title: Exosc3_EpiLC_Input

data_processing:
Adapters were trimmed from reads using Trim Galore (Martin, 2011). Reads were mapped to mm10 using bowtie2 (v2.4.1)(Langmead and Salzberg, 2012) with default parameters. BAM files were filtered using sambamba (v.0.5.6), removing reads that are duplicated, unmapped, and removing all secondary alignments (i.e. keeping the best genomic alignment location for multimapping reads). BigWigs were generated on the filtered BAM files using deepTools (v3.5.0) (Ramirez et al., 2016) with RPKM normalization. Peaks were called on filtered BAM files using MACS2 (v2.1.0) (Zhang et al., 2008) using the a q-value cutoff of 0.05, and the –broad parameter for H3K9me3 and H3K27ac.
Assembly: mm10
Supplementary files format and content: ChIP-Seq coverage in bigWig format

source_name: EpiLC

extract_protocol:
H3K9me3: Approximately 1x107 control and Exosc3 cKO pluripotent stem cells were dissociated from culture and fixed in 50 mL of N2B27 media with 1% methanol free formaldehyde for 10 minutes at room temperature. Fixation was quenched using .125 M glycine for 5 mins at room temperature. Pellets were then washed 3x with ice-cold DPBS supplemented with Halt protease and phosphatase inhibitors (Thermo Scientific, 78446). Pellets were frozen in -80°C overnight. Frozen pellets were then thawed on ice and 10x106 cells were lysed with 1 mL of LB1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton x-100) for 20 minutes rotating in 4°C. Chromatin was pelleted and supernatant was then discarded. Nuclear envelope of the chromatin fraction was lysed with 1 mL LB2 (Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 M EGTA), rotating for 10 minutes at room temperature. Pellets after LB2 lysis were resuspended in 300 µL of LB3 (Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 M EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine). Chromatin was sonicated in LB3 was aliquoted in 100 µL increments in micro AFA Fiber Crimp-Cap 6x16mm tubes (Covaris, 520091). Chromatin was sheared on a Covaris instrument with peak power set to 450 for 700 seconds. Aliquots of sheared chromatin were pooled for immunoprecipitation. Antibody was coupled to Protein A Dynabeads (Invitrogen, 10001D) for 4 hours rotating in 4°C. Coupled beads were washed 3x with 0.05% BSA in DPBS. Antibody bound beads were then added to chromatin in LB3 overnight rotating in 4°C. Beads were washed 8 times with RIPA buffer (500 mM Hepes-KOH pH 7.6, 100 mM LiCl, 0.5 M EDTA, 1% NP-40, 0.7% Na- Deoxycholate). An additional wash with TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 50 mM NaCl) prior to elution. Bound chromatin was eluted in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) shaking for 30 minutes at 65°C. Decrosslinking was achieved by the addition of 8 µL 5 M NaCl to 210 µL of eluted chromatin. RNA and protein were digested by using 500 µg/mL RNase (Invitrogen, AM2271) and 22 mg/mL proteinase K (Invitrogen, AM2546) for 2 hours at 55°C. DNA for library preparation and sequencing was purified using MinElute PCR Purification Kit (Qiagen, 28004).     H3K27ac and Rbp1: Cell fixation and quenching were done exactly as described above. Approximately 10x106 cells were lysed for 15 minutes on ice in 500 µL of cell lysis buffer 1 (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% NP-40). Nuclei were pelleted and subsequently lysed in 500 µL of nuclear lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 10 minutes on ice. Chromatin was then sheared using the Diagnode Bioruptor Plus for 30 cycles set to 30 seconds on and 30 seconds off. Sheared chromatin was then precleared using species specific IgG for 2 hours at 4°C. Antibodies for protein of interests bound to chromatin were couple to Protein A Dynabeads (Invitrogen, 10001D). Coupled beads were added to precleared chromatin and rotated overnight at 4°C. Beads bound to chromatin were then resuspended with 1 mL of IP wash I buffer (20 mM Tris-HCl pH 8, 2 mM EDTA, 50 mM NaCl, 1% Triton x-100, 0.01%SDS). Beads were bound to a magnetic stand and washed twice with a high salt buffer (20 mM Tris-pH 8, 2 mM EDTA, 500 mM NaCL, 1% Triton x-100, 0.01% SDS0 and once with IP wash II buffer (10 mM Tris ph8, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1 % Na- Deoxycholate). DNA was eluted twice by applying 100 µL of elution buffer (1.25% SDS, 100 mM NaHCO3) to each sample and incubating at 65°C shaking at 800 rpm. Decrosslinking and DNA purification were identical to the steps described above.
Paired-end libraries from purified DNA were prepared using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) per manufacturer recommendations. Size selection of DNA prior to library was not performed.

