title: Scr2_Unsorted_T14

description: library transduced cells screen day14_unsorted rep2

value: genome-wide sgRNA library transduced


title: hDE_H3K4me2_rep2

status: Public on Aug 17 2023

type: SRA

city: Worcester

first: René

last: Maehr

state: MA

address: 368 Plantation St

department: Program in Molecular Medicine/Diabetes Center of Excellence

country: USA

institute: UMass Medical School

library_source: genomic

data_processing:
Base calling: fastq files were obtained from Illumina Basespace under default parameters.
Alignment, Peak-calling and signal generation: Samples were aligned, peaks were called and the bigwig files were generated using the pipeline from https://github.com/ENCODE-DCC/chip-seq-pipeline2/tree/v1.6.1
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak files from the encode pipeline for each sample (except for Input sample)

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Approximately 3-5 million cells were used for each histone ChIPseq experiment. Cells were cross-linked with 1% formaldehyde for 10 minutes, followed by quenching with 125mM glycine for 4-5 minutes and washed for twice with PBS. The cell pellet was lysed in cell lysis buffer (20mM Tris-HCl, pH8, 85mM KCl, 0.5% NP-40) supplemented with 1x protease inhibitor cocktail (Roche, 11836170001) on ice for 20 minutes then pelleted at 5000rpm for 10 minutes. The pellet was resuspended in sonication buffer (10mM Tris pH7.5, 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS) with 1x protease inhibitor cocktail and incubated for 10 minutes at 4oC. In order to achieve 200-700nt DNA fragmentation range, nuclei were sonicated (Bronson sonifier model 250 with the following conditions: Amplitude = 15%, Time interval = 3 min (total of 8-12min) and pulse ON/OFF = 0.7sec/1.3sec). Chromatin was pre-cleared with Dynabeads Protein A (Invitrogen, 10002D) for 1 hour and incubated with antibody overnight at 4C. On the following day, 30-40ul of Dynabeads Protein A were added to the chromatin and antibody mix for 2-3 hours and then the captured immuno-complexes were washed as follows – 1x low-salt buffer, 1x High-salt buffer, 1x LiCl salt buffer and 1x TE. And the washed immuno-complexes were eluted in ChIP-DNA elution buffer (10mM TriHcl pH8, 100mM NaCl, 20mM EDTA and 1% SDS) for 20 minutes, reverse cross-linked overnight at 65C, followed by proteinase K treatment (Invitrogen, 25530-049), RNase A (Thermo Fischer Scientific, ENO531) treatment and Phenol:Chloroform:isoamyl alcohol extraction.
The illumina library construction steps were carried out with 5-10ng of purified ChIP’ed DNA. During the library construction, PCR purification was performed after every step using Qiagen kit (QIAquick PCR purification 28104 or QIAquick gel extraction 28706). The library reaction steps with ChIP’ed DNA as follows: 1.) End-repair - T4 PNK (NEB, M0201L), Klenow fragment (NEB, M0210S), T4 DNA Polymerase (NEB, M0203L) and dNTP mix (Thermo Fischer Scientific, 18427013) incubated at RT for 45min, 2.) 3’ end A-base addition - 3’ -> 5’ exo- Klenow fragment (NEB, M0212L) and dATP (NEB, N0440S) incubated at 37oC for 30min, 3.) Adapter ligation - T4 DNA ligase (NEB, M0202M) and illumina adapters incubated at 16C overnight and 4.) PCR amplification - 2x PfU Ultra Hotstart master mix (Agilent, 600850-51) for 10-14 cycles. The amplified libraries were size selected for 200-450nt on 2% Agarose E-gel (Thermo Fischer Scientific, G402002).

tag: cell line

tag: cell type

value: hDE

tag: chip antibody


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Gelding - KARYO_MAUZEEN

type: RNA

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Horse_60K_2016_01_22 021322 GE 8x60K (AMID 081421) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 081421_D_F_20160126). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 6 out of 45 microarrays. At this step, 42126 spots out of 62976 were selected.  The mean signal of the 16 first samples and 29 last ones were subtracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 30265 rows each corresponding to a unique ProbeName (provided as data Matrix).

molecule: total RNA

organism: Equus caballus

source_name: Whole blood

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Venous blood (10 ml) was collected from 51 horses using EDTA tubes (BD Vacutainer®). In order to stabilized intracellular RNA, 0.8 ml of venous blood was transferred in a tube containing 0.8 ml of Lysis Buffer DL (Macherey-Nagel, Düren, Germany). After homogenization, the samples were maintained at -20°C until RNA extraction. Total RNA was extracted using the NucleoSpin® RNA Blood kit (Macherey-Nagel, Düren, Germany). The manufacturer’s protocol was modified to obtained sufficient ARN quantities for the Microarray gene expression analyses: extraction was carried out from 1.6 ml of the mix blood and Lysis Buffer DL. Twenty µl of proteinase K was then added to complete blood lysis. To adjust RNA binding conditions, 0.8 ml of 70% ethanol was added. The following steps were not modified, except the elution that was carried out with 40 µl of RNase free water. Total RNA quality was assessed using RNA Pico chips on a Bioanalyser 2100 (Agilent, Boeblingen, Germany) and and its concentration was measured on a Nano Drop One Spectrophotometer (ThermoScientific, Illkirch, France).

tag: alert

tag: horse type

value: Gelding

tag: animal

tag: washbatch


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - RINALDO_ROUGE

tag: agressiveness


title: Scr1_Unsorted_T14

city: Boston

first: Nicholas

middle: J

last: Kramer

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: library transduced cells screen day14_unsorted rep1

data_processing:
sgRNA abundance and enrichment analysis using both MAGeCK and casTLE software comparing sorted vs unsorted cells
Assembly: sgRNA library (see PubMed 28474669)
Supplementary files format and content: csv files of differential representation of sgRNAs collapsed to gene level
Library strategy: sgRNA barcode sequencing

extract_protocol:
Genomic DNA extraction using QIAamp DNA Blood Maxi Kit from methanol fixed, FACS sorted cells
PCR based library construction for Illumina sequencing

treatment_protocol: sgRNA library transduced K562-Cas9 cells, methanol fixed, and FACS stained for COX1 and COX4

tag: genotype

value: Cas9 stable expression

tag: treatment

tag: cell population


title: Scr2_High_T10

description: library transduced cells screen day10_COX1_COX4_High_PopA rep2


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Gelding - APERO_ROUSSELIERE


title: Whole blood - Ag.0_Al.L_Ap.L_St.0 - Gelding - SUESTE_DES_LIBAUX

tag: welfare score


title: Whole blood - Ag.0_Al.0_Ap.L_St.0 - Gelding - SANS_PAREIL


title: hESC_Input

value: hESC


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - BOGOSSE_DU_LEVANT


title: Scr1_High_T10

description: library transduced cells screen day10_COX1_COX4_High_PopA rep1


title: Scr2_Low_T10

description: library transduced cells screen day10_COX1_COX4_Low_PopB rep2


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Gelding - ROLLO_DU_VILLAGE


title: Whole blood - Ag.0_Al.L_Ap.0_St.0 - Gelding - VOLCAN_DES_FONTAINES


title: Whole blood - Ag.0_Al.H_Ap.H_St.0 - Gelding - LIAISON

tag: unresponsiveness

value: LIAISON


title: Whole blood - Ag.L_Al.0_Ap.H_St.L - Gelding - QUEZAC_DU_NOYER


title: hES_H3K4me2_rep2


title: Scr1_Low_T10

description: library transduced cells screen day10_COX1_COX4_Low_PopB rep1


title: Scr1_Unsorted_T10

description: library transduced cells screen day10_unsorted rep1


title: Whole blood - Ag.L_Al.L_Ap.0_St.L - Gelding - QUERIZAC

value: QUERIZAC


title: Whole blood - Ag.L_Al.L_Ap.0_St.L - Gelding - AMOUR_DE_VOUGON


title: hES_H3K27me3_rep1_re-analyzed


title: Scr2_T0

description: library transduced cells screen day0 rep2


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - DA_VINCI


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Gelding - OLD_DREAM


title: hPFE_input

value: hPFE


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Gelding - QUIRO_DE_MELS


title: ATAC-seq_hDE_rep2_re-analyzed

data_processing:
Base calling: fastq files were obtained from Illumina Basespace under default parameters.
Alignment, Peak-calling and signal generation: Samples were aligned, signal tracks generated and bases called using the encode pipeline workflow from https://github.com/ENCODE-DCC/atac-seq-pipeline/tree/v1.9.1
Consensus peaks and downstream visualization: diffbind was used to obtain a consensus peakset, motifs were found with gimmemotifs. Custom visualizations for the manuscript were made with R/python
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak files from the encode pipeline for each sample

extract_protocol:
Samples were processed according to (PMID 30995470) ]. Briefly, approximately 50,000 cells were pelleted at 750 x g for 15 minutes at 4°C. After the addition of lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAl CA-630), nuclei were pelleted at 750 x g for 15 minutes at 4°C and the supernatant was discarded. Transposase reaction was performed at 37°C for 30 minutes.
The purified, tagmented DNA was amplified for 9–10 cycles and size selected using AMPure XP beads (Beckman Coulter, A63881) as follows: 0.55X volume of 2X concentrated AMPure beads was added to the amplified DNA and incubated for 5 minutes at room temperature. The supernatant, containing low-molecular weight DNA, was collected in a separate tube by removing the beads using a magnetic rack. 1X volume of AMPure beads was added to the supernatant and incubated for 5 min at room temperature. The beads were washed twice with 75% ethanol and then air-dried. The final purified library was eluted in EB buffer and sequenced (paired-end, 75–75) on an Illumina NextSeq500 platform.


title: ATAC-seq_hDE_rep1_re-analyzed


title: ATAC-seq_hES_rep2_re-analyzed


title: ATAC-seq_hES_rep1_re-analyzed


title: Whole blood - Ag.H_Al.0_Ap.0_St.0 - Mare - TONTOUTA_VIENNOISE

value: Mare


title: hPFE_H3K27me3_rep2


title: hPFE_H3k27me3_rep1


title: hAFE_rep2

library_source: transcriptomic single cell

data_processing:
The alignment, demultiplexing, barcoded processing and gene counting was done as described in the Methods with STAR aligner (v2.7.10), Picard tools (v2.26.10), and Drop-seq tools (v2.5.1).
Further downstream processing was done with Scanpy v1.9.1
Assembly: hg38
Supplementary files format and content: Tab-separated digital gene expression matrices containing cell identifiers and raw gene expression counts for each sample

extract_protocol:
Cells were washed once with PBS and lifted using TryplE
Following the Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/),  sorted single cell suspensions were resuspended at 1x105 cells per mL in PBS + 0.01% BSA. The diluted cell suspension, barcoded Oligo-dT beads (Chemgenes, MACOSKO-2011-10), and droplet generation oil (Biorad, 1864006) was run through a PDMS co-flow microfluidic droplet generation device (Nanoshift, custom built based on Macosko et al. datafile 1 [Macosko et al., 2015] at flow rates of 4,000 μL per hour, 4,000 μL per hour, and 15,000 μL per hour, respectively. Droplet breakage, bead isolation, and cDNA synthesis were performed as described (Macosko et al., 2015). cDNA libraries were tagmented with Nextera XT DNA Library Preparation kit (Illumina, FC-131-1024) and sequencing libraries were amplified and individually barcoded. Agencourt AMPure XP beads (Beckman Coulter, A63881) were used for purification of cDNA and sequencing libraries according to the manufacturer’s instructions. Final sequencing libraries were analyzed on an Agilent High Sensitivity DNA bioanalyzer chip to determine average basepair size and final library concentrations were determined with a Qubit High Sensitivity DNA assay kit (Invitrogen, Q32854).  Drop-seq libraries were sequenced at paired-end (20-50) on a Nextseq500 using a Nextseq500/550 High Output v2 75-cycle kit (Illumina, FC-404-2005).

