

organism: Oryza sativa Indica Group

growth_protocol: Plants were grown in paddy fields during the growing season in Beijing, China (40.22°N, 116.20°E) or Hainan, China (18.51°N, 110.04°E)

extract_protocol:
Wild-type and Osrdr6-mei anthers at the leptotene-like stage, determined according to floret length were collected and frozen in liquid nitrogen. The plant materials (wild type and Osrdr6-mei) used for the assays were obtained from the offspring of Osrdr6-mei/+. Anthers with wild-type genotype of OsRDR6 were used as the control group, while anthers with Osrdr6-mei genotype were used as the mutant group. Each sample contains fresh anthers from 3 independent plants. And both of these groups were set up three sets of biological repeats. In this condition, the repeatability of data is good. The same sample collection method is used for transcriptome sequencing and  WGBS.
Small RNA library construction and sequencing were completed by Oebiotech corporation, Shanghai, China (http://www.oebiotech.com/)   Total RNA samples used for small RNA sequencing were also used for transcriptional sequencing. Library construction and sequencing were completed by Oebiotech corporation, Shanghai, China (http://www.oebiotech.com/).  Wild-type and Osrdr6-mei anthers at the leptotene-like stage (as the same stage as used for small RNA sequencing), determined according to floret length were collected and frozen in liquid nitrogen. Library construction and sequencing were completed by Oebiotech corporation, Shanghai, China (http://www.oebiotech.com/).

treatment_protocol: Osrdr6-mei was derived from indica rice cultivar Zhongxian 3037 exposed to 60Co-γ-ray radiation.Zhongxian 3037 (Obtained from the offspring of Osrdr6-mei/+) was used as the wild type.

tag: cultivar

value: Zhongxian 3037

tag: genotype/variation

value: Osrdr6-mei mutant

value: leptotene-like stage

value: anthers


title: D0_ATACseq

status: Public on Jun 05 2021

type: SRA

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

library_source: genomic

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina
Adaptors were removed using Cutadapt and Trimmomatic
For RNA-Seq samples reads were mapped to the human reference genome hg38 using TopHat v2.1.1 with default parameters. Assembly of mapped reads was performed with Cufflinks v2.2.1 and values of Fragments Per Kilobase of transcript per million Mapped reads (FPKM) were calculated for all annotated genes and transcripts.
For ATAC-Seq samples we used ENCODE ATAC-Seq pipeline (http://www.encodeproject.org/atac-seq/) . Paired-end reads were aligned to hg38 using Bowtie2. Next, we used SAMTools [PMID:19505943] to remove unmapped reads, fragments with unmapped mates, non-primary alignment reads, and reads failing platform quality checks. Low quality reads (MAPQ < 30) and reads which mapped to mitochondrial DNA were also excluded. Optical and PCR duplicates were also removed using Picard tools (http://broadinstitute.github.io/picard). To accurately locate the center of each transposon-binding event, the remaining reads were offset by +4 and -5 for positive and negative strands respectively . ATAC-Seq peak regions were called for each sample using MACS2 with parameters --shift 75 --extsize 150 --nomodel --keep-dup all --call-summits. Resulting peaks which overlapped with ENCODE blacklisted regions were filtered out.
For both RNA-Seq and ATAC-Seq we calculated raw read counts using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: FPKM_mat and count_mat are tab-delimited files containing FPKM and raw counts. Each column represents a sample and each row represents a gene
Supplementary_files_format_and_content: Bigwig files were obtained with the bamCoverage function from deepTools. Values represent number of reads per bin. We used a bin size of 50.

molecule: genomic DNA

organism: Homo sapiens

source_name: H9 pluripotent stem cells

growth_protocol: The human embryonic stem cell line H9 (WA09)-GFP, which has constitutive expression of enhanced Green Fluorescent Protein (GPF), was used for all experiments. Prior to differentiation, cells were cultured in supplemented Knock Out (Gibco ®) medium, previously conditioned with mitotically inactivated mouse embryonic fibroblasts (MEFs) with fresh FGF-2 (10 ng/ml; Sigma), over a Matrigel (BD ®) matrix, until they reached 75% confluency.

extract_protocol:
Briefly, 50,000 cells were detached from each induction plate at the previously defined time-points and washed with cold PBS. Next 50 μl of cold lysis buffer was added to the cell pellet.
The Tn5-mediated tagmentation and adapter incorporation were performed with the Nextera DNA Library Prep Kit (Illumina) following manufacturer’s protocol at 37ºC for 30 min. The transposed DNA was purified using Qiagen MinElute PCR Purification Kit (Qiagen). To amplify DNA fragments, we used NEBNext High-Fidelity PCR Master Mix (New England Biolabs).

treatment_protocol: The floor-plate dopaminergic differentiation procedure was described previously (Kriks et al., 2011) with minor modifications (Carballo-Molina et al., 2016).

tag: induction day


title: Osrdr6-meiBS-seq rep-1

country: China

description:
processed data file:
CpGw100s50diff.csv
CHGw100s50diff.csv
CHHw100s50diff.csv
r6_1.Clean

tag: tag

tag: tissue


title: NS-KO D27 rep2

city: Beijing

first: Sunyang

last: YING

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District, Beijing

department: State key laboratory of stem cell and reproductive biology

institute: Chinese Academy of Sciences

description: tRNA derived fragments

library_source: transcriptomic

data_processing:
Basecalling was performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5’, 3’-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
tRNA sequences of cytoplasmic were downloaded from GtRNAdb. tRNA sequences of mitochondrial were predicted with tRANscan-SE software. To generate the mature tRNA libraries, we removed the predicted intronic sequences (if present) and added an additional 3’-terminal “CCA” to each tRNA. To generate the precursor tRNA libraries, we included 40 nucleotides of flanking genomic sequence on either side of the original tRNA sequence.
The abundance of tRF & tiRNA is evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). For each tRF & tiRNA, estimated the expression level using the mapped reads number and given an ID. Then the tRF & tiRNA are filtered if CPM less than 20 in all samples.
tRFdb & GtRNAdb
Supplementary_files_format_and_content: [Aligned Results, txt]: The trimmed reads (14-40nt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. [Trimmed Sequence Data, fastq]: Subsequently, the 5’, 3’-adapter sequence are trimmed from the clean reads by cutadapt and the reads with lengths shorter than 14nt or longer than 40 were discarded. The trimmed reads are collapsed into FASTA format. The identifier line, which begin with‘>’, gives a name that are divided into three parts by underline. The first part of the character indicate sample name, the second part of the integer indicate rank the i-th out of all sequences, the third part is made up of character and integer. For example, the identifier line ‘>samplei_1_x123’, the character ‘samplei’indicate sample name, the integer ‘1’ indicate rank the first out of all sequences, the character ‘x’as an identifier and the subsequent integer ‘123’indicate the sequence have occur 123 time. [xlsx files]: the data of expressed tRFs and differentially expressed tRFs, and their normalized data.

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Isolate mice liver and remove gall bladder. Cut the liver into small pieces and place them in RNAlater (Thermo). Liver tissues were ground in liquid nitrogen after added lysis buffer. Then extract the RNAs  with mirVana™ miRNA Isolation Kit (Thermo, AM1561). Isolate 14-40 nt RNAs by PAGE.
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’ -adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Pretreated total RNA of each sample was taken for tRF & tiRNA-seq library preparation. Library preparation procedures included: 1) 3’-adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~134-160bp PCR amplified fragments (corresponding to ~14-40nt small RNAs). The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results, and used for sequencing on the instrument.
tRF-seq

treatment_protocol: Once or repeated injections of CCl4 (Sigma) were performed respectively to produce acute and long-term liver injuries. Corn oil was used to dilute CCl4 (Sigma) to form 40% CCl4 and intraperitoneal injected into 9-12-week-old male mice at 2 ml kg-1 body mass.

tag: strain

value: liver

tag: age

value: 8-12 week

tag: gender

value: male

tag: genotype

tag: ccl4-treated time

value: Day 27


title: miCLIP mESC WT rep1, technical rep1

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

description:
Co-immunoprecipitated RNA fragments
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.noC2T.plus.bw
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.noC2T.minus.bw
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.C2T.plus.bw
miCLIP_mESC_WT_1.merged.v2uniqMD.duprm.C2T.minus.bw

data_processing:
miCLIP data processing:
Reads were mapped to the respective genome and its annotation (GENCODE release 31 for all human samples, GENCODE release M23 for all mouse samples) using STAR (v2.7.3a). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999), soft-clipping was prohibited on the 5'end of reads (--alignEndsType Extend5pOfRead1) and only uniquely mapping reads were kept for further analysis (--outFilterMultimapNmax 1).
Following mapping, BAM files were sorted and indexed (SAMtools v1.9) and duplicate reads were removed (UMI-tools v1.0.0).
After removing duplicates, all mutations found in reads were extracted using the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK, v1.1.3). The list was filtered for C-to-T mutations using basic Bash commands and kept in BED file format. Based on the filtered list of C-to-T mutations, deduplicated reads were separated into two BAM files holding reads with and without C-to-T mutation, respectively, using SAMtools and basic Bash commands. The BAM file of reads without C-to-T mutation was transformed to a BED file using bedtools bamtobed (BEDTools v2.27.1) and considering only the 5' mapping position of each read. Afterwards, the BED file was sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream (since this nucleotide is considered as the crosslinked nucleotide) using bedtools genomecov (BEDTools v2.27.1). Similarly, the BED files of C-to-T mutations were also sorted and summarized to strand-specific bedGraph files using bedtools genomecov. Finally, all bedGraph files were transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite (v365).
RNAseq data processing:
Reads were mapped to the mouse genome and its annotation based on GENCODE release M23 using STAR (v2.6.1b). When running STAR, up to 4% mismatches were allowed per read (--outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999). SAMtools was used to remove secondary alignments and keep only one location for multimapping reads (-F 256).
For differential expression analysis, mapped reads were counted with htseq-count (v0.12.4, -s reverse) into gene annotation based on GENCODE release M23 [PMID: 25260700].
Genome_build: mm10 (GRCm38.p6), hg38 (GRCh38.p12)
Supplementary_files_format_and_content: *.C2T.plus.bw, *.C2T.minus.bw: bigwig files of positions with C-to-T mutations and their counts. They were generated by filtering for C-to-T mutations in the list of all found mutations, which were output of the Perl script parseAlignment.pl of the CLIP Tool Kit (CTK). The filtered list was in BED file format and was then sorted and summarized to strand-specific bedGraph files using bedtools genomecov, which were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: *.noC2T.plus.bw, *.noC2T.minus.bw: bigwig files of positions upstream of reads without C-to-T mutation and their counts. They were generated by first removing all reads with C-to-T mutation from the BAM files and then transforming the resulting BAM file to a BED file using bedtools bamtobed considering only the 5' mapping position of each read. The BED file was then sorted and summarized to strand-specific bedGraph files which were shifted by one base pair upstream using bedtools genomecov. bedGraph files were then transformed to bigWig track files using bedGraphToBigWig of the UCSC tool suite.
Supplementary_files_format_and_content: The samples miCLIP_mESC_WT_1 and miCLIP_mESC_Mettl3_KO_1 were sequenced in two technical replicates (miCLIP_mESC_WT_1_1 + miCLIP_mESC_WT_1_2 and miCLIP_mESC_Mettl3_KO_1_1 + miCLIP_mESC_Mettl3_KO_1_2), for which we provide separate raw data files (fastq.gz), but have merged their bigwig tracks after processing into miCLIP_mESC_WT_1.merged... and miCLIP_mESC_Mettl3_KO_1.merged...
Supplementary_files_format_and_content: *.txt: count tables of reads mapping to genes generated by counting reads with htseq-count (v0.12.4, -s reverse) into gene annotation based on GENCODE release M23 [PMID: 25260700].
Supplementary_files_format_and_content: *.bed: bed files with predicted m6A sites by m6Aboost. In brief, bam files with reads without C-to-T mutation were used for peak calling with PureCLIP (v1.3.1) individually on each replicate for each condition. PureCLIP significant sites per replicate were then filtered for presence in at least two replicates for a given condition. m6Aboost was applied to the reproducible peaks to predict m6A sites.

