title: CK5_input

city: Beijign

first: Danping

last: Fan

address: Yinghua Donglu

institute: Institute of Clinical Medical Science, China-Japan Friendship Hospital

data_processing:
Library strategy: MeRIP-seq
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: homo sapiens Ensembl release-101
Supplementary_files_format_and_content: .xlsx files include gene expression and methylation level

source_name: peripheral blood mononuclear cells of control

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Total RNA  was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA).The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to create the final cDNA library in accordance with the protocol for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, cat.e7530L, USA).

value: peripheral blood mononuclear cells

tag: antibody

tag: disease state

value: non


title: KO3_polyribosome-bound-mRNA

status: Public on Mar 23 2022

type: SRA

city: Guangzhou

first: Jie

last: Chen

address: No. 58, Zhongshan 2nd Road, Yuexiu District, Guangzhou

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

description:
polyA RNA
Polyribosome-bound-RNA-seq

library_source: transcriptomic

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
scRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline. Gene expression matrix was created by using Seurat (V3.1.5) pipeline.
Genome_build: hg38, GRCH38，mm10
Supplementary_files_format_and_content: matrix table with raw gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: HNSCC

growth_protocol: SCC15 cells were cultured in DMEM/F12 (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) . Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).  HNSCC samples were harvested from the tongue of mice and single cell suspensions were prepared for 10× genomics processing.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set. scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s protocol.

treatment_protocol: SCC15 cells were  transfected with sgRNAs for knockout of METTL1. SCC15 cells with normal expression of METTL1 were used as control. Mettl1-/- and wild type mice were induced with 4NQO to establish murine HNSCC model.

tag: cell type

value: HNSCC cells

tag: treatment

value: The polyribosome-bound-mRNAs were isolated from total RNA by ultra-centrifugation

tag: genotype


title: CK4_IP

data_processing:
Library strategy: MeRIP-seq
Library strategy: MeRIP-seq
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: homo sapiens Ensembl release-101
Supplementary_files_format_and_content: .xlsx files include gene expression and methylation level

molecule: total RNA

value: m6A antibody IP


title: Control differentation repl. 1

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC.
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome.
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=no”. The gene annotation used for quantification was Ensembl version 104.
Assembly: GRCh38
Supplementary files format and content: raw read count in TSV format

source_name: Skeletal muscle cell line

growth_protocol: Immortalized human skeletal muscle cells (7304.1) were cultured in growth medium (F10 (Gibco) medium supplemented with 15% FCS, 1 ng/ml bFGF, 10 ng/ml EGF and 0.4 ug/ml Dexamethasone). Differentiation was induced using differentiation medium (DMEM (Gibco), without any supplements) for 24h

extract_protocol:
RNA was extracted using Qiazol, precipitated using chloroform followed by RNA isolation using the PureLink™ RNA Mini Kit (Invitrogen) according to the manual.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions

treatment_protocol: Cell cultures, at roughly 50% confluence, were transfected with 10 nM siRNA using Lipofectamine RNAiMAX transfection reagent and grown for 48h in transfection medium (80% proliferation medium and 20% OptiMEM). Subsequently, medium was replaced with either normal proliferation or differentiation medium.

value: 7304.1 Skeletal muscle cell line

value: Untreated


title: KO2_polyribosome-bound-mRNA

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: Rat5_Naive

city: Stony Brook

first: Martin

last: Kaczocha

state: NY

address: Health Sciences Center, L4-077

country: USA

institute: Stony Brook University

data_processing:
Pair-end reads were aligned to the rat genome using HISAT2
transcript counts were quantified with FeatureCounts, and differentially expressed genes (DEGs) were identified with DESeq2 package (Usegalaxy.org)
Gene expression fold-change ≥ 1.5 and false discovery rate (FDR) < 0.05 were set as the threshold values for subsequent analysis
Gene set enrichment analysis with ClusterProfiler was performed in R (https://learn.gencore.bio.nyu.edu)
Genome_build: rat genome (RGSC 6.0/rn6)

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (#12183018A, Invitrogen/Thermo Fisher Scientific) following the manufacturer’s instructions, and treated on column to degrade contaminating DNA with PureLink DNase (#12185-010, Invitrogen/Thermo Fisher Scientific).  Purified total RNA was eluted from the column with RNase-free water.
mRNA-Seq was performed by Novogene (Davis Lab, Sacramento CA), sequencing libraries were generated and subsequently tested for their quality (Library QC) with Qubit, real-time PCR for quantification and BioAnalyzer for size distribution detection.  The Illumina NovaSeq platforms were used for a paired-end 150 bp sequencing strategy to sequence the cDNA libraries.

treatment_protocol: Naïve (no procedures), sham (anesthesia, skin incision, sutures), and TKA (anesthesia and complete TKA surgery)

tag: strain

value: Sprague Dawley

tag: Sex

value: Female

value: naïve

tag: tissue/cell type

value: DRGs collected from the left side at levels L3 and L4


title: Control proliferation repl. 2


title: RRBS_Btau_fibro_5aza0

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

library_source: genomic

data_processing:
Reads were trimmed with Trim Galore v0.4.4 to remove adapter sequences and low-quality ends with a Phred score below 20. Trim Galore was run in –non_directional and –rrbs mode to remove two additional bases artificially introduced at the MspI restriction sites.
Reads were aligned to the corresponding genome with Bismark v0.18.2 with default parameters.
A maximum of two mismatches and an insertion size for paired-end sequences of between 30 and 400 bp were allowed.
Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 10X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 10X sequencing depth.

molecule: genomic DNA

organism: Bos taurus

source_name: Primary dermal fibroblasts

growth_protocol: Primary dermal fibroblasts were grown in DMEM-GlutaMax supplemented with 10% fetal bovine serum and 50U/mL penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were digested 5 hours by MspI (Thermo Scientific), end-repaired and A-tailed with Klenow fragment exo- (Thermo Scientific), and ligated to methylated adapters with T4 DNA ligase (Thermo Scientific) in Tango 1X buffer. Size selection was performed by gel excision from a 3% agarose 0.5X TBE gel to select fragments ranging from 150 to 400 bp. DNA was purified using the MinElute gel extraction kit (Qiagen) and bisulfite-converted twice with the EpiTect bisulfite kit (Qiagen), following the manufacturer’s instructions. Final libraries were amplified using the Pfu Turbo Cx hotstart DNA polymerase (Agilent) with 12 to 14 PCR cycles. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).

treatment_protocol: Fibroblasts were treated with 1 µM final concentration of 5-AzadC (Sigma A3656) for 72 hours and the medium was renewed every day.

tag: genome build

value: Control (not treated)

tag: tissue

value: Primary dermal fibroblasts


title: CK4_input


title: Control differentation repl. 3


title: Control proliferation repl. 3


title: GM12878-Fixed-20k-Nextera_TD-55C-Homemade_Tn5-Rep3

city: Tucson

first: Hao

last: Zhang

state: AZ

address: 1230 N Cherry Ave

department: CMM

institute: The University of Arizona

data_processing:
The paired-end reads were preprocessed using Trimmomatic v0.36 to trim the Nextera adaptors and low quality reads with the parameter setting as “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20”.
The trimmed reads were mapped to either the hg19 human genome or mm10 mouse genome reference contigent upon the sample source using Bowtie2 v2,2.9 with the parameter setting as “-X 2000 -3 1” to restrict the maximum fragment length of 2000 bp and trim 1 base from the 3’ end of each read before alignment. Following mapping, only the reads confidently (MAPQ ≥ 10) mapped to assembled nuclear chromosomes, and in proper pairs (we used the “-f3” and “-F12” options in SAMtools v1.4) were preserved for downstream analysis.
Picard v2.20.2 “MarkDuplicates” was used to remove duplicate reads and estimate library complexity.
Peaks were called by MACS2 v2.1.2 using deduplicated bed files and considering a 200 bp window centered on the read start using the parameters “--nomodel --keep-dup all --extsize 200 --shift -100”. Because each peak may have multiple summits (and will therefore be listed multiple times in the resulting peak bed file), the peaks output from MACS2 were then merged into a single peak set for each sample using bedtools “merge”.
Genome_build: Data from GM12878 were mapped to hg19 and data from mouse lungs were mapped to mm10
Supplementary_files_format_and_content: Matrix of the number of reads overlapping each peak for each GM12878 sample was generated by "multiBamSummary" (deepTools v3.5.1) using deduplicated bam files and a non-overlapping peak set that combined the peaks identified from each condition. The first column contains the coordinates for each peak.
Supplementary_files_format_and_content: Matrix with deviation scores for each motif and each GM12878 sample was computed by chromVAR v1.12.0. The first column shows the human motif ID from JASPAR CORE database.