value: hAFE


title: Whole blood - Ag.0_Al.0_Ap.L_St.0 - Gelding - SINATRA_DU_VILLAGE


title: hAFE_rep1


title: Whole blood - Ag.H_Al.0_Ap.H_St.L - Gelding - CRYSTAL_WHIT


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - VIDOCK_DE_RIOL


title: hPFE_H3K27ac_rep2


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - ASANKHYEYA

value: ASANKHYEYA


title: hDE_rep1


title: hAFE_H3K27me3_rep2


title: A549 cells, radiotherapy, rep1

city: Hamilton

first: Theodoros

last: Tsakiridis

address: 699 Concession St

country: Canada

institute: McMaster University

description:
RT A
Annotated_rlog_Normalized_DESeq2_Control_vs_RT.xls

library_source: transcriptomic

data_processing:
The sequencing data were uploaded to the Galaxy web platform and the public server at usegalaxy.org was used to process the data.
Raw RNA-seq reads were obtained from an Illumina HiSeq as 50bp single-end reads in FASTQ format with approximately 25 million reads per sample.
Raw reads underwent quality control and alignment against the GRCh38/hg38 genome using FastQC, Cutadapt and HISAT2.
Aligned reads per gene were then processed through featureCounts and DESeq2
Assembly: hg38
Supplementary files format and content: Excel file of DESeq2 normalized counts (control vs canagliflozin)
Supplementary files format and content: Excel file of DESeq2 normalized counts (control vs radiotherapy)

growth_protocol: A549 cells were maintained in DMEM (Wisent) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic in a humidified incubator with 5% CO2 at 37C

extract_protocol:
The RNeasy Mini Kit (QIAGEN) was used for total RNA purification. 1 ug of total RNA was used for construction of sequencing libraries.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with vehicle (DMSO; Sigma), 10 mM canagliflozin (MedChemExpress LLC) dissolved in DMSO or 5Gy (6 MV X-ray beams)

value: NSCLC cells

value: WT

value: 5 Gy + DMSO


title: A549 cells, vehicle control, rep3

description:
Control C
Annotated_rlog_Normalized_DESeq2_Control_vs_CANA.xlsx
Annotated_rlog_Normalized_DESeq2_Control_vs_RT.xls

value: DMSO


title: hAFE_H3K27ac_rep2


title: hESC_rep1


title: HeLa_WT_H3K27me3_eSPAN

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
library strategy: eSPAN
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.

source_name: HeLa

growth_protocol: Mouse E14 ES cells (a gift from Dr. Thomas Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere. HeLa and HEK 293T cells were cultured in DMEM medium supplemented with 10% (vol/vol) FBS and 1% penicillin/streptomycin. Primary mouse B cells were isolated from the spleen of 1-month old wild-type C57BL6 mice. B cells were activated and cultured as in Tubbs, A. et al. (2018).

extract_protocol:
eSPAN in mESC, mouse B cells and HeLa  cells were performed exactly as previously described (Li et al., 2020).GRO-seq (global run-on sequencing) was performed as previous described (Barbieri, E. et al., 2020).
GRO-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For CUT&TAG, CUT&RUN and eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

tag: experiments

tag: antibody vendor

value: Zhang Lab

tag: antibody cat.#


title: HeLa_WT_H4K20me2_eSPAN


title: hDE_Input


title: HeLa_POLE4KO_H3K9me3_CT

data_processing:
library strategy: CUT&TAG
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.


title: Whole blood - Ag.0_Al.0_Ap.L_St.0 - Mare - KATANIA

value: KATANIA


title: hDE_H3K27me3_rep2


title: Whole blood - Ag.H_Al.0_Ap.0_St.0 - Mare - SOUS_ENTENDU


title: hDE_H3K27me3_rep1


title: HeLa_POLE3KO_H3K9me3_eSPAN_rep2


title: HeLa_POLE4KO_H3K9me3_eSPAN_rep2


title: A549 cells, vehicle control, rep1

description:
Control A
Annotated_rlog_Normalized_DESeq2_Control_vs_CANA.xlsx
Annotated_rlog_Normalized_DESeq2_Control_vs_RT.xls


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Gelding - STARGATE

value: STARGATE


title: HeLa_POLE3KO_H3K9me3_eSPAN_rep1


title: hDE_H3K27ac_rep2

value: hDE


title: HeLa_WT_H3K9me3_eSPAN_rep2


title: RvsW-2005

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

description: RvsW

hyb_protocol: Just before hybridization, the oligos were fixed on the chip by exposure to 100 MJ of UV light in a UV Stratalinker 2400 crosslinker (Stratagene, La Jolla, California, USA).  The slides were then soaked twice in 0.2% sodium dodecyl sulfate (SDS) for 1 min. The probe solution was denatured at 100 °C for 1 min, cooled on ice for 2 min, stabilized at 37 °C for 5 min and injected into the hybridization chamber of the HS 4800 Hybridization Station (Tecan, Durham, North Carolina, USA). The slides were incubated at 37 °C for 16 h with medium agitation and then washed sequentially at 30 °C in 1X saline-sodium citrate (SSC)/0.1% SDS for 1 min 3 times, in 0.1X SSC/0.1% SDS for 1 min 3 times and finally in 0.1X SSC for 30 s.

scan_protocol: Microarrays were scanned using a GenePix 4000B fluorescence reader using GenePix Pro version 4 image acquisition software (Axon Instruments, Canada).

data_processing: Spot quantification and quality control was done using Maia version 2.75 (doi: 10.1093/bioinformatics/btl644). Bad quality spots and those with intensities above 50000 were filtered before further analyses. Data analyses were performed using the R/Bioconductor (doi: 10.1186/gb-2004-5-10-r80) package limma (doi: 10.2202/1544-6115.1027). Background correction was done using the normexp method (doi: 10.1093/bioinformatics/btm412). Array normalization was carried out using the limma function ‘normalizeWithinArrays’ (doi: 10.1016/s1046-2023(03)00155-5) and the method ‘printtiploess’.

organism: Vitis vinifera

source_name: berry skin

label_protocol: Fluorescently (Cy3/Cy5) labelled antisense RNA (aRNA) targets were obtained using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Austin, Texas, USA) according to manufacturer’s instructions. Six hundred pmol Cy3- and Cy5-labelled aRNA were pooled together, fragmented and adjusted to 100 µL with hybridization buffer.

growth_protocol: Ripening berries belonging to the Vitis vinifera cultivars cv. ‘Béquignol Noir’ (some of which presented the variegated berries), and ‘Béquignol blanc’ were sampled from a grapevine germplasm collection (INRA, France) at five weeks after the onset of ripening/ veraison (5WAV) at two consecutive years (2005 and 2006).

extract_protocol: RNA were extracted as described in Reid et al., 2006 (doi: 10.1186/1471-2229-6-27).

tag: skin color

value: white

tag: year

value: red


title: hES_H3K27me3_rep2_re-analyzed

tag: cell line

tag: cell type

value: hESC


title: Whole blood - Ag.H_Al.0_Ap.0_St.0 - Gelding - SIR_SANDRINO_DU_HANS

value: Gelding


title: hES_H3K27ac_rep2_re-analyzed

tag: chip antibody


title: ATAC-seq_hPFE_rep1


title: RvsW-2006

description: RvsW


title: ATAC-seq_hAFE_rep2


title: A549 cells, radiotherapy, rep3

description:
RT C
Annotated_rlog_Normalized_DESeq2_Control_vs_RT.xls


title: A549 cells, radiotherapy, rep2

description:
RT B
Annotated_rlog_Normalized_DESeq2_Control_vs_RT.xls


title: AFE_B

description:
B_RA_0nM.h5
B_RA_100nM.h5
B_RA_10uM.h5
B_RA_1uM.h5

data_processing:
To generate demultiplexed count matrices from fastq files, cellranger multi was used with GRCh38 genome version 2020-A as reference.
Further downstream processing was done with Scanpy v1.9.1
Assembly: hg38
Supplementary files format and content: Processed files contain 10x raw counts CellRanger v6.1.2 in HDF5 Feature-Barcode Matrix Format

extract_protocol:
Cells were washed once with PBS, singularized using TrypLE and resuspended in PBS + 0.5%BSA (FACS buffer) at the concentration of 1x10^6 cells/ml.
Approximately 500,000 cells for each sample were pelleted at 500 x g for 5 min at 4℃ and resuspended in 100 μL FACS buffer supplemented with 500 ng of one of four Hashtag Antibodies: A0251 anti-human Hashtag 1 Antibody (Biolegend 394601) for 0 nM RA, A0252 anti-human Hashtag 2 Antibody (Biolegend 394603) for 100 nM RA, A0253 anti-human Hashtag 3 Antibody (Biolegend 394605) for 1 μM RA, A0254 anti-human Hashtag 4 Antibody (Biolegend 394607) for 10 μM RA. Samples were incubated on ice for 30 min and then washed twice with 1 mL of FACS buffer. Cells were pelleted as before and resuspended in 250 μL FACS Buffer. Cells were filtered through 40 μM cell strainers (Fisher Scientific; 22363547) and counted on a hemocytometer. Equal counts of each of the four concentrations were combined and cells were recounted using a hemocytometer.  9,900 cells were used to generate 10X scRNAseq library using Chromium Next GEM Single Cell 3’ v3.1 reagents according to manufacturer’s instructions (10X Genomics; CG000206 Rev D). Hashtag libraries were prepared according to the manufacturer’s protocol (BioLegend). scRNAseq libraries were indexed using 10X SI-GA-B10 and SI-GA-B11 indices and HTO libraries were indexed using D701 (CGAGTAAT) and D702 (TCTCCGGA) indices. Libraries were sequenced on a Nextseq 550 using a High Output v2.5 75-cycle kit (Illumina, 20024906) to a mean read depth of 57,698 and 59,121 reads per cell for the two RNA replicates and 567 and 770 reads per cell for the respective hashtag libraries.