source_name: WT mouse embryonic stem cells (mESC)

growth_protocol: Mouse embryonic stem cells (mESC) with wildtype and Mettl3 knockout genotype were taken from a previous publication (PMID: 25569111) and cultured as described therein. The HEK293T cell line was cultured in DMEM (Life Technologies) containing 10% FBS (Life Technologies), 1% L-glutamine (Life Technologies) and 1% penicillin-streptomycin (Life Technologies) at 37°C with 5% CO2.

extract_protocol:
For RNA extraction from HEK293T cells and mESCs, cells were washed in ice-cold PBS and collected on ice for the isolation of total RNA using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommended protocol. Poly(A)+ RNA was extracted using Oligo d(T)25 Magnetic Beads using the manufacturer’s recommended protocol. Poly(A)+ concentration was measured using Qubit™ RNA HS Assay Kit (ThermoFisher Scientific). The quality of poly(A)+ RNA was ensured using High sensitivity RNA screen tapes for the 2200 Tape station system (Agilent). If a predominant peak for ribosomal RNA was still detectable an additional round of poly(A) selection was performed. Mouse heart RNA was purchased from Takara Clontech (order number 636202): RNA isolated by a modified guanidinium thiocyanate method followed by poly A+ RNA selection with two rounds of oligo(dT)-cellulose columns.
RNA-seq: NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol beginning with fragmentation step (Part # 15031047 Rev. E). Libraries were prepared with a starting amount of 73ng for imb_koenig_2019_21 and amplified in 10 PCR cycles.Libraries were profiled in a DNA 1000 on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).  All 6 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput Flowcell, SR for 1x 84 cycles plus 1x 7 cycles for the index read.
miCLIP2: Briefly, 1 µg of polyA selected and fragmented RNA was incubated with an m6A antibody [Synaptic Systems, 202 003] and crosslinked twice at 150 mJ/cm² at 254 nm followed by immunoprecipitation with protein A Dynabeads. After stringent washing, the 3’ end of the RNA was dephosphorylated using T4 PNK and subsequently pre-adenylated L3-App linker was ligated. The 5’ end was radioactively labelled and the samples were purified by SDS PAGE and transferred to a nitrocellulose membrane. After exposure to a Fuji film, the protein-RNA complexes were isolated and elution of the RNA was accomplished by proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Reverse transcription was perform for cDNA synthesis using RT primers against the L3-App linker. The cDNA was purified using MyONE Silane bead clean up system and the 5’ linker was ligated. A pre-amplification PCR with 6 cycles was performed and subsequently the samples were size-selected using ProNex beads. To prevent overamplification of the library, the PCR cycles were optimised to a minimum. For the preparative PCR, the minimum amount of PCR cycles was used followed by a second size selection step using ProNex beads. Libraries were profiled in a High Sensitivity D1000 ScreenTape on a Tape station 2200 (Agilent) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples in an experiment were pooled in equimolar ratio and sequenced on one NextSeq 500 High Output Flowcell, 75 cycle kit.

treatment_protocol: In the case of mESCs, Mettl3 knockout (KO) cells were taken from a previous publication (PMID: 25569111).

tag: cell type

value: mouse embryonic stem cells (mESC)

tag: miclip antibody

value: rabbit anti-m6A antibody (Synaptic Systems, order number 202 003)


title: NS-KO D27 rep1

description: tRNA derived fragments


title: CAF3-CON1

city: Wuhan

first: Tian

last: Fang

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp  paired-end reads, according to the manufacturer’ s instructions.
Raw data (raw reads) of fastq format were firstly processed through primary quality  control. In this step, clean data (clean reads) were obtained by removing read pairs that  contain N more than 3 or the proportion of base with quality value below 5 is more than 20%,  in any end,or adapter sequence was founded. All the downstream analyses were based on the  clean data with high quality.
Paired-end clean reads were aligned to the reference genome using TopHat. We selected  TopHat as the mapping tool for that TopHat can generate a database of splice junctions based  on the gene model annotation file and thus a better mapping result than other non-splice  mapping tools.
HTSeq was used to count the reads numbers mapped to each gene.
Differential expression analysis between two conditions was performed using the  DEGSeq R package (1.20.0). Differentially expressed genes were defined as those for which  the adjusted P-value below 0.05 and the log2(Fold change) more than 1.
Supplementary_files_format_and_content: fpkms

source_name: primary cancer-associated fibroblasts

growth_protocol: Primary cancer-associated fibroblasts were isolated from tumor specimens and cultured in DMEM/F-12 1:1 medium with 10% FBS and 1×PS in a humidified atmosphere incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells in a T75 culture flask were digested and washed with PBS, then dissoved in 1ml trizol and then stored in -80℃ for futher RNA isolation.
A total amount of 2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep  Kit for Illumina following manufacturer’ s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using  poly-T oligo-attached magnetic beads. Fragmentation was carried out using fragmentation buffer. First strand cDNA was synthesized and second strand cDNA synthesis was  subsequently performed. Remaining overhangs were converted into blunt ends. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated.  Then the PCR was performed. At last, Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 350bp.

treatment_protocol: When the confluence reach 60-70%, the medium were replaced with new complete medium containing 20uM niraparib or 30uM olaparib and incubated for 72h.

tag: disease state

value: ovarian cancer

value: primary cancer-associated fibroblasts (CAFs)

tag: treatment

value: DMSO for 72h


title: Wild-type BS-seq rep-2

description:
processed data file:
CpGw100s50diff.csv
CHGw100s50diff.csv
CHHw100s50diff.csv
RR6_2.Clean

source_name: Wild-type BS-seq

value: wild type


title: Wild-type BS-seq rep-1

description:
processed data file:
CpGw100s50diff.csv
CHGw100s50diff.csv
CHHw100s50diff.csv
RR6_1.Clean


title: AGS cells with DMSO

city: beijing

first: sichong

last: han

address: No. 15 North Third Ring East Road, Chaoyang District

institute: beijing university of chemical technology

description: NC

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
The trimmed reads were aligned to the reference genome (hg38) using Hisat2 software (v2.0.4)
The transcript abundances for each sample were estimated with StringTie (v1.2.3), , and the FPKM value for gene and transcript levels were calculated with R package Ballgown (v2.6.0)
The differential expression analysis of FPKM was based on Significance B using Perseus software (1.5.3.2)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: gastric cancer cells

growth_protocol: The human gastric cancer AGS cells were cultured in RPMI-1640 medium with 10% fetal bovine serum, 100 units/mL penicillin and 100 mg/mL streptomycin in 37C

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.Briefly, the purified total RNA was subjected to rRNA removal, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3 'end plus A, linker, enrichment and other steps to complete the sequencing sample library construct.

treatment_protocol: AGS cells were seeded in 6-well plates with 12 µM SFA or 18 µM SFE treatment, and were treated with DMSO as negative control.After cultured for 48h, cells were treated with trizol reagent to extract total RNA.

tag: cell line

value: AGS cells

value: DMSO as negative control


title: AGS cells with SFA treatment

value: SFA treatment


title: Osrdr6-meimRNA-seq rep-2 [r6_a_rep2]

description:
processed data file:
part_RR6_A_r6_a_all_FPKM.csv
Sample_r6_a_2

source_name: Osrdr6-mei mRNA-seq

value: Zhongxian 3037

tag: molecule subtype

value: mRNA


title: SSF-1784_P24_CTRL-

city: Barcelona

first: Carlota

last: Dobaño

address: Rosselló 153

country: Spain

institute: ISGlobal, Hospital Clínic - Universitat de Barcelona

data_processing:
reads were aligned using BWA Aln version 0.7.10 using UCSC RefSeq (Human 19) with mitochondrial genes added
Quantified samples were then quality controlled using mapping summary statistics to remove low quality samples based on predetermined minimum values for the total number of mapped reads, percent of mapped reads mapped to the human genome, etc.
Downstream analysis was applied only to reads that mapped uniquely to a UMI and only mapped to isoforms of the same gene (UMI.unq).
The TMM normalization method was applied to account for differing number of read counts and to address unwanted technical variation. The voom transformation from the limma R package  was applied to transform the data into a form appropriate for linear models.
Genome_build: hg19
Supplementary_files_format_and_content: concatenated_unique_refseq_umi_counts.tsv contains the count matrix for all samples/cells

molecule: polyA RNA

organism: blank sample

source_name: Water

extract_protocol:
RNA was extracted at the Center for Infectious Disease Research (CIDR, Seattle) using the Promega SV 96 RNA Isolation kit following the manufacturer’s protocol. Samples kept in RNAprotect were centrifuged at 4,000g for 7 minutes at 4°C, cell pellets were resuspended in 150 μL RLT Buffer, and 150 μL of 70% ethanol was added prior to processing with Promega SV 96 RNA Isolation kit. RNAs were eluted with 100 μL nuclease free water. Each 96-well extraction batch was spot checked by Bioanalyzer using Agilent RNA 6000 Pico chip and had an average RIN score of 7.4. RNA samples were distributed in 384 well plates for library preparation. Samples from the same individuals were in the same plate and key study variables (vaccine, site and cases-controls) were checked for balance across plates to avoid batch effects.
An optimized version of Digital Gene Expression (DGE) was used, further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from antigen-stimulated PBMCs was linked to unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Then, cDNA from multiple cells were pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3′ ends and preserving strand information. Nextera XT library preparation and sequence paired-ends were employed on an Illumina NextSeq instrument at the Broad Institute.
SCRB-Seq

tag: plate

tag: pid

tag: stimulation

tag: visit

tag: site

tag: vaccine

tag: case

tag: match

tag: sid

tag: waz

tag: haz

tag: hb

tag: Sex


title: CAF1-OLA1

tag: disease state

tag: cell type

value: olaparib 30um for 72h


title: NS-KO D3 rep2

description: tRNA derived fragments

tag: strain

tag: tissue

tag: age

tag: gender

tag: genotype

tag: ccl4-treated time

value: Day 3


title: Osrdr6-meimRNA-seq rep-1 [r6_a_rep1]

description:
processed data file:
part_RR6_A_r6_a_all_FPKM.csv
Sample_r6_a

tag: cultivar

tag: genotype/variation

value: Osrdr6-mei mutant

tag: tag

value: leptotene-like stage

value: anthers

tag: molecule subtype


title: NS-KO D3 rep1

description: tRNA derived fragments

value: liver

value: 8-12 week

value: male


title: SSF-1784_A2_CTRL-

tag: plate

tag: pid

tag: stimulation

tag: visit

tag: site

tag: vaccine

tag: case

tag: match

tag: sid


title: CAF1-CON3

tag: disease state

value: ovarian cancer

tag: cell type

tag: treatment


title: AGS cells with SFE treatment

tag: cell line

value: SFE treatment


title: CAF1-OLA3

value: primary cancer-associated fibroblasts (CAFs)