growth_protocol: The GM12878 cell line was cultured at 37°C with 5% CO2 in RPMI 1640 medium (GIBCO, cat. no. 11875-093) containing 15% FBS (GIBCO, cat. no. 10437-028), 100 U/ml Penicillin Streptomycin (GIBCO, cat. no. 15140-122). Cells were counted and split to 300,000 cells/ml three times a week

extract_protocol:
1) Nuclei isolation from native GM12878:  ~2 million native cells were collected and washed using 4 ml 1X PBS (pH 7.4, Gibco, cat. no. 10-010-023) supplemented with 0.04% BSA (PBSB), and then resuspended in 200 μl of ATAC-seq lysis buffer. Lysis buffer was made by supplementing ATAC resuspension buffer (RSB) with detergents. RSB buffer is 10 mM Tris-HCl (pH 7.5, Invitrogen, cat. no. 15567027), 10 mM NaCl (Invitrogen, cat. no. AM9759) and 3 mM MgCl2 (Invitrogen, cat. no. AM9530G) in nuclease free water. RSB was made in bulk and stored at 4°C long-term. On the day of the experiment, the ATAC lysis buffer was made by adding 0.1% IGEPAL (Sigma, cat. no. I3021), 0.01% digitonin (Invitrogen, cat. no. BN2006), and 0.1% Tween-20 (Bio-Rad, cat. no. 1610781) to RSB. Detergent percentages reported are final concentrations. After resuspending cell pellets in the lysis buffer, they were incubated on ice for 3 min, and then the lysis was stopped by adding 1 ml RSB containing 0.1% Tween-20. Nuclei were then centrifuged at 500 r.c.f for 10 min at 4 °C and resuspended in 200 ul of PBSB. The nuclei were counted and diluted to 3,100 nuclei/μl with PBSB. Then, 6.6 μl of diluted nuclei (20,460 total nuclei) were transferred to 12.4 μl of transposition reaction (10 μl of 2X Tagmentation buffer, 0.2 μl of 1% digitonin, 0.2 μl of 10% Tween-20, and 2 μl of H2O). We then added 1 μl of transposase to the transposition mix containing nuclei. Tagmentation was carried out on a thermocycler at either 37°C or 55°C for 30 min. Tagmented DNA was cleaned up using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer (Zymo, cat. no. D4004). 2) Nuclei isolation from fixed GM12878: the frozen, fixed cells (~ 2 million) were incubated in a 37°C water bath until thawed (~ 1 min). After thawing, the cells stored in 1 ml freezing buffer were diluted with 3 ml of PBSB. The fixed cells were collected by centrifuging at 500 r.c.f for 10 min at 4°C, resuspended again in 1 ml PBSB, and then centrifuged at 500 r.c.f for 5 min at 4°C to wash the cells. Following washing, the nuclei were isolated and tagmented as described in the ATAC-seq protocol for native samples described above. After tagmentation, crosslinks were then reversed for the fixed, tagmented nuclei by adding 60 μl of reverse-crosslinking buffer containing 0.067% SDS and 1.33 mg/ml Proteinase K (Qiagen, cat. no. 19133) in Qiagen Buffer EB (final concentration of 0.05% SDS and 1 mg/ml Proteinase K) directly to the tagmentation reactions, and incubating the samples at 65°C for 15 hours in a thermomixer with shaking at 1,000 r.p.m. Following crosslink reversal, tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer. 3) The isolation of mouse lung nuclei was performed following the single-nucleus isolation protocol described by Joshi Nikita and Misharin Alexander. In brief, we cut a ~0.1-0.2 g piece from the lung sample removed from -80°C and kept it on dry ice until use. The tissue block was thawed almost completely on ice for 1 min, and then injected with 1 ml of cell lysis buffer, which was made of 1x cOmplete protease inhibitor cocktail (1 tablet per 10 ml solution, Sigma-Aldrich, Cat. 11836153001) in Nuclei EZ prep buffer (Sigma-Aldrich, Cat. NUC101), into the center of the tissue with a 30G needle and syringe. Following lysis buffer injection, the tissue was chopped into small pieces with scissors and then transferred along with the lysing buffer into a gentleMACS C tube (Miltenyi Biotec, Cat. 130-096-334). An additional 1 ml of lysing buffer was added into the C tube to make a final volume of 2 ml. The minced tissue was then homogenized using a gentleMACS tissue dissociator by running the ‘m_lung_01’ program followed by the first 20 sec of the ‘m_lung_02’ program. After homogenization, tissue lysate was briefly centrifuged to reduce foam and then passed through a 40 μm cell strainer in a 50ml tube. After passing the sample through, the strainer was rinsed with 4 ml of washing buffer (PBS with 1% BSA). The nuclei were counted with Trypan blue in the presence of 2X Omni buffer (20 mM Tris HCl (pH 7.5), 10 mM MgCl2 and 20% Dimethyl Formamide), and then collected by centrifugation at 500 r.c.f for 5 min at 4°C. Then, we removed the supernatant and resuspended the nuclei to a concentration of 4-5 million nuclei/ml in a nuclei freezing buffer containing 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat .no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), and 2% protease inhibitor (Sigma, cat. no. P8340). 1 ml aliquots of the nuclei were flash frozen in liquid nitrogen and then transferred to a liquid nitrogen dewar for long-term storage.
5 μl of purified DNA out of 10 μl purified product was amplified in a 25 μl PCR reaction containing NEBNext PCR master mix (1X final), 0.5X SYBR Green and 1.25 μM of Ad1 primer from Buenrostro JD. et al., 2013 and 1.25 μM of an N7 primer containing custom barcodes. Samples were amplified on a Bio-Rad CFX Connect Real-time cycler using the following program: 72°C for 5 min; 98°C for 30s; cycling at 98°C for 10 s, 63°C for 30 s, 72°C for 1 min; samples were monitored and stopped when it appeared that their exponential amplification was leveling off. At this point the samples were allowed to incubate at 72°C for an additional minute to fully extend the library. All native samples were stopped after 9 cycles and fixed samples were stopped after 10 cycles. PCR products were cleaned up with Ampure XP beads. A double size selection was performed to remove DNA fragments larger than ~1500 bp (with 0.4X AMPure XP beads) and smaller than ~100 bp (with 1.5X AMPure XP beads). To do this, we added 25 μl of Qiagen Buffer EB to each PCR reaction to bring the volume to 50 μl, and then added 20 μl of beads (homogenizing the mixture well by pipetting), followed by a 5 min incubation at RT. The samples were then put on a magnet stand to bind the beads. 68 μl of the supernatant was transferred to a new 1.5 ml tube and an additional 53 μl of beads were added to the supernatant and resuspended thoroughly (we estimated that 19.4 μl of the 68 μl transferred was bead buffer and 48.6 μl was sample, so to get to 1.5X beads for the second selection we needed to add an additional 72.9 - 19.4 μl of beads, which we rounded off to 53 μl). After another 5 min at RT, the samples were placed on the magnet to clear the beads and the supernatant was discarded. Beads were washed twice with 200 μl of 80% EtOH (made fresh for each experiment). After the second wash, the beads were briefly spun, and any residual ethanol was removed. The beads were then put back on the magnet stand and air dried for 1 min. Then, beads were removed from the magnet and resuspended in 22 μl of Buffer EB, incubated for 2 min at RT and then placed on the magnet stand again. 20 μl of supernatant was transferred to a new tube. The 96 ATAC-seq libraries of the GM12878 cell line and 72 libraries of mouse lungs were pooled separately and sequenced with 2x76 bp reads in two independent runs on an NextSeq 550 Platform using the High Output Kits.

treatment_protocol: For fixation, cells were washed and resuspended in 9.2 ml of RPMI medium without additives, then crosslinked with 270 μl of 37% formaldehyde (1% final, VWR, cat. no. MK501602) for 10 min at room temperature. The fixation reaction was quenched by adding 500 μl of 2.5 M glycine (0.125 M final, Sigma, 50046-50G) and incubated for 5 min at room temperature, and then on ice for 15 min. The fixed cells were collected and resuspend in the freezing buffer, which contains 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat. no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), 2% protease inhibitor (Sigma, cat. no. P8340). Then, 2 million cells per aliquot were flash frozen in liquid nitrogen for long-term storage.

tag: cell line

value: lymphoblastoid

tag: nuclei state

value: Fixed

tag: nuclei input


title: KO1_polyribosome-bound-mRNA

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: RNA-seq_Btau_fibro_5aza1_1

data_processing:
Reads were aligned to the corresponding genome with HISAT2 v2.0.5 using default parameters and Ensembl transcriptome index.
For data visualization, BigWig files of normalized read counts per base were generated with bamToBed from bedtools and bedGraphToBigWig from UCSC using only reads that map uniquely in the genome.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide bigWig files for visualization of RNA-seq tracks.

extract_protocol:
RNA samples were prepared using the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-seq libraries were prepared from 150 to 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina), according to the manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The depleted RNA was fragmented using divalent cations at 94°C and cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were blunted, adenylated and ligated to adapters using T4 DNA Ligase. The cDNA libraries were generated with 12 cycles of PCR amplification, purified using AMPure XP beads (Beckman-Coulter) and checked for quality and quantified using capillary electrophoresis

value: Treated 5-AzadC 1 microM


title: RNA-seq_Btau_fibro_5aza0_1


title: CK5_IP


title: GM12878-Fixed-20k-THS_TD-55C-Homemade_Tn5-Rep3


title: Control proliferation repl. 1


title: CK3_IP


title: Rat3_Naive

value: Male


title: GM12878-Fixed-20k-Omni_TD-55C-Homemade_Tn5-Rep3


title: GM12878-Fixed-20k-Nextera_TD-37C-Nextera_Tn5-Rep4


title: GM12878-Fixed-20k-THS_TD-55C-Nextera_Tn5-Rep3


title: WGBS_Btau_fibro

data_processing:
Low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 and adapter sequences were trimmed with Trim Galore v0.4.4 (parameters -q 20 --clip_R1 5 --clip_R2 10 --stringency 2).
Reads were mapped to the corresponding genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50
Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark v0.22.1 with the parameters --minimum_count 5 and --percentage_cutoff 50
Methylation calls were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 5X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. Bisulfite conversion was performed with the EZ DNA Methylation-Gold kit (Zymo), and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA library Kit (Swift Biosciences) following the manufacturer’s instructions. 4 to 6 cycles were used for the final PCR amplification of the WGBS libraries. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).

value: No treatment


title: SF8628 with shRNAs and 6Gy radiation 02

city: Aurora

first: Bridget

last: Sanford

state: CO

department: Pediatrics

institute: University of Colorado

data_processing:
For RNA-seq: 1. adaptor trimming with trimmomatic 2. alignment with gsnap 3. FPKM produced with cufflinks
For shRNA library screening: 1. count generation with MAGeCK 2. normalization to read depth with MAGeCK 3. statistical testing by student's ttest with p value and adjusted pvalue
Assembly: hg38

source_name: Brain Tumor Cells

growth_protocol: SF8628 cells were routinely generated by replating adherent cells typically 1.5-2x106 cells on a tissue culture dish in DMEM media supplemented with 10% FBS, 1% AB/AM and 1% NEAA.