value: Anterior foregut endoderm

value: RA signalling


title: ATAC-seq_hAFE_rep1


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - TROUBLE_FETE

tag: alert

tag: horse type


title: hPFE_rep1

value: hPFE


title: A549 cells, canagliflozin, rep3

description:
CANA C
Annotated_rlog_Normalized_DESeq2_Control_vs_CANA.xlsx

value: 10 mM canagliflozin


title: AFE_A

description:
A_RA_0nM.h5
A_RA_100nM.h5
A_RA_10uM.h5
A_RA_1uM.h5


title: Whole blood - Ag.L_Al.L_Ap.0_St.L - Gelding - CALGARY_CHAMPEIX

tag: animal

tag: washbatch


title: A549 cells, canagliflozin, rep2

description:
CANA B
Annotated_rlog_Normalized_DESeq2_Control_vs_CANA.xlsx

tag: genotype


title: hDE_rep2


title: A549 cells, canagliflozin, rep1

description:
CANA A
Annotated_rlog_Normalized_DESeq2_Control_vs_CANA.xlsx

tag: treatment


title: TRAPSeq_5

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Sequencing results were quality checked using FastQC (version 0.11.7).
Illumina sequencing adaptors were removed using Trimmomatic (version 0.38) (Bolger et al., 2014), and reads aligning to the mouse rRNAs were removed using bowtie2 (version 2.3.5) (Dobin et al., 2013).
Surviving reads were then aligned to the mouse transcriptome (Ensembl Release 93) using STAR (version 2.7.0d) (Langmead and Salzberg, 2012).
The number of reads mapped to each gene were counted using htseq-count (version 0.9.1).
Genome_build: Mouse: Ensembl 93
Supplementary_files_format_and_content: Gene counts

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was extracted from the input and TRAP samples using the RNA Clean & Concentrator Kit (Zymo Research). RNA quality and concentration were measured using a NanoDrop spectrophotometer and a High Sensitivity RNA ScreenTape (Agilent Technologies). All samples had RNA integrity scores >7.0.
Barcoded libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) and the NEBNext rRNA Depletion Kit (NEB #E6310), according to the manufacturers’ instructions. Each library was screened for quality and adapter dimers on a High Sensitivity D1000 ScreenTape (Agilent Technologies), then sequenced on an Illumina HiSeq 3000 using 150bp, single-end reads.

tag: sample group

value: TRAP

value: Astrocytes

tag: mouse id


title: HTO_B


title: hESC_rep3


title: Whole blood - Ag.L_Al.L_Ap.0_St.L - Mare - HERA

tag: welfare score

value: Mare

value: HERA


title: hESC_rep2


title: TRAPSeq_4


title: N2156_JM103-hIPS-d35+2-30.10.20

city: Hannover

first: Joachim

middle: D.

last: Meissner

address: Carl-Neuberg-Str. 1

department: Molecular and Cellular Physiology

institute: Hannover Medical School

description:
processed data file:
Galaxy25-(N2147-N2156_All_d37_vs_d35_DESeq2_result_overview).tabular

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (v 1.4.2). The pipeline uses Nextflow ( v20.01.0) workflow tool and includes read trimming (Trim Galore! v0.6.4), alignment (STAR v2.6.1d), and counting (featureCounts  v1.6.4).
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool v2.11.40.2) with default settings except for “Output normalized counts table”, “Turn off outliers filtering”, and “Turn off independent filtering”, all of which were set to “True”.
Genome_build: GRCh38.p13; release 34
Supplementary_files_format_and_content: Tab-delimited text files include normalized espression values as a matrix table for all or a part of the samples (DESeq2 output)

source_name: hiPSC

extract_protocol:
Total RNA was isolated from hESC-CMs and hiPSC-CMs cultivated for 37 days or replated on day 35 and cultivated for 2 more days using the peqGOLD Total RNA Kit (Peqlab, a VWR Life Science brand) according to the manufacturer's instructions.
70ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs).

value: hiPSC-CMs

tag: replicates

value: technical replicate B

tag: cultivation

value: plated for 35 days on laminin-coated glass coverslips and replated for 2 more days


title: A549 cells, vehicle control, rep2

description:
Control B
Annotated_rlog_Normalized_DESeq2_Control_vs_CANA.xlsx
Annotated_rlog_Normalized_DESeq2_Control_vs_RT.xls

value: NSCLC cells

value: WT

value: DMSO


title: TRAPSeq_2


title: N2154_JM103-hIPS-d35+2-30.10.20

value: technical replicate A


title: N2153_JM102-hIPS-d37-30.10.20

value: plated for 37 days on laminin-coated glass coverslips


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Mare - VELOCE_DE_RIVERLAND

tag: agressiveness


title: Whole blood - Ag.L_Al.0_Ap.H_St.0 - Gelding - UN_AMOUR_DEL_CABALERO

tag: unresponsiveness

value: Gelding


title: TRAPSeq_1


title: HeLa_POLE3KO_H3K9me3_CT

tag: experiments

tag: antibody vendor

value: Zhang Lab

tag: antibody cat.#


title: N2152_JM101-hES-d35+2-23.10.20

description:
processed data file:
Galaxy25-(N2147-N2156_All_d37_vs_d35_DESeq2_result_overview).tabular; Galaxy26-(N2147-N2156_hES_d37_vs_d35_DESeq2_result_overview).tabular

source_name: hES

tag: cell type

value: hES-CMs

value: biological replicate C


title: HeLa_WT_H3K9me3_CT

tag: chip antibody


title: RNASeq_5

value: Input


title: Whole blood - Ag.H_Al.0_Ap.L_St.0 - Gelding - PARADOR_DU_FOUSSAL

tag: horse type


title: Whole blood - Ag.0_Al.L_Ap.L_St.H - Gelding - RICHEBOY_DE_THOISY

tag: animal


title: Whole blood - Ag.0_Al.0_Ap.H_St.0 - Gelding - RIESLING_LES_PARTS

tag: washbatch


title: N2150_JM97-hES-35+2-17.07.20

value: biological replicate B


title: WvsR-2005

description: WvsR

tag: skin color

value: red

tag: year

value: white


title: N2148_JM93-hES-d35+2-13.07.20

value: biological replicate A


title: Whole blood - Ag.0_Al.0_Ap.0_St.H - Mare - ALDEA_DESCAZAL

tag: alert

value: Mare


title: RNASeq_2

tag: sample group

value: Astrocytes

tag: mouse id


title: hepatocytes, tKO_9

city: Brooklyn

first: Mulin

last: He

state: New York

address: 310 Clarkson Avenue, Apt.615

institute: SUNY Downstate Health Sciences Univ

description: AllSamples.GeneExpression.FPKM.txt

data_processing:
For liver samples from wild-type (WT) and Smsr-KO mice, the raw data of sequence reads were trimmed using Trimmomatic (v.0.36).
For isolated primary hepatocytes from WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice, the raw sequencing reads were trimmed using SOAPnuke (v.1.5.2).
The trimmed reads were further mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner (v.2.5.2b) and Bowtie2 (v.2.2.5) respectively.
Then, the extracted gene hit counts were used for differential expression analysis using DESeq2 (v.1.30.1).
Assembly: mm10
Supplementary files format and content: raw counts, TPM values, or FPKM values for each sample

source_name: liver

extract_protocol:
For SMSrKO mice, total RNA was extracted from sWAT using an RNeasy Plus Micro Kit (Qiagen). RNA samples were quantified using a Qubit 4 fluorometer (Thermo Fisher Scientific), and RNA integrity was determined using a 4200 TapeStation System (Agilent Technologies).
For SMSrKO mice, the RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit s (NEB) and sequenced on an Illumina HiSeq.
For WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice, hepatocyte samples were isolated from two months old WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice (n=3 per group) using a two-step collagenase method.
RNA was extracted from primary hepatocytes with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was checked using 2200 TapeStation system (Agilent Technologies).

tag: tissue

value: liver

value: hepatocytes

tag: genotype


title: D-Biotin

type: protein

city: Shanghai

first: Jing

last: Zhong

address: 1200,Cailun Road, Shanghai

country: China

institute: Shanghai University of Traditional Chinese Medicine

description: Biotin was spotted on 20000 spots on human proteome  microarray.

hyb_protocol: Briefly, proteome microarrays were blocked with blocking buffer (5% BSA in 0.1% Tween 20, PBST) for 1 h at room temperature with gentle agitation. Biotin-HDCA and biotin were diluted to 100 μM in PBST and incubated on proteome microarray at room temperature for 1 h (Biotin-HDCA was synthesized by Xi'an Ruixi Biological Technology Co.,Ltd). After washing with PBST three times, microarray was incubated with 0.1% Cy5-Streptavidn solution for 20 min at room temperature in the dark, followed by three 5-min washes in PBST.

scan_protocol: The microarray was spun dry at 100 × g for 2 min and scanned with GenePixTM 4000B (Axon Instruments, CA).

data_processing: GenePixTM Pro v6.0 was used for data analysis. The median fluorescence signal at each site (F635_Median) was divided by the background (B635_Median) for data analysis, that is, original signal strength (I) = F635_Median/B635_Median. The median and SD of I were calculated to obtain the corrected data Z-Score (corrected signal strength) for each site.

molecule: protein

source_name: Compound

tag: concentration


title: Acta2 R179C, SMC, Rep 1

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

data_processing:
Reads aligned to mm10 genome using bwa (v.0.7.12)
Peaks called using MACS2 (v2.1.0)
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: Primary aortic SMC

growth_protocol: Lonza SMC medium

extract_protocol:
Cells permeabilized, processed for transposase reaction, indexed PCR and DNA purification according to Active Motif cultured cell ATAC-seq kit specifications
Unique indexed illumina primer pairs used to amplify tagmented DNA sequences following transposase reaction.

treatment_protocol: Serum starved 24 hours

tag: cell line

value: Primary aortic SMC


title: HeLa_POLE4KO_H3K9me3_eSPAN_rep1

tag: experiments


title: Biotinylated HDCA

description: Biotin-HDCA was spotted on 20000 spots on human proteome  microarray.


title: mES_POLE3MPP8KO1_Groctr_rep1

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.
Library strategy: GRO-seq

source_name: mESC

tag: molecule subtype

value: nascent RNA


title: mES_POLE3MPP8KO2_Groctr_rep2


title: hepatocytes, tKO_8

description: AllSamples.GeneExpression.FPKM.txt


title: NKO-Wtres_cmcRep2

data_processing:
Adapter and QC trimming by Trimmomatic then alignment to GRCh38/hg38 human genome using STAR
Samtools mpileup to produce text pileup output from aligned BAM files
Custom python scripts to count variants caused by CMC treatment in mpileup output
Assembly: hg38
Supplementary files format and content: txt files of deletions counted at each position across the mitochondrial genome normalized to total reads in CMC treated relative to untreated samples

extract_protocol:
Mtiochondria were isolated by subcellular fractionation followed by RNA extraction using Trizol and isopropanol precipitations
CMC treatment of purified RNA followed by library construction using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara)

value: NME6 KO + WT-NME6 cDNA

tag: treatment

value: 0.5M CMC


title: Whole blood - Ag.0_Al.0_Ap.L_St.0 - Gelding - DOMINGO_DE_HUS

tag: welfare score

value: Gelding


title: RNASeq_1

tag: cell type


title: WvsR-2006

description: WvsR


title: NKO-Wtres_cmcRep1


title: hepatocytes, dKO_6

description: AllSamples.GeneExpression.FPKM.txt


title: NKO-WTres_Minus

value: Untreated


title: mES_MPP8KO_GroG2M_rep1


title: mES_MPP8KO_GroG2M_rep2


title: mES_MPP8KO_GroS_rep1


title: mES_MPP8KO_GroG1_rep2


title: HeLa_WT_H3K9me3_eSPAN_rep1

value: WT

tag: chip antibody

tag: antibody vendor

value: Zhang Lab

tag: antibody cat.#


title: mES_MPP8KO1_Groctr_rep1


title: hepatocytes, dKO_4

description: AllSamples.GeneExpression.FPKM.txt


title: N2155_JM102-hIPS-d37-30.10.20

value: hiPSC-CMs

tag: replicates

value: technical replicate B

tag: cultivation

value: plated for 37 days on laminin-coated glass coverslips


title: VK1-2

city: Beijing

first: Ying

last: Shang

address: Anxiangbeili Street

institute: Strategic Support Force Medical Center

description: VK1 treatment

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: HG38

source_name: Jurkat T cells

growth_protocol: The cells were cultured in RPMI 1640 medium (HyClone, USA) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS; Gibco BRL, USA), antibiotics (penicillin 100U/ml and streptomycin 100μg/ml; Livning Biotechnology, Beijing, China) at 37 °C under 5% CO2 in air.

