title: GATA1_UV

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Commercially synthesized, high-density, single-stranded DNA microarrays from Agilent were first double-stranded via primer extension as done in previous assays (Berger et al, Nature Biotechnology 2006; Shen et al, Cell Systems 2018). The arrays were partially irradiated with UVC such that only some chambers were exposed to UVC while others were not. In order to irradiate only certain parts of the array, and protect the rest from UV irradiation, a cover/gasket slide was cut to the desired size are used to partially cover the DNA array. Next, the gasket slide was fully covered using Cryo-Babies® labels, and the array-gasket slide sandwich was placed in an open container with 1x PBS. To irradiate the DNA on the array, we used a Stratalinker® UV Crosslinker 1800 instrument and conducted a series of irradiations with UVC. Using the energy mode, the container was irradiated with 100 J/m2, randomly repositioned inside the crosslinker 15 times to achieve 1,500 J/m2. Midway through the series, the PBS was replaced in order to keep the solution at room temperature. This procedure resulted in a DNA array with some chambers of the array irradiated by UV and others not irradiated. Samples with the “UV” condition used irradiated chambers while those with a “Non-UV” condition used non-irradiated chambers. The arrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk for 1 hour as done in prior assays (Shen et al, Cell Systems 2018). Proteins were incubated at the indicated concentration using the buffers referred to in the manuscript for 1 hour. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min (Shen et al, Cell Systems 2018). Then the arrays were incubated with either Penta-His Alexa488-conjugated antibody and Penta-His Alexa647-conjugated antibody (1:20 and 1:40 ratio respectively) in a buffer with 2% (wt/vol) milk and 0.05% Tween for 1 hour (buffer details described in the manuscript). After incubation, the arrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min as done in prior work (Shen et al, Cell Systems 2018).

scan_protocol: Protein bound microarrays were scanned at 635nm using a GenePix 4400A at multiple laser power and gain settings to best capture the signal and avoid saturation of spots. The resulting TIF images were processed using GenePix Pro 7.3.

data_processing: The raw data collected using the GenePix® 4400A microarray scanner was processed using the Seed and Wobble suite (Berger et al, Nature Biotechnology 2006), with modifications to adapt the k-mer data to our UV-Bind universal design, as described in the manuscript. For each unique sequence tested, median values over the spots containing that sequence were used unless otherwise noted (i.e. for the universal design sequences and for the competition tests). The number of replicate spots for each sequence varied between 3 and 20, depending on the DNA library. Processing of k-mers and PWMs using Seed-and-Wobble was done using the adjusted signal (i.e. Alexa488Adjusted or Alexa635Adjusted column) in the alldata.txt file as done by default (Berger et al, Nature Biotechnology 2006).

label: Alexa 635

molecule: protein

source_name: Human GATA1

label_protocol: Label protocol is detailed in the manuscript for all tested proteins and antibodies.

growth_protocol: Cell growth protocol is detailed in the manuscript for all tested proteins and antibodies.

extract_protocol: Extract protocol is detailed in the manuscript for all tested proteins and antibodies.

tag: protein

tag: protein concentration

tag: array condition

value: UV


title: P53_NonUV

status: Public on Jan 20 2023

country: USA

organism: Homo sapiens

source_name: Human P53

value: Non-UV


title: priB_TriC_Spt5_IgG1poolcapture_ctrl_clone2_rep2

type: SRA

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

description: Tri-C

library_source: genomic

data_processing:
Library strategy: Tri-C
Tri-C
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: mm9
Supplementary files format and content: Tab separated matrix showing normalized interaction counts

molecule: genomic DNA

organism: Mus musculus

source_name: primary B-cells

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms

tag: capture probe

value: IgG1 pool capture

tag: treatment

value: WT

tag: clone

value: clone 2

tag: replicate

value: replicate 2


title: TmR_plko_s2_S04: control-repeat2

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

description: cell lines were made using lentivirus

library_source: transcriptomic

data_processing:
Reads were counted against gencode v29 transcripts and summarized to the gene level with tximport in R
Genome_build: GRh38.p12
Genome_build: Gencode version 29
Supplementary_files_format_and_content: raw counts per gene, ensembl gene IDs, comma-separated values

molecule: total RNA

source_name: tamoxifen resistant breast tumor cells

growth_protocol: Cells were grown in Iscoves media usings erum and Pen/Strep

extract_protocol:
Cells were trypsinized and then single cells were lysed using lysis buffer from Invitrogen RNA extration kit. Total RNA was isolated using standarad procedure following manufacture's protocol.
Library construction protocol was using standard protocol from Illumina

treatment_protocol: Cells were treated with trypsin for single cell isolation. DLL1 KD was made using lentivius mediated shRNAs from Sigma

tag: tissue

value: tamoxifen resistant breast tumor cells

tag: condition

value: control


title: Y24_1

city: Grand Forks

first: Lin

last: Yan

state: North Dakota

address: 2420 2nd Ave N

institute: USDA- Grand Forks Human Nutrition Research Center

description:
Y24_1
mRNA

data_processing:
Raw data (fastQ format) processed via fastp which clean data (clean reads) were obtained by removing reads containing adapter and pol-N- sequences. GC and phret scores were calculated at this time.
Clean paired-end reads were aligned to reference genome (obtained from NCBI) via STAR (version v2.5).
Quantification via HTSeq v0.6.1.
Differential Analysis via DESeq 2 (version v2_1.6.3, padju<0.05).
Enrichment Analysis via ClusterProfiler (version v2.4.3 with padj<0.05). Alternative splicing via rMATS (version v3.2.1 on default parameters) and Fusion gene analysis via STAR-Fusion (version v0.8.0 on default parameters).
Assembly: mm10
Supplementary files format and content: readcount_genename.xls: Raw counts of sequencing reads (before normalization) is provided in the matrix file. Column 1 provides the Ensembl ID, Column B-AQ provide the raw counts for each sample, columns AR-AY provide gene description (name, chromosomes, location, etc.)

source_name: Liver

extract_protocol:
Liver tissues were extracted via Qiazol method (RNeasy Tissue Lipid kit, Qiagen, MD USA). Concentration quantified via Spectrophometry 8000 (Thermofisher) and integrity on Qubit. Samples were sent off to Novogene USA for the complete analysis (mRNA methylation to total analysis of data).
Sequencing libraries were generated from 1 μg RNA per sample via NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. Library preparations were sequenced on an Illumina platform where paired-end reads were generated.

value: Liver

tag: Sex

value: Female

value: Standard diet (LF)

tag: time

value: Light phase (Zeitgeber time 0-12)

tag: time point

tag: strain


title: rne(5p) replicate 2

city: Freiburg

first: Ute

middle: A.

last: Hoffmann

address: Schänzlestr. 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

data_processing:
Basecalls were performed online during the sequencing procedure with Real-Time Analysis (RTA) software v2.4.11 and System Suite v2.1.2.1. bcl2fastq script v2.18.0.12 was used for coversion of bcl2 files to de-multiplexed gzipped fastq files
Transcript, TSS and PSS data sets were demultiplexed using BBDuk (PSS adapter: CTGAAGCT and TSS adapter: TAATGCGC were used for sorting and could match within the first 23nt of a read. Following adapter removal, the 2 subsequent bases were removed)
Sequenced reads were trimmed for adaptor sequences and low-quality base calls using cutadapt (Galaxy v1.16.5), then aligned using bowtie2 (Galaxy v2.3.4.3+galaxy0) –very-sensitive
Reads were filtered for a minimum mapping quality of 20 using bamtools filter (Galaxy v2.4.1)
Transcript pattern reads were assigned to annotated regions using htseq-count (Galaxy v0.9.1+galaxy1)
Transcript coverage files and 5’ end counts of PSS and TSS reads were created using bedtools Genome coverage (Galaxy v2.29.2)
DESeq2 (v1.30.1) was used  to classify PSS and TSS positions
TSS positions with a TSS-reads/transcript coverage ratio < 0.02 and > 2.00 were excluded. Furthermore, only TSS-positions with a maximum distance of 20nt to TSS identified by Kopf et al., 2014, were used in further analyses.
PSS determined previously (Hoffmann et al., 2021, doi: 10.1101/2021.07.27.453982) were included in the set of PSS to test
DESeq2 (v1.30.1) was used to evaluate differential expression at newly determined PSS and TSS positions and for htseq-count files
Genome_build: GCF_000009725.1
Supplementary_files_format_and_content: gff file with PSS and TSS positions determined as part of this analysis
Supplementary_files_format_and_content: Comma-delimited matrix tables with normalized read counts for RNA features (for transcript data), PSS or TSS (PSS, TSS data set, respectively)

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture

growth_protocol: WT Synechocystis sp. PCC 6803 and strains rne(WT) as well as rne(5p) were grown in BG-11 (Rippka et al., 1979) medium supplemented with 0.3% (w/v) sodium thiosulphate and 10mM (w/v) TES pH 8.0 at constant shaking (135 rpm) and 30 µm mol photons m-2 s-1 white light illumination

extract_protocol:
20 ml culture were collected by vacuum filtration through 0.8 µm polyethersulphone filter disks (Pall, Germany). Filters were immediately transferred to 1.6 ml PGTX solution (Pinto et al., 2009), vortexed, frozen in liquid nitrogen and stored at -80°C. RNA was extracted according to Pinto et al. (2009) with modifications as described in Wallner et al. (2020).
For RNA Sequencing, biological triplicates of WT and rne(WT) as well as biological duplicates of rne(5p) were used. Residual DNA was removed from samples containing each 10 µg RNA by three subsequent incubation steps with Ambion TURBO DNase (Thermo Fisher Scientific, Germany). For each step, 2 U TurboDNase was added, followed by 20 min incubation at 37°C. RNA was recovered using RNA Clean & Concentrator kits (Zymo Research, USA). RNA integrity was controlled for on a Fragment Analyzer using the High Sensitivity RNA Analysis Kit (Advanced Analytical Technologies, Germany). cDNA libraries were constructed and sequenced as a service provided by vertis Biotechnologie AG (Germany) according to the tagRNA-Seq protocol (Innocenti et al., 2015). Ribosomal RNAs were depleted using in-house depletion probes. 5‘-P RNA fragments were ligated to the 5‘ Illumina TruSeq sequencing adapter carrying the sequence tag CTGAAGCT. After incubation with 5‘-phosphate-dependent exoribonuclease Terminator Exonuclease (TEX, Lucigen), samples were treated with RNA 5‘ Polyphosphatase (5‘PP, Lucigen). The 5‘ Illumina TruSeq sequencing adapter carrying sequence tag TAATGCGC was ligated to newly formed 5‘-P RNA ends. RNA was fragmented and an oligonucleotide adapter was ligated to the resulting 3‘ ends. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3‘ adapter as primer. First-strand cDNA was purified and the 5‘ Illumina TruSeq sequencing adapter was ligated to the 3‘ end of the antisense cDNA. This was followed by PCR amplification to about 10-20 ng/µl using a high fidelity DNA polymerase. cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). Samples were pooled in approximately equimolar amounts and the cDNA pool in the size range of 200 – 600 bp was eluted from a preparative agarose gel.

value: untreated


title: PBMC_PDA-2_ETS1_CutTag

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

country: China

institute: Central People's Hospital of Zhanjiang

data_processing:
For CUT&Tag data processing, FASTQC was used to measure the date quality distribution.
The clean reads were then aligned to reference genome sequences using the bwa program.
Peaks were called using MACS2 peak caller with q-value < 0.05.
Genome-wide normalized signal coverage tracks were visualized in the IGV.
Assembly: hg38
Supplementary files format and content: bigWig files include peaks for each sample, respectively.