title: NS-KO D0 rep2

description: tRNA derived fragments

tag: strain

tag: tissue

tag: age

tag: gender

tag: genotype

tag: ccl4-treated time

value: Day 0


title: CAF1-OLA2


title: CAF1-CON2

value: DMSO for 72h


title: SSF-1783_P24_CTRL-

tag: plate

tag: pid

tag: stimulation

tag: waz

tag: haz

tag: hb

tag: Sex


title: NS-KO D0 rep1

description: tRNA derived fragments


title: WT D27 rep2

description: tRNA derived fragments

value: wild type

value: Day 27


title: Wild-type mRNA-seq rep-2 [RR6_A_rep2]

description:
processed data file:
part_RR6_A_r6_a_all_FPKM.csv
Sample_RR6_A_2

source_name: Wild-type mRNA-seq

tag: cultivar

value: Zhongxian 3037

tag: genotype/variation

tag: tag

tag: molecule subtype


title: CAF1-CON1

tag: disease state

tag: cell type

tag: treatment


title: SSF-1783_A2_CTRL-

tag: visit

tag: site

tag: age

tag: vaccine

tag: case

tag: match

tag: sid


title: Osrdr6-mei smallRNA-seq rep-3

description:
processed data file:
PhaseLoci_21nt.xlsx
PhaseLoci_24nt.xlsx
Sample_r6_a_3.deadaptor

source_name: Osrdr6-mei smallRNA-seq

tag: tissue

value: mRNA


title: Wild-type mRNA-seq rep-1 [RR6_A_rep1]

description:
processed data file:
part_RR6_A_r6_a_all_FPKM.csv
Sample_RR6_A


title: SSF-1782_A2_CTRL-

tag: plate

tag: pid

tag: stimulation

tag: waz

tag: haz

tag: hb


title: WT D27 rep1

description: tRNA derived fragments

tag: strain

tag: gender

tag: genotype

tag: ccl4-treated time


title: ChIP-Seq of Corylus heterophylla: ChIP of rapid ovule growth

city: Siping

first: Yunqing

last: Cheng

address: Haifeng street

institute: Jilin Normal University

data_processing:
Three pairs of input control and antibody-treated ChIP-Seq libraries were constructed and high-throughput sequencing was performed using the Illumina Novaseq 6000 platform.
Clean reads were aligned to the reference Corylus heterophylla genome using Bowtie2.
For peak calling, the Bowtie2 alignment output for the six libraries was used together as input for Model-based Analysis of ChIP-Seq (MACS2).
Subsequently, each peak’s signal value in the genome was obtained using the Reads Per Kilobase calculation method per Million mapped reads (RPKM).
Genome_build: Corylus heterophylla (PRJNA664441)
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigWig files

organism: Corylus heterophylla

source_name: ChIP of Ov3.1

extract_protocol:
Ovules [>0.1 g (g fresh weight) ] were isolated manually from the pistillate inflorescences or fruit clusters;  thereafter, only medium-sized ovules, among all isolated ovules from the same development stage, were immediately treated with 1% formaldehyde before placing in liquid nitrogen.
The chromatin complexes were isolated and sonicated to shear DNA into 200–600 bp fragments. Thereafter, the anti-ChARF3 antibody was used for immunoprecipitation of samples, excluding input controls. After reverse cross-linking, protein digestion, and DNA precipitation, immunoprecipitated DNA was recovered and quantified using a Qubit 4.0 Fluorimeter (Invitrogen, Carlsbad, USA). After dilution to 1.5 ng/μL, the DNA quality and insert size were evaluated using agarose gel electrophoresis.

value: ovule

tag: developmental stage

value: rapid ovule growth

tag: cultivar

value: wild germiplasm

tag: chip antibody

value: polyclonal antibody against ChARF3


title: SSF-1782_P24_CTRL-

tag: cell type

tag: visit

tag: site

tag: age

tag: vaccine

tag: case

tag: Sex


title: ChIP-Seq of Corylus heterophylla: Input of rapid ovule growth

source_name: Input of Ov3.1

tag: tissue


title: SSF-1781_P24_CTRL-

tag: plate

tag: pid

tag: stimulation

tag: match

tag: sid

tag: waz

tag: haz


title: Osrdr6-mei smallRNA-seq rep-2

description:
processed data file:
PhaseLoci_21nt.xlsx
PhaseLoci_24nt.xlsx
Sample_r6_a_2.deadaptor

tag: cultivar

tag: genotype/variation

value: Osrdr6-mei mutant

tag: tag

value: leptotene-like stage

value: anthers

tag: molecule subtype

value: Small RNA


title: WT D3 rep2

description: tRNA derived fragments

tag: strain

value: liver

value: 8-12 week

tag: gender

value: male

tag: genotype

tag: ccl4-treated time

value: Day 3


title: WT D3 rep1

description: tRNA derived fragments

tag: age


title: SSF-1781_A2_CTRL-

tag: cell type

tag: visit

tag: site

tag: vaccine

tag: case

tag: hb

tag: Sex


title: ChIP-Seq of Corylus heterophylla: Input of ovule formation

source_name: Input of Ov1.1

tag: tissue

tag: developmental stage

value: ovule formation


title: SSF-1780_P24_CTRL-

tag: plate

tag: pid

tag: stimulation

tag: match

tag: sid

tag: waz

tag: haz


title: WT D0 rep2

description: tRNA derived fragments

tag: strain

tag: age

tag: gender

tag: genotype

value: wild type

tag: ccl4-treated time

value: Day 0


title: Osrdr6-mei smallRNA-seq rep-1

description:
processed data file:
PhaseLoci_21nt.xlsx
PhaseLoci_24nt.xlsx
Sample_r6_a.deadaptor

tag: cultivar

value: Zhongxian 3037

tag: genotype/variation

tag: tag

tag: molecule subtype


title: Wild-type smallRNA-seq rep-3

description:
processed data file:
PhaseLoci_21nt.xlsx
PhaseLoci_24nt.xlsx
Sample_RR6_A_3.deadaptor

source_name: Wild-type smallRNA-seq

tag: tissue


title: WT D0 rep1

description: tRNA derived fragments


title: SSF-1780_A2_CTRL-

tag: cell type

tag: plate

tag: visit

tag: site

tag: vaccine

tag: case

tag: hb

tag: Sex


title: ChIP-Seq of Corylus heterophylla: ChIP of ovule formation

source_name: ChIP of Ov1.1

tag: developmental stage

tag: chip antibody


title: Wild-type smallRNA-seq rep-2

description:
processed data file:
PhaseLoci_21nt.xlsx
PhaseLoci_24nt.xlsx
Sample_RR6_A_2.deadaptor


title: Wild-type smallRNA-seq rep-1

description:
processed data file:
PhaseLoci_21nt.xlsx
PhaseLoci_24nt.xlsx
Sample_RR6_A.deadaptor


title: HYR__c47998_e6244b__20210412_mouse_cortex_sbmerged_S4

status: Public on Jun 04 2021

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Barcode reads (read 2) were trimmed using trimgalore (trim_galore -j 2 -o . $R1 $R2 --paired --gzip), corrected to a whitelist allowing 1 mismatch (custom seq script inVSN pipeline version 41df185308 [develop_atac]), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
Cell barcodes were written to the bam as a CB SAM tag using SAMtools and AWK (custom VSN pipeline version 41df185308 [develop_atac] script) (samtools view -h HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5.bwa.out.possorted.bam | mawk '/^@/ {print;next} {N=split($1,n,"_"); NN=split(n[1],nbc,"-"); ucorr_bc=""; corr_bc=""; if(NN==1){ # BioRad data with format {corrected_bc}_qname; corr_bc="CB:Z:" nbc[1];} if(NN==2){ucorr_bc="CR:Z:" nbc[1]; if(length(nbc[2])>0){corr_bc="
Reads were mapped to reference genomes using bwa-mem and duplicate-marked using samtools markdup by the VSN pipeline version 41df185308 [develop_atac] (bwa mem -t 8 genome.fa $R1.fq.gz $R2.fq.gz | samtools fixmate -@ 6 -m -u -O bam - - | samtools sort -@ 6 -u -O bam - | samtools markdup -@ 6 -f markdup.log - bwa.out.possorted.bam).
Fragments files were generated using Sinto (sinto fragments -b $bam -m 30 --barcodetag CB --use_chrom "(?i)^chr" --min_distance 10 --max_distance 5000 --chunksize 5000000 -p 2 -f $fragments.bed)
Per-cluster differentially accessible region were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='cell_type_finetuned', var_features=variable_regions, contrasts=None, adjpval_thr=0.05, log2fc_thr=np.log2(1.5), n_cpu=12)) and written to BED format using a custom python script.
Per-cluster coverage bigwigs were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (bw_paths, bed_paths = export_pseudobulk(input_data = cistopic '0.1.dev214+gc72ef83.d20210522'_obj.cell_data, variable = 'cell_type_finetuned', chromsizes = chromsizes, bed_path = bed_path, bigwig_path = bw_path, path_to_fragments = fragments_dict, n_cpu = nclusters, normalize_bigwig = True, remove_duplicates = True))
Aggregate genome coverage bigwigs were generated using DeepTools 3.5.0 (bamCoverage -b ${file} -o ${file%.bam}.RPGCnormalized.bw -bs 1 -p 4 --normalizeUsing RPGC  --effectiveGenomeSize 2913022398)
For HyDrop-RNA samples (prefix HYR):
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Reads were mapped  to reference genomes and expression matrices were generated using STAR version: 2.7.8a_2021-04-27 in STARsolo mode (STAR --runThreadN 6 --runMode alignReads --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --genomeDir "${star_reference_dir}" --readFilesIn "${fastq_R1_filename}" "${fastq_R2_filename}" --readFilesCommand 'gzip -c -d' --soloCBwhitelist "${whitelist_part1_filename}" "${whitelist_part2_filename}" "${whitelist_part3_filename}" --soloType CB_UMI_Complex --soloCBposition 0_0_0_9 0_20_0_29 0_40_0_49 --soloUMIposition 0_50_0_57 --sjdbGTFfile $sjdbgtf --soloCellFilter CellRanger2.2 2000 0.99 10 --soloCBmatchWLtype 1MM --outFilterMultimapNmax 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY --outFileNamePrefix ${bam_filename%bam} --outReadsUnmapped Fastx --quantMode GeneCounts --bamRemoveDuplicatesType UniqueIdentical --soloFeatures Gene GeneFull Velocyto)
For the optimisation samples (HYR__1ec4a0__20200929_Exo_S1 HYR__3ac717__20201006_non-exo_S2 HYR__70afb2__20201006_TSO-LNA_S3 HYR__c6c4b7__20201016_gtp_S4 HYR__d0a5b4__20201023_klenow_S5 HYR__f0eb5a__20201023_bst_S6), FASTQs were downsampled to match the reads per cell depth of the lowest sample and re-mapped using the same STAR parameters to generate the DOWNSAMPLED expression matrices.
Genome_build: For human samples: hg38, for mouse samples: mm10, for hybrid samples: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary_files_format_and_content: For HyDrop-ATAC samples (prefix HYA): standard tab-separated fragments files, tar archive with per-cluster differentially accessible region bed files, tar archive with per-cluster genome coverage bigwig
Supplementary_files_format_and_content: For HyDrop-RNA samples (prefix HYR): STARsolo gene expression matrix in MEX format

molecule: nuclear RNA

source_name: Mouse cortex nuclei

growth_protocol: Female wild-type P56 BL/6 mice were kept according to standard animal husbandry practices were maintained in a specific pathogen-free facility under standard housing conditions with continuous access to food and water. Mice used in the study were 1–8-weeks old and were maintained on 14 h light, 10 h dark light cycle from 7 to 21 h.