extract_protocol:
The purified total RNA was subjected to mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end-repair, A-tailing, adapter ligation, and enrichment to construct sequencing libraries.
The qualified libraries were applied to the Illumina NovaSeq6000 sequencing platform (Illumina, CA, USA) for PE150 sequencing mode.

treatment_protocol: Jurkat T cells (1 × 107 cells) were seeded in flask and incubated with culture medium containing 50 μM VK1 for 15 h.

value: Jurkat T cells

value: VK1 treatment


title: VK1-1

description: VK1 treatment


title: HTO_A

value: Anterior foregut endoderm

value: RA signalling


title: VK1-3

description: VK1 treatment


title: Whole blood - Ag.0_Al.0_Ap.H_St.0 - Mare - CARO_DESBOIS

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 081421_D_F_20160126). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 6 out of 45 microarrays. At this step, 42126 spots out of 62976 were selected.  The mean signal of the 16 first samples and 29 last ones were subtracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 30265 rows each corresponding to a unique ProbeName (provided as data Matrix).

tag: unresponsiveness

tag: horse type

value: Mare

tag: animal

tag: washbatch


title: N2151_JM100-hES-d37-23.10.20

value: hES-CMs

value: biological replicate C


title: RNASeq_4

tag: sample group

value: Input

value: Astrocytes

tag: mouse id


title: N2149_JM96-hES-37-17.07.20

value: biological replicate B


title: N2147_JM92-hES-d37-13.07.20

value: biological replicate A


title: Acta2 R179C, SMC, Rep 2

tag: cell line

value: Primary aortic SMC

tag: genotype


title: Whole blood - Ag.H_Al.0_Ap.0_St.0 - Mare - D_AMOUR

tag: agressiveness


title: Control, SMC, Rep 1

value: WT


title: NKO-Wtres_cmcRep3

value: NME6 KO + WT-NME6 cDNA

tag: treatment

value: 0.5M CMC


title: Control, SMC, Rep 2


title: CD4+ B12(VHH)-CAR-T cells stimulated with IMR5 tumor cells, scRNA-seq

city: Bethesda

first: Mitchell

last: Ho

state: MD

address: 37 Convent Drive, Rm5002

department: LMB/CCR

institute: NCI

description: Illumina

data_processing:
Raw Fastq Sequencing data was initially quality controlled with FASTQC version 0.11.9 to ensure reliable data quality.
Cutadapt version 3.4 was utilized to trim nucleotide bases from Read 1 that were not relevant for cell barcode identification.
Subsequently Alevin Salmon version 1.4.0 was utilized for cell barcode identification and gene expression quantification.
AlevinQC v. 1.10.0 was utilized to quality control the Alevin Salmon data processing step to ensure accurate estimation of cell barcodes identified.
Assembly: Human Reference - Release 36 (GRCh38.p13).

source_name: primary T cells

extract_protocol:
Cells were lysed in sealed microchambers and then mRNA was captured by barcoded microbeads
cDNA production occurs in the sealed micro chambers through action of reverse transcriptase.  cDNA amplification protocol was developed in-house using a commercially available polymerase. Illumina library preparation was done using the manufacturer’s protocol and Nextera XD library preparation kit (Illumina, FC-131-1096).

value: primary T cells

value: CD4+ T cell

value: stimulated with IMR5 cells


title: Whole blood - Ag.H_Al.H_Ap.0_St.0 - Mare - ATHENA_CHAMPEIX

tag: alert

tag: welfare score


title: hepatocytes, WT_2

description: AllSamples.GeneExpression.FPKM.txt

tag: tissue

value: liver

tag: cell type

value: hepatocytes


title: hepatocytes, tKO_7

description: AllSamples.GeneExpression.FPKM.txt


title: mES_MPP8KO2_Groctr_rep2

tag: experiments

tag: molecule subtype

value: nascent RNA


title: mES_MCM22A_Triptolide_H3K27me3_eSPAN

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.
Library strategy: CUT&TAG

tag: chip antibody

tag: antibody vendor

value: Cell Signaling

tag: antibody catalog#


title: mES_MPP8KO_GroS_rep2


title: hepatocytes, dKO_5

description: AllSamples.GeneExpression.FPKM.txt


title: C2

description: Control

value: Jurkat T cells

value: No medication required


title: mES_MCM22A_DMSO_H3K27me3_eSPAN


title: C1

description: Control


title: mES_MPP8KO_GroG1_rep1


title: mES_WT2_Groctr_rep2


title: hepatocytes, WT_3

description: AllSamples.GeneExpression.FPKM.txt


title: mES_POLE4KO_Triptolide_H3K9me3_CT_rep1

value: Zhang Lab


title: HeLa_TASORKD_H3K9me3_CT_rep1

value: TASORKD


title: mES_WT_Triptolide_H3K9me3_CT_rep1


title: mES_WT_DMSO_H3K9me3_CT_rep1


title: mES_WT1_Groctr_rep1


title: mES_MCM22A_DMSO_H3K27me3_CT


title: mES_MCM22A_Triptolide_H3K27me3_CT


title: dbp2_TTseq_1

city: West Lafayette

first: Elizabeth

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

data_processing:
Raw reads were cleaned (adpater trimming, quality-trimming, removal of reads less than 50bp) was performed using Fastp toolkit.
Coordinates for predicted non-coding transcripts (CUTs, SUTs and XUTs) and coding genes  in Saccharomyces cerevisiae were collected.
Genes and non-coding transcripts that have overlapping coordinates and located on opposite strands were determined using R-packages
Read counts for gene and antisense coordinates were determined using featurecounts.
Data was further filtered to keep the longest non-coding transcript per gene.
Differential expression was determined (treatment vs control) using coordinates for 1,669 non-coding transcripts and yeast genes was performed using edgeR.
Assembly: Saccharomyces_cerevisiae.R64
Library strategy: TT-seq

organism: Saccharomyces cerevisiae

source_name: cultures

growth_protocol: Yeast strains transformed with an empty URA vector, pRS426, were grown at 30˚C in SD-URA + 2% glucose media to an OD600 of 0.5.

extract_protocol:
RNA was extracted using a hot phenol protocol. RNAs were sonicated to an average size of 1 kb in a Covaris sonicator. 4-thiouracil-containing RNAs were biotin-labeled using EZ-link biotin (Sigma) at a final concentration of 0.2 mg/mL for 2 hours at room temperature. Treated RNAs were extracted twice with chloroform and ethanol precipitated. Biotinylated RNAs were enriched using the µMACS Streptavidin kit (Miltenyi) as per manufacturer’s instructions. Enriched RNAs were ribodepleted using a Ribominus yeast/bacteria ribodepletion kit (Thermofisher) and size selected using an RNA Clean and Concentrator-5 kit (Zymo Research).
Using the NEBNext Ultra II Directional RNA Library kit (NEB)

treatment_protocol:
Cultures were then treated with 4-thiouracil at a final concentration of 0.32 mg/mL for 10 minutes at 30˚C.
Cultures were then fast cooled in a dry ice/ethanol bath before pellets were harvested by centrifugation and stored at -80˚C.

value: cultures

value: DBP2 knockout


title: hepatocytes, WT_1

description: AllSamples.GeneExpression.FPKM.txt


title: WT_TTseq_3


title: mES_WT_Triptolide_H3K9me3_CT_rep2


title: mES_POLE4KO_Triptolide_H3K9me3_CT_rep2


title: mES_WT_Triptolide_H3K9me3_eSPAN_rep2

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.
Library strategy: eSPAN


title: HeLa_MPP8KD_H3K9me3_CT_rep2


title: dbp2_TTseq_3


title: mES_POLE4KO_Triptolide_H3K9me3_eSPAN_rep1


title: HeLa_TASORKD_H3K9me3_CT_rep2


title: mES_POLE4KO_Triptolide_H3K9me3_eSPAN_rep2


title: dbp2_TTseq_2


title: mES_WT_Triptolide_H3K9me3_eSPAN_rep1


title: WT_TTseq_2


title: HeLa_WT_H3K9me3_CT2


title: mES_POLE4KO_DMSO_H3K9me3_eSPAN_rep2


title: mES_WT_DMSO_H3K9me3_eSPAN_rep4


title: HeLa_MPP8KD_H3K9me3_CT_rep1


title: mES_POLE4KO_DMSO_H3K9me3_eSPAN_rep1


title: HeLa_WT_TASOR_eSPAN_rep1

value: Anti-TASOR

value: GeneTex


title: mES_POLE4KO_DMSO_H3K9me3_CT_rep1


title: WT_TTseq_1

value: WT


title: mES_WT_DMSO_H3K9me3_eSPAN_rep3


title: HeLa_TASORKD1_H3K9me3_eSPAN_rep1


title: Islets, 22mM Glucose + 5uMO304, 48h, rep5

city: Umeå

first: Stefan

last: Norlin

address: Trastvägen 4F

department: UCMM

country: Sweden

institute: Umeå University

data_processing:
Fastq quality control (FastQC)
Mapping performed using STAR.
Read counts were obtained using STAR/featurecounts on gene level
Assembly: GRCm39 , version 103, ensembl.org
Supplementary files format and content: comma-delimited textfile containing raw counts for each sample

molecule: polyA RNA

source_name: Islets of Langerhans

growth_protocol: Mice were killed by cervical dislocation and the pancreata were perfused with 2.5 ml cold collagenase (without Mg2+/Ca2+, GIBCO #14180). The pancreata were then dissected out and incubated at 37 °C for 10–15 min. Collagenase activity was stopped by adding 25 ml of Hanks’ solution (with Mg2+/Ca2+, GIBCO #14060) and vigorous shaking released the islets from the rest of the pancreatic tissue. Islets were rinsed in icecold Hanks’ three times and then picked manually under a stereo microscope. Islets were then cultured for 48h in media (RPMI 1640 medium [GIBCO #11879-0], 1% fetal bovine serum [GIBCO #10500-064], 10 mM HEPES [Umeå University, Laboratory medicine], 1 mM sodium pyruvate [Gibco, #11360-039], 50μM 2-mercaptoethanol [Gibco, #31350-010], 50U/ml Pen:Strep [Gibco #15140-122]) supplemented with 11mM glucose or 22mM glucose +/- 5μM O304