source_name: peripheral blood mononuclear cells

growth_protocol: The peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll (Cytiva, 17544202, Marlborough, MA, USA) according to the manufacturer’s instructions.hTERT RPE-1 cells (ATCC, CRL-4000) were cultured in F12/DMEM (1:1) supplemented with 10% fetal bovine serum (FBS, Gemini, 900-108) and 0.01mg/ml hygromycin B under 5% CO2 at 37°C.

extract_protocol:
10,000 fresh cells were counted and processed according to Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) instructions. Briefly, ConA beads were added to the cell pellet and incubation at room temperature for 10 min. Subsequently, the mixed complexes were incubated overnight at 4°C with primary antibody. The following day, the cells were washed and incubated with diluted secondary antibody at room temperature for 2 h. Antibody-protein-DNA complexes were then linked by pA/G-Tnp by incubation at room temperature for 1 h. After washing, the eluted complexes were subsequently sheared by adding 5 × TTBL. The proteinase K and DNA extract beads were used for obtaining eluted DNA.
Sequencing libraries were established after 11 cycles of PCR amplification. Selected size-selected were proceeded using AMPure XP beads and the DNA were sequenced on the Illumina Hiseq-PE150 platform to a depth of 2.5 × 107 reads.

value: peripheral blood mononuclear cells

tag: cell line

tag: cell type

value: PBMCs

tag: genotype


title: PBMC_PDA-1_ETS1_CutTag


title: priB_TriC_Spt5_IgG1poolcapture_ctrl_clone2_rep1

description: Tri-C

value: replicate 1


title: rne(WT) replicate 3

value: rne(WT)


title: Y16_3

description:
Y16_3
mRNA

value: Dark phase (Zeitgeber time 12-24)


title: rne(5p) replicate 1


title: PBMC_CTRL-1_ETS1_CutTag


title: PBMC_CTRL-1_IgG_CutTag


title: rne(WT) replicate 2


title: PBMC_CTRL-2_ETS1_CutTag


title: GATA1_NonUV

value: Non-UV


title: priB_TriC_Spt5_IgG1poolcapture_ctrl_clone1_rep3

description: Tri-C

value: IgG1 pool capture

value: clone 1

value: replicate 3


title: Y14_1

description:
Y14_1
mRNA


title: Glioblastoma, low-functional connectivity, patient 3

city: San Francisco

first: Abrar

last: Choudhury

state: California

institute: University of California, San Francisco

library_source: transcriptomic single cell

data_processing:
Library demultiplexing, read alignment to the hg38 human reference genome, identification of empty droplets, and UMI quantification was performed using CellRanger v3.0.2
Single cell UMI count data were processed in R v3.6.1 with the Seurat v3.0.1 package using the sctransform workflow, with scaling based on regression of UMI count and percentage of reads attributed to mitochondrial genes per cell.
Assembly: hg38
Supplementary files format and content: Matrix table with the number of unique molecular identifiers for every feature (gene) by row and every barcode (cell) by column
Supplementary files format and content: Sequences corresponding to every barcode in the matrix table
Supplementary files format and content: Sequences corresponding to every feature in the matrix table

molecule: polyA RNA

source_name: glioblastoma

extract_protocol:
Fresh glioblastomas were dissociated into single cells by mincing and then treating with papain, trypsin, and RBC lysis buffer. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.

value: glioblastoma

tag: functional connectivity

value: low

tag: age

value: M


title: priB_TriC_Spt5_IgG1poolcapture_ctrl_clone1_rep1

description: Tri-C

value: WT


title: Y13_3

description:
Y13_3
mRNA

value: Liver

value: Female


title: rne(WT) replicate 1


title: priB_TriC_Spt5_IgG1poolcapture_dep_clone1_rep3

description: Tri-C

value: Spt5 62h activated, last 32h depleted with 4HT


title: priB_TriC_B18AIDKO_IgG1capture_72h_clone2_rep3

description: Tri-C

value: 72h activated

value: clone 2


title: Glioblastoma, high-functional connectivity, patient 3

value: high


title: WT replicate 2

value: untreated


title: WT replicate 3


title: Y14_3

description:
Y14_3
mRNA

value: Standard diet (LF)

value: Light phase (Zeitgeber time 0-12)


title: WT replicate 1


title: Y8_3

description:
Y8_3
mRNA

value: Dark phase (Zeitgeber time 12-24)


title: priB_TriC_B18AIDKO_IgG1capture_72h_clone2_rep2

description: Tri-C

value: IgG1 pool capture

value: replicate 2


title: priB_TriC_B18AIDKO_IgG1capture_72h_clone2_rep1

description: Tri-C

value: replicate 1


title: Glioblastoma, high-functional connectivity, patient 2

value: glioblastoma


title: priB_TriC_B18AIDKO_IgG1capture_72h_clone1_rep3

description: Tri-C

value: clone 1

value: replicate 3


title: Y8_2

description:
Y8_2
mRNA


title: Glioblastoma, low-functional connectivity, patient 1

value: low

value: F


title: priB_TriC_B18AIDKO_IgG1capture_72h_clone1_rep2

description: Tri-C


title: Y11_3

description:
Y11_3
mRNA

value: Liver

value: Female


title: Glioblastoma, low-functional connectivity, patient 2

value: M


title: Y7_2

description:
Y7_2
mRNA


title: Glioblastoma, high-functional connectivity, patient 1


title: Y5_2

description:
Y5_2
mRNA


title: priB_TriC_B18AIDKO_IgG1capture_48h_clone2_rep3

description: Tri-C

value: 48h activated

value: clone 2


title: final_rep1

city: Bethesda

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

institute: NIH

description:
Lihui_Counts_2020_03_05
ER_K20_GFP high.gene_summary

data_processing:
sgRNA sequences were obtained per sample by extracting 20 bps followed by the index sequence of “TTGTGGAAAGGACGAAACACCG” on the de-multiplexed FASTQ files from Illumina’s NGS sequencer using the Cutadapt software, version 2.8
FASTQC, version 0.11.9 was used to assess the sequencing quality.
MAGeCK, version 0.5.9, was used to quantify and to identify differentially expressed sgRNAs.
MAGeCK count command was run on the merged two-half libraries of A and B to quantify.
Differentially expressed sgRNAs with statistical significance were determined by running the MAGeCK test command in paired mode.
Assembly: library_A_B
Supplementary files format and content: Lihui_Counts_2020_03_05.xlsx: MS Excel file and it contains raw and normalized counts
Supplementary files format and content: ER_K20_GFP high.gene_summary.xlsx: MS Excel file and it contains deregulated genes with fold change, p-values and adjusted p-values

extract_protocol:
Genomic DNA was extracted from each cell population using a QIAGEN Blood Maxi kit (for GFP low cells) or QIAGEN Blood Midi kit (for GFP high cells).
sgRNAs sequences were amplified from genomic DNA samples using the Herculase II Fusion DNA Polymerase (Agilent Technologies) in two PCR steps as follows. In the first PCR, the genomic region containing sgRNAs were amplified from 130 µg total DNA using the following primers: Forward: 5’-AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG-3’; Reverse: 5’-CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC-3’. In total, 13 PCR reactions were performed in parallel, with 10 µg genomic DNA in each reaction using Herculase II Fusion DNA Polymerase (Agilent) for 18 cycles and the resulting PCR products were combined. In the second step PCR, 5 µl of first PCR product was used in a 100 µl reaction volume and 24 PCR cycles was used. The primers used for the second PCR include stagger sequences of variable lengths and a 6bp barcode for multiplexing of different biological samples. The 2nd step PCR primers were used as the following: Forward: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (1-9bp variable length sequence)-(6bp barcode)tcttgtggaaaggacgaaacaccg-3’; Reverse: 5’-CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT tctactattctttcccctgcactgt-3’.
sgRNAs amplified from genomic DNA

treatment_protocol: Cells were infected with the GeckoV2 libraries (A, B) in duplicates.

value: Kidney

value: wild type

value: cells stably expressing the ERGFP_K20 reporter were infected with GeckoV2 libraries (A, B)

tag: sorting

value: GFP high


title: Y3_1

description:
Y3_1
mRNA

value: Standard diet (LF)

value: Dark phase (Zeitgeber time 12-24)


title: priB_TriC_B18AIDKO_IgG1capture_48h_clone2_rep2

description: Tri-C

value: IgG1 pool capture

value: replicate 2


title: TBP_UV

scan_protocol: Protein bound microarrays were scanned at 488nm or 635nm using a GenePix 4400A at multiple laser power and gain settings to best capture the signal and avoid saturation of spots. The resulting TIF images were processed using GenePix Pro 7.3.

label: Alexa 488

organism: Arabidopsis thaliana

source_name: Arabidopsis TBP

tag: protein

value: TBP

tag: protein concentration

tag: array condition

value: UV


title: Y1_3

description:
Y1_3
mRNA

tag: treatment


title: initial_rep2

value: GFP low


title: hDPSCs

type: RNA

city: Seoul

first: SoYoung

last: Park

state: Korea,Seoul

address: Seoul, Republic of Korea,, 1 Gwanak-ro, Gwanak-gu, Seoul, 86-509

country: South Korea

institute: Seoul National University

hyb_protocol: Approximately 5.5 ug of labeled DNA target was hybrized to Affymetrix GeneChip Array at 45 °C for 15 hour

scan_protocol: Hybridized arrays were washed and stainined on a GeneChip Fluidics station 450 and scanned on a GCS3000 Scanner (Affymetrix)

data_processing:
Array data export processing and analysis was performed using Affymetrix GeneChip command console softeware (AGCC)
Affymetrix power Tools, R 3.1.2

label: biotin

source_name: Tooth

label_protocol: The sence cDNA was then frgmented and  biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Termial labeling kit

growth_protocol: Human dental pulp-derived mesenchymal stromal cells (hDPSCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C °C

extract_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) amplication kit as descirbed by the manufacturer

treatment_protocol: To detect the osteogenic differentiation capability of hDPSCs, they were cultured in 50 μg/mL ascorbic acid (Sigma-Aldrich) and 10 mM β-glycerophosphate (Sigma-Aldrich) in DMEM containing 10% FBS and 1% penicillin-streptomycin.

value: hDPSCs


title: initial_rep1


title: priB_TriC_B18AIDKO_IgG1capture_48h_clone2_rep1

description: Tri-C

tag: capture probe

tag: clone

tag: replicate

value: replicate 1


title: Y1_1

description:
Y1_1
mRNA

tag: tissue

value: Liver

tag: Sex

value: Female


title: UVDDB

source_name: Human UV-DDB

value: UVDDB


title: Y4_1

description:
Y4_1
mRNA

tag: time

tag: time point


title: priB_TriC_B18AIDKO_IgG1capture_48h_clone1_rep2

description: Tri-C

value: 48h activated

value: clone 1


title: priB_TriC_B18AIDKO_IgG1capture_48h_clone1_rep1

description: Tri-C


title: final_rep2

tag: cell line

value: Kidney

value: wild type


title: LT3

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

institute: Korea University College of Medicine

data_processing:
Sequencing reads were trimmed for bases with base quality score less than 20
Trimmed sequencing reads were aligned to human transcriptome mm10 using HISAT2
Mapped reads were converted to the count table using HTSeq v0.8
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing the raw count data for all samples

source_name: Bone marrow mesenchymal stem cells from CFA-inflammed mice treated with LTbR-Ig (48h).