extract_protocol:
1. RNA-seq samples: Total RNA was extracted by ethanol precipiation in ddH2O. 2. Genomic DNA samples: Genomic DNA was extracted with AL Buffer and Ethanol precipitation in AE Buffer.
1. RNA-seq samples: Total RNA was extracted using Qiagen miRNeasy Mini kit. 2. Genomic DNA samples: Genomic DNA was extracted with Qiagen DNeasy Blood and Tissue Mini Kit.
RNA-Seq: Libraries were prepared by using the TruSeq Library Preparation Kit v2 (Agilent). Directional mRNA sequencing was performed at the University of Colorado Anschutz Medical Campus Genomics and Microarray Core on a HiSeq 2500 sequencing system (Illumina) using single-pass 125 bp reads (1 × 125) and approximately 50 million reads per sample. DNA Repair shRNA screen: Sample library preparation was performed using primers from transomic (TRP60001) and KOD HOT Start DNA polymerase kit (Millipore 17086).

treatment_protocol: 1. RNA-seq samples: 2x106 SF8628 Cells were plated in a tissue culture dish on day 0 in triplicate for each group (6Gy Radiation and Unirradiated). On Day 1, cells were exposed to 6Gy radiation or no radiation. Cells were collected at 6hrs after radiation in Qiazol and the total RNA was extracted. 2. DNA Repair shRNA Screen samples: SF8628 Cells were plated on day 0 and was transduced with a human lentiviral pooled shRNA library on day 1. On day 3, cells were treated with puromycin for selection. Then, on day 5, cells were split into 4 plates. Two of the plates received 6Gy radiation and two plates did not receive any further treatments. Cells were passaged regularly to maintain an MOI of 0.3. 21 days after radiation, cells were collected and the genomic DNA was extracted from the 2 samples in duplicates.

value: Diffuse Midline Glioma

tag: gene characteristics

value: H3.3K27M, WEE1 Amplified, BRAF WT, TP53 Mutant

value: shRNA pool transduction followed by 6Gy Radiation


title: KO2_Input

description:
polyA RNA
Polyribosome-bound-RNA-seq

value: HNSCC cells


title: KO3_Input

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: SF8628 with shRNAs and no radiation 02

value: shRNA pool transduction followed by no treatment


title: SF8628 with shRNAs and no radiation 01


title: Rat1_Naive


title: CK3_input

value: peripheral blood mononuclear cells

value: non


title: CK2_IP

value: m6A antibody IP


title: KO1_Input

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: GM12878-Fixed-20k-Omni_TD-55C-Nextera_Tn5-Rep3


title: WT3_polyribosome-bound-mRNA

description:
polyA RNA
Polyribosome-bound-RNA-seq

value: The polyribosome-bound-mRNAs were isolated from total RNA by ultra-centrifugation

value: normal


title: CK2_input


title: WT2_polyribosome-bound-mRNA

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: RRBS_Hsap_sperm

data_processing:
Reads were trimmed with Trim Galore v0.4.4 to remove adapter sequences and low-quality ends with a Phred score below 20. Trim Galore was run in –non_directional and –rrbs mode to remove two additional bases artificially introduced at the MspI restriction sites.
Reads were aligned to the corresponding genome with Bismark v0.18.2 with default parameters.
A maximum of two mismatches and an insertion size for paired-end sequences of between 30 and 400 bp were allowed.
Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 10X.
Assembly: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
Supplementary files format and content: We provide IGV files containing methylation scores for all CGs with at least 10X sequencing depth.

source_name: Sperm

value: Sperm


title: SF8628 with shRNAs and 6Gy radiation 01


title: CK1_IP


title: GM12878-Fixed-20k-Nextera_TD-55C-Nextera_Tn5-Rep3


title: LX-2 cells, MPI MT 3

city: New York

first: Jaime

last: Chu

address: 1 Gustave L. Levy Place, Annenberg 14-12

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were trimmed using Trimmomatic v.0.36, and trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v2.5.2b.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2, and differential gene expression analysis was performed using DESeq2(3) by Genewiz.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential_expression_analysis_table.xlsx

source_name: LX-2 (human hepatic stellate cell line)

growth_protocol: LX-2 human HSCs  were maintained in Dulbecco’s modified Eagle’s medium with 10% FBS, L-glutamine, and penicillin/streptomycin) and routinely tested for mycoplasma using the Venor GeM Mycoplasma Detection Kit (Sigma-Aldrich).

extract_protocol:
Cells were collected in TRIzol Reagent (Life Technologies) and total RNA was purified following the supplied protocol.
mRNA was enriched by poly(A) selection, fragmented cDNA synthesized by random priming. 5’-phosphorylated and dA-tailed library was ligated to adapter.
Illumina HiSeq 2x150

value: hepatic stellate cells

value: MPI exon 3 mutant


title: CK1_input


title: GM12878-Fixed-20k-Nextera_TD-37C-Homemade_Tn5-Rep3

value: lymphoblastoid

value: Fixed


title: WT1_polyribosome-bound-mRNA

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: LX-2 cells, MPI MT 2


title: LX-2 cells, MPI MT 1


title: GM12878-Fixed-20k-THS_TD-37C-Homemade_Tn5-Rep3


title: RA5_IP

source_name: peripheral blood mononuclear cells of rheumatoid arthritis patient

value: rheumatoid arthritis


title: GM12878-Fixed-20k-THS_TD-37C-Nextera_Tn5-Rep3


title: WT3_Input

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: LX-2 cells, WT 3

value: WT


title: GM12878-Fixed-20k-Omni_TD-37C-Homemade_Tn5-Rep3


title: RA5_input


title: RA4_IP


title: WT2_Input

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: GM12878-Fixed-20k-Omni_TD-37C-Nextera_Tn5-Rep3


title: GM12878-Fixed-20k-Nextera_TD-37C-Nextera_Tn5-Rep3


title: LX-2 cells, WT 2


title: WT1_Input

description:
polyA RNA
Polyribosome-bound-RNA-seq


title: RA4_input


title: SSP-25 cells knocked down for JMJD6 rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: SSP-25 cells knocked down for JMJD6

data_processing:
Sequencing was performed on an Illumina HiSeq 3000 in 100-base single-end mode, respectively.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: SSP-25 cells knocked down for JMJD6

extract_protocol:
RNA was extracted using Maxwell(R) RSC simplyRNA tissue kit (Promega).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Transfection was performed using the protocol from the manufacturer (Origene) with control (scrambled) or specific siRNA. The efficacy of transfection was monitored in 48 hours by western blot and real-time PCR.

value: Cholangiocarcinoma cell lines SSP-25


title: GM12878-Fixed-20k-THS_TD-55C-Homemade_Tn5-Rep2


title: SSP-25 cells knocked down for JMJD6 rep2

description: SSP-25 cells knocked down for JMJD6


title: RA3_IP


title: 22_Naïve_PRC2i: GTTTCG

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: bulk RNAseq

data_processing:
Quality assessment of bulk RNA-sequencing data was performed using FastQC (v0.11.8). Samples were mapped to the human GRCh38.p12 reference genome with corresponding GENCODE v31/Ensembl 97  using STAR (v2.7.1a). Count table was generated using featureCounts (v2.0.1) with default parameters. Downstream analyses were performed with the R package DESeq2 (v1.26.0). Samples were filtered to keep genes that had more than 1 count in at least 2 conditions and counts were transformed to the log2 scale with rlog function, which minimizes differences between samples for rows with small counts, and which normalizes with respect to library size.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: normalized counts (.csv format)

source_name: Human embryonic pluripotent stem cells

growth_protocol: Human PSCs were grown in a 5% O2 and 5% CO2 incubator under humidified conditions at 37 °C. H9 primed PSCs were cultured in feeder-free conditions on plates pre-coated with 0.5 μg/cm2 Vitronectin (ThermoFisher Scientific) in complete TeSR-E8™ medium (Stem Cell Technologies). Cells were passaged using a 5 min incubation at room temperature with 0.5 mM EDTA in PBS. 2.5 μM UNC1999 (Sigma) was applied the day after passaging for 4 days, with media changed daily. H9 reset naïve PSCs were cultured in feeder-free conditions in PDGLX media, composed of a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N-2 supplement, 0.5x B-27 supplement, 2 mM L-Glutamine, 50 U/ml Penicillin-Streptomycin, 0.1 mM beta-mercaptoethanol (all from ThermoFisher Scientific) – supplemented with 1 μM PD0325901, 20 ng/ml human LIF (Wellcome-MRC Cambridge Stem Cell Institute), 2 μM Gö6983 (PKCi; Tocris) and 2 µM XAV939 (Sigma). A 1:300 dilution of Geltrex™ matrix (ThermoFisher Scientific) was added directly to media containing passaged cells to ensure adherence. Cells were passaged using a 5 min incubation at 37 °C with Accutase (BioLegend). 1 μM UNC1999 was applied the day after passaging for 4 days, with media changed daily.

extract_protocol:
RNA extraction 0.5 million cells per sample was performed with RNeasy Micro Kit (Qiagen, 74004) following the manufacturer’s protocol.
mRNA-seq libraries were prepared starting from 500 pg of input RNA, followed by library preparation with KAPA Stranded mRNA-Seq Kit (Illumina, 07962193001) with KAPA Single-Indexed Adapter Kit Set A and B (Illumina, KR1317) following manufacturer’s protocol. Libraries were pooled with a desired library concentration of 7 nM. The quality of input RNA, cDNA and individual libraries was assessed using an Agilent 2100 Bioanalyzer system at the KU Leuven Nucleomics core. Sequencing was performed at the KU Leuven Genomics Core on a HiSeq4000 (Illumina) sequencer in single-end mode (50 bp), yielding an average of 29 million reads per sample

treatment_protocol: For treated pirmed samples  2.5 μM UNC1999 (Sigma) was applied the day after passaging for 4 days, with media changed daily. For treated naïve samples 1 μM UNC1999 was applied the day after passaging for 4 days, with media changed daily.