extract_protocol:
Cortex was separated from female P56 BL/6 mouse brains, immediately snap-frozen in liquid nitrogen and preserved in -80 °C. A ~1 cm3 frozen piece of mouse cortex tissue was transferred to 1 mL of ice-cold homogenisation buffer (320 mM Sucrose, 10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgAcetate, 1 mM DTT, 0.1 mM EDTA, 0.1% IGEPAL, 1X cOmplete Protease Inhibitor Cocktail) in a Dounce homogenizer mortar and thawed for 3 minutes. The tissue was homogenised with 10 strokes of pestle A and 5 strokes of pestle B until a homogeneous cell suspension was achieved. The resulting homogenate was filtered through a 40 μm Flowmi strainer. The mortar was washed with 1.65 mL of ice-cold homogenisation buffer to collect any remaining cells. 2.65 mL of ice-cold gradient medium was added to 1.65 mL of homogenate. 4 mL of 29% iodoxanol cushion (129.2 mM Sucrose, 77.5 mM KCl, 15.5 mM MgCl, 31 mM Tris-HCl pH 7.5, 29% Iodoxanol) was loaded into an ultracentrifuge. 5.3 mL of sample was gently layered on top of the 29% iodoxanol cushion without mixing both phases. Sample was centrifuged at 10 000 xg, 4°C for 30 minutes and the supernatant was gently removed without disturbing the nuclei pellet. Nuclei were resuspended in 100 μL of Nuclei buffer. Cells were resuspended in 85 μL of RT mix (1x Maxima RT Buffer, 0.9 mM dNTPs, 25 mM DTT, 1.3 mM GTP, 15 % Optiprep, 1.3 U/uL RNAse inhibitor, 15 U/uL Maxima hRT, 12.5 uM TSO, 4.4% PEG-8000). RT mix was co-encapsulated with 35 μL of freshly thawed HyDrop-RNA beads in RAN oil on the Onyx microfluidics platform. The resulting emulsion was collected in aliquots of 50 μL total volume and thermocycled according to the RT program (42 °C for 90 min., 11 cycles of [50 °C for 2 min., 42 °C for 2 min.], 85 °C for 5 min., followed by a final hold on 4 °C). 125 μL of recovery agent (20% PFO in HFE), 55 μL of GITC Buffer (5 M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4) and 5 μL of 1 M DTT was added to each separate aliquot of 50 μL thermocycled emulsion and incubated on ice for 5 minutes. 99 μL of Ampure XP beads was added to the aqueous phase and incubated for 10 minutes. Ampure beads were pelleted on a Nd magnet and washed twice with 80% EtOH. Elution was performed in 50 μL of EB-DTT-Tween (10 mM DTT, 0.1% Tween-20 in EB). Exonuclease treatment was performed by adding 3 μL of 10x NEBuffer 3.1, 3 μL of ExoI, and 4 μL of dH2O to 30 μL of eluted library. The ExoI reaction mix was incubated at 37 °C for 5 min., 80 °C for 1 min. followed by a final hold at 4 °C. 2 μL of 1 M DTT was added and a 0.8X Ampure XP purification was performed according to manufacturer’s recommendations. cDNA was eluted in 40.5 μL of EB-DTT (10 mM DTT in EB) and added to ISPCR mix (40 μL library, 50 μL 2x KAPA HiFi, 10 μL 10 uM TSO-P primer). PCR cycling was performed according to the ISPCR program (95 °C for 3 min., 13 cycles of [98 °C for 20s, 63 °C for 20s, 72 °C for 3 min.], 72 °C for 5 min. followed by a final hold at 4 °C. 2 μL of 1M DTT was added and a 0.6x Ampure XP purification was performed according to manufacturer’s recommendations. cDNA was eluted in 28.5 μL of EB-DTT.
Final sequencing library was prepared according to the following customised NEB Ultra II FS protocol. 80 ng of amplified cDNA was fragmented in Ultra II fragmentation mix (26 μL of amplified cDNA, 7 μL of NEBNext Ultra II FS Reaction Buffer, 2 μL of NEBNext Ultra II FS Enzyme Mix) on the following thermocycling program: 37 °C for 10 min., 65 °C for 30 min. and a final hold at 4 °C. 15 μL of EB was added and a 0.8X Ampure purification was performed according to manufacturer’s recommendation and eluted in 35 μL. Fragmented library was adapter-ligated in NEBNext Ultra II adapter ligation mix (35 μL of fragmented library, 30 μL of NEBNext Ultra II Ligation Master Mix, 1 μL of NEBNext Ligation Enhancer, 2.5 μL of NEBNext Adapter for Illumina) at 20 °C for 15 min., with 4 °C final hold. 28.5 μL of EB was added and a 0.8X Ampure purification was performed according to manufacturer’s recommendation and eluted in 30 μL. Eluted library was amplified in PCR master mix (50 μL 2x KAPA HiFi, 10 μL 10 uM Hy-i7 primer, 10 μL 10 uM Hy-i5 primer, 30 μL eluted library) in the following thermocycling program: 95 °C for 3 min., 13 cycles of [98 °C for 20 s, 64 °C for 30 s, 72 °C for 30 s], 72 °C for 5 min. and a final hold at 4 °C. Sequencing-ready library was purified using a 0.8X Ampure purification and eluted in 30 μL of EB.

tag: strain

tag: tissue/cell line

value: Cerebral cortex


title: HYA__combined__20210323_cortex_phu_dv_etssb_1-2_S2

description:
processed data file: HYA__combined__20210323_cortex_phu_dv_etssb.cluster_bigwigs.tar.gz
processed data file: HYA__combined__20210323_cortex_phu_dv_etssb.cluster_dars.tar.gz

extract_protocol:
Cortex was separated from female P56 BL/6 mouse brains, immediately snap-frozen in liquid nitrogen and preserved in -80 °C. A ~1 cm3 frozen piece of mouse cortex tissue was transferred to 1 mL of ice-cold homogenisation buffer (320 mM Sucrose, 10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgAcetate, 1 mM DTT, 0.1 mM EDTA, 0.1% IGEPAL, 1X cOmplete Protease Inhibitor Cocktail) in a Dounce homogenizer mortar and thawed for 3 minutes. The tissue was homogenised with 10 strokes of pestle A and 5 strokes of pestle B until a homogeneous cell suspension was achieved. The resulting homogenate was filtered through a 40 μm Flowmi strainer. The mortar was washed with 1.65 mL of ice-cold homogenisation buffer to collect any remaining cells. 2.65 mL of ice-cold gradient medium was added to 1.65 mL of homogenate. 4 mL of 29% iodoxanol cushion (129.2 mM Sucrose, 77.5 mM KCl, 15.5 mM MgCl, 31 mM Tris-HCl pH 7.5, 29% Iodoxanol) was loaded into an ultracentrifuge. 5.3 mL of sample was gently layered on top of the 29% iodoxanol cushion without mixing both phases. Sample was centrifuged at 10 000 xg, 4°C for 30 minutes and the supernatant was gently removed without disturbing the nuclei pellet. Nuclei were resuspended in 100 μL of Nuclei buffer. 50 000 nuclei were resuspended in 50 μL of ATAC Reaction Mix (10% DMF, 10% Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/uL Tn5, 70 uM Pitstop, 0.1% Tween-20, 0.01% Digitonin) and incubated at 37 °C for 1 hour without shaking. 100 μL of 0.1% BSA in PBS was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes and resuspended in 40 μL of 0.1% BSA in PBS. Tagmented nuclei were added to 100 μL of PCR mix (1.3X Phusion HF Buffer, 15% Optiprep, 1.3 mM dNTPs, 39 mM DTT, 0.065 U/uL Phusion HF Polymerase, 0.065 U/uL Deep Vent Polymerase, 0.013 U/uL ET SSB). PCR mix was co-encapsulated with 35 μL of freshly thawed HyDrop-ATAC beads in RAN oil on the Onyx microfluidics platform. The resulting emulsion was collected in aliquots of 50 μL total volume and thermocycled according to the PCR1 program (72 °C 15 min., 98 °C 3 min., 13 PCR cycles of [98 °C 10 s, 63 °C 30 s, 72 °C 1 min.], followed by a final hold on 4 °C). 125 μL of recovery agent (20% PFO in HFE), 55 μL of GITC Buffer (5 M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4) and 5 μL of 1 M DTT was added to each separate aliquot of 50 μL thermocycled emulsion and incubated on ice for 5 minutes. 5 μL of Dynabeads was added to the aqueous phase and incubated for 10 minutes. Dynabeads were pelleted on a Nd magnet and washed twice with 80% EtOH. Elution was performed in 50 μL of EB-DTT-Tween (10 mM DTT, 0.1% Tween-20 in EB). A 1X Ampure bead purification was performed according to manufacturer’s recommendations. Elution was performed in 30 μL of EB-DTT (10 mM DTT in EB).
Eluted library was further amplified in 100 μL of PCR2 mix (1X KAPA HiFi, 1 uM index i7 primer, 1 uM index i5 primer). Final library was purified in a 0.4X-1.2X double-sided Ampure purification and eluted in 25 μL of EB-DTT (10 mM DTT in EB).


title: HYA__combined__20210323_cortex_phu_dv_etssb_1-3_S3


title: HYA__combined__20210323_cortex_phu_dv_etssb_1-4_S4


title: HYA__combined__20210323_cortex_phu_dv_etssb_1-1_S1


title: HYR__666332__20210412_mouse_cortex_a_S1


title: An.stephensi infected with CSPmut rep2

city: ChongQing

first: Jian

last: Zhang

address: Gaotanyan Main Street

institute: Army Medical University (Third Military Medical University)

data_processing:
Paired-end sequencing of the library was performed on the HiSeq XTen sequencers (Illumina, San Diego, CA).
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data.
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters.
DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples.
Genome_build: The reference genome downloaded from VectorBase（Anopheles_stephensi__AsteI2 genome）
Supplementary_files_format_and_content: Processed data with gene expression level was provided in file "gene_expression.addAnno.xls".

organism: Anopheles stephensi

source_name: whole mosquito

growth_protocol: Anopheles stephensi(A.stephensi) was maintained at 27°C in 70-80% relative humidity and fed a 10% sugar solution(with 0.5% PABA).

extract_protocol:
Total RNA was extracted using the Trizol Reagent (Invitrogen, Carlsbad, USA) from a pool of 15 mosquitoes infected with CSPwt or CSPmut parasites.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For the infection of CSPwt or CSPmut, 3- to 5-day-old female adults were fed on BALB/c mice with over 0.1%gametocytemia, and kept at 23-24°C.