extract_protocol:
Long bones were flushed with HBSS supplemented with 2% of heat-inactivated fetal bovine serum, Penicillin/Streptomycin, L-glutamine, HEPES, and 200 U/mL Collagenase IV (Worthington Biochemical Corporation) and digested for 30 min at 37°C. Cell clumps were dissociated by gentle pipetting. Cells were filtered through a 100 mm nylon mesh and washed with HBSS/2% FBS. Hematopoietic cells were depleted by staining with biotin-conjugated CD45 and Ter119 antibodies, and using Dynabeads ® Biotin Binder (Invitrogen #11047). Following depletion of hematopoietic cells, the remaining cells were stained with antibodies against CD31, CD144 and PDGFRb. BM MSCs were identified as CD45- Ter119- CD31- CD144- PDGFRb+ cells. Sorting was performed using a BD FACS Aria II. Cells were sorted directly into 350 mL RLT plus buffer (Qiagen) and RNA extracted using the RNeasy® Plus Micro Kit (Qiagen #74034). RNA sequencing was performed by the Yale Center for Genome Analysis using the Illumina HiSeq2500 system, with paired-end 2 x 76 bp read length.
Libraries were prepared after poly-A selection

value: Bone Marrow

tag: cell type

value: Bone Marrow Lepr+ Mesenchymal Stem Cells

value: CFA and LTbR-Ig 3


title: STAT3_NonUV

source_name: Human STAT3

value: Non-UV


title: STAT3_UV


title: SLE3

city: Taipei

first: Szu-Ting

last: Chen

address: No. 155, 2nd Sec. Li Nong Street

department: Clincal medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Cutadapt (V1.9.1)
The adapters were cut off, and reads were trimmed when the quality dropped below 20. Reads of length <75 were discarded.
Raw reads (>21 million reads per sample) were aligned to the human reference genome (ENSEMBL, Homo_sapiens. GRCh37.91) via Hisat2 (v2.0.1).
The transcript levels were displayed as reads per kilobase of transcript per million mapped reads (RPKM) obtained from HT-seq (V 0.6.1).
Assembly: GRCh37.91
Supplementary files format and content: All_gene_expression.txt: Tab-delimited text file includes RPKM values for all Samples.

source_name: CD14+ monocyte

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen) and 1ug of total RNA was used for the libraries preparation.
Next-generation sequencing library preparations were constructed according to the manufacturer’s protocol (Illumina HiSeq/Novaseq and MGI2000).

treatment_protocol: Human healthy monocytes were treated with 3000 U of the IFNA2 for 6 hours if the group was the one for IFN treatment (H-IFN)

value: female

value: CD14+ monocyte

tag: disease state

value: SLE

value: no treatment

value: 0 hour


title: TBP_NonUV

value: TBP


title: SLE4

value: male


title: ETS1_UV_r2

source_name: Human ETS1

value: UV


title: SLE2


title: LT2

value: CFA and LTbR-Ig 2


title: ETS1_UV_r1


title: priB_TriC_B18AIDKO_IgG1capture_48h_clone1_rep3

description: Tri-C

value: IgG1 pool capture

value: 48h activated

value: replicate 3


title: LT1

value: CFA and LTbR-Ig 1


title: priB_TriC_B18AIDKO_IgG1capture_72h_clone1_rep1

description: Tri-C

value: 72h activated

value: clone 1

value: replicate 1


title: H3-IFNA

value: Healthy

value: 6 hours


title: priB_TriC_B18AIDKO_IgG1capture_0h_clone2_rep1+3

description: Tri-C

value: WT

value: clone 2


title: P53_UV


title: HEL3

source_name: Bone marrow mesenchymal stem cells from CFA-inflammed mice treated with control HEL-Ig (48h).

value: Bone Marrow

value: Bone Marrow Lepr+ Mesenchymal Stem Cells

value: CFA and Hel-Ig 3


title: priB_TriC_B18AIDKO_IgG1capture_0h_clone2_rep2

description: Tri-C

value: replicate 2


title: H2-IFNA

value: male

value: CD14+ monocyte


title: priB_TriC_B18AIDKO_IgG1capture_0h_clone1_rep2

description: Tri-C

value: IgG1 pool capture


title: H1-IFNA

value: female


title: ETS1_NonUV_r1

value: Non-UV


title: HEL2

value: CFA and Hel-Ig 2


title: priB_TriC_B18AIDKO_IgG1capture_0h_clone1_rep1+3

description: Tri-C


title: H3

value: no treatment

value: 0 hour


title: HEL1

value: CFA and Hel-Ig 1


title: priB_TriC_B18AIDKO_hs4capture_72h_rep3

description: Tri-C

value: hs4 capture

value: 72h activated

value: clone 1

value: replicate 3


title: H2

value: Healthy


title: ELK1_UV

source_name: Human ELK1

value: UV


title: priB_TriC_B18AIDKO_hs4capture_72h_rep2

description: Tri-C


title: H1


title: CTR3

source_name: Bone marrow mesenchymal stem cells from untreated control mice.

value: Bone Marrow

value: Bone Marrow Lepr+ Mesenchymal Stem Cells

value: Control 2


title: ELK1_NonUV


title: CTR1

value: Control 1


title: ETS1_NonUV_r2


title: priB_TriC_B18AIDKO_hs4capture_72h_rep1

description: Tri-C

value: replicate 1


title: BPC_tumor_306_LECs_rep4

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

data_processing:
Adapter sequences and low quality base pairs at the 5 prime and 3 prime ends of the reads were trimmed using Trimmomatic 0.38
Star2.6 was used align reads to NCBI’s mm10 mouse genome and quantify genes.
Assembly: mm10
Supplementary files format and content: RNA180216AL_raw.xlsx: excel spreadsheet (.xlsx) of raw transcript counts
Supplementary files format and content: RNA180216AL_norm.xlsx: excel spreadsheet (.xlsx) of RPKM values

source_name: BPC melanoma - ear pinna

extract_protocol:
RNA extracted using Qiagen Rneasy Micro Kit
RNA libraries for RNA-seq were prepared using Takara SMART-Seq v4 Ultra low Input RNA kit following manufacturer's protocols.

value: BPC melanoma - ear pinna

value: lymphatic endothelial cell

tag: genotype

value: BrafCA/+; pten l/l; Cre+

value: female


title: BPC_tumor_303_LECs_rep3


title: EGR1_UV

source_name: Human EGR1


title: hDPSCs, W146, Day7

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 1.3.4d, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: hDPSCs

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
To detect the osteogenic differentiation capability of hDPSCs, they were cultured in 50 μg/mL ascorbic acid (Sigma-Aldrich) and 10 mM β-glycerophosphate (Sigma-Aldrich) in DMEM containing 10% FBS and 1% penicillin-streptomycin.
hDPSCs were plated in 48-well plates and treated with inhibitors in osteogenic differentiation medium, and the medium was changed every 2~3day.

tag: drug

value: hDPSCs

value: osteogenic differentiation

value: Day 7


title: BPC_tumor_278_LECs_rep2

value: male


title: priB_TriC_B18AIDKO_hs4capture_48h_rep2

description: Tri-C

source_name: primary B-cells

value: hs4 capture

value: 48h activated

value: clone 1

value: replicate 2


title: CREB1_UV

source_name: Human CREB1

value: UV


title: hDPSCs, ML354, Day7


title: CREB1_NonUV

value: Non-UV


title: BPC_tumor_275_LECs_rep1


title: hDPSCs, FSLLRY-NH2, Day7


title: priB_TriC_B18AIDKO_hs4capture_0h_rep2

description: Tri-C

value: WT


title: naïve_skin_LECs_rep3

source_name: naïve skin - ear pinna

value: naïve skin - ear pinna

value: BrafCA/+; pten l/l; Cre-


title: priB_TriC_B18AIDKO_hs4capture_48h_rep3

description: Tri-C

value: replicate 3


title: hDPSCs, ZM241385, Day7


title: priB_TriC_B18AIDKO_hs4capture_0h_rep1+3

description: Tri-C

value: replicate 1


title: hDPSCs, Ki16425, Day7


title: hDPSCs, FR171113, Day7


title: UVDDB_ETS1

source_name: Human UV-DDB and ETS1

value: 250nM UVDDB| 35nM ETS1


title: priB_TriC_B18AIDKO_Emucapture_72h_rep3

description: Tri-C

value: Emu capture

value: 72h activated


title: hDPSCs, osteoControl, Day7

description: osteoControl

value: osteoControl

value: hDPSCs

value: osteogenic differentiation


title: naïve_skin_LECs_rep2

value: lymphatic endothelial cell

value: BrafCA/+; pten l/l; Cre-/Braf+/+;pten l/l Cre+

value: female


title: naïve_skin_LECs_rep1

value: pooled male and female


title: priB_TriC_B18AIDKO_Emucapture_72h_rep2

description: Tri-C

value: clone 1

value: replicate 2


title: priB_TriC_B18AIDKO_hs4capture_48h_rep1

description: Tri-C

value: hs4 capture

value: 48h activated


title: priB_PROseq_rest_rep2

description:
nascent RNA
PRO-seq

data_processing:
Library strategy: PRO-seq
PRO-seq
Identical reads were collapsed using sort -k 10,10 -u.
The 3' adaptors were removed using cutadapt (v1.4.2 Read1: cutadapt -O 5 -a NNNNTGGAATTCTCGGTGCC ) and 9 nucleotides from their 5′ were removed.
The trimmed reads were reverse complemented using fastx_reverse_complement (http://hannonlab.cshl.edu/fastx_toolkit ).
Trimmed reads >18 were aligned using bowtie (v 1.0.0, -v 2 --best --strata --tryhard -m 1 --chunkmbs 256).
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools (v2.27, bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+', bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools (bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024).
Normalised coverage tracks were created by dividing the coverage at each position with the total number of aligned reads per million.
Spike-in normalised coverage tracks of the 3’ position were created using bedtools genomecov (v2.27,  bedtools genomecov -3  -bg -scale,  bedtools genomecov -3  -bg -scale '+', bedtools genomecov -3  -bg -scale '-‘)
Assembly: hybrid mouse drosophila genome (GRCm38 and drosophila FlyBase release 5)
Supplementary files format and content: bigWigs of rpm-normalized and spike-in normalized read densities

extract_protocol:
To isolate nuclei, murine and Drosphila S2 cells were resuspended in cold Buffer IA (160 mM Sucrose, 10 mM Tris-Cl pH 8, 3 mM CaCl2, 2 mM MgAc2, 0.5% NP-40, 1 mM DTT added fresh), incubated on ice for 3 min and centrifuged at 700 g for 5 min. The pellet was resuspended in nuclei resuspension buffer NRB (50 mM Tris-Cl pH 8, 40% Glycerol, 5 mM MgCl2, 0.1 mM EDTA). For each run-on, 107 nuclei of the sample and 10% Drosophila S2 nuclei were combined in a total of 100 µL NRB and incubated at 30°C for 3 min with 100 µL 2x NRO buffer including 5µl of each 1mM NTPs. Reactions were terminated with TRIzol and RNA extracted as per the manufacturer's protocol.
3’ ligation was performed at 16°C overnight with adapter 5’5Phos/NNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT-3’. RNA was reverse transcribed by SuperScript III RT with RP1 Illumina primer to generate cDNA libraries. Libraries were amplified with barcoding Illumina RPI-x primers and the universal forward primer RP1 using KAPA HiFi Real-Time PCR Library Amplification Kit. Amplified libraries were subjected to gel electrophoresis on 2.5% low melting agarose gel and amplicons from 150 to 350 bp were extracted from the gel, multiplexed and sequenced on Illumina platform NextSeq 550 SR75.