value: H9 human embryonic stem cells

value: EZH2i (Abcam ab146152 UNC1999, EZH2 methyltransferase inhibitor)


title: GM12878-Fixed-20k-Omni_TD-55C-Homemade_Tn5-Rep2


title: 21_Naïve: GTGGCC

description: bulk RNAseq

value: untreated


title: 19_Naïve: GTGAAA

description: bulk RNAseq


title: GM12878-Fixed-20k-Nextera_TD-55C-Homemade_Tn5-Rep2


title: SSP-25 cells knocked down for control

description: SSP-25 cells knocked down for control

source_name: SSP-25 cells knocked down for control


title: SSP-25 cells knocked down for JMJD6 rep1

description: SSP-25 cells knocked down for JMJD6


title: GM12878-Fixed-20k-THS_TD-55C-Nextera_Tn5-Rep2


title: 18_Primed_PRC2i: GTCCGC

description: bulk RNAseq


title: RA2_IP


title: GM12878-Fixed-20k-Omni_TD-55C-Nextera_Tn5-Rep2


title: LX-2 cells, WT 1


title: 20_Naïve: GGCTAC

description: bulk RNAseq


title: GM12878-Fixed-20k-Nextera_TD-55C-Nextera_Tn5-Rep2


title: RA1_input


title: 13_Primed: CTTGTA

description: bulk RNAseq


title: GM12878-Fixed-20k-THS_TD-37C-Homemade_Tn5-Rep2


title: FRG2_BM_sample11_190802

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

description: Low index

data_processing:
NovaSeqTM 6000 (Illumina, San Diego, CA, USA) running in a 50-bp pair-end mode.
Reads were mapped on human genome using Tophat/Bowtie2
Annotation of the aligned reads was carried out using Htseq count
Differential analysis was performed using edgeR R package
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD34+ from bone marrow

extract_protocol:
Twenty ml PB were withdrawn by venipuncture and collected in EDTA-coated tubes for cell analysis using flow cytometry, isolation of CD34+HSPC for molecular studies, and collection of plasma for biochemistry. BM cells were isolated from the femoral head by flushing with PBS and filtering on 70-μm cell strainer. PB-mononuclear cells (MNCs) and BM-MNCs were isolated using Histopaque Ficoll by centrifugation at 1.200 rpm for 20 min at 25°C and were collected and washed with PBS. PB-MNCs and BM-MNCs were assessed for viability by Trypan Blue and an average of 50X107 cells were immunomagnetically sorted using Diamond CD34+ HSPC Isolation Kit Human. The purity of selected cells was assessed by flow cytometry.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Library Prep Gold)
Bead-based rRNA depletion, cDNA synthesis, and PCR

tag: tag

value: CD34+ from bone marrow


title: BD-MSC-3

type: RNA

city: Nantong

first: Jianmei

last: Gu

address: 30 Tongyang North Road

department: Clinical Laboratory Medicine

institute: Affiliated Cancer Hospital of Nantong University

description: gene expression in BD-MSCs

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was   fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x   Agilent fragmentation buffer and 2x Agilent blocking agent following the   manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of   2x Agilent hybridization buffer was added to the fragmentation mixture and   hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a   rotating Agilent hybridization oven. After hybridization, microarrays were washed 1   minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C   GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray   Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area   61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set   to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1   (Agilent) using default parameters to obtain background subtracted and spatially   detrended Processed Signal intensities as the raw data. Raw data were normalized   in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2   samples flagged as Detected were maintained.

source_name: patients3 with benign diseases

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: BM samples from newly diagnosed MM patients and BD patients were harvested from their iliac crest.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Under aseptic conditions, 3-4 ml of BM was collected and placed into EDTA anticoagulant tubes. Then, BM mononuclear cells were isolated using human BM mononuclear lymphocytes separating medium (Biological Products Technology; Tianjin Haoyang; China). Primary BMSCs were cultured and selected in plastic flasks and used at the third to fourth passage.

tag: gender

value: male

value: bone marrow

tag: age


title: GM12878-Fixed-20k-Omni_TD-37C-Homemade_Tn5-Rep2


title: BD-MSC-1

description: gene expression in BD-MSCs

source_name: patients1 with benign diseases

value: female


title: MM-MSC-3

description: gene expression in MM-MSCs

source_name: patients3 with MM


title: RA3_input

value: peripheral blood mononuclear cells

tag: antibody


title: 16_Primed_PRC2i: ATGTCA

description: bulk RNAseq


title: 23_Naïve_PRC2i: CGTACG

description: bulk RNAseq


title: TAP_2_0mm, replicate 3

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
LCM isolated tapetal cells from fixed 2.0 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome

organism: Zea mays

source_name: LCM isolated tapetal cells

growth_protocol: Maize (Zea mays) W23 bz2 inbred line plants were grown in Stanford, CA, USA under greenhouse conditions (31℃/21℃, 14 h day/10 h night light cycle with supplemental LED and UV-A lamps providing ~50% of summer sun conditions).

extract_protocol:
Total RNA was isolated from three different LCM cell samples and FA samples at 1.5 mm and 2.0 mm using the RNAqueous™-Micro Kit (Invitrogen).
RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples.

treatment_protocol: Anthers were dissected from tassels and then measured using a micrometer (Fisher Scientific).

value: Isolated tapetal cells from fixed 2.0 mm maize anthers

value: W23 inbred

tag: Stage


title: GM12878-Fixed-20k-Omni_TD-37C-Nextera_Tn5-Rep2

tag: cell type


title: 17_Primed_PRC2i: CCGTCC

description: bulk RNAseq

tag: treatment


title: TAP_2_0mm, replicate 2

tag: genotype


title: OSC_2_0mm, replicate 2

description:
LCM isolated outer cell layers from fixed 2.0 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

source_name: LCM isolated outer cells

value: Isolated outer cell layers from fixed 2.0 mm maize anthers


title: RA2_input

data_processing:
Library strategy: MeRIP-seq
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: homo sapiens Ensembl release-101
Supplementary_files_format_and_content: .xlsx files include gene expression and methylation level

tag: disease state


title: GM12878-Fixed-20k-THS_TD-55C-Homemade_Tn5-Rep1


title: GM12878-Fixed-20k-Nextera_TD-37C-Homemade_Tn5-Rep2


title: FRG2_BM_sample8_190802

description: Low index


title: FRG2_PB_sample9_190802

description: Low index

source_name: CD34+ from peripheral blood

value: CD34+ from peripheral blood


title: GM12878-Fixed-20k-THS_TD-37C-Nextera_Tn5-Rep2

value: lymphoblastoid


title: TAP_2_0mm, replicate 1


title: FRG2_BM_sample6_190802

description: High index


title: FRG2_BM_sample4_190802

description: High index


title: RA1_IP

value: m6A antibody IP


title: 1.5 mm FA_rep2

city: Stanford

first: Xue

last: Zhou

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

description: Fixed anthers

data_processing:
Paired-end RNA-seq Read1 contained a 10 bp unique molecular identifier (UMI) and sample barcodes, and Read2 contained the transcript sequence. Each UMI was processed and attached to the Read2 metadata using fastp
Barcodes were used to demultiplexed Read2 into a separate file for each library using fastq-multx
After trimming the adapters by Trim Galore, the reads were mapped to version 4 of the B73 maize genome using Hisat2
Genome_build: Version 4 of the B73 maize genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Anthers

growth_protocol: Maize (Zea mays) W23 bz2 inbred line plants were grown in Stanford, CA, USA under greenhouse conditions (31 ℃/21 ℃, 14 h day/10 h night light cycle with supplemental LED and UV-A lamps providing ~50% of summer sun conditions).

extract_protocol:
Total RNA was isolated from three different LCM cell samples and FA samples at 1.5 mm and 2.0 mm using the RNAqueous™-Micro Kit
RNA-seq libraries were prepared using CEL-seq2

tag: develpmental stage

value: Wild type_W23


title: GM12878-Fixed-20k-Omni_TD-55C-Homemade_Tn5-Rep1

value: Fixed


title: ME_2_0mm, replicate 3

description:
LCM isolated meiocytes from fixed 2.0 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

source_name: LCM isolated meiocytes

value: Isolated meiocytes from fixed 2.0 mm maize anthers


title: 24_Naïve_PRC2i: GAGTGG

description: bulk RNAseq

value: H9 human embryonic stem cells


title: OSC_2_0mm, replicate 1


title: 15_Primed: AGTTCC

description: bulk RNAseq


title: RRBS_Hsap_fibro_5aza0

source_name: Primary dermal fibroblasts

tag: Sex

value: Female

value: Control (not treated)

value: Primary dermal fibroblasts


title: MM-MSC-1

description: gene expression in MM-MSCs

source_name: patients1 with MM

value: male


title: FRG2_PB_sample10_190802

description: Low index


title: SK-N-BE2 GNE987 10nm_rep2

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample …

source_name: Neuroblastoma cells

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

value: 10nM GNE987


title: GM12878-Fixed-20k-Nextera_TD-55C-Homemade_Tn5-Rep1


title: GM12878-Fixed-20k-Nextera_TD-37C-Nextera_Tn5-Rep2


title: RNA-seq_Hsap_fibro_5aza1_2

tag: genome build

value: Treated 5-AzadC 1 microM


title: SK-N-BE2 GNE987 10nm_rep1


title: RRBS_Hsap_fibro_5aza1

tag: tissue


title: GM12878-Fixed-20k-THS_TD-55C-Nextera_Tn5-Rep1

tag: cell line


title: W23_2_0mm, replicate 2

description:
A fixed 2.0 mm single anther of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

source_name: single anther

value: Fixed 2.0 mm maize anther


title: 14_Primed: AGTCAA

description: bulk RNAseq

value: untreated


title: SK-N-BE2 GNE987 0nm_rep2

value: DMSO


title: RNA-seq_Hsap_fibro_5aza1_3


title: ME_2_0mm, replicate 2

value: W23 inbred


title: GM12878-Fixed-20k-THS_TD-37C-Homemade_Tn5-Rep1

value: lymphoblastoid

tag: nuclei state


title: FRG2_PB_sample5_190802

description: High index

value: CD34+ from peripheral blood


title: d4 TSC EZH2i 10X scRNAseq_2

description:
10X Genomics scRNAseq
scRNAseq_Sigma_hiPSCs_D4_TSCs_UNC1999_countMtx.csv