extract_protocol:
Total RNA from isolated islets was prepared using RNeasy Micro Kit (Qiagen #74004)
Sequencing libraries were prepared from 150ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (#1000000040498)

treatment_protocol: Islets were treated for 48h in growth media supplemented with 11mM glucose or 22mM glucose +/- 5μM O304

value: Islets of Langerhans


title: Islets, 22mM Glucose + Vehicle, 48h, rep5


title: HeLa_WT_MPP8_eSPAN_rep1

value: Proteintech


title: Islets, 11mM Glucose + Vehicle, 48h, rep5


title: mES_WT_MidS_H3K9me3_CT_rep2


title: mES_WT_DMSO_H3K9me3_eSPAN_rep1


title: mES_WT_nextG1_H3K9me3_CT_rep2


title: HeLa_MPP8KD2_H3K9me3_eSPAN_rep1


title: mES_WT_nextG1_H3K9me3_eSPAN_rep3


title: mES_WT_nextG1_H3K9me3_eSPAN_rep2


title: HeLa_MPP8KD1_H3K9me3_eSPAN_rep1


title: Islets, 22mM Glucose + 5uMO304, 48h, rep4


title: mES_WT_LateS_H3K9me3_eSPAN_rep2


title: Islets, 11mM Glucose + 5uMO304, 48h, rep4


title: mES_WT_MidS_H3K9me3_eSPAN_rep2


title: mES_WT_LateS_H3K9me3_eSPAN_rep3


title: mES_WT_DMSO_H3K9me3_eSPAN_rep2


title: Islets, 11mM Glucose + 5uMO304, 48h, rep5


title: HeLa_POLE4KD_H3K9me3_CT_rep2


title: Islets, 22mM Glucose + Vehicle, 48h, rep4


title: mES_TASORM2_H3K9me3_CT_rep1


title: mES_TASORM3_H3K9me3_CT_rep1


title: HeLa_POLE3KD_H3K9me3_CT_rep2


title: mES_WT_LateS_H3K9me3_CT_rep2


title: HeLa_TASORKD2_H3K9me3_eSPAN_rep1


title: Islets, 11mM Glucose + Vehicle, 48h, rep4


title: HEK293_HA_RPB1_rep2

city: Austin

first: Yan

middle: Jessie

address: 100 E. 24th Street

institute: University of Texas-Austin

data_processing:
Base-calling was performed by Novogene Inc. with the latest Illumina software
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.2.7.1 with the default significance cut-off q-value <=0.1 for broad peaks
bigWig files were generated using the bedGraph files of scores outputted from MACS2.
Assembly: hg38
Supplementary files format and content: bigWig files for all experimental samples

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed 2mM DSG for 15 minutes followed by 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorupter UCD-200
ChIP-seq libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina with barcode primers from NEBNext® Multiplex Oligos. 5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 300-500bp in length using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: For inhibition study, cells were treated with 2μM of Flavopiridol for 4 hours prior to fixation

value: Human embryonic kidney

value: HA (Cell signaling, #3724)


title: mES_TASORM1_H3K9me3_CT_rep2


title: Islets, 22mM Glucose + 5uMO304, 48h, rep3


title: mES_TASORM1_H3K9me3_CT_rep1


title: HEK293_HA_RPB1_rep1


title: mES_Ctrl_H3K9me3_CT3


title: Islets, 22mM Glucose + Vehicle, 48h, rep3


title: Islets, 11mM Glucose + 5uMO304, 48h, rep3


title: mES_TASORM3_H3K9me3_eSPAN_rep1


title: mES_TASORM2_H3K9me3_eSPAN_rep2


title: HEK293_HA_CHERPdeltaCID_rep1


title: mES_TASORM3_H3K9me3_eSPAN_rep2


title: Islets, 11mM Glucose + Vehicle, 48h, rep3


title: mES_TASORM1_H3K9me3_eSPAN_rep3


title: mES_TASORM2_H3K9me3_CT_rep2


title: mES_TASORM2_H3K9me3_eSPAN_rep1


title: Islets, 22mM Glucose + 5uMO304, 48h, rep2


title: mES_TASORM1_H3K9me3_eSPAN_rep1


title: mES_Ctrl_H3K9me3_CT2


title: HCT116, IGF2BP3, IgG RNase I, in-lysate 0.1 U/μL, on-bead 0.025 U/μL

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

data_processing:
library strategy: PAR-CLIP
Basecalling was performed using Real-Time Analysis (RTA) v1.18.54.4. BCL files were converted to demultiplexed fastq files with bcl2fastq v2.20.0.422. Tiles within the rages 1150-1223, 2101-2125, 2254-2278 and 1242 were excluded due to low quality of produced reads.
For the demultiplexed data sets unique molecular identifiers were extracted and adapter sequences were trimmed using UMI-tools v1.1.1. The reads were size and quality trimmed using trimmomatic v0.30 to have the length between 18 and 45 nt.
The reads then were mapped to the GENCODE human genome assembly GRCh38.p13 with bowtie v0.12.7 allowing up to 3 mismatches and deduplicated using UMI-tools v1.1.1. IGF2BP3-binding clusters were called with PARalyzer v1.5 (.ini file parameters: BANDWIDTH=3, CONVERSION=T>C, MINIMUM_READ_COUNT_PER_GROUP=5, MINIMUM_READ_COUNT_PER_CLUSTER=2, MINIMUM_READ_COUNT_FOR_KDE=3, MINIMUM_CLUSTER_SIZE=11, MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2, MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2,  MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1, MINIMUM_READ_LENGTH=18, MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=1)
Assembly: hg38
Supplementary files format and content: csv, PARalyzer output (clusters)

growth_protocol: HCT116 conditionally expressing Tet-OsTIR1 were obtained from Masato Kanemaki Lab and cultured in McCoy's 5A (Modified) Medium (Sigma) with 10% Fetal Bovine Serum (Gibco), 2 mM Glutamine (Sigma), 1% Pen/Step (Sigma).