value: resting


title: D56_TPT

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
Basecalling was performed using BCL2Fastq2.
Sequenced reads were trimmed for adaptor sequence and filtered for low quality sequences using TrimGalore, then mapped to hg38 whole genome using HISAT2 with parameters: --fr  --q --x
Read counts were calculated with HTSeq (htseq-count) using the following parameters:  --stranded=reverse.  Mapped files were counted against the Gencode v37.
Data filtering was performed before differential expression analysis with EdgeR. Filtering removed any gene which did not achieve 10 counts per million in at least 3 samples. Differential expression analysis was performed between TPT- and DMSO-treated groups; significance was determined at an FDR corrected p-value < 0.05 and an absolute fold change in expression of greater than 2.
Assembly: hg38
Supplementary files format and content: total host gene counts; ERCC spike-in counts; HIV counts

source_name: CD4+ T-cell RNA extract

extract_protocol:
Total RNA was extracted from cell samples using the RNeasy micro kit (QIAGEN, Cat. No. 74004) with the addition of an on-column DNase treatment (RNase-free DNase Set, QIAGEN, Cat. No. 79254).
Paired end ribodepleted RNA stranded libraries were prepared for sequencing using standard Illumina protocols.
RNA-Seq was conducted using Illumina NovaSeq 6000 sequencer

treatment_protocol: Cells were plated at 500,000 cells per well in 200 ul RPMI-1640 media containing 5% human serum on a 96-well tissue culture plate and either treated with TPT (10 uM) or DMSO for a period of 24 hours.

value: CD4+ T cell

tag: infection status

value: Model of HIV latency

value: 10 uM TPT


title: priB_PROseq_rest_rep1

description:
nascent RNA
PRO-seq


title: EGR1_NonUV

tag: protein

value: Non-UV


title: priB_TriC_B18AIDKO_Emucapture_72h_rep1

description: Tri-C

value: Emu capture

value: 72h activated

value: replicate 1


title: priB_TriC_B18AIDKO_Emucapture_48h_rep3

description: Tri-C

value: replicate 3


title: D56_DMSO

value: DMSO


title: MYC_UV

source_name: Human c-MYC

value: c-MYC and MAX

tag: protein concentration

value: 500nM c-MYC|100nM MAX

value: UV


title: ETS1_NonUV

tag: array condition


title: ETS1_UV


title: MYC_NonUV


title: 64PP_UV_r2

type: other

description: Antibody

hyb_protocol: Commercially synthesized, high-density, single-stranded DNA microarrays from Agilent were first double-stranded via primer extension as done in previous assays (Berger et al, Nature Biotechnology 2006; Shen et al, Cell Systems 2018). The arrays were partially irradiated with UVC such that only some chambers were exposed to UVC while others were not. In order to irradiate only certain parts of the array, and protect the rest from UV irradiation, a cover/gasket slide was cut to the desired size are used to partially cover the DNA array. Next, the gasket slide was fully covered using Cryo-Babies® labels, and the array-gasket slide sandwich was placed in an open container with 1x PBS. To irradiate the DNA on the array, we used a Stratalinker® UV Crosslinker 1800 instrument and conducted a series of irradiations with UVC. Using the energy mode, the container was irradiated with 100 J/m2 , randomly repositioned inside the crosslinker 15 times to achieve 1,500 J/m2 . Midway through the series, the PBS was replaced in order to keep the solution at room temperature. This procedure resulted in a DNA array with some chambers of the array irradiated by UV and others not irradiated. Samples with the “UV” condition used irradiated chambers while those with a “Non-UV” condition used non-irradiated chambers. The arrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk for 1 hour as done in prior assays (Shen et al, Cell Systems 2018). Antibodies for CPD and 6-4PP were incubated in a 1:400 and 1:80 ratio respectively in a 1x PBS buffer of 2% (wt/vol) milk and 0.05% Tween for 1 hour. After incubation, the arrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min as done in prior work (Shen et al, Cell Systems 2018). Then the arrays were incubated with a secondary antibody of conjugated anti-mouse 488 at 1.3% volume in a PBS buffer with 2% (wt/vol) milk and 0.05% Tween for 1 hour. The arrays were then washed as previously described.

scan_protocol: Anti-CPD and anti-6-4PP bound microarrays were scanned at 488nm using a GenePix 4400A at multiple laser power and gain settings to best capture the signal and avoid saturation of spots. The resulting TIF images were processed using GenePix Pro 7.3.

molecule: other

source_name: Mouse Anti-6-4PP

tag: antibody

value: Anti-6-4 Photoproduct

tag: antibody ratio


title: priB_TriC_B18AIDKO_Emucapture_48h_rep2

description: Tri-C

tag: capture probe

tag: treatment

tag: clone

value: clone 1

value: replicate 2


title: D47_TPT


title: 64PP_NonUV_r2

description: Antibody


title: priB_Rad21_ChIPseq_Spt5depleted

description: CHIP-seq

data_processing:
ChIP-seq
The 3' adaptors were removed using cutadapt (v1.4.2, Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were aligned to a hybrid mouse drosophila genome (mouse genome build NCBI m37, GCA_000001635.18, drosophila FlyBase release 5) using bowtie (v 1.0.0, -v 2 --best --strata --tryhard -m 1 --chunkmbs 256)
Replicates were pooled with samtools merge 1.9, the number of reads mapping to the Drosophila genome were counted with samtools flagstat and spike-in normalization factors were computed as 1,000,000/number of Drosophila reads
genome-wide coverage tracks were computed with deeptools bamCoverage 3.3.0 using --ignoreDuplicates --nomalizeUsing CPM --scaleFactor 1.61717/1.25156 for H3K09me3 WT/KD and using --ignoreDuplicates --nomalizeUsing CPM --exactScaling for H3 WT and KD
H3K09me3 broad peaks for each condition were called on pooled reads with epic2 0.0.41 using -gn mm9 -fdr 0.01 -fs 200 with IgG ChiP-seq as input
Assembly: NCBI m37, GCA_000001635.18, drosophila FlyBase release 5
Supplementary files format and content: broadPeak format files containing the output of epic2 for H3K09me3 data sets for WT and KD

extract_protocol:
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, libraries were prepared following the NEB Next Ulta II DNA library kit. Libraries were amplified with the kappa library amplification qCR master mix

value: Spt5 depleted


title: D55_TPT


title: priB_TriC_B18AIDKO_Emucapture_48h_rep1

description: Tri-C

value: 48h activated

tag: replicate


title: priB_Rad21_ChIPseq_control

description: CHIP-seq

value: control


title: priB_PROseq_act_rep2

description:
nascent RNA
PRO-seq

value: 72h LPS-IL4 activated


title: 64PP_UV_r1

description: Antibody


title: priB_TriC_B18AIDKO_Emucapture_0h_rep2

description: Tri-C

value: WT


title: priB_PROseq_act_rep1

description:
nascent RNA
PRO-seq


title: D47_DMSO

value: CD4+ T cell

value: Model of HIV latency


title: priB_TriC_B18AIDKO_Emucapture_0h_rep1+3

description: Tri-C

value: Emu capture


title: Y8_1

description:
Y8_1
mRNA

source_name: Liver

tag: tissue

value: Liver

tag: Sex

value: Female

value: Standard diet (LF)

tag: time

value: Dark phase (Zeitgeber time 12-24)

tag: strain


title: D55_DMSO

tag: cell type

value: DMSO


title: 64PP_NonUV_r1

description: Antibody

value: Non-UV


title: Group 2, rep 3, AAV sh-RNA MYTHO, 3 weeks

status: Public on Jan 19 2023

city: Montreal

first: Gilles

last: Gouspillou

state: Québec

address: 141 Avenue du Président Kennedy

department: Département des sciences de l'activité physique

country: Canada

institute: UQAM

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the Robust Multichip Analysis (SST-RMA) procedure. The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters.                                                                                Array Type: Clariom_S_Mouse  Analysis Type: Expression (Gene)                                                                                Genome Version: mm10 (Mus musculus)  Annotation: Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

source_name: Gastroc skeletal muscle, AAV sh-RNA MYTHO

label_protocol: Microarray was performed at the McGill University and Génome Québec Innovation Centre (Montréal, QC). Raw data were analyze using default parameters from the Transcriptome Analysis Console (TAC) 4.0.1 software (Affymetrix) using default parameters.

extract_protocol: Total RNA was isolated by Trizol, according to the manufacturer’s instructions.

value: Gastroc skeletal muscle

value: male

tag: strain background

value: C57/Bl6j mice

tag: age


title: Group 2, rep 2, AAV sh-RNA MYTHO, 3 weeks


title: Group 2, rep 1, AAV sh-RNA MYTHO, 3 weeks


title: Group 2, rep 4, AAV sh-RNA MYTHO, 3 weeks


title: Group 2, rep 3, AAV sh-RNA MYTHO

hyb_protocol: not provided

scan_protocol: not provided Microarray was performed at the McGill University and Génome Québec Innovation Centre (Montréal, QC). Raw data were analyze using default parameters from the Transcriptome Analysis Console (TAC) 4.0.1 software (Affymetrix) using default parameters.

data_processing:
The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the Robust Multichip Analysis (SST-RMA) procedure. The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters.                                                                                Array Type: Clariom_S_Mouse
Analysis Type: Expression (Gene)
Genome Version: mm10 (Mus musculus)
Annotation: Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

label_protocol: not provided

value: AAV sh-RNA MYTHO

tag: background strain


title: Group 2, rep 4, AAV sh-RNA MYTHO


title: Group 2, rep 1, AAV sh-RNA MYTHO


title: CPD_UV_r1

description: Antibody

data_processing: The raw data collected using the GenePix® 4400A microarray scanner was processed using the Seed and Wobble suite (Berger et al, Nature Biotechnology 2006), with modifications to adapt the k-mer data to our UV-Bind universal design, as described in the manuscript. For each unique sequence tested, median values over the spots containing that sequence were used unless otherwise noted (i.e. for the universal design sequences and for the competition tests). The number of replicate spots for each sequence varied between 3 and 20, depending on the DNA library. Processing of k-mers and PWMs using Seed-and-Wobble was done using the adjusted signal (i.e. Alexa488Adjusted or Alexa635Adjusted column) in the alldata.txt file as done by default (Berger et al, Nature Biotechnology 2006).

source_name: Mouse Anti-CPD

extract_protocol: Extract protocol is detailed in the manuscript for all tested proteins and antibodies.