data_processing:
Cell ranger (v4.0.0) was used to process, align and summarize unique molecular identifier (UMI) counts for individual single-cell samples against the 10X genomics pre-built human GRCh38 (hg38) GENCODE v32/Ensembl 98 and mouse GRCm28 (mm10) GENCODE vM23/Ensembl 98 reference genome dataset (version 2020-A, July 7 2020). Gene Ensembl IDs were converted into gene symbols using R Package biomaRt (v2.64.3). Downstream analyses were performed with the R package Seurat (v4.0.1) (https://satijalab.org/seurat/). Human cells were retained and mouse cells (MEFs) were filtered out by adjusting number of counts per cell (nCount_RNA) and number of mapped genes per cell (nFeature_RNA) to only keep cells that were mostly mapped to the human GRCh38 (hg38) genome (for naive cells: nCount_RNA < 40000, nCount_RNA > 3000, nFeature_RNA < 8000 and nFeature_RNA > 1500; for d4 of naive to TSC conversion cells: nCount_RNA < 300000, nCount_RNA > 10000, nFeature_RNA < 12000 and nFeature_RNA > 3000). Naive cells with more than 25% of mitochondrial counts were filtered out. D4 TSC converted cells with more than 30% of mitochondrial counts were filtered out. Read count tables for multiple samples were merged and cell counts were normalized with Seurat global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell by the total expression, multiplies this by 10.000 scale factor, and log-transforms the result.
Genome_build: Human GRCh38 (hg38) GENCODE v32/Ensembl 98 and mouse GRCm28 (mm10) GENCODE vM23/Ensembl 98 reference genome dataset (version 2020-A, July 7 2020).
Supplementary_files_format_and_content: Non-normalized count matrix (.csv format)

source_name: Human induced pluripotent stem cells

growth_protocol: Sigma iCas9 naive hiPSCs were cultured on MEF feeders at 37°C under hypoxic (5% O2, 5% CO2) conditions with filter sterilized PXGL medium which consists on: 1:1 mixture of DMEM/F12 (Gibco, 31330-038) and Neurobasal (Gibco, 21103-049), 0.5% N2-supplement (Gibco, 17502-048), 1% B27-supplement (Gibco, 17504-044), 2 mM L-Glutamine (Gibco, 25030-081) and 1% penicillin-streptomycin (Gibco, 15140-122), 1 μM PD0325901 (Axon Medchem, 1408), 2 μM XAV939 (Sigma, X3004), 2 μM Gö6983 (Tocris, 2285), 10 ng/mL human LIF (PeproTech, 300-05-5UG), 0.1 mM β-mercapto-EtOH (Gibco, 31350-010) and 10 μM Y-27632 (Tocris, 1254). XAV939 and Y-27632 were always added fresh to the medium, which was changed daily. Naive hPSCs were passaged every four days in a ratio of 1:2 by single-cell dissociation with TryplETM Express Enzyme (ThermoFisher, 12605-036) (10-15 min at 37°C) followed by filtering through a Falcon 40 μm Cell Strainer (Corning, 352340). The conversion from naive hPSCs to TSCs was performed as previously described by Castel et al., 2020 and Dong et al., 2020. In brief, cell culture plates were coated with 5 μg/mL Collagen IV (Corning, 354233) 37°C overnight. Naive hPSCs were single-cell dissociated with TryplETM Express Enzyme (10-15 min at 37°C) followed by filtering through a Falcon 40 μm Cell Strainer. After washing the prepared plate once with 1X phosphate buffered saline (PBS) (ThermoFisher, 10010-023), naive cells were seeded on Collagen IV in filter sterilized TSC medium [DMEM/F12 (Gibco, 31330-038) supplemented with 0.3% bovine serum albumin (BSA) (Sigma-Aldrich, A9418-50G), 0.2% FBS (Gibco, 10270), 0.5% penicillin-streptomycin (Gibco, 15140-122), 1% insulin-transferrin-selenium-ethanolamine supplement (ITS-X) (ThermoFisher, 51500-056), 8.5169 μM L-ascorbic acid (Sigma-Aldrich, 50-81-7), 0.5 μM A83-01 (PeproTech, 9094360), 1 μM SB431542 (Axon Medchem, 1661), 50 ng/mL human epidermal growth factor (hEGF) (Miltenyi Biotec, 140-033-715.02), 2 μM CHIR-99021 (Axon Medchem, 99021), 0.8 mM valproic acid (Sigma-Aldrich, 1069-66-5), 0.1 mM β-mercapto-EtOH and 5 μM Y-27632]. Y-27632 was always added fresh to the medium, which was changed daily.

extract_protocol:
Cells were washed with 1X PBS before dissociation from the culture dish by TryplETM Express Enzyme (ThermoFisher, 12605-036) incubation for 8 minutes at 37°C. Single cell suspension was filtered through a Falcon 40 µm Cell Strainer and centrifuged at 200G for 5 min. After resuspension in 1X PBS with 0.04% BSA, the single cell suspension was counted with a Luna-FL automated Fluorescence Cell Counter (Logos Biosystems).
The cells were loaded onto the 10X Chomium Single Cell Platform (10X Genomics) at a concentration of 1.000 cells per μL (Next GEM Single Cell 3’library and Gel Bead Kit v3.1) according to the manufacturer’s protocol (10X User Guide, Revision D). Cells were loaded targeting 4.000 cells each run. Generation of gel beads in emulsion (GEM), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed according to the manufacturer’s protocol. Individual sample quality was assessed using a Bioanalyze Tapestation (Agilent). Qubit 2.0 (ThermoFisher) and KAPA Library Quantification Kit for Illumina Platform (KAPA Biosystems) were used for library quantification before pooling. The final library pool was sequenced on the NovaSeq6000 (Illumina) instrument using the NovaSeq SP kit (Illumina) for 2 lanes of 100-base-pair paired-end reads at the KU Leuven Genomics Core.

treatment_protocol: To inhibit EZH2, 1 μM of EZH1/2 methyltranferase inhibitor (Abcam, ab146152, UNC1999) was added fresh to the medium.

value: TSC-derived iCas9 Sigma hiPSC line

value: EZH2i (Abcam ab146152 UNC1999, EZH2 methyltransferase inhibitor)


title: d4 TSC EZH2i 10X scRNAseq_1


title: RNA-seq_Hsap_fibro_5aza0_1


title: RNA-seq_Hsap_fibro_5aza1_1


title: ME_2_0mm, replicate 1

value: Isolated meiocytes from fixed 2.0 mm maize anthers


title: GM12878-Fixed-20k-Omni_TD-55C-Nextera_Tn5-Rep1

value: Fixed

tag: nuclei input


title: Naïve_UNC1999_IgG_Replicate_2

data_processing:
Standard Illumina base-calling pipeline.
Reads were trimmed using trim galore v0.6.5 using default parameters to remove the standard Illumina adapter sequence, and mapped to the human genome GRCh38 and Drosophila genome BDGP6 using Bowtie2. BAM files were imported into SeqMonk.
Genome_build: GRCh38 and BDGP6
Supplementary_files_format_and_content: A tab-separated file of log2 RPM read counts per 1kb. Fields are chomosome, start, end, log2 RPM values for each sample.

organism:
Drosophila melanogaster
Homo sapiens

source_name: Human embryonic stem cells (ESCs) and Drosophila Schneider 2 cells (S2)

growth_protocol: Human pluripotent stem cells (hPSCs) were grown in a 5% O2 and 5% CO2 incubator under humidified conditions at 37 °C. H9 primed hPSCs were cultured in feeder-free conditions on plates pre-coated with Vitronectin in complete TeSR-E8™ medium. H9 chemically reset naive hPSCs were cultured on Geltrex-coated plates in PXGL medium, which consists of a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2-supplement, 0.5x B27-supplement, 2 mM L-Glutamine, 1x penicillin-streptomycin, 0.1 mM β-mercaptoethanol, 1 μM PD0325901, 2 μM XAV939, 2 μM Gö6983 and 20 ng/mL human LIF. Drosophila S2 cells were grown in a non-humidified incubator at 28°C without additional CO2 in normoxic conditions. Drosophila S2 were cultured in T75 flasks in Schneider’s Drosophila medium  supplemented with 10% heat inactivated FBS.

extract_protocol:
Concanavalin A conjugated paramagnetic beads were resuspended and washed twice on a magnetic rack in a bead activation buffer composed of: 20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2. Naive or primed hPSCs and Drosophila S2 cells were dissociated and counted. Cell pellets were then washed twice with a wash buffer composed of: 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine and supplemented with EDTA-free protease inhibitor. 50,000 human cells and 20,000 Drosophila cells were added in wash buffer to Concanavalin A beads and incubated for 10 min at RT with rotation to immobilise cells. Concanavalin A beads were then collected with a magnetic rack, the supernatant discarded and beads were resuspended in antibody buffer, composed of wash buffer supplemented with 0.08% Digitonin and 2 mM EDTA. 1 μg of antibody was added to beads which were then incubated overnight at 4 °C with rotation to allow permeabilisation and target binding. Antibodies used were: rabbit anti-Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology, 9733), rabbit anti-IgG (Invitrogen, 31188) and anti-Histone H2Av spike-in antibody (Active Motif, 61686). The following day, beads were washed twice with digitonin buffer, composed of wash buffer supplemented with 0.08% Digitonin. To 50 μl digitonin buffer, 2.5 μl CUTANA™ pA/G MNase (EpiCypher, 15-1016) was added and incubated for 10 min at RT to promote pA/G MNase binding to the antibody constant region. Beads were again washed twice with digitonin buffer and MNase was activated with 2 mM CaCl2 and incubated for 2 h at close to 0 °C to facilitate chromatin fragmentation under sites of antibody binding. MNase activity was terminated by adding 100 μl stop buffer, composed of 340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/ml RNase A and 50 μg/ml Glycogen. Cleaved DNA fragments were released from nuclei by incubation for 10 min at 37 °C, spinning for 5 min at 16,000 xg at 4 °C and collecting the supernatant from the beads on a magnetic rack. DNA was then purified by incubation with 1 μl SDS (20 %) and 1.5 μl Proteinase K (20 mg/ml) at 70 °C for 10 min, followed by a 1.8x AMPure XP bead (Beckman Coulter) clean-up into DNA lo-bind tubes (Eppendorf) and eluted in 50 μl 0.1x TE.
Libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina (NEB) using the manufacturer’s protocol, with libraries indexed using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2) (NEB). Following library preparation, library fragment size and concentration were determined using the Qubit fluorometer double stranded DNA high sensitivity assay kit, using an Agilent Bioanalyzer 2100 and by KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq500 instrument as HighOutput 75 bp paired-end reads at the Babraham Institute Next Generation Sequencing Facility.
CUT&RUN

treatment_protocol: 2.5 μM UNC1999 was applied to primed hPSCs the day after passaging for 4 days. 1 μM UNC1999 was applied to naïve hPSCs the day after passaging for 4 days.