tag: ChIP

value: Input


title: Exosc3_mESC_Input

status: Public on Oct 01 2023

type: SRA

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

tag: genotype


title: Ungrafted,Day7,Intact,Rep2

city: Uppsala

first: Ai

last: Zhang

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

library_source: transcriptomic

data_processing:
The residual rRNA contamination was removed using SortMeRNA
adapter and low-quality sequences were removed using the fastp software
The cleaned reads were aligned to version 1.0 of the Norway spruce genome using STAR
The number of reads was counted using htseq
Differentially expressed genes were identified using the DESeq2
Assembly: Picea abies reference genome v1.0
Supplementary files format and content: Matrix table with raw gene counts for each gene and each sample

molecule: total RNA

organism: Picea abies

source_name: cell line: FP-96. Skogsgård

extract_protocol:
Total RNA was extracted using a modified CTAB/LiCl method(Azevedo et al., 2003). Briefly, frozen tissue was ground into a fine powder. Extraction buffer was prepared (100 mM Tris-HC1 (pH 8), 2% (w/v) CTAB, 30 mM EDTA, 2 M NaCI, 0.05% (w/v) spermidine, 2% (w/v) PVPP, 2% (v/v) 2-mercaptoethanol, proteinase K (10 mg/mL) to a final concentration of 1.5 mg/mL) and warmed for 10 min at 42℃, then added to the ground frozen tissue and incubated for at 42℃for 90 min.  Chloroform-isoamyl alcohol (24:1 [v/v]) was added to extract RNA. After vortexing and centrifuging at 15,000 g for 15 min at 4℃, the top aqueous phase was transferred to a new tube and ¼ vol of 10 M LiC1 was added, allowing overnight precipitation at 4℃. Samples were centrifuged at 15,000 g for 30 min and supernatant discarded. Finally, the pellet was washed with 2 M LiCl twice and dissolved in RNase-free water. RNA concentration was measured using Qubit 2.0. The RNA Integrity Number (RIN) was analyzed by using an Agilent 2100 Bioanalyzer with RNA 6000 Nano kit. The RINs of all samples were above 8.0.
1 ug total RNA per sample was used for RNA-seq library preparation. mRNA isolation was performed using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S), followed directly by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7760S) and NEBNext Multiplex Oligos for Illumina (NEB #E7600S) for library construction. The quality of DNA libraries was checked by with an Agilent 2100 Bioanalyzer DNA High Sensitivity Kit.

tag: tissue

value: hypocotyl

tag: cell type

value: Intact

value: WT

tag: treatment

value: ungrafting


title: Exosc3_EpiLC_cKO_H3K27ac_Rep1


title: Recessive yellow sample Mc1rE, scRNA-seq, pairs with Nonagouti_RecessiveYellow

city: Bethesda

first: Dawn

last: Watkins-Chow

state: Maryland

address: 9000 Rockville Pike

institute: NIH

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) was used for alignment, barcode counting, and UMI counting
Downstream processing (filtering and differential analysis) of the data was performed with Partek Flow™ Genomic Analysis Software
Assembly: mm39
Supplementary files format and content: Tab-separated values (.TSV)
Supplementary files format and content: Matrix (.mtx)

source_name: Skin

extract_protocol:
FACS-isolated melanocytes were captured in a solution of 1xPBS + 0.04% FBS. Cell viability and concentration were analyzed using a Luna-FX7 cell counter
Gel Bead-in-Emulsions were prepared by loading cells onto a Chromium Chip G and run using the Chromium controller per 10x Genomics' specififcations. cDNA libraries were generated with Chromium Single Cell 3’ GEM, Library and Gel Bead Kit V3.1.