value: Anti-Cyclobutane Pyrimidine Dimer

value: UV


title: Group 2, rep 2, AAV sh-RNA MYTHO


title: Group 1, rep 2, AAV sh-RNA scrmb

source_name: Gastroc skeletal muscle, AAV sh-RNA scrmb

value: AAV sh-RNA scrmb


title: Group 1, rep 1, AAV sh-RNA scrmb


title: Group 1, rep 4, AAV sh-RNA scrmb


title: CPD_UV_r2

description: Antibody


title: CPD_NonUV_r2

description: Antibody


title: Group 1, rep 3, AAV sh-RNA scrmb


title: CPD_NonUV_r1

description: Antibody


title: Group 1, rep 4, AAV sh-RNA scrmb, 3 weeks


title: Patient24165

city: Aurora

first: Petter

last: Bjornstad

state: Colorado

institute: University of Colorado School of Medicine

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the cellranger v6 (10x Genomics) pipeline.
SoupX was employed, as noted per sample in the supplemental materials for this manuscript, using default parameters.
Integration was conducted with RunHarmony, embedded within Seurat v4.0.0.
Assembly: hg38, v. GRCh38-2020-A
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: Kidney cortex

extract_protocol:
Cortical human kidney biopsies that had been stored in Cryostor were subjected to a cellular RNA extraction protocol from the Kidney Precision Medicine Project.
Library construction was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics)

treatment_protocol: Where indicated, patients were prescribed and had been administered an SGLT2 inhibitor, averaging 6 months treatment prior to kidney biopsy

value: Kidney cortex

value: Kidney and immune cells

tag: disease state

value: Healthy control


title: Patient34064

description: 10x Genomics


title: Patient34332

description: 10x Genomics

value: Male


title: Patient24164

description: 10x Genomics

value: SGLT2 inhibitor


title: Group 1, rep 3, AAV sh-RNA scrmb, 3 weeks


title: Patient24163

description: 10x Genomics


title: Group 1, rep 1, AAV sh-RNA scrmb, 3 weeks


title: Group 1, rep 2, AAV sh-RNA scrmb, 3 weeks


title: Patient24024

description: 10x Genomics


title: Patient24162

description: 10x Genomics


title: Patient23984

description: 10x Genomics

value: Female


title: Patient23644

description: 10x Genomics


title: Patient23453

description: 10x Genomics


title: Patient23642

description: 10x Genomics


title: Patient23982

description: 10x Genomics


title: Patient23981

description: 10x Genomics


title: Patient23454

description: 10x Genomics


title: Patient23452

description: 10x Genomics


title: Patient23451

description: 10x Genomics


title: Patient23274

description: 10x Genomics


title: WT_2

city: padova

first: Maria

last: Pennuto

state: Padova

address: via ugo bassi 58b

country: Italy

institute: University of Padua

hyb_protocol: Agilent protocols

scan_protocol: Agilent protocols

data_processing: Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09). Data were pre-processed with Agi4x44PreProcess R package 1.16.0: after import, data were processed for background correction and between array normalization (quantile). After probe filtering (remove controls and well above BG probes), replicated probes were summarized using the median of the intensities.

source_name: 3 month old wild type mouse

label_protocol: Agilent protocols

extract_protocol: total RNA

value: Quadriceps

tag: genotype

value: WT


title: 113Q_1

source_name: 3 month old 113Q mouse


title: Patient23272

description: 10x Genomics


title: Patient23271

description: 10x Genomics


title: WT_4


title: 113Q_3


title: WT_1


title: 113Q_2


title: WT_3


title: TfhCM_rep2

city: Canberra

first: Xin

last: Gao

state: ACT

address: 131 Garran Rd

department: Immunology

country: Australia

institute: The Australian National University

data_processing:
Illumina Casava1.7 software used for basecalling.
The mapping of raw reads into count files was performed by Galaxy's standardized protocol: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html
Genome_build: hg38
Supplementary_files_format_and_content: Merged matrix table with counts for all genes in all samples
Supplementary_files_format_and_content: raw counts

source_name: Buffy coat

extract_protocol:
Indicated cell subsets were FACS-purified from PBMC. 300000-500000 cells per sample were further processed for RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

tag: cell subtype

value: TfhCM


title: TfhEM_rep2

value: TfhEM


title: Patient24023

description: 10x Genomics


title: TfhEM_rep1


title: TEM_rep2

value: TEM


title: Patient24021

description: 10x Genomics


title: TCM_rep2

value: TCM


title: TEM_rep1


title: TCM_rep1


title: Patient23643

description: 10x Genomics


title: Naïve_CD4_rep2


title: Naïve_CD4_rep1


title: Mouse_C57BL/6xJF1_EPC_rep1 [CxJ_EPC1]

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

country: Japan

institute: Nara Medical University

description:
WGBS (rPBAT)
mouse_ectoplacentalcone_maternal_rep1-3_x1.bw
mouse_ectoplacentalcone_maternal_rep1-3_x5.bw
mouse_ectoplacentalcone_paternal_rep1-3_x1.bw
mouse_ectoplacentalcone_paternal_rep1-3_x5.bw

data_processing:
>Sequencing reads were trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to diploid rat or mouse pseudogenomes using MEA and Bismark.
>Duplicate reads were removed and the number of methylated and unmethylated reads overlapping each CpG of the rat or mouse genome was reported. This resulted in total (allele-agnostic), maternal- and paternal-specific CpG report files.
>Replicates and reciprocal crosses were merged for visualization and analyses.
>CpGs covered by at least 5 (total) or 1 (maternal or paternal) sequencing reads were assessed for methylation levels and genome-wide tracks were sunsequently generated for visualization.
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample

source_name: EPC

extract_protocol:
Genomic DNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One hundred nanograms of genomic DNA from JF1 (female) and C57BL/6 (male) mouse hybrids were prepared for Methyl-seq (Illumina) library construction. Twenty nanograms of genomic DNA from the other mouse and rat hybrid crosses were prepared for rPBAT or tPBAT library construction.

treatment_protocol: E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains. E7.25 F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to whole genome bisulphite sequencing.

value: F1 hybrid resulting from female C57BL/6N and male JF1/Ms mice

value: embryonic days 7.25

value: wild type

value: EPC

value: female


title: Infect WT HSC using antibody against BATF2 replication #2

city: Houston

first: Duy

middle: Tri

last: Le

state: Texas

address: 1102 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
FASTQ files were preprocessed using HTS stream
CUT&RUN alignment (Bowtie2)
Peaks were called uing MACS v2.2 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: narrow peaks
Library strategy: CUT&RUN sequencing

source_name: Hematopoietic Stem Cells

growth_protocol: HSCs were isolated via whole bone marrow from naïve or infected mice

extract_protocol:
Leg and hip bones were isolated and HSCs were purified via FACS sorting following mechanical isolation and c-kit+ magnetic cell enrichment. HSCs (LK CD150+ CD48-) were washed with Wash Buffer (50mL total with 20 mM HEPES pH 7.5, 150mM NaCl, 0.5 mM Spermidine, and one Roche Complete protein inhibitor tablet) and bound to Concanavalin A-coated magnetic beads (Bang Laboratories L200731C) for 15 minutes room temperature. Sample slurries were magnetically separated, washed, and incubated with primary antibody diluted in wash buffer containing 0.05% digitonin (Dig Wash) overnight at 4 °C. Slurries were then magnetically separated and washed with Dig Wash three times and then incubated with protein A-MNase (pA-MN, Epicypher 15-1016) for 1 hour at 4 °C. Slurries were magnetically separated and washed, resuspended in 200uL Dig Wash, and placed on an iced heating block. 2uL of 2mM CaCl2 was added to catalyze the pA-MN reaction and digestion. After 45 minutes, one equal volume of Stop Buffer (340mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 ug/mL RNase A, 2 pg/mL heterologous spike-in DNA) was added to end the reaction, and sample slurries were then incubated for 30 minutes at 37 °C to release fragments and then magnetically separated. The supernatant was collected, and DNA was purified via phenol-chloroform extraction and ethanol precipitation. Samples were resuspended in molecular-grade water after ethanol precipitation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were in the presence of 1-month M. avium infection.

value: murine Hematopoietic stem cells

value: 1-month Mycobacterium avium infection


title: Infect BATF2 KO HSC using antibody against BATF2


title: Infect WT HSC using antibody against H3K27ac replication #2


title: Mouse_C57BL/6xJF1_EPC_rep2 [CxJ_EPC2]


title: Mouse_C57BL/6xJF1_Epiblast_rep1 [CxJ_EB1]

description:
WGBS (rPBAT)
mouse_epiblast_maternal_rep1-3_x1.bw
mouse_epiblast_maternal_rep1-3_x5.bw
mouse_epiblast_paternal_rep1-3_x1.bw
mouse_epiblast_paternal_rep1-3_x5.bw

source_name: epiblast

value: epiblast


title: Mouse_C57BL/6xJF1_Epiblast_rep2 [CxJ_EB2]


title: TfhCM_rep1


title: Mouse_JF1xC57BL/6_EPC_rep1

data_processing:
>Reads were trimmed using Trimmomatic (v0.32) to remove 2 nucleotides of the 5’ end of read 2
>Sequencing reads were further trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to genome build mm10 or rn6 using STAR (v2.4.0.i) and PCR duplicate reads were flagged using Picard MarkDuplicates (v1.92).
>Library quality was assessed using samtools flagstat (v1.1) and Picard CollectRNASeqMetrics.
>Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using samtools parameters: samtools view -bh -q 255 -F 1540.
>NCBI RefSeq mouse transcript annotations (n=106,520 isoforms, 35,977 genes) were downloaded from the UCSC Table Browser (last updated 2017-11-16). NCBI RefSeq rat transcript annotations (n=69,194 isoforms, 30,871 transcripts) were downloaded from the UCSC Table Browser (last updated 2018-03-09).
>Gene expression values were calculated by averaging read coverage over exons using VisRseq (v0.9.12) and normalized to the total number of aligned reads and transcript length in kilobases (RPKM).
>Genome browser compatible normalized bigWigs were generated using bedtools genomecov (v2.22.1).
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One nanogram of embryonic total RNA was reverse transcribed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio) according to the manufacturer's protocol.

treatment_protocol: E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains as well as between strains BN/CrlCrlj and F334/NSlc (F344/N rat). E7.25  F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to strand-specific RNA-sequencing.

value: F1 hybrid resulting from female JF1/Ms and male C57BL/6N mice


title: Mouse_C57BL/6xJF1_EPC_rep1


title: Mouse_JF1xC57BL/6_Epiblast_rep2


title: Mouse_JF1xC57BL/6_Epiblast_rep1


title: Mouse_C57BL/6xJF1_EPC_rep2


title: Mouse_JF1xC57BL/6_EPC_rep2


title: Mouse_C57BL/6xJF1_Epiblast_rep1


title: no guide control biol rep 3

city: Leiden

first: Niels

last: Geijsen

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: LUMC

data_processing:
Reads were trimmed with TrimGalore
Trimmed reads were mapped to the genome (GRCh37) using STAR
Count table was constructed with featureCounts (parameters: fc_group_features = 'gene_id', fc_count_type = 'exon', fc_group_features_type = 'gene_biotype', fc_extra_attributes = 'gene_name', normalize_counts = true, biotypeQC = true)
downstream analysis was performed in R using DEseq2
Assembly: GRCh37
Supplementary files format and content: tab delimited count table

growth_protocol: HAP1-dEGFP cells were cultured in IMDM 10% FBS supplemented with 10 ug/ml puromycin. Cells were grown in a 37C, 5% CO2 incubator with humidified atmosphere.

extract_protocol:
RNA was harvested in TRIzol and purified using the zymo RNA clean and concentration -5 kit, including an in column DNase treatment. Next, PolyA RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S).
libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L)

treatment_protocol: Cells were transduced using iTOP (D'Astolfo et al. 2015, Cell). crRNAs were prepared by in vitro transcription. LbuCas13a protein was expressed in E. coli and purified in house.