value: Naive ESCs (H9 line) and Drosophila S2

tag: cut and run antibodies

value: IgG (Invitrogen, 31188) and Histone H2Av spike-in antibody (Active Motif, 61686)


title: RNA-seq_Hsap_fibro_5aza0_3

value: Female

value: Control (not treated)

value: Primary dermal fibroblasts


title: TAP_1_5mm, replicate 1

description:
LCM isolated tapetal cells from fixed 1.5 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

value: Isolated tapetal cells from fixed 1.5 mm maize anthers


title: W23_2_0mm, replicate 1


title: FRG2_PB_sample7_190802

description: High index

tag: tag


title: SK-N-BE2 GNE987 0nm_rep1

value: Neuroblastoma cells


title: Naïve_UNC1999_IgG_Replicate_1


title: GM12878-Fixed-20k-Nextera_TD-55C-Nextera_Tn5-Rep1


title: GM12878-Fixed-20k-Nextera_TD-37C-Homemade_Tn5-Rep1


title: OSC_1_5mm, replicate 1

description:
LCM isolated outer cell layers from fixed 1.5 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

value: Isolated outer cell layers from fixed 1.5 mm maize anthers


title: RNA-seq_Hsap_fibro_5aza0_2


title: Naïve EZH2i 10X scRNAseq_1

description:
10X Genomics scRNAseq
scRNAseq_Sigma_hiPSCs_Naive_UNC1999_countMtx.csv

value: naive iCas9 Sigma hiPSC line


title: OSC_1_5mm, replicate 2


title: TAP_1_5mm, replicate 2


title: GM12878-Fixed-20k-Omni_TD-37C-Homemade_Tn5-Rep1


title: WGBS_Hsap_fibro

value: No treatment


title: d4 TSC 10X scRNAseq_2

description:
10X Genomics scRNAseq
scRNAseq_Sigma_hiPSCs_D4_TSCs_countMtx.csv

value: untreated


title: GM12878-Fixed-20k-Nextera_TD-37C-Nextera_Tn5-Rep1

value: lymphoblastoid


title: GM12878-Native-20k-THS_TD-55C-Homemade_Tn5-Rep4

value: Native


title: Naïve_UNC1999_H3K27me3_Replicate_2

value: Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology, 9733)


title: d4 TSC 10X scRNAseq_1

value: TSC-derived iCas9 Sigma hiPSC line


title: GM12878-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep4


title: GM12878-Fixed-20k-THS_TD-37C-Nextera_Tn5-Rep1


title: ME_1_5mm, replicate 2

description:
LCM isolated meiocytes from fixed 1.5 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

value: Isolated meiocytes from fixed 1.5 mm maize anthers

value: W23 inbred


title: GM12878-Fixed-20k-Omni_TD-37C-Nextera_Tn5-Rep1

value: Fixed


title: ME_1_5mm, replicate 1


title: Naïve EZH2i 10X scRNAseq_2

value: EZH2i (Abcam ab146152 UNC1999, EZH2 methyltransferase inhibitor)


title: W23_1_5mm, replicate 1

description:
A fixed 1.5 mm single anther of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.

value: Fixed 1.5 mm maize anther


title: W23_1_5mm, replicate 2


title: Naïve_IgG_Replicate_1

value: Naive ESCs (H9 line) and Drosophila S2

value: IgG (Invitrogen, 31188) and Histone H2Av spike-in antibody (Active Motif, 61686)


title: GM12878-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep4


title: Naïve 10X scRNAseq_2

description:
10X Genomics scRNAseq
scRNAseq_Sigma_hiPSCs_Naive_countMtx.csv


title: Naïve_UNC1999_H3K27me3_Replicate_1


title: Naïve 10X scRNAseq_1


title: GM12878-Native-20k-THS_TD-55C-Nextera_Tn5-Rep4


title: BRAF7

first: Yariv

last: Houvras

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were then aligned to the zebrafish genome (GRCz10) using Star v2.3
The Ensemble transcriptome was used to identify genes
Differential gene expression was analyzed using DESeq2
Assembly: GRCz10
Supplementary files format and content: DESeq2 was used to normalize gene expression and to identify differentially regulated genes

organism: Danio rerio

source_name: thyroid tumor

growth_protocol: Transgenic zebrafish were created by injecting tol2 transposon vectors into zebrafish to drive expression of either CCDC6-RET or BRAF(V600E) under control of the zebrafish thyroglobulin promoter

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy extraction kit
RNA-seq libraries were prepared according to the Illumina TruSeq RNA protocol. cDNA libraries were then run on the HiSeq platform to obtain 50 bp paired-end reads.

treatment_protocol: Zebrafish were raised until thyroid cancers were identified as visible  lesions. Thyroid tumors were harvested and RNA was extracted

value: Thyroid cancer

value: BRAF(V600E) transgenic zebrafish


title: Naïve_H3K27me3_Replicate_2


title: B3T-IP

city: Wuhan

first: gaocai

last: li

state: HuBei

address: JIefang Avenve 1277, Jianghan District

department: Department of Orthopeadics

institute: wuhan union hospital

data_processing:
Library strategy: Me-RIP-seq
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38  by using Bowtie2.
Only unique mapping paired reads were sorted using samtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called  using the exomePeak R package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peak files were generated using the exomePeak R package

source_name: nucleus pulposus cells

growth_protocol: Nucleus pulposus cells were cultured at 37℃ with 5% CO2

extract_protocol:
RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

treatment_protocol: Three groups of nucleus pulposus cells were untreated as normal cells, and other three groups of nucleus pulposus cells were treated with 20nM TNF-α for 24 h as senescent cells

value: human primary nucleus pulposus cells

value: senescent

value: 20nM TNF-alpha for 24 h


title: BRAF2


title: B1T-IP


title: BRAF6


title: B3N-IP

value: normal

value: untreated


title: BRAF3


title: Primed_UNC1999_IgG_Replicate_1

value: Primed ESCs (H9 line) and Drosophila S2


title: Primed_UNC1999_IgG_Replicate_2


title: GM12878-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep4

data_processing:
The paired-end reads were preprocessed using Trimmomatic v0.36 to trim the Nextera adaptors and low quality reads with the parameter setting as “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20”.
The trimmed reads were mapped to either the hg19 human genome or mm10 mouse genome reference contigent upon the sample source using Bowtie2 v2,2.9 with the parameter setting as “-X 2000 -3 1” to restrict the maximum fragment length of 2000 bp and trim 1 base from the 3’ end of each read before alignment. Following mapping, only the reads confidently (MAPQ ≥ 10) mapped to assembled nuclear chromosomes, and in proper pairs (we used the “-f3” and “-F12” options in SAMtools v1.4) were preserved for downstream analysis.
Picard v2.20.2 “MarkDuplicates” was used to remove duplicate reads and estimate library complexity.
Peaks were called by MACS2 v2.1.2 using deduplicated bed files and considering a 200 bp window centered on the read start using the parameters “--nomodel --keep-dup all --extsize 200 --shift -100”. Because each peak may have multiple summits (and will therefore be listed multiple times in the resulting peak bed file), the peaks output from MACS2 were then merged into a single peak set for each sample using bedtools “merge”.
Genome_build: Data from GM12878 were mapped to hg19 and data from mouse lungs were mapped to mm10
Supplementary_files_format_and_content: Matrix of the number of reads overlapping each peak for each GM12878 sample was generated by "multiBamSummary" (deepTools v3.5.1) using deduplicated bam files and a non-overlapping peak set that combined the peaks identified from each condition. The first column contains the coordinates for each peak.
Supplementary_files_format_and_content: Matrix with deviation scores for each motif and each GM12878 sample was computed by chromVAR v1.12.0. The first column shows the human motif ID from JASPAR CORE database.

value: lymphoblastoid

value: Native


title: GM12878-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep4


title: RET6

value: CCDC6-RET transgenic zebrafish


title: B2N-IP


title: RET5


title: Primed_IgG_Replicate_1


title: B1N-IP


title: GM12878-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep4


title: RET3


title: GM12878-Native-20k-THS_TD-37C-Nextera_Tn5-Rep4


title: B3T-Input


title: B2T-Input


title: Primed_UNC1999_H3K27me3_Replicate_1

value: Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology, 9733)


title: Naïve_H3K27me3_Replicate_1


title: B2T-IP


title: RET2


title: GM12878-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep4


title: Primed_H3K27me3_Replicate_2


title: Primed_H3K27me3_Replicate_1


title: B1T-Input


title: GM12878-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep4


title: B3N-Input


title: B2N-Input


title: GM12878-Native-20k-THS_TD-37C-Homemade_Tn5-Rep4


title: Liver SZ5

city: Beijing

first: Yanmin

address: 1 Xian Nong Tan Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped   to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA from liver tissues was isolated using TRIzol reagent according to the manu-facturer's instructions and RNA integrity was assessed using the RNA Nano 6000 As-say Kit of the Bioanalyzer2100 system (Agilent Technologies, CA, USA). mRNA was purified using poly-T oligo-attached magnetic beads.
After fragmentation, libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumi-na® according to the manufacturer’s instructions.