value: whole mosquito

tag: treatment

value: infected with CSPmut plasmodium

tag: days after infection


title: ChIP-Seq of Corylus heterophylla: Input of early ovule growth

source_name: Input of Ov2.1

value: ovule

value: early ovule growth

tag: cultivar

value: wild germiplasm


title: An.stephensi infected with CSPmut rep1


title: An.stephensi infected with CSPwt rep1

value: infected with CSPwt plasmodium


title: ATAC-Hmel_ros_HW-2

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

country: USA

institute: Cornell University

data_processing:
Alignment to Hmel2 genome using Bowtie2
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
The genome assemblies used for alignment can be found here on LepBase:
Hmel2: http://download.lepbase.org/v4/sequence/Heliconius_melpomene_melpomene_Hmel2_-_scaffolds.fa.gz
Genome_build: Hmel2
Supplementary_files_format_and_content: bigWig

organism: Heliconius melpomene rosina

source_name: Whole wing tissue

extract_protocol:
Nuclei from whole wing tissue were treated with hyperactive Tn5 as described in the ATAC-seq protocol
Libraries were prepared as described in the ATAC-seq protocol

value: Day 3 Post-Pupation


title: ATAC-Hmel_ros_FW-2


title: ChIP-Seq of Corylus heterophylla: ChIP of early ovule growth

source_name: ChIP of Ov2.1

value: polyclonal antibody against ChARF3


title: ATAC-Hmel_ros_FW-1


title: An.stephensi infected with CSPwt rep2


title: KC-A242-11

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The raw sequencing data was trimmed using skewer package.
The reads were mapped to the transcriptome using STAR
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene expression matrix

source_name: mPanIN

extract_protocol:
No RNA extraction protocol is applicable. We dissected individual lesion from a 12 um frozen section and directly lysed it in the lysis buffer and applied single cell transcriptome amplification assay (MATQ-seq).
cDNA libraries were prepared for sequencing using standard Illumina Truseq protocols

value: pancreatic intraepithelial neoplasia

tag: genotype


title: pool5_eyfp

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description: Contains libraries Liver_IL12_Trx_I_rep1, Liver_IL12_Trx_I_rep2, Liver_IL12_Trx_J_rep1, Liver_IL12_Trx_J_rep2, Liver_IL12_Trx_K, Tumor_IL12_Trx_I_rep1, Tumor_IL12_Trx_I_rep2, Tumor_IL12_Trx_J_rep1, Tumor_IL12_Trx_J_rep2, Tumor_IL12_Trx_K

data_processing:
Sequencing and basecalling was carried out on NextSeq_2_1_0.
Fastq files were generated from Illumina base calls through bcl2fastq with the following flags/parameters: —adapter-stringency 0.9 --barcode-mismatches 0 --fastq-compression-level 4 --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --min-log-level INFO --minimum-trimmed-read-length 0 --processing-threads 8 --no-lane-splitting --mask-short-adapter-reads 0 --use-bases-mask y*,y*,y*,y*()
To accurately quantify Il12b (p40) transcript counts, we therefore added the IRES-EYFP-bGH-Poly(A)-loxP as an artificial chromosome to the ensemble reference genome and IRES-EYFP-bGH-Poly(A)-loxP transcript and exon annotations to the ensemble gtf reference genome annotation file.
Processing of fastq files leading to pre-filtered count matrices (including alignment, genome mapping) was performed through STAR-solo
Single cell data filtering and normalization: We applied count filters on total and mitochondrial counts in order to retain high quality transcriptomes. We manually determined library-specific thresholds on total counts (ranging from 120 to 400 counts) and fraction of counts coming from mitochondrial genes (ranging from 12% to 15%) based on the empirical distributions of these magnitudes in each library. Subsequently, expression matrices were normalized to 10,000 counts per cell.
Dimensionality reduction and visualization of single cell data: To attain a low dimensional embedding of the transcriptomes, we first determined a set of highly variable genes based on the corrected Fano Factor (V-statistic) as defined in Klein et al. (2015) (Klein et al., 2015). We then performed PCA on the expression matrix resulting from retaining only highly-variable genes (160 components), computed a kNN graph (k=10), and obtained a UMAP 2D embedding of the pooled libraries.
Cell multiplet removal: We employed Scrublet (Wolock et al., 2019) to remove transcriptomes derived from two or more cells entering the same microfluidic droplet. We considered the cells with the top 1.9% doublet scores assigned by Scrublet as putative multiplets and verified that they co-localized in the UMAP embedding. This threshold was suggested by the software based on the distribution of doublet scores.
Genome_build: Mus_musculus.GRCm38.99
Genome_build: + IRESeYFP (IRESeYFP.fa) appended as additional chromosome (./extra)
Supplementary_files_format_and_content: Raw counts (tsv.gz): library identity, barcode, and raw counts for all cells included in each pool
Supplementary_files_format_and_content: Library barcodes: library identity, barcode for all cells across all pools
Supplementary_files_format_and_content: pool1_raw_counts.tsv.gz: Liver_CD45pos_NT_A, Liver_CD45pos_NT_B, Liver_CD45pos_Trx_A, Liver_CD45pos_Trx_B
Supplementary_files_format_and_content: pool2_raw_counts.tsv.gz: Liver_CD45pos_NT_C, Liver_CD45pos_NT_D, Liver_CD45pos_Trx_C, Liver_CD45pos_Trx_D
Supplementary_files_format_and_content: pool3_raw_counts.tsv.gz: Liver_CD45pos_NT_E, Liver_CD45pos_NT_G, Liver_CD45pos_Trx_E, Liver_CD45pos_Trx_G
Supplementary_files_format_and_content: pool4_raw_counts.tsv.gz: Liver_CD45pos_NT_F, Liver_CD45pos_NT_H, Liver_CD45pos_Trx_F, Liver_CD45pos_Trx_H
Supplementary_files_format_and_content: pool5_raw_counts.tsv.gz: Liver_IL12_Trx_I_rep1, Liver_IL12_Trx_I_rep2, Liver_IL12_Trx_J_rep1, Liver_IL12_Trx_J_rep2, Liver_IL12_Trx_K, Tumor_IL12_Trx_I_rep1, Tumor_IL12_Trx_I_rep2, Tumor_IL12_Trx_J_rep1, Tumor_IL12_Trx_J_rep2, Tumor_IL12_Trx_K

source_name: Liver, MC38 murine colon carcinoma

growth_protocol: IL-12p40-IRES-EYFP (Jackson Labs Cat #006412) mice were injected in the flank with MC38 tumor cells, which were allowed to grow for 7 days.

extract_protocol:
Two days after the anti-CD40 treatment time point, mice were sacrificed and livers and tumors were isolated for generating single cell suspensions. Tissues were enzymatically digested, passed through a cell strainer, and cells were stained for CD45 and labeled with 7AAD; CD45+ cells or IL-12-EYFP+ cells were sorted using a BD FACSAria sorter. InDrops single cell RNA sequencing was performed.
A microfluidic device was used to co-encapsulate individual cells and polyacrylamide beads carrying barcoding reverse transcription (RT) primers and lysis reagents into 2-3 nl droplets, followed by primer release and RT at 50°C. After the RT reaction, droplets were broken, and the resulting barcoded cDNA was taken through the following sequencing library preparation steps 1) second strand synthesis, 2) in vitro transcription providing linear amplification of the material, 3) fragmentation of the amplified RNA, 4) a second reverse transcription using random hexamer primers bearing a universal PCR primer annealing site, and 5) indexing PCR, yielding a sequencing-ready library.

treatment_protocol: Tumor-bearing mice were injected intraperitoneally with 5 mg / kg agonist anti-CD40 monoclonal antibody, or left untreated

tag: tag

value: EYFP+

value: IL-12p40-IRES-EYFP transgene


title: pool3_cd45

description: Contains libraries Liver_CD45pos_NT_E, Liver_CD45pos_NT_G, Liver_CD45pos_Trx_E, Liver_CD45pos_Trx_G

source_name: Liver

value: Untreated, aCD40


title: KC-A242-8

tag: tissue


title: pool4_cd45

description: Contains libraries Liver_CD45pos_NT_F, Liver_CD45pos_NT_H, Liver_CD45pos_Trx_F, Liver_CD45pos_Trx_H


title: KC-A242-9


title: pool2_cd45

description: Contains libraries Liver_CD45pos_NT_C, Liver_CD45pos_NT_D, Liver_CD45pos_Trx_C, Liver_CD45pos_Trx_D


title: KC-A242-5


title: KC-A242-7


title: HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5


title: pool1_cd45

description: Contains libraries Liver_CD45pos_NT_A, Liver_CD45pos_NT_B, Liver_CD45pos_Trx_A, Liver_CD45pos_Trx_B


title: KC-A242-4


title: KC-A242-3


title: KC-663-8


title: KC-A242-2


title: KC-663-7


title: KC-A242-6


title: KC-A242-1


title: KC-663-6


title: KC-663-5


title: ATAC-Hmel_ros_HW-1


title: KC-663-4


title: KC-663-9


title: KC-663-1


title: KC-663-3


title: KC-A242-10


title: AKC-mt2-9


title: AKC-mt2-10


title: AKC-mt2-7


title: AKC-mt2-8


title: AKC-mt2-6


title: AKC-mt2-5


title: AKC-mt2-1


title: AKC-mt2-2


title: AKC-363-11


title: AKC-363-14


title: AKC-363-13


title: AKC-mt2-4


title: AKC-mt2-3


title: BPs lysogen Mycobacterium chelonae rep 2

city: Orono

first: Sally

middle: Dixon

last: Molloy

state: Maine

address: 5735 Hitchner Hall, University of Maine

institute: The University of Maine

data_processing:
Base  calls were performed on an Illumina HiSeq 2500 using the Real Time Analysis Software.   Reads were checked for consistency  across Lanes and concatenated
Reads were processed using TrimGalore to remove reads with a quality score <30.  the first 9 bases on the 5' end and the last base on the 3' end were removed.
Though rRNA was depleted from the samples sequenced, we removed remaining rRNA reads by aligning the reads to the rRNA region of the M. chelonae genome, using Bowtie2 and retaining only the reads that did not align to rRNA region.
Reads were quantitated using Salmon, the non-rRNA fastq files, and a fasta file of coding sequences for M. chelonae downloaded from GenBank.  The following parameters were specified: mate pairs oriented toward each other, read 1 represented the reverse strand, bias was corrected for GC content.  The remaining parameters used the default for the program.
The output file is a tsv format, Only the column used raw read counts was used.
Data was processed using the R script DESeq2, to obtain read depth, log2FC, and false discovery rate.
Genome_build: NZ_CP007220.1  Annotation Date  :: 04/05/2017
Supplementary_files_format_and_content: TSV files with Salmon output for expression levels

organism: Mycobacteroides chelonae

source_name: mid-log phase cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to an OD(600) of 1.0

extract_protocol:
total RNA was extracted using the Rneasy Mini Kit, rRNA was depleted using Ribo-Zero (Illumina)
Libraries were constructed using the TruSeqClusterKitv3

treatment_protocol: M. chelonae cells either carried the BPs prophage (BPs lysogen) or did not (M. chelonae WT)

value: Host strain:Mycobacterium chelonae ATCC 35752; phage:Mycobacterium phage BPs

tag: growth phase

value: mid-log


title: AKC-363-5


title: KC-663-2


title: BPs lysogen Mycobacterium chelonae rep 1


title: AKC-363-7


title: AKC-363-4


title: AKC-363-6


title: BPs lysogen Mycobacterium chelonae rep 3


title: AKC-363-8


title: Mycobacterium chelonae WT rep 2

value: Mycobacterium chelonae ATCC 35752


title: Mycobacterium chelonae WT rep 3


title: AKC-363-3


title: E13epi

city: Bethesda

first: Shaohe

last: Wang

state: Maryland

address: 9000 Rockville Pike, Bldg 30, Rm 403

department: DIR

institute: NIDCR, NIH

data_processing:
Base-calling was performed using Illumina's RTA v2.1 on the NextSeq 500 sequencer.
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings.
The filtered features, barcodes and matrix output files were used for further analysis using the Python libraries Scanpy (v1.6.0) (Wolf et al., 2018) and scVelo (v0.2.2) (Bergen et al., 2020).
Genome_build: GRCm38.v11b-2.1.0
Supplementary_files_format_and_content: The processed files are the filtered feature-barcode matrix output from the cellranger pipeline. Filtered here means that it contains only detected cellular barcodes, instead of every barcode from fixed list of known-good barcode sequences. Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. It also contains gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively.