tag: cell line

value: near haploid chronic myelogenous leukemia KBM-7 derived

value: iTOP transduction with only LbuCas13a protein


title: empty transduction biol rep 3

value: empty iTOP transduction


title: non targeting control biol rep 1

value: iTOP transduction with LbuCas13a protein and non-targeting crRNA


title: gfp targeting control biol rep 1

value: iTOP transduction with LbuCas13a protein and dEGFP targeting crRNA


title: gfp targeting control biol rep 3


title: no guide control biol rep 2


title: no guide control biol rep 1


title: non targeting control biol rep 3


title: Nontumor, Male, White, Age 70.3 [Sample 22]

city: Silver Spring

first: Thomas

last: Biel

address: 10903 New Hampshire Ave

department: OBP

institute: FDA

data_processing:
BaseSpace TopHat Alignment v1.0.1
Read mapping using TopHat 2 aligner
FPKM estimation of reference genes and transcripts using Cufflinks 2
Read count and normalization were analyzed using Students T tests, one-way ANOVAs, and two-way ANOVAs
Assembly: Homo Sapiens UCSC hg19 (RefSeq and Gencode gene annotations)
Supplementary files format and content: tab-delimited excel file contain RPKM values for each Sample

source_name: Pancreas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using Illumina Truseq Stranded Total RNA protocol

value: Pancreas

tag: race

value: White

tag: gender

value: Male


title: Infect BATF2 HSC using antibody against H3K27ac

tag: treatment


title: gfp targeting control biol rep 2


title: empty transduction biol rep 1


title: non targeting control biol rep 2


title: empty transduction biol rep 2


title: Nontumor, Male, White, Age 45.3 [Sample 19]


title: Nontumor, Female, White, Age 40.2 [Sample 16]

value: Female


title: Nontumor, Female, White, Age 56.4 [Sample 21]


title: Nontumor, Female, White, Age 44.2 [Sample 8]


title: Nontumor, Female, Black, Age 33.1 [Sample 17]

value: Black


title: Nontumor, Female, Black, Age 25.2 [Sample 11]


title: Tumor, Female, White, Age Age 73.6 [Sample 31]

source_name: Pancreatic adenocarcinoma

value: Pancreatic adenocarcinoma


title: Nontumor, Female, Black, Age 59.7 [Sample 10]


title: Nontumor, Female, White, Age 45.6 [Sample 20]


title: Tumor, Male, White, Age 70.9 [Sample 32]


title: Mouse_C57BL/6xJF1_Epiblast_rep2

value: F1 hybrid resulting from female C57BL/6N and male JF1/Ms mice

value: embryonic days 7.25

value: wild type


title: Tumor, Female, White, Age 58.7 [Sample 30]


title: Nontumor, Male, White, Age 56.6 [Sample 18]


title: Tumor, Male, White, Age 65.2 [Sample 29]


title: Tumor, Female, White, Age 56.2 [Sample 27]


title: Tumor, Female, Black, Age 73.4 [Sample 6]


title: Tumor, Male, Black, Age 74.4 [Sample 25]


title: Tumor, Female, White, Age 63.4 [Sample 28]


title: Tumor, Male, Black, Age 74.4 [Sample 12]


title: Nontumor, Female, White, Age 30.2 [Sample 9]


title: Tumor, Male, Black, Age 63.5 [Sample 26]


title: Tumor, Female, White, Age 56.2 [Sample 5]


title: Panc1_KO_2_y_H6

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
Lexogen BlueBee QuantSeq FWD Analyses pipeline
Cutadapt to remove artifacts and adapter sequences
FASTQC report for trimmed reads
STAR aligner
Assembly: hg38
Supplementary files format and content: raw count table at the gene level for all samples

source_name: Panc1 cells

growth_protocol: DMEM basal media (Gibco) supplemented with high glucose, GlutaMax (Gibco), and penicillin/streptomycin

extract_protocol:
Norgen toal RNA extraction kit with Dnase treatment
Lexogen QuantSeq 3'RNAseq FWD kit

treatment_protocol: SAM: Over expresssion: MiaPaCa2 or P10.05 cells containg lentiMPHv2 plasmid were co-transfected with psPAX2, pMD2G, and lentiSAMv2 lentiviral plasmids containing NTC1or ANGPTL4 sgRNA using Lipofecatming 2000 Transfection Reagent (ThermoFisher). KO: MiaPaCa2 cells or Panc1 cells transfected with DsiRNA for ANGPTL4 or NTC using RNAi transfection reagent (ThermoFisher). Gemcitabine treatment: Cells were treated with or without 1.5nM of gemcitabine for 24 hours before RNA extraction using Norgen's total RNA extraction kit.

value: Gemcitabine

tag: replicate #

tag: angptl4 expression condition

value: altered with DsiRNA


title: Nontumor, Male, White, Age 40.9 [Sample 15]

tag: tissue


title: Tumor, Male, White, Age 67.2 [Sample 7]


title: Tumor, Male, White, Age 78.5 [Sample 3]


title: Tumor, Male, Black, Age 48.5 [Sample 24]


title: Tumor, Male, White, Age 76.8 [Sample 4]


title: MP2_KO_2_y_H2

source_name: MiaPaCa2 cells


title: Panc1_KO_2_y_H5


title: Panc1_KO_2_y_H4


title: Panc1_KO_2_n_G5

value: media


title: MP2_KO_2_y_H1


title: MP2_KO_2_n_G2


title: Panc1_KO_2_n_G6


title: MP2_KO_2_n_G1


title: MP2_KO_2_n_G3


title: Panc1_KO_2_n_G4


title: Panc1_plain_y_F6

value: not altered


title: Panc1_plain_y_F5


title: Panc1_plain_y_F4


title: MP2_KO_1_y_F3


title: Tumor, Male, White, Age 72.8 [Sample 1]


title: Panc1_plain_n_E6


title: MP2_KO_1_y_F1


title: MP2_KO_1_y_F2


title: MP2_KO_2_y_H3


title: MP2_KO_1_n_E3


title: Panc1_plain_n_E4


title: Panc1_plain_n_E5


title: MP2_KO_1_n_E2


title: MP2_sam_2_y_D2

value: altered with CRISPR


title: P10.05_sam_2_y_D5

source_name: P10.05 cells


title: MP2_sam_2_y_D1


title: P10.05_sam_2_y_D6


title: P10.05_sam_2_n_C5


title: P10.05_sam_2_n_C6


title: P10.05_sam_2_n_C4


title: P10.05_plain_y_B5


title: MP2_sam_2_n_C1


title: P10.05_plain_y_B4


title: MP2_plain_y_B3


title: P10.05_plain_y_B6


title: MP2_sam_2_n_C3


title: MP2_sam_2_n_C2


title: MP2_plain_y_B2


title: MP2_plain_y_B1


title: P10.05_plain_n_A5


title: P10.05_plain_n_A4


title: MP2_KO_1_n_E1


title: MP2_sam_2_y_D3


title: P10.05_sam_2_y_D4_new


title: 2017-079

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

data_processing:
The quality control was done using fastQC.
The data was processed using the alignment-free quantification software Kallisto (v0.46).
Genome_build: GRCh38.p12 (Ensembl v96)
Supplementary_files_format_and_content: Matrix table with a gene counts for every transcript and every sample
Supplementary_files_format_and_content: Raw counts

source_name: Post-mortem substantia nigra

extract_protocol:
The tissue samples were homogenized (6875D Freezer/Mill Spex). 50mg amount of sample was used for RNA isolation using the inhouse Tecan robot using AllPrep DNA/RNA/Protein kit (Qiagen) as mentioned in the protocol DOI:10.1007/978-1-4939-8695-8_19.
1 µg of total RNA was used for library preparation using TruSeq stranded mRNA library preparation kit (Illumina) as per the protocol provided by the manufacturer.

value: Parkinson's disease

value: Substantia nigra

tag: age at death (years)

tag: post-mortem delay (h

tag: braak

tag: amyloid

tag: braak lb

tag: apoe

tag: ph-csf

tag: brain weight (g)


title: 2017-059

tag: disease state


title: MP2_plain_n_A2


title: 2017-041

value: O


title: 2017-056


title: 2016-051

value: B


title: 2017-016

value: Non-demented control


title: 2012-067

value: Male

value: A


title: 2017-012


title: 2016-023


title: 2001-139

value: Female

value: C


title: 2016-016


title: 1997-042


title: 1996-105


title: P10.05_plain_n_A6


title: 2000-025


title: Izq.STG139.M5.13

city: Madrid

first: María José

last: Jiménez

state: Madrid

address: C. de Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: Spanish National Cancer Research Centre

data_processing:
RNA-seq processing:
Read adapters and poly A tails were removed with BBDuk v38.38. Then, human reads were separated from mice ones using Xenome v1.0.1 and those classified as “human”, “both” or “ambiguous” were selected. Processed reads were analyzed with the Nextpresso pipeline v1.9.2.5, as follows: Single-end reads were downsampled to 8,500,000 reads with seqtk. Sequencing quality was checked with FastQC v0.11.7 and FastQ Screen v0.13.0. Reads were aligned to the human reference genome (GRCh38) with TopHat v2.0.10 using Bowtie v1.0.0.0 and Samtools v0.1.19.0 (-library-type fr-secondstrand), allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes) using the human gene annotation from GENCODE (gencode.v34.GRCh38.Ensembl100). Differential expression was performed with DESeq2 v1.12.4, using a 0.05 FDR.  Genes were ranked according to the log2 Fold Change and GSEAPreranked v2.2.2 was used to perform gene set enrichment analysis for Hallmark, Biocarta, Reactome and KEGG v7.1 signatures, setting 1000 gene set permutations and a classic enrichment statistic. Only those signatures with significant enrichment levels (FDR q-value < 0.05) were considered.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: Human breast cancer orthoxenografts

growth_protocol: Dissociated breast tumor cells mixed 1:1 with Matrigel Basement Membrane (BD Biosciences) were transplanted orthotopically in the inguinal mammary gland of 10/12-week old NSG mice.

extract_protocol:
Total RNA was isolated from cell lysates or tumors pieces using TRIzol (Thermo Fisher Scientific) or Maxwell® RSC simplyRNA Tissue Kit (AS1340 Promega), following the manufacturer’s instructions.
Total RNA samples (300ng) were processed with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. RNA Quality scores were 7.7 on average (range 4.2-9.2) when assayed on a PerkinElmer LabChip analyzer. Library generation was initiated by reverse transcription with oligodT priming, and a second strand synthesis was performed from random primers. Primers from both steps contained Illumina-compatible sequences. Libraries were completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries were purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: When tumors reached 5 mm of diameter mice were randomized for mock, h-RANKL (0.75 mg/kg, 4-6 doses, twice per week; Amgen Inc), h-RANK-Fc treatment (10 mg/kg, three times per week; Amgen Inc), denosumab (10 mg/kg, three times per week; XGEVA®). Mice were sacrificed 24 h after the last treatment and RNA extracted from the tumors.