value: Skin

tag: strain

tag: age


title: Exosc3_EpiLC_CTRL_H3K27ac_Rep2

value: CTRL


title: Exosc3_EpiLC_CTRL_H3K27ac_Rep1


title: Grafted,Day3,Rootstock,Rep1

value: Rootstock

value: grafting


title: Exosc3_mESC_cKO_H3K27ac_Rep2


title: Exosc3_mESC_cKO_H3K27ac_Rep1


title: Grafted,Day3,Scion,Rep2

value: Scion


title: Grafted,Day3,Scion,Rep3


title: Exosc3_mESC_CTRL_H3K27ac_Rep2


title: Grafted,Day3,Scion,Rep1


title: Exosc3_mESC_CTRL_H3K27ac_Rep1


title: Grafted,Day7,Scion,Rep3


title: Exosc3_EpiLC_cKO_H3K9me3_Rep2


title: Ungrafted,Day3,Intact,Rep3


title: Exosc3_EpiLC_cKO_H3K9me3_Rep1


title: Ungrafted,Day3,Intact,Rep1


title: Ungrafted,Day3,Intact,Rep2


title: Exosc3_EpiLC_cKO_H3K27ac_Rep2


title: Ungrafted,Day7,Intact,Rep1


title: Grafted,Day1,Rootstock,Rep2


title: Grafted,Day1,Rootstock,Rep3


title: Exosc3_EpiLC_CTRL_H3K9me3_Rep1


title: Grafted,Day3,Rootstock,Rep3


title: Grafted,Day1,Scion,Rep3


title: Exosc3_mESC_cKO_H3K9me3_Rep2


title: Exosc3_mESC_cKO_H3K9me3_Rep1


title: Exosc3_mESC_CTRL_H3K9me3_Rep2


title: Grafted,Day1,Scion,Rep2


title: Grafted,Day3,Rootstock,Rep2


title: Exosc3_mESC_CTRL_H3K9me3_Rep1


title: Grafted,Day1,Scion,Rep1


title: Grafted,Day1,Rootstock,Rep1


title: Ungrafted,Day1,Intact,Rep1


title: Ungrafted,Day1,Intact,Rep2


title: Ungrafted,Day1,Intact,Rep3


title: Ungrafted,Day0,Intact,Rep3


title: Exosc3_EpiLC_cKO_Pol2-8WG16_Rep1


title: Exosc3_EpiLC_CTRL_Pol2-8WG16_Rep2


title: Exosc3_EpiLC_cKO_Pol2-8WG16_Rep2


title: Exosc3_mESC_cKO_Pol2-8WG16_Rep1


title: Exosc3_mESC_cKO_Pol2-8WG16_Rep2


title: Exosc3_mESC_CTRL_Pol2-8WG16_Rep1


title: sRNAseq of KRAS silenced MEF cells

city: Seattle

first: Inyoul

last: Lee

state: WA

address: 401 Terry Ave. North

institute: Institute for Systems Biology

data_processing:
small RNA analysis pipeline, sRNAnalyser (http://srnanalyzer.systemsbiology.net)
Small RNA sequence reads were trimmed for adaptor sequence/low-quality sequence using "Cutadapt" and "Prinseq"
Trimmed and duplicated sequence reads were merged into a single sequence while maintaining reads counts using "fastx_collapser" in FASTX_TOOLKIT.
Read count extraction was performed using sRNAnalyzer PisaR_v.1.6
Supplementary files format and content: processed data files represent the complete small RNA read counts

source_name: KRAS silenced MEF cells

extract_protocol:
Total RNA was prepared from cells or cell-derived extracellular vesicles using miRNeasy Serum/Plasma advanced kit (Qiagen).
Small RNA (sRNA) libraries for sRNA-seq were prepared using NEXTFLEX Small RNA-seq kit v3 (PerkinElmer) following manufacturer's protocols (v19.01). The quality of libraries was assessed with the Agilent 2100 Bioanalyzer with the High Sensitivity DNA chip. The library concentrations were assessed by NEBNext Library Quant Kit (New Englans Biolabs). The libraries were pooled (2nM final concentration).

value: Mouse Embryonic Fibroblast (MEF)

value: KRAS shRNA


title: Exosc3_mESC_CTRL_Pol2-8WG16_Rep2


title: sRNAseq of Plasmids treated MEF-derived EV (46_MEF 64+53_S46)

source_name: Plasmids treated MEF-derived EV

value: extracellular vesicles (EVs)

value: Plasmids CD64 and TP53


title: Ungrafted,Day0,Intact,Rep1


title: sRNAseq of KRAS silenced MEF-derived EV

source_name: KRAS silenced MEF-derived EV


title: Exosc3_EpiLC_CTRL_H3K9me3_Rep2


title: Exosc3_EpiLC_cKO_Pol2-CTD4H8_Rep1


title: sRNAseq of Plasmids treated MEF-derived EV (06_MEF_64_53_S06)


title: Exosc3_EpiLC_CTRL_Pol2-CTD4H8_Rep2


title: sRNAseq of Mouse embryonic fibroblast (MEF)-derived EV, control

value: Control-No Treatment


title: sRNAseq of Plasmids CD64 and TP53 sequencially treated BMSC-derived EV

organism: Homo sapiens

value: Bone Marrow Stem Cells (BMSCs)


title: Exosc3_EpiLC_CTRL_Pol2-CTD4H8_Rep1


title: sRNAseq of PBS treated MEF-derived EV

source_name: PBS treated MEF-derived EV

value: PBS


title: Exosc3_mESC_cKO_Pol2-CTD4H8_Rep2


title: Exosc3_mESC_cKO_Pol2-CTD4H8_Rep1


title: sRNAseq of PBS treated human BMSCs

source_name: PBS treated human BMSCs


title: Ungrafted,Day0,Intact,Rep2


title: Exosc3_mESC_CTRL_Pol2-CTD4H8_Rep1


title: sRNAseq of TP53 Plasmid treated BMSCs

source_name: TP53 Plasmid treated BMSCs


title: sRNAseq of Human BMSC control cells

source_name: Human BMSC control cells


title: sRNAseq of Plasmids cd64_TP53 treated BMSC-derived EV


title: Exosc3_EpiLC_cKO_Pol2-CTD4H8_Rep2


title: sRNAseq of PBS treated BMSC-derived EV

source_name: PBS treated BMSC-derived EV


title: sRNAseq of Control BMSC-derived EV

source_name: Control BMSC-derived EV


title: Squirrel_Chx10pos

first: Joshua

middle: William

last: Hahn

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: SpeTri2.0
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