source_name: Salivary gland epithelium

extract_protocol:
Mouse submandibular salivary glands were isolated from 13-day mouse embryos as previously described (Sequeira et al., 2013). Briefly, a scalpel (Fine Science Tools, 10011-00 and 10003-12) was used to decapitate the mouse embryo. While the detached head was held on its side with one prong of forceps (Fine Science Tools, 11251-20) pierced through the top, a scalpel was used to slice across the mouth opening to isolate the mandible and tongue, between which the submandibular glands were sandwiched. Under a dissecting microscope, the detached mandible tissue was placed on a glass plate with the tongue facing down. A pair of forceps was used to slice through the midline of the mandible tissue to expose the tongue and the two submandibular glands attached to the base of the tongue. After surrounding tissues were removed, glands were detached using forceps and collected into a 35-mm dish with 3 mL DMEM/F-12 (Thermo Fisher, 11039047) media until all embryos were dissected. To isolate the epithelial rudiments, 4 to 6 glands (see Salivary gland isolation and culture) were treated with 150 µL 2 units/mL dispase (Thermo Fisher, 17105041; diluted in DMEM/F-12) in a well of a Pyrex spot plate (Fisher Scientific 13-748B) for 15 min at 37°C. The glands were washed twice with 5% BSA (MilliporeSigma, A8577; diluted in DMEM/F-12) in the same well to quench the dispase activity. The mesenchyme of each gland was removed using a pair of forceps (Fine Science Tools, 11254-20) and a tungsten needle (Fine Science Tools, 10130-05 and 26016-12) under a dissecting microscope. The forceps were mostly used to hold the gland still, whereas the needle was gently inserted between the mesenchyme and epithelium to separate them. Isolated epithelial rudiments were transferred to a new well of the spot plate with 150 µL DMEM/F-12 media using low-retention pipette tips (cut for larger opening; Rainin, 30389190) for temporary storage until all glands were processed. A total of 8 isolated epithelial rudiments were collected and rinsed in 1 mL HBSS (Thermo Fisher, 14170161) in a 2 mL protein LoBind tube (Eppendorf, 022431102). After the rudiments were pelleted by centrifugation at 100× g for 30 seconds, liquid was removed as much as possible using a 1 mL pipette followed by a 200 µL pipette under a dissecting microscope to avoid accidentally discarding the samples. 100 µL Accutase (Innovative Cell Technologies, AT104) was added to the tube, which was immediately incubated for 2 minutes in a 37°C water bath to disrupt cell-cell adhesion. While being monitored under a dissecting microscope, the epithelial rudiments were triturated using a 200 µL pipet set at 50 µL using a low-retention tip (Rainin, 30389187) for 2 min, when most cells were clearly dissociated. 900 µL 10% fetal bovine serum (FBS; GE Healthcare/Cytiva, SH30070.03) diluted in PBS was added to quench the Accutase. The 1 mL cell suspension was passed through a 40 µm Flowmi (VWR, H13680-0040) cell strainer into a polyethylene terephthalate (PET) 15 mL tube (Corning, 430053). It is critical to use PET tubes instead of polypropylene tubes for efficient cell recovery. Cells were pelleted by centrifugation at 100× g for 2 minutes in a swinging-bucket rotor. After the supernatant was carefully removed, cells were resuspended in 1% FBS in PBS and pelleted again. About 50 µL liquid was retained to resuspend the cells. 15 µL was taken to determine the cell density and viability using an automated cell counter (Nexcelom Cellometer Auto 2000) with the AO/PI (acridine orange / propidium iodide) staining solution (Nexcelom, CS2-0106). The live cell density was 797,000 per mL with a viability at 92.0%. The remaining cell suspension was used for single cell capture on a 10X Genomics Chromium platform.
Single cell capture and library construction were performed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit (v2 Chemistry) following the manufacturer’s instructions. The libraries were sequenced on an Illumina NextSeq500 sequencer.

value: ICR (CD-1)

value: wild type

tag: age

value: embryonic day 13

value: Submandibular salivary gland

tag: cell type

value: Epithelial cells


title: HepG2-control-rep14

city: Uppsala

first: Claes

last: Wadelius

state: Uppsala

address: Husargatan 3 PO BOX 815, BMC B11:4

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala universitet

description:
R233
YY1_KD_feature_counts.txt

data_processing:
Reads were quality trimmed using Trim Galore (0.6.4)
Reads were aligned to human hg19 genome with HISAT2 version 2.1.0
The aligned PE reads were mapped to gene with featureCounts version 1.6.4
Gene differential expression was carried out with the R package DESeq2 v.1.26.0
The GO and KEGG pathways analysis were done by the R package clusterProfiler version 3.14.3.
Genome_build: hg19
Supplementary_files_format_and_content: raw read conunts that mapped to gene

source_name: HepG2 cells

growth_protocol: HepG2 cells were maintained in RPMI1640 basal medium supplemented with 10% fetal bovine serum and 2 mM L-glutamine.

extract_protocol:
Total RNA was isolated from TRIzol reagent with the PureLink RNA Mini Kit (12183018A, Thermo Fisher Scientific) following the manufacturer’s instructions. The optional on-column PureLink DNase (12185010, Thermo Fisher Scientific) treatment was carried out to get rid of trace amount of genomic DNA during RNA extraction.
The library was constructed with QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina (016, Lexogen) following protocol from the manufacture.

treatment_protocol: To knock down the expression of YY1, HepG2 cells were transduced with lentivirus expressing both shRNA and artificial miRNA targeting YY1. The HepG2 cells transduced with the control virus were used as the controls.

value: Human  hepatocyte carcinoma

value: HepG2 cells

value: control


title: Mycobacterium chelonae WT rep 1


title: AKC-363-10


title: HepG2-control-rep12

description:
R231
YY1_KD_feature_counts.txt


title: HepG2-control-rep11

description:
R230
YY1_KD_feature_counts.txt


title: MEF_siSET8_H4K20me1_Async_ChIP-seq

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
ChIP-seq reads were aligned to the mm10 or hg19 genome assemblies using bowtie version 1.1.2 (PMID: 19261174) and the settings -m 1 -S
Mapped reads were sorted using samtools version 1.10 (PMID: 19505943).
Sorted mapped reads were imported into EaSeq version 1.111 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: mm10; hg19
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Both U2OS and MEF cell lines were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% Penicillin–Streptomycin. MEF cells were in addition supplemented with non-essential amino acids.

extract_protocol:
Cells were formaldehyde fixed and lysed in ice-Cold IP buffer and sonicated to an average length of 300 to 1000 bp fragments using Bioruptor bath-based sonicator. After checking for fragment size 500 µg of chromatin lysate was pre-cleared with 40 µl of Protein-A sepharose beads (BSA blocked) for 1 h and incubated overnight at 4ºC on rotation with 5 µg of primary ChIP-grade antibody. Blocked Protein-A sepharose beads were then added next day to the chromatin and  incubated at 4ºC on rotation for 3-4 h. Samples were subsequently washed and DNA was decrosslinked overnight and purified using Qiagen PCR purification columns.
Chipped DNA was quantified using Qubit dsDNA HS kit. Libraries were prepared from 5 ng of Chipped DNA using NEBNext Ultra II library preparation kit according to manusfacturer's protocol.

treatment_protocol: U2OS and MEF cells were treated with either scramble siRNA sequence or siRNA against SET8 according to mansufacturer's protocol.

value: Mouse Embryonic Fibroblasts

tag: sirna

value: H4K20me1:abcam, ab9051

tag: cell cycle stage

value: Asynchronous


title: MEF_siSET8_Input_Async_ChIP-seq

value: No antibody


title: AKC-363-9

value: pancreatic intraepithelial neoplasia


title: MEF_siCtrl_Input_Async_ChIP-seq

value: siCtrl


title: HepG2-control-rep10

description:
R226
YY1_KD_feature_counts.txt


title: MEF_siCtrl_H4K20me1_Async_ChIP-seq


title: HepG2-control-rep9

description:
R225
YY1_KD_feature_counts.txt


title: AKC-363-2


title: HepG2-YY-KD-rep7

description:
R222
YY1_KD_feature_counts.txt


title: HepG2-YY-KD-rep8

description:
R223
YY1_KD_feature_counts.txt


title: AKC-363-1


title: HepG2-YY-KD-rep6

description:
R221
YY1_KD_feature_counts.txt


title: MEF_siSET8_Async_repl1_ATAC-seq

data_processing:
Paired-end reads were trimmed for Nextera transposase adapter sequences using Trimmomatic (v0.32) (PMID: 24695404) in palindrome mode with default settings except ILLUMINACLIP:2:30:10:1:true MINLEN:25.
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) before and after trimming to confirm the removal of any 3’ adapter sequences and the insertion Tn5 motif in the 5’-ends.
Trimmed PE reads were mapped to the mm10 or hg19 assembly (canonical chromosomes only) using bowtie2 v.2.2.9 (PMID: 22388286) with default settings except -k 2 -X 2000 --no-mixed --no-discordant.
Sorting (SortSam) and labeling duplicates (MarkDuplicates) with Picard tools (v. 2.6.0-27-g915ffa7-SNAPSHOT) (https://broadinstitute.github.io/picard/)
Addition of a NH tag (number of reported alignments)
Filtering to exclude unmapped, multimapping, and mitochondrial reads (samtools view -f 2 -F 4 and custom filter) (PMID: 19505943).
Filtered bam files were converted to bed format using bedtools bamtobed (v2.26.0-92-g88cd6c5) (PMID: 20110278).
Sorted mapped reads were imported into EaSeq version 1.111 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: mm10; hg19
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

extract_protocol:
Nuclei were prepared from 50,000 cells and subjected to tagmentation reaction. DNA was extracted and PCR amplified using Nextera Index primers (FC-121-1011) for paired-end sequencing.    DNA was size selected and using Ampure XP magnetic beads. Libraries were quantified using KAPA SYBR FAST qPCR Master mix (KK4932) to determine the optimal number of PCR cycles. After running the remaining number of PCR cycles, libraries were purified with Ampure XP beads (with size slection). Libraries were quantified using the Qubit DNA HS Kit, and for quality control, 1 μl of each sample was run on Bioanalyzer High Sensitivity DNA Chip.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (FC-121-1030, FC-121-1011). In all, 2 nM of all libraries were pooled and 1.5 pM were analyzed on Illumina NextSeq500 (500/550 High Output v2 Kit—150 cycles).

value: Async

tag: replicate


title: MEF_siSET8_Async_repl4_ATAC-seq


title: MEF_siSET8_Async_repl3_ATAC-seq


title: MEF_siSET8_Async_repl2_ATAC-seq


title: MEF_siCtrl_Async_repl3_ATAC-seq


title: HepG2-YY-KD-rep4

description:
R219
YY1_KD_feature_counts.txt


title: HepG2-control-rep13

description:
R232
YY1_KD_feature_counts.txt


title: MEF_siCtrl_Async_repl4_ATAC-seq


title: HepG2-YY-KD-rep3

description:
R218
YY1_KD_feature_counts.txt


title: MEF_siCtrl_Async_repl2_ATAC-seq


title: MEF_siCtrl_Async_repl1_ATAC-seq


title: HepG2-control-rep5

description:
R209
YY1_KD_feature_counts.txt


title: HepG2-YY-KD-rep2

description:
YY1_KD_feature_counts.txt
R217


title: HepG2-YY-KD-rep1

description:
R216
YY1_KD_feature_counts.txt


title: HepG2-control-rep7

description:
R211
YY1_KD_feature_counts.txt


title: RNAseq_Control_replicate_2

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

data_processing:
Raw reads were aligned to the NCBIm37 mouse reference genome (mm9) using HiSat2 (version 2.0.0) using options -N 1 -L 20 -i S, 1, 0.5 -D 25 -R 5 --pen-noncansplice 20 --mp 1, 0 --sp 3, 0 and providing a list of known splice sites. Expression levels were quantified using featureCounts with RefSeq gene annotation and normalized as TPM using custom scripts.
Genome_build: UCSC mm9/NCBIm37
Supplementary_files_format_and_content: Tab-delimited text files of raw gene counts for each sample.