tag: strain

tag: diet

value: High-fat diet

tag: sz-a treatment

value: yes


title: Newman 30 min rep 3

city: Brno

first: Adela

last: Finstrlova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Masaryk University

data_processing:
Raw reads quality control with FastQC
Quality trimming and filtering performed using Trimmomatic toolkit (v 0.36) with the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 SLIDINGWINDOW:4:15 LEADING:22 TRAILING:22 MINLEN:20 AVGQUAL:22
Alignment to the reference genome and read counting using using STAR v 2.5.2b with the following parameters: outFilterMultimapScoreRange 0, outFilterMatchNmin 30, outFilterMatchNminOverLread, 0.95, outFilterMismatchNmax 999, outFilterMismatchNoverLmax 0.02, outFilterMismatchNoverReadLmax 1, alignIntronMin 20, alignIntronMax 1
Normalization of counts within the triplicates and DGE analysis was performed with DESeq2 package
Genome_build: Staphylococcus aureus SH1000 de novo sequenced genome (Bioproject Accession: PRJNA769253), Staphylococcus aureus Newman (Genbank Accession: NC_009641.1), Staphylococcus virus K (GenBank Accession: NC_005880.2 )
Supplementary_files_format_and_content: csv file with raw counts generated using aligner STAR for each sample
Supplementary_files_format_and_content: csv file with normalized counts generated using DESeq2 for each sample
Supplementary_files_format_and_content: csv file with DESeq2 results for each sampling time

organism: Staphylococcus aureus

source_name: Staphylococcus aureus Newman growing exponentionally in MPB infected with phage K

growth_protocol: MPB exponential growth

extract_protocol:
The total RNA was extracted using organic extraction with TRIzol. Genomic DNA was removed using a Turbo DNA-free kit. The rrRNA depletion was performed using a RiboMinus Bacteria 2.0 Transcriptome Isolation Kit according to the manufacturer’s instructions.
Sequencing libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit, following the standard protocol.

value: Newman

tag: infection

value: Staphylococcus virus K

tag: time

value: 30 min


title: BRAF1

value: Thyroid cancer


title: GM12878-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep3

extract_protocol:
1) Nuclei isolation from native GM12878:  ~2 million native cells were collected and washed using 4 ml 1X PBS (pH 7.4, Gibco, cat. no. 10-010-023) supplemented with 0.04% BSA (PBSB), and then resuspended in 200 μl of ATAC-seq lysis buffer. Lysis buffer was made by supplementing ATAC resuspension buffer (RSB) with detergents. RSB buffer is 10 mM Tris-HCl (pH 7.5, Invitrogen, cat. no. 15567027), 10 mM NaCl (Invitrogen, cat. no. AM9759) and 3 mM MgCl2 (Invitrogen, cat. no. AM9530G) in nuclease free water. RSB was made in bulk and stored at 4°C long-term. On the day of the experiment, the ATAC lysis buffer was made by adding 0.1% IGEPAL (Sigma, cat. no. I3021), 0.01% digitonin (Invitrogen, cat. no. BN2006), and 0.1% Tween-20 (Bio-Rad, cat. no. 1610781) to RSB. Detergent percentages reported are final concentrations. After resuspending cell pellets in the lysis buffer, they were incubated on ice for 3 min, and then the lysis was stopped by adding 1 ml RSB containing 0.1% Tween-20. Nuclei were then centrifuged at 500 r.c.f for 10 min at 4 °C and resuspended in 200 ul of PBSB. The nuclei were counted and diluted to 3,100 nuclei/μl with PBSB. Then, 6.6 μl of diluted nuclei (20,460 total nuclei) were transferred to 12.4 μl of transposition reaction (10 μl of 2X Tagmentation buffer, 0.2 μl of 1% digitonin, 0.2 μl of 10% Tween-20, and 2 μl of H2O). We then added 1 μl of transposase to the transposition mix containing nuclei. Tagmentation was carried out on a thermocycler at either 37°C or 55°C for 30 min. Tagmented DNA was cleaned up using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer (Zymo, cat. no. D4004). 2) Nuclei isolation from fixed GM12878: the frozen, fixed cells (~ 2 million) were incubated in a 37°C water bath until thawed (~ 1 min). After thawing, the cells stored in 1 ml freezing buffer were diluted with 3 ml of PBSB. The fixed cells were collected by centrifuging at 500 r.c.f for 10 min at 4°C, resuspended again in 1 ml PBSB, and then centrifuged at 500 r.c.f for 5 min at 4°C to wash the cells. Following washing, the nuclei were isolated and tagmented as described in the ATAC-seq protocol for native samples described above. After tagmentation, crosslinks were then reversed for the fixed, tagmented nuclei by adding 60 μl of reverse-crosslinking buffer containing 0.067% SDS and 1.33 mg/ml Proteinase K (Qiagen, cat. no. 19133) in Qiagen Buffer EB (final concentration of 0.05% SDS and 1 mg/ml Proteinase K) directly to the tagmentation reactions, and incubating the samples at 65°C for 15 hours in a thermomixer with shaking at 1,000 r.p.m. Following crosslink reversal, tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer. 3) The isolation of mouse lung nuclei was performed following the single-nucleus isolation protocol described by Joshi Nikita and Misharin Alexander. In brief, we cut a ~0.1-0.2 g piece from the lung sample removed from -80°C and kept it on dry ice until use. The tissue block was thawed almost completely on ice for 1 min, and then injected with 1 ml of cell lysis buffer, which was made of 1x cOmplete protease inhibitor cocktail (1 tablet per 10 ml solution, Sigma-Aldrich, Cat. 11836153001) in Nuclei EZ prep buffer (Sigma-Aldrich, Cat. NUC101), into the center of the tissue with a 30G needle and syringe. Following lysis buffer injection, the tissue was chopped into small pieces with scissors and then transferred along with the lysing buffer into a gentleMACS C tube (Miltenyi Biotec, Cat. 130-096-334). An additional 1 ml of lysing buffer was added into the C tube to make a final volume of 2 ml. The minced tissue was then homogenized using a gentleMACS tissue dissociator by running the ‘m_lung_01’ program followed by the first 20 sec of the ‘m_lung_02’ program. After homogenization, tissue lysate was briefly centrifuged to reduce foam and then passed through a 40 μm cell strainer in a 50ml tube. After passing the sample through, the strainer was rinsed with 4 ml of washing buffer (PBS with 1% BSA). The nuclei were counted with Trypan blue in the presence of 2X Omni buffer (20 mM Tris HCl (pH 7.5), 10 mM MgCl2 and 20% Dimethyl Formamide), and then collected by centrifugation at 500 r.c.f for 5 min at 4°C. Then, we removed the supernatant and resuspended the nuclei to a concentration of 4-5 million nuclei/ml in a nuclei freezing buffer containing 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat .no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), and 2% protease inhibitor (Sigma, cat. no. P8340). 1 ml aliquots of the nuclei were flash frozen in liquid nitrogen and then transferred to a liquid nitrogen dewar for long-term storage.
5 μl of purified DNA out of 10 μl purified product was amplified in a 25 μl PCR reaction containing NEBNext PCR master mix (1X final), 0.5X SYBR Green and 1.25 μM of Ad1 primer from Buenrostro JD. et al., 2013 and 1.25 μM of an N7 primer containing custom barcodes. Samples were amplified on a Bio-Rad CFX Connect Real-time cycler using the following program: 72°C for 5 min; 98°C for 30s; cycling at 98°C for 10 s, 63°C for 30 s, 72°C for 1 min; samples were monitored and stopped when it appeared that their exponential amplification was leveling off. At this point the samples were allowed to incubate at 72°C for an additional minute to fully extend the library. All native samples were stopped after 9 cycles and fixed samples were stopped after 10 cycles. PCR products were cleaned up with Ampure XP beads. A double size selection was performed to remove DNA fragments larger than ~1500 bp (with 0.4X AMPure XP beads) and smaller than ~100 bp (with 1.5X AMPure XP beads). To do this, we added 25 μl of Qiagen Buffer EB to each PCR reaction to bring the volume to 50 μl, and then added 20 μl of beads (homogenizing the mixture well by pipetting), followed by a 5 min incubation at RT. The samples were then put on a magnet stand to bind the beads. 68 μl of the supernatant was transferred to a new 1.5 ml tube and an additional 53 μl of beads were added to the supernatant and resuspended thoroughly (we estimated that 19.4 μl of the 68 μl transferred was bead buffer and 48.6 μl was sample, so to get to 1.5X beads for the second selection we needed to add an additional 72.9 - 19.4 μl of beads, which we rounded off to 53 μl). After another 5 min at RT, the samples were placed on the magnet to clear the beads and the supernatant was discarded. Beads were washed twice with 200 μl of 80% EtOH (made fresh for each experiment). After the second wash, the beads were briefly spun, and any residual ethanol was removed. The beads were then put back on the magnet stand and air dried for 1 min. Then, beads were removed from the magnet and resuspended in 22 μl of Buffer EB, incubated for 2 min at RT and then placed on the magnet stand again. 20 μl of supernatant was transferred to a new tube. The 96 ATAC-seq libraries of the GM12878 cell line and 72 libraries of mouse lungs were pooled separately and sequenced with 2x76 bp reads in two independent runs on an NextSeq 550 Platform using the High Output Kits.

tag: cell type


title: Liver SZ6


title: Liver SZ4


title: Primed_IgG_Replicate_2

value: IgG (Invitrogen, 31188) and Histone H2Av spike-in antibody (Active Motif, 61686)


title: GM12878-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep3


title: B1N-Input

value: human primary nucleus pulposus cells

tag: Stage

tag: treatment


title: Newman 30 min rep 2


title: Liver SZ3


title: GM12878-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep4


title: 18SD07417

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a), with the annotation of known genes from gencode v33.
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode v33
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with raw counts from salmon for each sample

extract_protocol:
RNA was extracted from FFPE sections with the RNeasy FFPE Kit (Qiagen)
RNA libraries were prepared with the TruSeq RNA exome kit (Illumina).