extract_protocol:
Five 15 cm (diameter) dishes of 60 % confluent cells per condition were put on ice, washed with ice-cold PBS (Sigma) and crosslinked with the UV light at 365nm with 0.15 J/cm2 and pelleted. Cell pellets were lysed in 1250 μL of ice-cold lysis buffer (25 mM HEPES pH 7.3, 150 mM NaCl, 0.5% NP-40, 0.5 mM EDTA, 10% Glycerol, 0.1% SDS, 0.2% Sodium Deoxycholate, 1x protease inhibitors cocktail, 0.1mM DTT), by incubation on ice for 15 min with intermittent vortexing and passing three times through the 27G needle. The lysate was clarified by centrifugation for 20 min at 20,000g at +4ºC. 1100 μL of the supernatant was taken for the in-lysate RNase digestion on a rotator for 15 min at room temperature. The RNase I (Ambion) was used at 0.1 or 0.05 U/μL and RNase T1 (Thermo Scientific) at 1 or 0.25 U/μL. For IP 50 μg of Proteintech anti-IGF2BP3 antibody (14642-1-AP, lot 00090203) or Proteintech IgG control (30000-0-AP) were coupled to the 200 μL of protein G Dynabeads (Invitrogen) in 1 mL of lysis buffer for 20 min rotating at room temperature, washed three times with 1 mL of the lysis buffer, resuspended in the original bead volume (200 μL) and added to 1 mL of the RNase treated lysate. The IP was incubated on a rotator at +4ºC for 4 hours, washed twice and resuspended in 1 mL of the lysis buffer. For the on-beads RNase treatment RNase I (Ambion) was added at 0.05 or 0.025 U/μL and RNase T1 (Thermo Scientific) at 1 or 0.25 U/μL. For RNase treatment, the samples were incubated on the rotator for 15 min at room temperature and cooled on ice for 5 min. Then the beads were washed three times with 1 mL of ice-cold high salt wash buffer (25 mM HEPES pH 7.3, 400 mM NaCl, 0.5% NP-40, 0.5 mM EDTA, 10% Glycerol, 1x protease inhibitors cocktail, 0.1mM DTT), with 3 min incubations on ice after each wash step.
Library strategy: PAR-CLIP For dephosphorylation of the crosslinked RNA fragments, the beads were washed once with 1 mL of PNK wash buffer (20 mM Tris-HCl pH 6.5, 10 mM MgCl2, 0.2% Tween20, 0.1mM DTT), resuspended in 200 μL of dephosphorylation mix (1x PNK buffer pH 6.5 (70 mM Tris-HCl pH 6.5, 10 mM MgCl2, 1 mM DTT), 100 U T4 polynucleotide kinase (NEB), 20 U SUPERase·In (Invitrogen)) and incubated at 37 °C for 30 min with shaking at 1100 rpm. Afterwards, the beads were kept on ice and washed once with 1 mL of PNK wash buffer, incubated in 1 mL of high salt wash buffer for 5 min on ice and washed once more with 1 mL of PNK wash buffer. For 3’ adapter ligation (ordered as /5Phos/NNNNNATCGTAGATCGGAAGAGCACACGTCTGAA/3AzideN/, pre-adenylated using 5’ DNA Adenylation Kit (NEB) and conjugated to the IRdye-800CW-DBCO (LiCor) was via “click” chemistry at 37 °C for 2 hours as described in (Zarnegar et al. 2016), the beads were resuspended in 200 μL of the ligation reaction mix (20% PEG8000, 1x T4 RNA Ligase Reaction Buffer (NEB), 1000 U T4 RNA Ligase 2 truncated KQ (NEB), 50 pmol 5' pre-adenylated IR-dye conjugated DNA adapter and 20 U SUPERase·In) and incubated at 25°C for 3 hours with shaking at 1100rpm in the dark. Next, the beads were transferred on ice and washed once with 1 mL of PNK wash buffer, incubated in 1 mL of high salt wash buffer for 5 min on ice, resuspended in 1 mL of PNK wash buffer and transferred to the new low-bind RNase-free 1.5 mL tube. The PNK wash buffer was removed and the crosslinked protein-RNA complexes were eluted in 40 μL of 1x SDS sample buffer without DTT at +70ºC for 10 min. DTT at 20mM concentration was added to the collected eluates and the samples were heated at +70ºC for 10 min and stored at -80ºC. Next, the crosslinked protein-RNA complexes were resolved on a 10 well 4-12% NuPAGE Novex Bis-Tris gel (Invitrogen) in 1x MOPS-SDS running buffer (Invitrogen) at 200 V for 65 min. The gel was visualized at 800nm using LI-COR Odyssey CLx near infrared imager and RBP-RNA complexes were size selected using imager’s grid. The bands corresponding to IGF2BP3-RNA complexes were excised from the gel and transferred to a low-bind RNase-free tube. For the samples with the RNase treatment conditions in-lysate and on-beads: RNase I 0.05 U/µl, RNase T1 1 U/µl proteinase K digestion was performed as described in (Acosta-Alvear et al. 2018). The gel piece was transferred to nuclease free water preequilibrated Pur-A-Lyzer Midi Dialysis Tube (MWCO 3.5 kDa, Sigma) with 200 μL 1x MOPS-SDS running buffer (Invitrogen) and electroelution was performed at 100 V for 2 h. The polarity of the electric current was reversed for 120 seconds, sample was transferred to the new 2 mL low-bind RNase-free tube with an equal volume of 2x Proteinase K buffer (100 mM HEPES pH 7.3, 100 mM NaCl, 20 mM EDTA, 2% SDS) and proteinase K (Invitrogen) at the final concentration of 1.2 mg/ml and incubated for 30 min at +55 ºC. For the samples with RNase treatment conditions: RNase I 0.05 U/µl in-lysate and 0.025 U/µl on-beads, RNase I 0.01 U/µl in-lysate and 0.025 U/µl on-beads, and RNase T1 0.25 U/µl in-lysate and on-beads gel extraction and protein digestion were performed as described in (Anastasakis et al. 2021). Gel pieces were transferred to 1.5 mL low-bind RNase-free tube, frozen at -80ºC, thawed at +55ºC and crashed with a single use RNase-free pellet pestle. Gel slurry was boiled in 2x proteinase K buffer with 50 mM DTT at +95ºC for 2 min and was subsequently incubated three times with fresh addition of proteinase K at 2.4 mg/ml, 1.5 mg/ml, and 2.4 mg/ml in 2x proteinase K buffer at +50 ºC for 30 min with shaking at 1100rpm. Extracted 3’ adapter-ligated RNA fragments were separated from the gel by centrifugation at 10,000g for 10 min through Spin-X centrifuge filter (Costar). For all samples, RNA was extracted with 1 mL of acidic phenol – chloroform – IAA (25:24:1, pH 4.0), isopropanol precipitated, resuspended 1x TBE-Urea dye (Invitrogen), denatured by heating at +75ºC for 2 min and resolved on a 10 well 15% TBE-Urea gel (Invitrogen) in 1x TBE running buffer (Invitrogen) at 180 V for 70 min. The gel was visualized at 800 nm using LI-COR Odyssey CLx near infrared imager and the 3’ adapter-ligated RNA fragments were size selected using imager’s grid. Gel pieces were transferred to 1.5 mL low-bind RNase-free tube, frozen at -80º C, thawed at +55º C and crashed with a single use RNase-free pellet pestle. 3’ adapter-ligated RNA fragments were extracted from the gel during overnight incubation rotating in 300 μL of RNA elution buffer at +4ºC (10mM Tris-HCl pH 7.0, 0.3 M NaOAc pH 5.5, 2mM EDTA, 20 U SUPERase·In). Extracted complexes were separated from the gel fragments by centrifugation at 10,000 g for 10 min through Spin-X centrifuge filter, ethanol precipitated and resuspended in 11.5 μL of nuclease-free water. For reverse transcription, 1 μL of 1 μM reverse transcription primer (/5Phos/RNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC) was added to the sample. The sample was incubated at +70 ºC for 10 min and transferred on ice. Then the components of the reverse transcription mix were added to the sample making final volume of 20 μL (1x Superscript IV buffer, dNTPs 0.2 mM each, 5 mM DTT, 10 U SUPERase·In, 200 U Superscript IV (Invitrogen)), the reaction was performed at +55 ºC for 20 min and inactivated at +80 ºC for 5 min. 2.2 µl of 1 M NaOH was added and RNA was hydrolyzed in 30 min incubation at 98 °C. The reaction was neutralized by addition of 2.2 µl of 1 M HCl. The reverse transcription reaction was purified on Oligo Clean & Concentrator columns (Zymo) according to the manufacturer’s instructions and eluted in 6 µl of nuclease-free water. cDNA was mixed with 6 µl of 2x TBE-Urea dye), denatured by heating at +75ºC for 2 min and resolved on a 10 well 10% TBE-Urea gel (Invitrogen) in 1x TBE running buffer at 180 V for 70 min. The gel was stained with SYBR gold (Invitrogen), visualized and the reverse transcription product was separated from the unreacted primer and no-insert products. Gel extraction was performed similarly as for the 3’ adapter-ligated RNA fragments using DNA elution buffer (10 mM Tris-HCl pH 8.0, 0.3 M NaOAc pH 5.5). After ethanol precipitation, the pellet was resuspended in 10 μL of circular ligation reaction mix (1x CircLigase II buffer, 2.5 mM MnCl2, 50 U CircLigase II (Lucigen)). Circular ligation was performed at +60°C for 2 hours and the enzyme was inactivated through heating at +80°C for 10 min. To amplify the libraries the PCR reactions were performed with NEB Phusion polymerase and index primers (NEB, E6609S). The reaction mix of 50 µl (1x High fidelity buffer, dNTPs 0.2 mM each, 500 nM NEB Universal primer, 500 nM NEB Index primer, 2 µl circularization reaction, 1 U Phusion polymerase) was run according to the following program: 98 °C, 30 sec; 20 cycles of 98 °C, 10 sec; 65 °C, 10 sec; 72 °C, 10 sec; 72 °C, 5 min. Typically, the number of cycles was 16-18 for IGF2BP3 IP and 22-23 for IgG control. Libraries were ethanol precipitated, resolved on 10 well of 6% TBE gel similarly to the cycle selection PCR, and separated from the no-insert library and unreacted primers. Gel extraction was performed similarly to the extraction after reverse transcription reaction, but the gel pieces were not heated higher than +30 °C. After ethanol precipitation, pellets were resuspended in 10 µl of nuclease-free water. Library size distribution and quantity were determined using Agilent Bioanalyzer 2100 with High Sensitivity DNA Kit (Agilent) and via qPCR with NEBNext Library Quant Kit for Illumina (NEB). Libraries were sequenced on a NovaSeq 6000 S1 at SR100 mode (Illumina) at the Vienna BioCenter NGS facility.

treatment_protocol: 4-thiouridine (4sU, Sigma) was added to the cell culture media 15 hours prior collection at 100µM.

value: human colorectal carcinoma

tag: par-clip antibody

value: IgG control (Proteintech, #30000-0-AP)

value: 4-thiouridine (4sU) 100 μM 15h


title: mES_TASORM1_H3K9me3_eSPAN_rep2


title: Islets, 11mM Glucose + 5uMO304, 48h, rep2


title: mES_TASORM1_H3K9me3_CT_rep3


title: HCT116, IGF2BP3, RNase T1, in-lysate 0.25 U/μL, on-bead 0.25 U/μL


title: mES_WT_TASOR_eSPAN_rep3


title: mES_WT_FlagTASOR_eSPAN_rep1

value: Anti-Flag

value: Sigma


title: mES_WT_TASOR_eSPAN_rep1


title: Islets, 22mM Glucose + Vehicle, 48h, rep2


title: HCT116, IGF2BP3, RNase I, in-lysate 0.05 U/μL, on-bead 0.025 U/μL


title: HEK293_HA_CHERPdeltaCID_rep2


title: HCT116, IGF2BP3, RNase I, in-lysate 0.05 U/μL, on-bead 0.05 U/μL


title: Islets, 22mM Glucose + 5uMO304, 48h, rep1


title: mES_MPP8KO_MPP8_CT


title: mES_WT_MPP8_CT_rep2


title: mES_MPP8W80A_H3K9me3_CT_rep2


title: Islets, 11mM Glucose + 5uMO304, 48h, rep1


title: HCT116, IGF2BP3, RNase I, in-lysate 0.1 U/μL, on-bead 0.025 U/μL


title: mES_MPP8KO_H3K9me3_CT_rep2


title: Islets, 22mM Glucose + Vehicle, 48h, rep1


title: HEK293_Input_2_Ser2treatment_rep1rep2

data_processing:
Base-calling was performed by Novogene Inc. with the latest Illumina software
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.5.0. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.2.7.1 with the default significance cut-off q-value <=0.1 for broad peaks
bigWig files were generated using the bedGraph files of scores outputted from MACS2.
Assembly: hg38
Supplementary files format and content: bigWig files outputted from MACS2 (except for input files).


title: mES_MPP8KO_H3K9me3_CT_rep1


title: HCT116, IGF2BP3, RNase T1, in-lysate 1 U/μL, on-bead 1 U/μL


title: HEK293_Input_1_HA_CHERP_rep1


title: mES_Ctr_H3K9me3_CT1


title: HEK293_HA_CHERP_Ser2_treatment_rep2


title: mES_MPP8W80A_H3K9me3_eSPAN_rep2


title: Islets, 11mM Glucose + Vehicle, 48h, rep1


title: pancreatic islets, Neurod1CKO

city: Vestec by Prague

first: Gabriela

last: Pavlínková

address: Průmyslová 595

department: Laboratory of Molecular Pathogenetics

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i

description: 10x Genomics

data_processing:
Libraries were controlled for contamination using fastq_screen v0.11.1. Reads were mapped against the mouse genome GRCm38 and counted using annotation genecode.vM8 using STAR v2.7.3a with parameters “--soloType CB_UMI_Simple --soloFeatures Gene –soloCBmatchWLtype 1MM_multi_pseudocounts –soloUMIdedup 1MM_Directional –soloUMIfiltering MultiGeneUMI”. Empty droplets were filtered out using emptyDrops command from DropletUtils package (v 1.14.1) with lower parameter set to 1000.
Assembly: mm10/GRCm38
Supplementary files format and content: bardcodes.tsv: list of cell barcodes
Supplementary files format and content: features.tsv: list of gene Ids
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format

source_name: Pancreas

extract_protocol:
Mouse pancreatic islets were isolated (and pooled) from four mice per each genotype perfusion of the common bile duct with Collagenase P (1 mg/ml; Merck) in HBS (Merck) supplemented with Actinomycin D (25μg/ ml; Merck) to stop transcription, digestion of the pancreases with 0.8 mM Collagenase P and purification of the islets by Ficoll discontinuous gradient. Single cell dispersion was carried out as follows: islets were settled by centrifugation (140 rcf, 4°C, 4 min), washed with 2 ml of HBS with Actinomycin D (2.5μg/ ml). Islets were centrifuged (140 rcf, 4°C, 4 min) again and Dulbecco’s PBS was used for the final wash. Digestion was performed with 0.6 ml of trypsin/0.53 mM EDTA 172 supplemented with Actinomycin D (25μg/ ml). Samples were incubated at 37°C for 5 min. Following incubation, trypsinization was stopped by adding of 1.2 ml of PBS with 10 mM EGTA supplemented with 10% fetal bovine serum (FBS; Merck). Cells were gently dispersed mechanically using a P1000 pipette. Cells were then spun down (800 rcf, 4°C, 10 min) and resuspended in PBS with 10 mM EGTA supplemented with 2% FBS.
Single-cell RNA-Seq (scRNA-Seq) libraries were prepared using Chromium Next GEM Single Cell 3' Kit v3.1 (1000268, 10X Genomics) according to the manufacturer’s protocol.