tag: cell type

value: Breast cancer PDX

tag: tumor subtype

value: Estrogen receptor negative

value: denosumab

tag: rank

value: RANK+


title: Izq.STG139.M5.14


title: Izq.STG139.M5.10

value: RANKL


title: 2009-039

tag: gender


title: Izq.STG139.M5.11

tag: treatment

value: RANK-Fc


title: Izq.AB521.X3.10


title: MP2_plain_n_A3

tag: cell line

value: media

tag: replicate #

value: not altered


title: MP2_plain_n_A1

tag: angptl4 expression condition


title: Izq.AB521.X3.8


title: Izq.AB521.X3.7

value: PBS


title: Der.AB521.X3.8


title: Der.AB521.X3.9


title: Der.AB521.X3.7


title: Der.AB521.X3.6


title: Der.AB521.X3.12


title: Der.AB521.X3.10


title: 2003-035

tag: tissue

value: Substantia nigra

tag: age at death (years)


title: De.STG139.M5.8


title: De.STG139.M5.7


title: De.STG139.M5.12


title: De.STG139.M5.14


title: De.STG139.M5.11


title: De.STG139.M5.10


title: DER.B3277.9


title: Izq.STG139.M5.7


title: DER.B3277.7


title: DER.B3277.3


title: DER.B3277.5


title: DER.B3277.1


title: DER.B3277.2


title: DER.B3277.10


title: DER.B3277.11


title: De.STG139.M5.9


title: DER.B3277.6


title: SCR_shRNA_Rep1

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

description: Chd4 WT (Replicate 1)

data_processing:
Fastq reads were trimmed for adapter and contaminating sequences using trimgalore v0.6.4. Trimmed reads were mapped to mm10 genome assembly and ERCC spike-in sequences using STAR v2.7.1a (default parameters)
Number of reads mapping to ENSEMBL defined gene annotations were determined using FeatureCounts (allowing multiassignment of reads and reads mapping to multiple positions are counted as 1/number of mapped positions).
Raw read counts were ERCC spike-in normalized using EDASeq_2.24.0 and RUVSeq_1.24.0. Differential gene expression was then performed using edgeR_3.32.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample along with spike-in ERCC control

source_name: 2i-derived ESC line: TCF2.2

growth_protocol: Mouse ES cells were cultured on 0.2% gelatin-coated dishes in serum-free 2i medium and passaged every 2-3 days using Accutase to detach cells.

extract_protocol:
To quantify nascent RNA synthesis affected by desired treatment, i.e., BRG1 inhibition or Chd4 shRNA KD, mouse ES cells were incubated with 500 µM 4-thiouridine for 5 min at 37°C and 5% CO2 and lysed in TRIzol which was then spiked in with external reference RNA (2.4 ng synthetic ERCC RNA mixture for per million mESC). Total RNA was extracted using phenol-chloroform method and precede to biotinylating by incubation with HPDP-Biotin for 2 hours. Nascent RNA was isolated from unlabeled RNA by streptavidin beads and eluted in 100 mM DTT followed by purification with MACHEREY-NAGEL NucleoSpin RNA kit according to the manufactory’s instruction.
Nascent RNA libraries were prepared using NEBNEXT Ultra II directional RNA preparation kit (E7760S) according to manufactory’s instruction, briefly, nascent RNA with different length were fragmentated into an average of 300 nt and reverse transcribed into stranded DNA using random primers, which was followed by 3-prime end indexing during PCR amplification.

treatment_protocol:
For BRG1 inhibition, ESCs were treated with 10 μM BRM/BRG1 ATP inhibitor-1, BRM014 (HY-119374, MedChemExpress) or DMSO for 3 hours.
For Chd4 knockdown, ESCs were transduced with Chd4 shRNA lentivirus or scrambled shRNA lentivirus followed by 24 hour incubation in 2i medium containing 1.5 μg/mL puromycin.

tag: strain

value: 2i-derived ESC line:TCF2.2

tag: genotype

value: Chd4 WT

value: Scrambed shRNA

tag: time

value: 24 hours


title: DMSO_Rep1

description: BRG1 WT (Replicate 1)

value: BRG1 WT

value: DMSO

value: 3 hours


title: DMSO_Rep2

description: BRG1 WT (Replicate 2)


title: SCR_shRNA_Rep2

description: Chd4 WT (Replicate 2)


title: Chd4_shRNA_Rep2

description: Chd4 shRNA (Replicate 2)

value: Chd4 KD

value: Chd4 shRNA KD


title: delta_biological_replicate_1

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Ave

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

description: chromatin accessibility

data_processing:
FastQC
Trimmomatic
Bowtie2
Picard Tools
MACS2
Assembly: mm10
Supplementary files format and content: Aligned BAM Files

source_name: FACS-sorted delta cells

extract_protocol:
mIns1-H2b-mCherry [1] x Rosa-LSL-YFP crossed to either Sst-Cre [44] or Gcg-Cre [45] triple transgenic mice were pooled by sex, each sample yielding a median of 20,000 cells, with islet isolation and FACS-sorting as previously described (Supplemental Fig. 1) [1, 46-48].
Single-end 50 bp reads were generated after library size selection yielded an average of 450 bp fragments and sequenced as previously described using NexteraDNA library protocol  [30].

value: delta

value: mouse

tag: status

value: healthy


title: delta_biological_replicate_2

description: chromatin accessibility


title: beta_biological_replicate_3

description: chromatin accessibility

source_name: FACS-sorted beta cells

value: beta


title: Chd4_shRNA_Rep1

description: Chd4 shRNA (Replicate 1)


title: BRM014_Rep1

description: BRG1 inhibitor (Replicate 1)

value: BRG1 inhibited

value: BRG1 inhibitor


title: alpha_biological_replicate_2

description: chromatin accessibility

source_name: FACS-sorted alpha cells

value: alpha


title: BRM014_Rep2

description: BRG1 inhibitor (Replicate 2)


title: TG-CCRR1

city: Harbin

first: Lihua

last: Sun

state: Heilongjiang

address: 157 Baojian Road

institute: Harbin Medical University

description: Gene expression

hyb_protocol: Each slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The raw data obtained from the chip scan is normalized by the limma package in the R software. The algorithm used is Quantile, and the normalized signal value is the signal value calculated by log2.

source_name: heart

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Alternate day and night for 12 hours, drinking water and eating normally

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Fresh heart tissue

tag: subgroup

value: CCRR transgenosis


title: TG-CCRR3

description: Gene expression


title: beta_biological_replicate_1

description: chromatin accessibility


title: MI-MI2

description: Gene expression after MI

value: MI


title: TG-CCRR-MI1

description: Gene expression after MI

value: CCRR transgenosis MI


title: TG-CCRR-MI3

description: Gene expression after MI


title: TG-CCRR2

description: Gene expression


title: WT3

description: Gene expression

value: WT


title: MI-MI3

description: Gene expression after MI


title: WT2

description: Gene expression


title: WT & cKO BMDC replicate 2

city: Taipei

first: Wen

last: Chang

address: 128 Sec 2 Academia Rd, Nankang

institute: Institute of Molecular Biology, Academia Sinica

description: Biological replicate 1 of 3. BMDC cells.

hyb_protocol: Agilent Gene Expression Hybridization Kits and wash kit were  used for hybridization according to the manufacturer’s instruction.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using the AgilentG3_GX_2 Color scan protocol for 8x60K high densitiy Micorarray Formats (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Red and Green PMT is set to 100%, the resulting file is a 20 bit tiff image).

data_processing: The raw microarray data (three biological replicates) were imported into GeneSpring software (Agilent, version 12.6.1). A total of 62,976 probes were then mapped to corresponding genes using the NCBI mm9 Mouse Genome Assembly (NCBI37; Jul2007).  After removing probes associated with unnamed genes, non-coding genes, and predicted genes, the probes with a signal intensity > 70 in at least two out of three replicates were selected to calculate the normalized log2 ratio of cKO/WT signals.

label: alexa 647

source_name: FAM21 cKO D8 BMDC cells

label_protocol: 10 µg of total RNA were primed with  anchored Oligo-(dT) at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase, and 10mM dNTP including amino-allyl-dUTP. (SuperScript Indirect cDNA Labeling System, Invitrogen).  After reaction, add 10μL 0.5M EDTA and 10μL 1N NaOH, incubate at 70℃ for 15 min to hydrolysis RNA followed by neutralization with addition of 25μL 1M HEPES pH 7.4. Then purified using QIAquick(Qaigen) kit, aa-cDNA was eluted from column with 60 μl 0.1M NaHCO3 pH 9.0.  The elute was added into a tube containing  Alexa 555 or Alexa 647 NHS ester. Coupled the dye at room temperature in the dark for 60-90 min.  The reaction was stopped by adding 15 μl of 4 M NH2OH-HCl in the dark for 15 min. Labeled cDNA was purified through QIAquick column.

growth_protocol: Bone marrow cells were flushed out of mouse femurs and tibias of C57BL/6 mice of 6-8 weeks old, treated with ACK lysis buffer (150mM NH4C ,10mM KHCO3 and 0.1mM EDTA) to remove red blood cells. These cells were then plated in 100mm non-TC petri dishes containing Rosewell Park Memorial Institute medium (RPMI) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 1% Penicillin and Streptomycin (Gibco), 2mM L-glutamine (Gibco), 1mM sodium pyruvate (Sigma), 20mM HEPES, and 10% growth supernatant of GM-CSF transduced J558L cells. Cell cultures were replenished with fresh medium every three days and BMDC purity was determined at day 8.

extract_protocol: RNA was extracted accrding to manufacturer's protocol by TRIzol method (Invitrogen). RNA pellet was then centrifuged and resuspended in DEPC water.

treatment_protocol: BMDC cells were harvested on Day 8 and spin down at 1200 rpm and the cell pellet was resuspended in TRIzol.

value: Bone marrow derived

tag: genotype/variation

value: FAM21 cKO

tag: age

value: 8 weeks

value: Female

label: alexa 555

source_name: WT D8 BMDC cells

value: wild type


title: WT-MI1

description: Gene expression after MI


title: TG-CCRR-MI2

description: Gene expression after MI


title: WT1

description: Gene expression


title: WT & cKO BMDC replicate 3


title: WT & cKO BMDC replicate 1


title: beta_biological_replicate_2

description: chromatin accessibility

tag: cell type


title: Adad2_wild_RNA_rep2

data_processing:
>Basecalls were performed using NextSeq 500/550 RTA software (v1.0) or HiSeq 2500 HCS (v2.2) and RTA (v1.18) software.
>FASTQ files were generated using bcl2fastq (v2.17.1.14 for RNA-seq and v1.8.4 for small RNA-seq).
>RNA-seq reads were aligned to the mm9 Mouse genome assembly using Bowtie2. Ensembl gene annotation (mm9, 26127 genes) were used to calculate RPKM values. RPKM values were log2-transformed using SeqMonk.
Assembly: mm9
Supplementary files format and content: A single text file that lists Ensembl gene RPKM log2 values for each sample

source_name: 24-day-old testis

extract_protocol:
Total RNA for transcriptome and small RNA analysis was purified from whole testes of postnatal 24-day-old mice using ISOGEN (Nippon Gene) according to manufacturer’s protocols.
RNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina).