value: Cutaneous tumor

value: melanoma


title: Primed_UNC1999_H3K27me3_Replicate_2


title: 18SD08551


title: Liver SZ2

last: Chen


title: Liver SZ1


title: Newman 20 min rep 2

value: 20 min


title: GM12878-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep3


title: 18SD03300


title: Liver HFD6

value: no


title: GM12878-Native-20k-THS_TD-55C-Homemade_Tn5-Rep3


title: GM12878-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep3


title: Liver HFD5


title: Newman 20 min rep 1


title: GM12878-Native-20k-THS_TD-37C-Homemade_Tn5-Rep3


title: 18SD03881


title: Newman 10 min rep 3

value: 10 min


title: Liver HFD4


title: 17SD09681


title: Newman 10 min rep 2


title: 18SD05258


title: Liver HFD2


title: Newman 10 min rep 1


title: GM12878-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep3

value: lymphoblastoid


title: GM12878-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep3

value: Native


title: GM12878-Native-20k-THS_TD-37C-Nextera_Tn5-Rep3


title: 17SD06291


title: Newman 5 min rep 3

value: 5 min


title: Newman 30 min rep 1


title: Liver HFD3


title: Liver HFD1


title: GM12878-Native-20k-THS_TD-55C-Nextera_Tn5-Rep3


title: GM12878-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep3


title: Newman 5 min rep 2


title: Newman 20 min rep 3


title: 19SD00840


title: 18SD04064


title: Liver CHOW6


title: Liver CHOW5

value: Normal chow


title: 16SD05200


title: Newman 5 min rep 1


title: GM12878-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep3


title: GM12878-Native-20k-THS_TD-55C-Homemade_Tn5-Rep2


title: 18SD00379


title: GM12878-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep2


title: Newman 2 min rep 3

value: 2 min


title: Newman 2 min rep 2


title: 17SD04859


title: Liver CHOW3


title: 17SD00357


title: Newman 2 min rep 1


title: GM12878-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep2


title: Liver CHOW2


title: 17SD06149


title: Newman 0 min rep 3

value: 0 min


title: GM12878-Native-20k-THS_TD-55C-Nextera_Tn5-Rep2


title: GM12878-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep2


title: Liver CHOW1


title: GM12878-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep2


title: Newman 0 min rep 2

value: Newman


title: 17SD09568


title: Mouse5, Uninjected side (control for GFP)

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

data_processing:
Reads were aligned using Kallisto version 0.43.1 using default settings, with specific input parameters of 100 bootstraps and 16 threads. The average mapping rate across samples was ~87% and read depth was ~ 15M reads per GFP sample, and ~ 40M reads per miR sample.
Differential gene expression was quantified using Sleuth version 0.30.0, aggregating abundance on Ensemble genes, with a two-step Likelihood Ratio Test and Wald Test
Genome_build: Ensemble transcriptome release 98 (119215 transcript targets), ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: ALL-RESULTS*txt files report normalized gene expression based on TPM values.

source_name: substantia nigra

extract_protocol:
Regions of substantia nigra were dissected, snap-frozen in liquid nitrogen and stored at -80 until processing. Tissue pieces were homogenized in 150-200 ul ice-cold lysis buffer (50 mM Tris, 120 mM NaCl, 5 mM EDTA, 1% triton-X100) with protease and phosphatase inhibitors (Sigma-Aldrich or Thermo Fisher Scientific) using disposable pellet pestles. Approximately 75-100 ul of lysate was transferred to 1-ml of TRIzol (Thermo Fisher Scientific) and stored at -80 till processing. Total RNA was isolated from TRIzol according to the manufacturer’s instructions (Thermo Fisher Scientific) and dissolved in TE (IDT) and quantified by nano-drop. RNA was DNase treated using DNA-free kit (Thermo Fisher Scientific). Total RNA samples isolated as described above were put over GeneJET RNA clean-up micro columns (cat# K0841, Thermo Fisher Scientific).
RNA quality assessment and sequencing were performed by the Iowa Institute of Human Genetics, Genomics Division, at the University of Iowa. RNA quality and concentrations were determined with the Agilent 2100 Bioanalyzer, and Dropsense or Little Lunatic (Unchained Labs, Pleasanton, CA) reads. RIN values for samples were all >7.5. Illumina TruSeq® Stranded mRNA Library Prep kits (Illumina, San Diego, CA) were used to prepare sequencing libraries from mRNA, followed by reverse transcription to cDNA, fragment purification and ligation to indexed (barcoded) adaptors.
Indexed libraries from AAV:miR-181 samples were prepared as a set and pooled for multiplex sequencing across two lanes on the Illumina HiSeq 4000 sequencer with 75-base paired-end reads. Indexed libraries from AAV:GFP samples were prepared as a set and pooled for multiplex sequencing across two lanes on the Illumina NovaSeq 6000 sequencer for 100 cycles with 50-base paired-end reads.

treatment_protocol: RNAseq was performed on RNA isolated from injected and non-injected SN regions harvested 3 weeks after stereotaxic injection of either AAV-hSYN1-miR-181 (1.65e10 vg; n=3 mice) or AAV-hSYN1-GFP (1e10 vg; N=5 mice).

value: substantia nigra

value: uninjected

tag: genotype

value: uninjected control for GFP overexpression


title: GM12878-Native-20k-THS_TD-37C-Homemade_Tn5-Rep2


title: 16SD06173


title: Newman 0 min rep 1

value: Staphylococcus virus K


title: Newman neg control rep 3

source_name: Staphylococcus aureus Newman growing exponentionally in MPB

value: before infection


title: GM12878-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep2


title: Mouse4, Uninjected side (control for GFP)


title: Newman neg control rep 2


title: GM12878-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep2


title: 17SD08795

value: Cutaneous tumor


title: Mouse2, Uninjected side (control for GFP)


title: Mouse3, Uninjected side (control for GFP)


title: 17SD05886

value: melanoma


title: 17SD08604


title: SH1000 30 min rep 3

source_name: Staphylococcus aureus SH1000 growing exponentionally in MPB infected with phage K

value: 30 min


title: GM12878-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep2


title: Newman neg control rep 1


title: Mouse4, GFP-injected side

value: injection of AAV-hSYN1-GFP

value: GFP overexpression


title: 17SD07867


title: Mouse3, GFP-injected side


title: GM12878-Native-20k-THS_TD-37C-Nextera_Tn5-Rep2

value: lymphoblastoid


title: LiverCHOW4

value: no


title: 15SD00496


title: SH1000 30 min rep 1


title: GM12878-Native-20k-THS_TD-55C-Homemade_Tn5-Rep1

value: Native


title: Mouse1, Uninjected side (control for GFP)


title: SH1000 30 min rep 2


title: GM12878-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep2


title: Mouse2, GFP-injected side


title: SH1000 20 min rep 3

value: 20 min


title: GM12878-Native-20k-Omni_TD-55C-Homemade_Tn5-Rep1


title: 16SD08442


title: 16SD00640


title: Mouse1, GFP-injected side


title: GM12878-Native-20k-Nextera_TD-55C-Homemade_Tn5-Rep1


title: E135-4_BKDL202569354

city: Shanghai

first: Luyue

last: Wang

state: 徐汇区

address: Yue yang road

institute: Shanghai institute of nutrition and health

data_processing:
FastQC (V0.11.3) and Trimmomatic (V0.39) were used for quality control.
Alignment and transcript counting of libraries was done using Cell Ranger (V3.0.1) with the default parameters,and the digital gene expression (DGE) matrices were obtained
The DGE matrices were analysed by a R package Seurat (v4.0.1)
Genome_build: House mouse transcriptome was established with Cell Ranger (V3.0.1) from GRCm38 and TdTomato sequence
Supplementary_files_format_and_content: Raw gene count matirx for each sample

source_name: E13.5 inner ear tissues

extract_protocol:
N/A
10x genomics
Single cell RNA-Seq (10x)

treatment_protocol: single cell suspension preparation method is described in method section of manuscript

value: inner ear

tag: age


title: SH1000 20 min rep 1


title: SH1000 20 min rep 2


title: 17SD00613


title: 17SD02595


title: 17SD06711


title: GM12878-Native-20k-THS_TD-55C-Nextera_Tn5-Rep1

first: Hao

institute: The University of Arizona


title: 14SD02351


title: E135-2_BKDL202569352


title: GM12878-Native-20k-Nextera_TD-55C-Nextera_Tn5-Rep1


title: GM12878-Native-20k-Omni_TD-55C-Nextera_Tn5-Rep1


title: E135-3_BKDL202569353


title: GM12878-Native-20k-THS_TD-37C-Homemade_Tn5-Rep1


title: E115-2_BKDL202569102

source_name: E11.5 otic and peri-otic tissues

value: otic and peri-otic


title: 14SD08906


title: E115-1_BKDL202569101


title: E115-3_BKDL202569103


title: 16SD07600


title: 15SD00550


title: SH1000 10 min rep 1

value: 10 min


title: SH1000 5 min rep 2

value: 5 min


title: GM12878-Native-20k-Omni_TD-37C-Homemade_Tn5-Rep1


title: SH1000 5 min rep 1


title: 15SD02313


title: GM12878-Native-20k-THS_TD-37C-Nextera_Tn5-Rep1


title: GM12878-Native-20k-Nextera_TD-37C-Homemade_Tn5-Rep1


title: Mettl1_KO2

city: Guangzhou

first: Jie

address: No. 58, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-sen University

description:
RNA
scRNA-seq

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
scRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline. Gene expression matrix was created by using Seurat (V3.1.5) pipeline.
Genome_build: hg38, GRCH38，mm10
Supplementary_files_format_and_content: matrix table with raw gene counts

source_name: tongue

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).  HNSCC samples were harvested from the tongue of mice and single cell suspensions were prepared for 10× genomics processing.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set. scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s protocol.


title: E95_BKDL190837054

source_name: E9.5 otic and peri-otic tissues


title: 16SD07599


title: SH1000 10 min rep 3


title: Mettl1_KO1

description:
RNA
scRNA-seq


title: GM12878-Native-20k-Omni_TD-37C-Nextera_Tn5-Rep1

city: Tucson

address: 1230 N Cherry Ave


title: SH1000 2 min rep 1

value: 2 min


title: 11SD06471


title: 16SD07597


title: SH1000 10 min rep 2


title: SH1000 2 min rep 2


title: Mettl1_WT2

description:
RNA
scRNA-seq

value: wild type


title: GM12878-Native-20k-Nextera_TD-37C-Nextera_Tn5-Rep1


title: SH1000 0 min rep 3

value: Staphylococcus virus K

value: 0 min


title: SH1000 5 min rep 3


title: E135-1_BKDL202569351


title: 14SD06045

value: Cutaneous tumor


title: Mettl1_WT1

description:
RNA
scRNA-seq


title: SH1000 0 min rep 2


title: 16SD07594

value: melanoma


title: SH1000 0 min rep 1


title: 12SD02832