value: Pancreas

tag: strain

value: mixed background

tag: age

value: 1 month

tag: Sex

value: pooled male and female


title: mES_MPP8W80A_H3K9me3_eSPAN_rep1

value: Zhang Lab


title: HEK293_HA_CHERP_Ser2_treatment_rep1

tag: cell line


title: mES_MPP8KO_BrdU

tag: genotype

value: Anti-BrdU


title: Islets, 11mM Glucose + Vehicle, 48h, rep2


title: pancreatic islets, control

description: 10x Genomics

value: control


title: mES_MPP8W80A_H3K9me3_CT_rep1


title: mES_WT_MPP8_eSPAN_rep1

value: WT


title: HEK293_HA_CHERP_rep2


title: mES_WT_POLE3MPP8KO_H3K9me3_CT_rep2


title: mES_WT_MPP8_eSPAN_rep2


title: mES_MPP8KO_H3K9me3_eSPAN_rep2


title: mES_WT_H3K9me3_CT_Ctrl1


title: mES_MPP8KO_H3K9me3_eSPAN_rep1


title: HEK293_HA_CHERP_rep1


title: mES_WT_POLE3MPP8KO_H3K9me3_CT_rep1


title: RPSUD4_cmcRep3

value: RPUSD4 knockdown

value: 0.5M CMC


title: NeuroD1ST_3 [RNA-seq]

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

institute: Czech Academy of Science

data_processing:
Raw reads were trimmed of Illumina sequencing adaptor and bases with reading quality lower than 20 using cutadapt v1.18 49. Reads shorter than 20 bp were filtered out.
Ribosomal RNA and reads mapping to UniVec database were filtered out using bowtie v1.2.2. with parameters -S -n 1 and SortMeRNA database
FASTQ files were mapped to the mouse genome using STAR [version 2.7.0c 48] GRCm38 primary assembly and annotation version M8
Count table was generated by Rsubread v2.0.1 package using default parameters without counting multi-mapping reads
Assembly: GRCm38.p6 (Ensembl)
Supplementary files format and content: Count_matrix.txt.gz: Compressed tab seprated text file containing raw counts for control and NeuroD1ST. Rows corresponds individual genes with ensembl ID and columns to samples.

growth_protocol: Cre/loxP system was used to delete Neurod1 from embryonic (E15.5) pancreatic cells with active Neurod1 promoter. TdTomato was used as Cre-activity reporter in this model.

extract_protocol:
The pancreata microdissected from E15.5 embryos were directly trypsinized and prepared for FACS. Briefly, tissue was dissociated using 0.05% trypsin/0.53 mM EDTA at 37°C for 5 min. Digestion was stopped by adding the FACS buffer (2% FBS and 10 mM EGTA in PBS), and cells were then 1x washed by FACS buffer. Finally, cell suspensions were filtered through 40 μm nylon mesh and immediately tdTomato+ cells were sorted using a flow cytometer (BD FACSAriaTM Fusion), through a 100 μm nozzle in 20 psi, operated with BD FACSDiva™ Software.
100 sorted cells were collected into the individual wells of 96-well plate containing 5 μl of lysis buffer of NEB Next single-cell low input RNA library prep kit for Illumina (New England Biolabs #E6420). The plates were frozen immediately on dry ice and stored at −80°C until the libraries were prepared following the manufacturer's instructions of previously mentioned NEB Next kit.

tag: developmental stage

value: endocrine cells


title: NeuroD1ST_4 [RNA-seq]


title: mES_WT_POLE3MPP8KO_H3K9me3_eSPAN_rep2


title: mES_MPP8KO_MPP8_eSPAN


title: NeuroD1ST_2 [RNA-seq]


title: mES_WT_POLE3MPP8KO_H3K9me3_eSPAN_rep1


title: Control_4 [RNA-seq]


title: NeuroD1ST_1 [RNA-seq]


title: RPUSD4_cmcRep1

city: Boston

first: Nicholas

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

tag: treatment


title: Control_1 [RNA-seq]


title: mES_WT_MPP8_CT_rep1


title: Control_3 [RNA-seq]


title: mES_WT_LateS_H3K9me3_CT_rep1


title: RPUSD4_UntrRep1

value: Untreated


title: Control_2 [RNA-seq]


title: mES_POLE4KO_GroG2M_rep2

data_processing:
library strategy: GRO-seq
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.

value: nascent RNA


title: NKO_cmcRep4

value: NME6 KO


title: mES_WT_MidS_H3K9me3_CT_rep1


title: mES_POLE4KO_GroS_rep2


title: mES_POLE4KO_GroG2M_rep1


title: mES_POLE4KO_GroG1_rep2


title: mES_WT_nextG1_H3K9me3_eSPAN_rep1


title: RPUSD4_cmcRep2


title: mES_POLE4KO_GroS_rep1


title: mES_POLE4KO_GroG1_rep1


title: NKO_cmcRep1


title: mES_POLE4KO_Groctr_rep1


title: mES_POLE4KO_Groctr_rep2


title: NKO_UntrRep2


title: mES_WT_MidS_H3K9me3_eSPAN_rep1


title: mES_POLE3KO_Groctr_rep2


title: mES_WT_nextG1_H3K9me3_CT_rep1


title: mES_POLE3KO_Groctr_rep1


title: mES_WT_GroS_rep2


title: mES_TASORKO_H3K9me3_CT_rep2

value: TASORKO


title: mES_WT_Groctr_rep2


title: mES_WT_GroG2M_rep2


title: mES_WT_GroG1_rep2


title: mES_TASORKO_H3K9me3_CT_rep1


title: mES_WT_FlagTASOR_eSPAN_rep2

value: Anti-Flag


title: NT_cmcRep3

value: wildtype, non-targeting sgRNA


title: mES_WT_GroG2M_rep1


title: NKO_cmcRep3


title: mES_WT_TASOR_eSPAN_rep2

value: Anti-TASOR

value: GeneTex


title: NT_cmcRep2


title: mES_WT_GroS_rep1


title: NKO_cmcRep2


title: mES_WT_Groctr_rep1


title: mES_WT_GroG1_rep1


title: mES_WT_LateS_H3K9me3_eSPAN_rep1


title: mB_WT_H3K27me3_CT

data_processing:
library strategy: CUT&TAG
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.

source_name: activate mouse B cells

value: Cell Signaling

tag: antibody cat.#


title: NKO_UntrRep1


title: mES_TASORKO_H3K9me3_eSPAN_rep2


title: NT_cmcRep1


title: mES_TASORKO_H3K9me3_eSPAN_rep1


title: mB_WT_H3K9me3_CT


title: NT_cmcRep4


title: mB_WT_H4K20me2_eSPAN

data_processing:
library strategy: eSPAN
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.

value: Diagenode


title: mB_WT_H3K27me3_eSPAN


title: mES_WT_MPP8_eSPAN_rep3

value: Proteintech


title: NT_UntrRep1


title: mB_WT_H3K9me3_eSPAN_rep2

value: Zhang Lab


title: mB_WT_H3K9me3_eSPAN_rep1


title: asyn_3 scRNA-Seq

first: Connor

last: Monahan

description:
single-cell RNA sequencing
DC014

data_processing:
10x Genomics
Assembly: mm10-2020-A
Supplementary files format and content: Unfiltered feature-barcode matrix

source_name: small intestine

extract_protocol:
10x Genomics Chromium 3' v3 chemistry
10x Genomics Chromium 3' v3 chemistry

value: small intestine

value: CD45+ cells


title: CFA_3 scRNA-Seq

description:
single-cell RNA sequencing
DC013

value: CFA only


title: HEK293 cells, shSCAF6, replicate 2

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Quality of raw reads was assessed using FastQC read quality reports (Galaxy).
Adapter Illumina sequences (--illumina) were trimmed off by TrimGalore! v.0.6.7 with default parameters.
Next, reads were aligned to human reference genome, GRCh38 version, using HISAT2 fast aligner v.2.2.1 with default parameters, except Reverse (RF) --rna-strandedness. Gencode v38 gtf file was used as annotation gtf.
Lastly, mapped fragments were quantified by featureCounts v.2.0.1 in Galaxy.
Assembly: GRCh38
Supplementary files format and content: tabular files including FeatureCounts for each Sample

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2

extract_protocol:
Total RNA was isolated using DirectZol RNA Miniprep kit (Zymo Research). 1.3-1.7 ug RNA per sample was used for library construction.
Libraries were prepared at the University of Texas Genomic Sequencing and Analysis Facility (GSAF) according to manufacturer’s instructions for the NEBNext Ultra II Direction RNA kit (NEB). Strandness of library was preserved using dUTP method.

treatment_protocol:
HEK293 cells were infected using MISSION shRNA lentiviral particles against SCAF6 (Sigma). Hexadimethrine bromide was added to the cells at a final concentration of 8 μg/ml.
Transduced cells were selected with puromycin at a concentration of 1 μg/ml for 7 days. The control cells were transfected with MISSION non-mammalian shRNA negative control plasmid (Sigma).

value: embryonic kidney cells

value: SCAF6 knockdown


title: mES_SUV39h1KO_H3K9me3_CT_rep2

first: Zhiguo

address: 1130 St. Nicholas Avenue

institute: Columbia University

extract_protocol:
eSPAN in mESC, mouse B cells and HeLa  cells were performed exactly as previously described (Li et al., 2020).GRO-seq (global run-on sequencing) was performed as previous described (Barbieri, E. et al., 2020).
GRO-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For CUT&TAG, CUT&RUN and eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.


title: mES_SUV39h1KO_H3K9me3_CT_rep1


title: mES_GLPKO_H3K9me3_CT_rep2

value: GLPKO


title: PBS_2 scRNA-Seq

description:
single-cell RNA sequencing
DC012

value: PBS


title: HEK293 cells, shSCAF6, replicate 1


title: asyn_2 scRNA-Seq

description:
single-cell RNA sequencing
DC009


title: mB_WT_H4K20me2_CT

value: WT


title: HEK293 cells, shControl, replicate 2


title: mES_GLPKO_H3K9me3_CT_rep1


title: mES_G9aKO_H3K9me3_CT_rep1


title: mES_G9aKO_H3K9me3_CT_rep2


title: HEK293 cells, shControl, replicate 1


title: NT_UntrRep2

last: Kramer

data_processing:
Adapter and QC trimming by Trimmomatic then alignment to GRCh38/hg38 human genome using STAR
Samtools mpileup to produce text pileup output from aligned BAM files
Custom python scripts to count variants caused by CMC treatment in mpileup output
Assembly: hg38
Supplementary files format and content: txt files of deletions counted at each position across the mitochondrial genome normalized to total reads in CMC treated relative to untreated samples

value: Untreated


title: mES_SUV39h1KO_H3K9me3_eSPAN_rep1

last: Zhang


title: CFA_2 scRNA-Seq

description:
single-cell RNA sequencing
DC008


title: Control 3 - Day 8, rep3

city: Hong Kong

first: Yin Yu

last: Lam

address: 102 Pokfulam Road

department: Department of Paediatrics and Adolescent Medicine

institute: The University of Hong Kong

description:
hiPSC3_Day8_Rep3
Poly-A mRNA-seq

data_processing:
Raw sequencing reads were filtered, aligned against GRCh38 genome with count matrix generated with Rsubread.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count_Matrix.csv: Comma-separated count matrix.

source_name: Human induced pluripotent stem cell-derived cardiomyocytes

extract_protocol:
Total RNA was isolated with TRIzol LS Reagent according to manufacturer's protocol.
Constructed with Illumina Stranded mRNA Prep according to manufacturer's protocol.