value: testis

tag: Sex

value: male


title: Adad2_homo_RNA_rep1

value: Adad2-knockout homozygous


title: alpha_biological_replicate_1

description: chromatin accessibility

value: mouse

value: healthy


title: Adad2_homo_RNA_rep2


title: H3.3 (Chd4 shRNA, Rep2)

description: H3.3 in Chd4 shRNA ESC

data_processing:
Reads were mapped to mouse genome assembly (mm10) using bowtie2
For Pol II Serine-5p, Serine-2p, H3.3 and H2A.Z ChIP-seq data in WT, BRG1 inhibitor  (BRM014) treated and Chd4 KDtreated mESCs, reads were mapped to a combined mouse (mm10) and drosophila (dm6) genome, and read counts were spike-in normalized (Orlando et al., 2014) followed by coverage normalization using total number of reads mapping in genomic regions outside peaks (background).
Assembly: mm10
Supplementary files format and content: Only properly mapped paired reads were used for analysis. Furthermore, we only used uniquely mapped and PCR duplicates (exact copies) were collapsed into single reads, that were extended to their fragment length by determining the read extension size using MASC2 (predictd parameter) (Zhang et al., 2008). Raw read counts were normalized to TPM using deeptools (bamCoverage) (Ramírez et al., 2014).

source_name: ESC

extract_protocol:
mES cells were fixed using 1% formaldehyde and lysed in ChIP lysis buffer (50 mM Tris PH 8.0, 100 mM NaCl, 5 mM EDTA PH 8.0, 0.5% SDS, 50 mM NaF, 20 mM b-glycerophosphate and protease inhibitor cocktail). Nuclei were isolated by spin down at full speed for 15 min and suspended in IP buffer (A 2:1 mix 2 of ChIP SDS lysis buffer and ChIP dilution buffer containing 100 mM Tris PH 8.0, 5 mM EDTA PH 8.0 and 5% Igepal CA630) followed by chromatin shearing to 200-500b and chromatin immunoprecipitation using indicated antibodies and protein G Sepharose beads. Precipitated chromatins were isolated by decrosslinking and purification with Qiaquick PCR purification kit and subjected to sequencing library preparation directly.
DNA libraries were prepared following NEBNext Ultra II DNA Library Kit for Illumina (New England Biolabs) guidelines.

treatment_protocol: For BRG1 inhibition, ESCs were treated with 10 μM BRM/BRG1 ATP inhibitor-1, BRM014 (HY-119374, MedChemExpress) or DMSO for 3 hours. For Chd4 knockdown, ESCs were transduced with Chd4 shRNA lentivirus or scrambled shRNA lentivirus followed by 2-days incubation in 2i medium containing 1.5 μg/mL puromycin.

value: 2i-derived ESC line:TCF2.2

tag: chip-antibody

value: ab176840, Abcam

value: Chd4 shRNA


title: H3.3 (Chd4 shRNA, Rep1)

description: H3.3 in Chd4 shRNA ESC


title: H3.3 (Chd4 WT, Rep2)

description: H3.3 in Chd4 WT ESC

value: Chd4 WT


title: H3.3 (Chd4 WT, Rep1)

description: H3.3 in Chd4 WT ESC


title: H2A.Z (Chd4 WT, Rep2)

description: H2A.Z in Chd4 WT ESC

value: ab4174, Abcam


title: H2A.Z (Chd4 shRNA, Rep2)

description: H2A.Z in Chd4 shRNA ESC


title: H3.3 (BRM014, Rep2)

description: H3.3 in BRM014 ESC


title: H2A.Z (Chd4 WT, Rep1)

description: H2A.Z in Chd4 WT ESC


title: H3.3 (Brg1 WT, Rep2)

description: H3.3 in BRG1 WT ESC

value: BRG1 WT


title: H2A.Z (BRM014, Rep2)

description: H2A.Z in BRM014 ESC


title: H2A.Z (BRM014, Rep1)

description: H2A.Z in BRM014 ESC


title: H3.3 (BRM014, Rep1)

description: H3.3 in BRM014 ESC


title: H3.3 (Brg1 WT, Rep1)

description: H3.3 in BRG1 WT ESC


title: Pol II (ser-2p) (Chd4 WT, Rep3)

description: Pol II (ser2p) in Chd4 WT ESC

value: ab238146, Abcam


title: Pol II (ser-2p) (Chd4 WT, Rep2)

description: Pol II (ser2p) in Chd4 WT ESC


title: Adad2_wild_RNA_rep1


title: Pol II (ser-2p) (Chd4 shRNA, Rep2)

description: Pol II (ser2p) in Chd4 shRNA ESC


title: Pol II (ser-2p) (Chd4 shRNA, Rep1)

description: Pol II (ser2p) in Chd4 shRNA ESC


title: H2A.Z (Brg1 WT, Rep1)

description: H2A.Z in BRG1 WT ESC


title: Pol II (ser-2p) (Chd4 shRNA, Rep3)

description: Pol II (ser2p) in Chd4 shRNA ESC


title: Pol II (ser-2p) (Chd4 WT, Rep1)

description: Pol II (ser2p) in Chd4 WT ESC


title: Pol II (ser-5p) (Chd4 shRNA, Rep3)

description: Pol II (ser5p) in Chd4 shRNA ESC

value: ab5131, Abcam


title: H2A.Z (Chd4 shRNA, Rep1)

description: H2A.Z in Chd4 shRNA ESC


title: Pol II (ser-5p) (Chd4 shRNA, Rep1)

description: Pol II (ser5p) in Chd4 shRNA ESC


title: Pol II (ser-5p) (Chd4 WT, Rep3)

description: Pol II (ser5p) in Chd4 WT ESC


title: Pol II (ser-5p) (Chd4 WT, Rep1)

description: Pol II (ser5p) in Chd4 WT ESC


title: Pol II (ser-2p) (BRM014, Rep3)

description: Pol II (ser2p) in BRM014 ESC


title: Pol II (ser-5p) (BRM014, Rep3)

description: Pol II (ser5p) in BRM014 ESC


title: Pol II (ser-2p) (Brg1 WT, Rep2)

description: Pol II (ser2p) in BRG1 WT ESC


title: Pol II (ser-2p) (Brg1 WT, Rep3)

description: Pol II (ser2p) in BRG1 WT ESC


title: Pol II (ser-5p) (BRM014, Rep2)

description: Pol II (ser5p) in BRM014 ESC


title: Pol II (ser-5p) (Chd4 shRNA, Rep2)

description: Pol II (ser5p) in Chd4 shRNA ESC


title: H2A.Z (Brg1 WT, Rep2)

description: H2A.Z in BRG1 WT ESC


title: Pol II (ser-5p) (BRM014, Rep1)

description: Pol II (ser5p) in BRM014 ESC


title: Pol II (ser-5p) (Brg1 WT, Rep3)

description: Pol II (ser5p) in BRG1 WT ESC


title: Pol II (ser-5p) (Brg1 WT, Rep2)

description: Pol II (ser5p) in BRG1 WT ESC


title: time-restricted feeding, SK2, 8PM

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
Sphingosine kinase 2, Female
TRF_SK2_8PM

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

organism: Drosophila melanogaster

source_name: indirect flight muscle

growth_protocol: All flies were kept at 22 °C, 50% humidity in a 12 h light/12 h dark (LD) cycle

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 50-bp single-read chemistry

treatment_protocol: ALF and TRF flies were subjected to vials with assigned diet at zeitgeber time zero (ZT0) 9AM (lights on), and were switched to either a food media vial (for ALF) or a 1.1% agar vial (for TRF) at 9 PM (lights off).

value: indirect flight muscle

value: Sphingosine kinase 2

tag: diet

value: normal

value: time-restricted feeding


title: time-restricted feeding, SK2, 8AM

description:
Sphingosine kinase 2, Female
TRF_SK2_8AM

value: Female

tag: treatment


title: time-restricted feeding, SK2, 4PM

description:
Sphingosine kinase 2, Female
TRF_SK2_4PM


title: time-restricted feeding, SK2, 12AM

description:
Sphingosine kinase 2, Female
TRF_SK2_12AM


title: time-restricted feeding, SK2, 4AM

description:
Sphingosine kinase 2, Female
TRF_SK2_4AM


title: IFCp4

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

data_processing:
Fastq files were aligned using Bismark v0.20.1 in PBAT mode against the GRCm38 genome where SNP positions between C57B6 and CBA were N masked using the SNPSplit_genome_preparation script.
Bismark BAM files were split into reads deriving from C57B6, CBA or Undefined BAM files using SNPsplit v0.4
Methylation calls were extracted from the split BAM files using the bismark methylation extractor with default parameters
Assembly: GRCm38
Supplementary files format and content: CpG methylation counts in Bismark coverage file format

source_name: mouse blastocyst

extract_protocol:
Blastocysts were individually collected and lysed in 10 μl of RLT buffer
DNA was purified using solid phase reversible immobilization (SPRI) beads and converted with bisulphite reagent using EZ DNA Methylation-Gold kit (ZYMO Research, D5005). DNA was eluted in EB buffer and individual blastocyst PBAT libraries were prepared as outlined below. First-strand synthesis was performed using Klenow exo-tagged (New England Biolabs) and a biotinylated oligo I (5-[Btn]CTACACGACGCTCTTCCGATCTNNNNNNNNN-3), followed by Exo-I treatment (New England Biolabs) and SPRI purification. Purified DNA was incubated with Dynabeads Strepatavidin M-280 beads (ThermoFisher Scientific) to capture biotinylated DNA and second strand synthesis was carried out using reverse oligo II (5’-TGCTGAACCGCTCTTCCGATCTNNNNNNNNN 3’). Libraries were amplified using indexed iPCRTag reverse primers (54) with KAPA HiFi (Kapa Biosystem) DNA polymerase for 15 PCR cycles and purified using SPRI beads (Agencourt Ampure XP bead). Libraries were quantitated and quality control was checked using Agilent High Sensitivity DNA kit and KAPA Illumina Library Quantifcation Kit for Illumina (KAPA Biosystems)
Bisulfite-Seq (PBAT)

value: mouse blastocyst

tag: oocyte collection_method

value: In vitro follicule culture oocyte maturation derived from prepubertal mouse


title: IFCp5


title: time-restricted feeding, SK2, 12PM

state: California

description:
Sphingosine kinase 2, Female
TRF_SK2_12PM


title: Pol II (ser-5p) (Brg1 WT, Rep1)

description: Pol II (ser5p) in BRG1 WT ESC


title: time-restricted feeding, HF, 8PM

description:
Canton-S+HFD, Female
TRF_HF_8PM

value: Canton-S

value: wild type

value: HFD


title: Pol II (ser-2p) (BRM014, Rep1)

description: Pol II (ser2p) in BRM014 ESC

value: 2i-derived ESC line:TCF2.2


title: time-restricted feeding, HF, 8AM

description:
Canton-S+HFD, Female
TRF_HF_8AM


title: IFCp3


title: Pol II (ser-2p) (BRM014, Rep2)

description: Pol II (ser2p) in BRM014 ESC


title: time-restricted feeding, HF, 4PM

description:
Canton-S+HFD, Female
TRF_HF_4PM


title: IFCp2


title: Pol II (ser-2p) (Brg1 WT, Rep1)

description: Pol II (ser2p) in BRG1 WT ESC


title: Pol II (ser-5p) (Chd4 WT, Rep2)

description: Pol II (ser5p) in Chd4 WT ESC


title: time-restricted feeding, HF, 4AM

description:
Canton-S+HFD, Female
TRF_HF_4AM


title: IFCp1


title: IFCa6

value: In vitro follicule culture oocyte maturation derived from adult mouse


title: IFCa5


title: time-restricted feeding, HF, 12AM

description:
Canton-S+HFD, Female
TRF_HF_12AM