source_name: newborn skin

extract_protocol:
Suction-blistered and control samples were collected at P2 and treated with 0.25% trypsin EDTA overnight at 4°C. The epidermis was minced with a scalpel and suspended in 10% FCS DMEM. The cell suspension was filtered through a 70 µm filter, and cell pellets were collected.
Library preparation was performed using an Illumina TruSeq RNA prep kit by following the manufacturer’s instructions. Briefly, following TRIzol extraction and chemical fragmentation, mRNA was purified with oligo-dT-attached magnetic beads and reverse transcribed into cDNA. Following a second strand synthesis step with DNA polymerase I and RNAse H, the resulting cDNA was subjected to end repair, A-tailing, and Illumina compatible adaptor ligation. Following purification and PCR-mediated enrichment, libraries were purified with AMPure XP beads.

treatment_protocol: Suction blisters were produced on the neonatal murine dorsal skin using a syringe and connector tubes. The negative pressure applied to the skin was 523.4±1.3 mmHg. The diameter of the syringe attached to the skin was 4 mm. The size of the typical blister was 3 mm in diameter.

value: epidermal cells

value: control skin


title: RNAseq_Control_replicate_1


title: RNAseq_Control_replicate_3


title: HepG2-control-rep8

description:
R224
YY1_KD_feature_counts.txt


title: HepG2-control-rep4

description:
R204
YY1_KD_feature_counts.txt


title: RNAseq_Blister_replicate_2

value: blister healing


title: HepG2-YY-KD-rep5

description:
R220
YY1_KD_feature_counts.txt


title: HepG2-control-rep2

description:
R202
YY1_KD_feature_counts.txt


title: HepG2-control-rep3

description:
R203
YY1_KD_feature_counts.txt


title: HepG2-control-rep6

description:
YY1_KD_feature_counts.txt
R210


title: RNAseq_Blister_replicate_1


title: HiC-Del8 2

city: Rotterdam

first: Niels

last: Galjart

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Centre

data_processing:
Hi-C read-pairs were mapped to the reference genome (mm10) using TADbit. Low quality bins (those presenting low contacts numbers) were removed as implemented in TADbit's 'filter_columns' routine. A single round of ICE normalization ('vanilla' normalization) was performed and contact matrices were corrected to achieve an average content of one interaction per cell.
Genome_build: mm10
Supplementary_files_format_and_content: 50kb contact matrices with raw contacts

source_name: ES cells

extract_protocol:
Cells were collected by centrifugation. Crosslinked nuclei were digested with MboI followed by fill-in with bio-dATP, in-situ ligation and DNA extraction.
DNA was sonicated and libraries were constructed using the the NEBNext DNA Library Prep Kit (New England Biolabs).

tag: gentoype


title: HiC-Del8 3


title: HepG2-control-rep1

description:
R201
YY1_KD_feature_counts.txt


title: HiC-Del8 1


title: HiC-WT 1

value: wild type


title: HiC-WT 3


title: SEM-TetOn-Tight-HDAC7_3

city: Badalona

first: Maribel

last: Parra

state: Barcelona

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

department: Lymphocyte Development and Disease

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Resulting bam files were analyzed with Bioconductor package metaseqR and subjected to differential expression analysis
Sequenced reads were mapped to hg19 whole genome using, for RNA-Seq reads, tophat2 with default settings. The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against hg19 with the --local and --very-sensitive options.
Reads overlapping the hg19 human exons were counted and filtered for several artifacts. The final gene counts were calculated as the sums of their exonic reads. The counts table was normalized using DESeq normalization and analyzed for differential expression using DESeq and the Bioconductor package metaseqR. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05 and an absolute log2 fold change greater than 1.5.
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: Genes with DESeq p-value less than 0.05 and fold change (for each contrast) greater than 0.58 or less than -0.58 in log2 scale, corresponding to 1.5 times up and down, respectively, on a natural scale, were considered differentially expressed.

source_name: SEM-K2 established cell line

growth_protocol: Cells were grown in RPMI complete medium (+10% FBS, +1% Penicllin Streptomycin)

extract_protocol:
Total RNA was extracted and purified with RN-easy mini column kit, following manufacturer's instructions
Paired-end mode with 75bp read length. 20 milion paired-end reads were generated per each sample

treatment_protocol: Where indicated, cells were treated with 1ug/ml of doxycycline for 48h before RNA extraction

tag: cell line

value: pro-B lymphocytes

tag: mll rearrangement

value: untreated


title: SEM-TetOn-Tight-HDAC7 +Doxy_1

value: doxycycline 1ug/ml 48h


title: RNAseq_Blister_replicate_3


title: SEM-TetOn-Tight-HDAC7 +Doxy_2


title: HiC-WT 2

tag: strain


title: SEM-TetOn-Tight-HDAC7_1


title: SEM-TetOn-Tight-control +Doxy_3


title: SEM-TetOn-Tight-HDAC7_2


title: KO rep3 mLN [RNA-seq]

city: Vienna

first: Katharina

middle: A

last: Mayer

address: Lazarettgasse 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Fastq generation, bcl2fastq v2.19.1.403
Alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir GRCm38_RSEM_index --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
Count normalization and transformation, DESeq2 v1.22.2
Genome_build: GRCm38
Supplementary_files_format_and_content: *.counts.tsv: Plain tab-delimited text, raw counts per gene, one file per sample.

source_name: CD4+ T cell

extract_protocol: RNA libraries were prepared for sequencing using the NEBNext SingleCell/Low Input Library Prep Kit and standard Illumina protocols.

treatment_protocol: WT and KO T cells were transferred in to Rag KO recipients to induce T cell transfer colitis; donor T cells were isolated from spleen and mLN after 6 weeks.

value: KO (CD4-Cre PRKAA1fl/fl)

value: CD4+ T cell mLN


title: KO rep2 mLN [RNA-seq]


title: SEM-TetOn-Tight-control +Doxy_2


title: SEM-TetOn-Tight-control +Doxy_1


title: KO rep1 mLN [RNA-seq]


title: WT rep4 mLN [RNA-seq]

value: WT (PRKAA1fl/fl)


title: SEM-TetOn-Tight-control_3


title: WT rep1 mLN [RNA-seq]


title: WT rep2 mLN [RNA-seq]


title: SEM-TetOn-Tight-control_2


title: KO rep4 spleen [RNA-seq]

value: CD4+ T cell spleen


title: SEM-TetOn-Tight-control_1


title: KO rep3 spleen [RNA-seq]


title: SEM-TetOn-Tight-HDAC7 +Doxy_3


title: KO rep2 spleen [RNA-seq]


title: KO rep4 mLN [RNA-seq]


title: OSUCLL CC122 1 24h rep 3

city: Columbus

last: Blachly

state: OH

address: B305 Starling-Loving Hall

institute: The Ohio State University

data_processing:
Reads were quantified without mapping using Salmon
Gene level counts were made by summing transcript level estimated counts
Between group differentially expressed genes were determined using DESeq2
Genome_build: Gencode 23
Supplementary_files_format_and_content: Count matrix

source_name: OSU-CLL cell line

growth_protocol: OSU-CLL cells are grown in suspension in RPMI 1640 with 10% FBS and antibiotics

extract_protocol:
Trizol
Illumina TruSeq stranded mRNA

treatment_protocol: Treatment with the indicated drug for 5 or 24 hours

tag: timepoint (h)

tag: dose (micromolar)


title: WT rep4 spleen [RNA-seq]


title: OSUCLL CC122 1 5h rep 3

tag: treatment


title: WT rep3 spleen [RNA-seq]


title: WT rep2 spleen [RNA-seq]


title: KO rep1 spleen [RNA-seq]


title: OSUCLL LEN 1 5h rep 3

value: LEN


title: OSUCLL CC122 0.1 24h rep 3


title: WT rep1 spleen [RNA-seq]


title: OSUCLL CC122 0.1 5h rep 3


title: OSUCLL DMSO 0 24h rep 3

value: DMSO


title: OSUCLL LEN 1 24h rep 2


title: OSUCLL DMSO 0 5h rep 3


title: microglial cells from lateral corpus callosum

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

data_processing:
NextSeq data were analysed using the 10x Genomics suite Cell Ranger 2.0.1 and specifically the function mkfastq.
Mapping with STAR against mus musculus reference genome, detecting the number of cells and genes per cell and finally quantifying gene expression
Genome_build: mm10
Supplementary_files_format_and_content: 3 tab-delimited file containing genes Ensembl Mus musculus Gene ID /Name association (genes.tsv), cell/barcode association (barcodes.tsv), gene/cell/expression association (matrix.mtx)

source_name: CX3CR1 mice fed with cuprizone for 4 weeks to induce demyelination

growth_protocol: cells were FACS sorted from tissue and directly processed for single cell library without culture and growth step

extract_protocol:
Single cells were processed using the Single cell 3’ Library, Gel beads & multiplex kit (10X Genomics, Pleasanton) as per the manufacter’s protocol.
Cells, were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with the Chromium Single Cell Controller (10X  genomics, Pleasanton),  where  all  generated  cDNA  share  a  common  10x  Barcode.  Libraries were generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions.

treatment_protocol: Tissues were dissociated using Gentle MACS according to manufacter's instructions

tag: agent

value: cuprizone


title: subventricular zone-derived cells mobilized to demyelinated corpus callosum

source_name: NestinCreERT2:RosaYFP mice fed with cuprizone for 4 weeks to induce demyelination

tag: genotype


title: OSUCLL CC122 1 24h rep 2


title: microglial cells from medial corpus callosum


title: OSUCLL CC122 0.1 24h rep 2


title: OSUCLL LEN 1 24h rep 3


title: SRFKO-2

city: Rochester

first: Eric

last: Small

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

data_processing:
Basecalls by bcl2fastq version 1.8.4
Quality filtering and adapter removal were performed using Trimmomatic version 0.32 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15".
Processed/cleaned reads were then mapped to the GRCm38 reference genome using the SHRiMP version 2.2.3 and the following parameters: " --qv-offset 33 --all-contigs".
Uniquely aligned and multi-mapped reads were counted within the gencode GRCm38 gene annotations, in a strand specific manner, using the cuffdiff tool from the cufflinks-2.0.2 package and the following parameters: “--FDR 0.05 -u -b GENOME”
Differential expression analyses and data normalization were performed using DESeq2-1.14.1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimitted gene counts

source_name: Epicardium-derived cells

growth_protocol: Hearts were removed from mouse embryos at  embryonic age 12.5. Ex vivo hearts were cultured for 48 hours in a mixture of M199/DMEM High Glucose media containing 1% FBS and 1% Pen-Strep. Hearts were maintained at conditions of 5% CO2 and 37℃.

extract_protocol:
Ex vivo heart explants were removed from culture media and whole heart tissue was digested with collagenase type IV and trypsin at 37℃ for 20 minutes. A single cell suspension was subjected to fluorescence-activated cell sorting to collect GFP-positive epicardium-derived cells directly into TRIzol to isolate RNA.
The Clontech Ultralow RNA Kit in conjunction with NexteraXT DNA Library Prep Kit was used for next generation sequencing library construction per manufacturer’s protocols.