value: Induced pluripotent stem cell-derived APLNR+ in vitro SHF progenitors

tag: disease state

value: Normal

tag: time point

value: 72h post-isolation


title: PBS_1 scRNA-Seq

city: New York

description:
single-cell RNA sequencing
DC007

tag: tissue

tag: cell type


title: mES_SUV39h1KO_H3K9me3_eSPAN_rep2

tag: experiments


title: mES_GLPKO_H3K9me3_eSPAN_rep2

tag: chip antibody


title: asyn_1 scRNA-Seq

description:
single-cell RNA sequencing
DC002


title: mES_G9aKO_H3K9me3_eSPAN_rep1

tag: antibody vendor


title: Control 3 - Day 8, rep1

description:
hiPSC3_Day8_Rep1
Poly-A mRNA-seq


title: mES_POLE4KO_H3K9me3_CR_rep2

data_processing:
library strategy: CUT&RUN
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.


title: Control 3 - Day 8, rep2

description:
hiPSC3_Day8_Rep2
Poly-A mRNA-seq


title: CFA_1 scRNA-Seq

description:
single-cell RNA sequencing
DC001


title: mES_WT_H3K9me3_CR_rep2


title: Control 3 - Day 7, rep3

description:
hiPSC3_Day7_Rep3
Poly-A mRNA-seq

value: 48h post-isolation


title: mES_POLE4KO_H3K9me3_CR_rep1


title: asyn_4

description: bulk RNA sequencing

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (v2.19) for converting FASTQ, adaptor trimming
kallisto (v0.44.0)
DESeq2
Assembly: pseudoalignment to a kallisto index from mouse transcriptomes GRCm38
Supplementary files format and content: FASTQ

source_name: ileum

extract_protocol:
TRIzol RNA extraction
TruSeq Stranded mRNA kit (Illumina)

value: ileum

value: Male


title: Control 3 - Day 7, rep2

description:
hiPSC3_Day7_Rep2
Poly-A mRNA-seq


title: mES_POLE3KO_H3K9me3_CR_rep1


title: Control 3 - Day 7, rep1

description:
hiPSC3_Day7_Rep1
Poly-A mRNA-seq


title: asyn_2

description: bulk RNA sequencing

value: Female


title: Control 3 - Day 6, rep3

description:
hiPSC3_Day6_Rep3
Poly-A mRNA-seq

value: 24h post-isolation


title: mES_GLPKO_H3K9me3_eSPAN_rep1

value: Zhang Lab


title: mES_POLE3KO_H3K9me3_CT_rep2


title: asyn_1

description: bulk RNA sequencing


title: mES_POLE3KO_H3K9me3_CT_rep1


title: asyn_3

description: bulk RNA sequencing


title: mES_POLE4KO_H3K9me3_eSPAN_rep2


title: mES_POLE4KO_H3K9me3_CT_rep1


title: Control 3 - Day 6, rep1

description:
hiPSC3_Day6_Rep1
Poly-A mRNA-seq


title: mES_POLE4KO_H3K9me3_eSPAN_rep1


title: CFA_3

description: bulk RNA sequencing


title: mES_POLE3KO_H3K9me3_CR_rep2


title: Control 3 - Day 6, rep2

description:
hiPSC3_Day6_Rep2
Poly-A mRNA-seq


title: mES_POLE3KO_H3K9me3_eSPAN_rep1


title: mES_POLE3KO_H3K9me3_eSPAN_rep2


title: CFA_4

description: bulk RNA sequencing


title: Control 3 - Day 5, rep3

description:
hiPSC3_Day5_Rep3
Poly-A mRNA-seq

value: 0h post-isolation


title: mES_WT_H3K9me3_CR_rep1


title: mES_SETDB1KD_H3K9me3_CT_rep2


title: mES_SETDB1KD_H3K9me3_CT_rep1


title: CFA_1

description: bulk RNA sequencing

value: CFA only


title: Control 3 - Day 5, rep1

description:
hiPSC3_Day5_Rep1
Poly-A mRNA-seq


title: Control 3 - Day 5, rep2

description:
hiPSC3_Day5_Rep2
Poly-A mRNA-seq


title: mES_POLE4KO_H3K9me3_CT_rep2


title: mES_SETDB1KD_H3K9me3_eSPAN_rep2


title: mES_WT_H3K9me3_CT_shCtr


title: mES_G9aKO_H3K9me3_eSPAN_rep2


title: H03

city: La Jolla

first: Stephanie

last: Cherqui

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
RNA-Seq data were processed using Kallisto (version 0.45.0), Mus musculus genome GRCm38 Ensembl version 94 annotation (Mus_musculus GRCm38.94 chr_patch_hapl_scaff.gtf)
Gene-level TPM values and gene annotations were computed using tximport and the biomaRt R package.
A custom python script was used to organize the data and log reduced using log2(TPM+1).
Assembly: Mus musculus genome GRCm38 Ensembl version 94 annotation (Mus_musculus GRCm38.94 chr_patch_hapl_scaff.gtf)
Supplementary files format and content: tab-separated values files include estimated counts (est_counts) and TPM.

source_name: Cortex

extract_protocol:
Hippocampus and cortex were dissected from brains and total RNA was isolated using Rneasy Tissue kit (Qiagen). RNA was assessed for quality using an Agilent Tapestatio 4200, and 50ng of RNA with an RNA Integrity Number greater than 8.0 were used to generate libraries.
RNA sequencing libraries using the Illumina® Stranded mRNA Prep (Illumina) following manufacturer’s instructions.

value: Cortex


title: mES_SETDB1KD_H3K9me3_eSPAN_rep1


title: mES_WT_H3K9me3_eSAPN_shCtr


title: Control 2 - Day 8, rep3

description:
hiPSC2_Day8_Rep3
Poly-A mRNA-seq


title: G03


title: mES_WT_G2M_H3K9me3_eSPAN_rep2


title: mES_WT_G2M_H3K9me3_eSPAN_rep1


title: Control 2 - Day 8, rep2

description:
hiPSC2_Day8_Rep2
Poly-A mRNA-seq


title: mES_WT_BrdU_rep1

value: Anti-BrdU

value: BD Biosciences


title: F03

value: Transplanted with GFP+ WT HSPCs


title: Control 2 - Day 8, rep1

description:
hiPSC2_Day8_Rep1
Poly-A mRNA-seq


title: CFA_2

description: bulk RNA sequencing


title: mES_WT_BrdU_rep2

value: WT


title: mES_WT_H4K5_K12ac_eSPAN_rep2


title: mES_WT_H4K5ac_eSPAN_rep2

value: Abcam


title: mES_WT_H4K5ac_eSPAN_rep1


title: mES_WT_H4K12ac_eSPAN_rep2


title: Control 2 - Day 7, rep3

description:
hiPSC2_Day7_Rep3
Poly-A mRNA-seq

value: Induced pluripotent stem cell-derived APLNR+ in vitro SHF progenitors


title: E03


title: Control 2 - Day 7, rep2

description:
hiPSC2_Day7_Rep2
Poly-A mRNA-seq

value: Normal


title: mES_WT_H4K5_K12ac_eSPAN_rep1


title: mES_WT_H4K12ac_eSPAN_rep1


title: Control 2 - Day 6, rep3

description:
hiPSC2_Day6_Rep3
Poly-A mRNA-seq


title: Control 2 - Day 7, rep1

description:
hiPSC2_Day7_Rep1
Poly-A mRNA-seq


title: mES_WT_H3K36me3_eSPAN_rep2

value: Active motif


title: B03

value: Mock, Transplanted with 5xFAD HSPCs


title: C03


title: mES_WT_H3K36me3_eSPAN_rep1


title: mES_WT_H3K4me3_eSPAN_rep2


title: Control 2 - Day 6, rep2

description:
hiPSC2_Day6_Rep2
Poly-A mRNA-seq


title: A03


title: mES_WT_H3K4me3_eSPAN_rep1


title: mES_WT_H3K36me2_eSPAN_rep2

value: Cell Signaling


title: H02


title: Control 2 - Day 6, rep1

description:
hiPSC2_Day6_Rep1
Poly-A mRNA-seq


title: D03


title: Control 2 - Day 5, rep3

description:
hiPSC2_Day5_Rep3
Poly-A mRNA-seq


title: F02


title: Control 2 - Day 5, rep1

description:
hiPSC2_Day5_Rep1
Poly-A mRNA-seq


title: mES_WT_MCM2_eSPAN_rep2


title: E02


title: Control 2 - Day 5, rep2

description:
hiPSC2_Day5_Rep2
Poly-A mRNA-seq


title: mES_WT_H4K20me2_eSPAN_rep1

value: Diagenode


title: mES_WT_H4K20me3_eSPAN_rep1


title: mES_WT_H4K20me3_eSPAN_rep2


title: mES_WT_H4K20me2_eSPAN_rep2


title: mES_WT_MCM2_eSPAN_rep1


title: mES_WT_H3K9me2_eSPAN_rep2


title: mES_WT_H3K9me2_eSPAN_rep1


title: C02

source_name: Hippocampus

value: Hippocampus


title: mES_WT_H3K27me3_eSPAN_rep2


title: Control 1 - Day 8, rep3

description:
hiPSC1_Day8_Rep3
Poly-A mRNA-seq

value: 72h post-isolation


title: mES_WT_H3K9me3_CT_rep2

value: Zhang Lab


title: B02


title: mES_WT_H3K27me3_eSPAN_rep1


title: mES_WT_H3K36me2_eSPAN_rep1


title: Control 1 - Day 8, rep2

description:
hiPSC1_Day8_Rep2
Poly-A mRNA-seq


title: Control 1 - Day 8, rep1

description:
hiPSC1_Day8_Rep1
Poly-A mRNA-seq


title: mES_WT_H3K9me3_CT_rep1


title: A02


title: mES_WT_H3K9me3_Ab2_eSPAN


title: mES_WT_H3K9me3_Ab3_eSPAN


title: Control 1 - Day 7, rep3

description:
hiPSC1_Day7_Rep3
Poly-A mRNA-seq

value: 48h post-isolation


title: G02


title: mES_WT_H3K9me3_Ab1_eSPAN


title: mES_WT_H3K9me3_Ab3_CT


title: H01


title: Control 1 - Day 7, rep2

description:
hiPSC1_Day7_Rep2
Poly-A mRNA-seq


title: D02


title: mES_WT_H3K9me3_Ab2_CT


title: G01


title: mES_WT_H3K9me3_eSPAN_rep2


title: Control 1 - Day 6, rep3

description:
hiPSC1_Day6_Rep3
Poly-A mRNA-seq

value: 24h post-isolation


title: Control 1 - Day 7, rep1

description:
hiPSC1_Day7_Rep1
Poly-A mRNA-seq


title: F01


title: Control 1 - Day 6, rep2

description:
hiPSC1_Day6_Rep2
Poly-A mRNA-seq


title: mES_WT_H3K9me3_eSPAN_rep1


title: E01


title: D01


title: Control 1 - Day 6, rep1

description:
hiPSC1_Day6_Rep1
Poly-A mRNA-seq


title: C01