treatment_protocol: All ex vivo SRF-flox/flox  hearts were treated with adenoviruses to express GFP.  Explants were also transduced with adenovirus expressing Cre-recombinase or  beta-galactosidase, as indicated. Adenoviral infection was at 10 E^6 pfu/ml. Adenoviruses are validated to infect the epicardaial cell layer of the heart. All cardiac explants  were  also treated with TGFb2 [2ng/mL] and PDGF-BB [20ng/mL] to induce epithelial-to-mesenchymal transition.

tag: background strain

value: Srf-flox/flox

tag: developmental stage

value: embryonic day 12.5

value: heart

value: epicardium-derived cells

value: adenovirus expressing Cre and GFP, each at 10 E^6 pfu/ml (48 hours) ; recombinant TGFb2 [2ng/mL] and PDGF-BB [20ng/mL] (48 hours)


title: OSUCLL LEN 1 5h rep 2


title: WT1noGFP-4

source_name: Non-epicardium-derived cells

tag: tissue

value: Non-epicardium-derived cells

value: adenovirus expressing b-galactosidase and GFP, each at 10 E^6 pfu/ml (48 hours) ; recombinant TGFb2 [2ng/mL]and PDGF-BB [20ng/mL] (24 hours)


title: OSUCLL DMSO 0 24h rep 2


title: OSUCLL CC122 1 5h rep 2


title: SRFKO-1


title: WT1noGFP-3


title: WT1noGFP-1


title: d8-3B OTHER: Med-Seq

description: LpnPI-digested genomic DNA

data_processing:
Library strategy: Med-Seq
RNA-Seq : Reads were aligned to the mouse genome (mm10 build) using HISAT2. Sample scaling and statistical analysis were performed using the R package DESeq2.
MedSeq : Raw fastq files were subjected to Illumina adaptor trimming and reads were filtered based on LpnPI restriction site occurrence between 13‐17 bp from either 5’ or 3’ end of the read. Reads that passed the filter were mapped to mm10 using bowtie2.1.0. BAM files were generated using SAMtools for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated from bam files using deepTools (bamCoverage). Bam files were generated from fastq files using different packages.

extract_protocol:
RNA-Seq : RNA was harvested from ES cells using Trizol reagent.
MedSeq : Genomic DNA was digested with LpnPI.
RNA-Seq samples were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting DNA libraries were sequenced according to the Illumina TruSeq Rapid  v2 protocol on an Illumina HiSeq2500 sequencer, generating single-end reads of 50bp.
MedSeq : LpnPI-digested genomic DNA was processed using the ThruPlex DNA–seq 96D kit (Rubicon Genomics cat#R400407). Stem‐loop adapters were blunt end ligated to repaired input DNA and amplified (4 +10 cycles) to include dual indexed barcodes to yield an indexed Illumina NGS library. Multiplexed samples were sequenced on Illumina HiSeq2500 systems for single read of 50 base pairs.

tag: enzyme

value: LpnPI


title: OSUCLL DMSO 0 5h rep 2


title: OSUCLL CC122 0.1 5h rep 2


title: d8-3A OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: d8-2B OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: OSUCLL LEN 1 24h rep 1


title: d8-2A OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: OSUCLL CC122 1 24h rep 1


title: OSUCLL CC122 0.1 24h rep 1


title: d8-1B OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: OSUCLL LEN 1 5h rep 1


title: d8-1A OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: GC2A OTHER: Med-Seq

description: LpnPI-digested genomic DNA

value: GFP-CTCF


title: OSUCLL DMSO 0 24h rep 1


title: OSUCLL CC122 0.1 5h rep 1


title: OSUCLL CC122 1 5h rep 1


title: GC2B OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: GC1A OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: mature 40S rep_1 NC

city: Jupiter

first: Haina

last: Huang

state: Florida

address: 130 scripps way c296

department: The integrative structural and computational biology

institute: The Scripps Research Institute

description: ribosomal RNA

data_processing:
removing adaptors with skewer
trimming reads with seqtk
running shapemapper aligning to 20S rRNA
… S.c.20S_rRNA_profile.txt were extracted for further analysis.
Supplementary_files_format_and_content: Extract "Modified_effective_depth" and "modified_rate" of each nucleotide for further analysis.

organism: Saccharomyces cerevisiae

source_name: ribosome mature 40S

growth_protocol: Cells were grown in YPD till mid-log phase before harvesting.

extract_protocol:
Phenol chloroform  precipitation
RNA-seq (DMS-MaPseq)

treatment_protocol: 1% DMS, 30°C, 5min

tag: dms treatment

value: untreated


title: mature 40S rep_3 NC

description: ribosomal RNA


title: mature 40S rep_2 DMS

description: ribosomal RNA

value: treated


title: Rio2_Δloop pre-40S rep_3 DMS

description: ribosomal RNA

source_name: ribosome pre-40S intermediate


title: mature 40S rep_3 DMS

description: ribosomal RNA


title: Rio2_Δloop pre-40S rep_4 DMS

description: ribosomal RNA


title: mature 40S rep_2 NC

description: ribosomal RNA


title: Rio2_Δloop pre-40S rep_4 NC

description: ribosomal RNA


title: mature 40S rep_1 DMS

description: ribosomal RNA


title: Rio2_Δloop pre-40S rep_3 NC

description: ribosomal RNA


title: Rio2_Δloop pre-40S rep_2 NC

description: ribosomal RNA


title: Rio2_Δloop pre-40S rep_2 DMS

description: ribosomal RNA


title: Rio2_Δloop pre-40S rep_1 DMS

description: ribosomal RNA


title: GC1B OTHER: Med-Seq

description: LpnPI-digested genomic DNA


title: Rio2_Δloop pre-40S rep_1 NC

description: ribosomal RNA


title: OSUCLL DMSO 0 5h rep 1


title: S15_YRR pre-40S rep_3 DMS

description: ribosomal RNA


title: E10.5_OV_IgG_ChIP_seq

city: New York

first: Jun

last: Li

address: 1425 Madsion Ave, 14th Fl, RM 14-02

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0). Only uniquely-mapped reads were retained and duplicates were removed.
Peak-calling was performed using MACS (v2.1.1) with qvalue (minimum FDR) cutoff of 0.05.
Motif enrichment analysis was performed using the Homer package (v4.8.3). The peak annotation and gene ontology analysis was performed using the GREAT program and Panther classification system.
Genome_build: mm10

source_name: E10.5 embryo otic region

extract_protocol:
The tissues were fixed with 1%FA in PBS for 60 min at RT. After washing, the tissues were homogenized to a fine powder using BeadBugTM high-energy benchtop homogenizer in the lysis buffer. Chromatin shearing was performed using the Bioruptor sonicator. After preclearing with Protein A beads, the chromatin was immunoprecipitated with antibodies. After IP, the beads were washed in sequential low salt buffer, high salt buffer, LiCl washing buffer and TE buffer.
The libraries were prepared using the ThruPlex DNA-seq Kit (Rubicon Genomics) and according to the manufacturer's instructions.

tag: antibody

value: IgG


title: E10.5_OV_Genomic input_ChIP_seq

value: input


title: E10.5_OV_Six1_ChIP_seq


title: E10.5_OV_H3K27me3_ChIP_seq


title: E10.5_OV_H3K27ac_ChIP_seq


title: S15_YRR pre-40S rep_1 DMS

description: ribosomal RNA


title: E10.5_OV_Brg1_ChIP_seq Eya1mt

value: Eya1 mutant


title: WT pre-40S rep_5 DMS

description: ribosomal RNA


title: S15_YRR pre-40S rep_1 NC

description: ribosomal RNA


title: E10.5_OV_Brg1_ChIP_seq WT replicate 2

value: WT


title: WT pre-40S rep_3 DMS

description: ribosomal RNA


title: Sample 3_Somatostatin-expressing cells: Delta cells (3)

city: Geneva

first: Marta

last: Perez Frances

state: Geneva

address: 1, rue Michel-Servet

country: Switzerland

institute: University of Geneva

data_processing:
cDNA libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina) and sequenced on an Illumina HiSeq 2500 (for δ-cells) and HiSeq4000 platform (for γ-cells) with single-end 100-bp reads (for δ-cells) or pair-end 100bp reads (for γ-cells).
All sequencing data were uploaded to, and aligned on the Galaxy project against Ensembl reference genome GRCm38.p6 (release 100) using STAR version 2.7.2b in 2-pass mapping mode. Aligned data were counted using HTSeq version 0.9.1 in union mode.
Analyses were performed in a pair-wise manner between YFP-positive samples and alpha cell samples, YFP-positive samples and beta cell samples and YFP-positive samples and delta cell samples using DESeq2 version 1.28.1. For each pairwise comparison, genes were discarded if they had fewer than 5 counts per sample on average.
After calculating differential expression between groups, log2 fold changes were shrunken using the normal estimator. Genes were considered to be differentially expressed if the absolute shrunken log2 fold changes were equal to or above 1, and adjusted p-values were equal to or below 0.05.
Genome_build: Ensembl reference genome GRCm38.p6 (release 100) using STAR version 2.7.2b in 2-pass mapping mode
Supplementary_files_format_and_content: Tab-separated values files (.tsv) containing gene and sample names

extract_protocol:
Islet cells were obtained from two-month-old doxycycline-treated Ppy-rtTA;TetO-Cre;R26-YFP and Sst-Cre;R26-YFP mice FAC-sorted in a Moflo Astrios (Beckman Coutler) or BD FACS Aria II system. Total mRNA was extracted from sorted YFP+ from both mice models using the Qiagen RNeasy Micro Kit.
Libraries preparation, RNA-sequencing and quality controls were performed in the Genomics Core Facility of the University of Geneva. Reverse transcription and cDNA amplification were performed using the SMARTer Ultra Low RNA kit (Clontech). cDNA libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina) and sequenced on an Illumina HiSeq 2500 (for δ-cells) and HiSeq4000 platform (for γ-cells) with single-end 100-bp reads (for δ-cells) or pair-end 100bp reads (for γ-cells).

treatment_protocol: Doxycycline (1 mg/ml) was administered in the drinking water one moths prior to the sample extract in order to YFP-label Ppy-expressing ells

tag: strain background

value: Mixed

tag: age

value: two-month-old

value: Endocrine pancreas - Islet of Langerhans

tag: cell type

value: Pancreatic islet cells

tag: genotype/variation


title: WT pre-40S rep_4 DMS

description: ribosomal RNA


title: WT pre-40S rep_4 NC

description: ribosomal RNA


title: WT pre-40S rep_5 NC

description: ribosomal RNA


title: WT pre-40S rep_3 NC

description: ribosomal RNA


title: WT pre-40S rep_2 DMS

description: ribosomal RNA


title: E10.5_OV_Brg1_ChIP_seq WT replicate 3


title: E10.5_OV_Brg1_ChIP_seq WT replicate 1


title: Sample 1_Somatostatin-expressing cells: Delta cells (1)


title: AKC-363-12

data_processing:
The raw sequencing data was trimmed using skewer package.
The reads were mapped to the transcriptome using STAR
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene expression matrix

source_name: mPanIN

extract_protocol:
No RNA extraction protocol is applicable. We dissected individual lesion from a 12 um frozen section and directly lysed it in the lysis buffer and applied single cell transcriptome amplification assay (MATQ-seq).
cDNA libraries were prepared for sequencing using standard Illumina Truseq protocols

value: pancreatic intraepithelial neoplasia


title: S15_YRR pre-40S rep_2 DMS

description: ribosomal RNA


title: Sample 2_Somatostatin-expressing cells: Delta cells (2)


title: WT pre-40S rep_2 NC

description: ribosomal RNA