molecule: nuclear RNA

organism: Ictidomys tridecemlineatus

source_name: Retina

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single nucleus RNA sequecning (10X Genomics)

value: Retina

tag: cell line

value: Retinal neurons


title: Squirrel_NeuNpos


title: Sheep_chx10 2

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Ovis aries


title: Sheep_NEUN 2


title: Sheep_NeuN1


title: Sheep_NeuN2


title: Sheep_neun 1


title: Sheep_Chx10


title: Sheep_neunpos_B3


title: Sheep_CHX10 1


title: Exosc3_EpiLC_CTRL_Pol2-8WG16_Rep1


title: Exosc3_mESC_CTRL_Pol2-CTD4H8_Rep2


title: sRNAseq of CD64 Plasmid treated BMSCs

source_name: CD64 Plasmid treated BMSCs

value: Plasmid CD64


title: PHD KO IR kidney

city: Tampa

first: Ratnakar

last: Tiwari

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida

description: 10X Genomics

data_processing:
Raw sequencing data in base call format (.bcl) was demultiplexed using Cell Ranger from 10x Genomics, converting the raw data into FASTQ format. Cell Ranger was also used for alignment of the FASTQ files to the mouse reference genome (mm10) and to count the number of reads from each cell that align to each gene
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
Injured kidneys from Cdh5-CreERT2;Phd1f/f, Phd2f/f, Phd3f/f and Cre- mice were collected on day 14 post unilateral IRI. Single-cell suspensions were prepared using Multi Tissue Dissociation Kit 2 (Miltenyi Biotec; Catalog # 130-110-203) following the instructions provided with the kit. Cell suspension was filtered through 100 µm and then 30 µm cell strainer.  Cell suspension was centrifuged at 400 x g for 10 minutes. Cell pellet was incubated with 1mL of RBC lysis buffer on ice for 1 minute. 10 mL neutralizing buffer (PBS with 2% Ffetal bovine serum) was added, and cells were recentrifuged at 400 x g for 5 minutes. Cell pellets were suspended in 10mL neutralizing buffer and centrifuged again at 100 x g for 5 minutes. Finally. cell pellet was suspended in 1X PBS with 0.04% BSA and filtered through 30 µm. Cell number and viability were analyzed using the Nexcelom Cellometer Auto 2000 with the AOPI fluorescent staining method.
The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics; Catalog # PN-1000286) and single Index Kit T Set A (10X Genomics; Catalog # PN-1000213) according to the manufacturer’s manual. For the cell hashing library, it was constructed according to Biolegend’s published protocol on HTO library preparation guidelines with single index adapters. Quality control for the constructed library was performed by the Agilent Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies; Catalog # 5067-4626) and Qubit DNA HS Assay Kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on an Illumina HiSeq 4000 sequencer with 2X50 paired-end kits using the following read lengths: 28 bp for Read1 for cell barcode and UMI, and 90 bp for Read2 for transcript.

value: kidney

value: Cdh5-CreERT2;Phd1f/f, Phd2f/f, Phd3f/f


title: LRJZ11

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

country: France

institute: IGBMC/PHENOMIN-ICS

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Alignment was performed with STAR version 2.5.3a on mm10 mus musculus genome
Quantification step was performed with htseq-count version 0.6.1p1 with annotations coming from Ensembl version 102
Assembly: mm10
Supplementary files format and content: tab-delimited text file provides raw read counts for each gene together with gene annotations. This file contains only genes with at least one read count in one sample.

molecule: polyA RNA

source_name: Mouse paired P5 lower incisors (males only). RNA extraction was performed using RNeasy plus micro kit (Qiagen).

extract_protocol:
Lower incisors of  4 control and 5 Rogdi -/-  postnatal 5 days males were pulled and frozen in dry ice.  RNA extraction was performed using RNeasy Plus Micro Kit (Qiagen).
P2685 : RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Rogdi -/-

tag: Sex

value: male


title: Control IR kidney

description: 10X Genomics

value: Cre-


title: LRJZ10

value: Mouse paired P5 lower incisors (males only). RNA extraction was performed using RNeasy plus micro kit (Qiagen).


title: LRJZ9


title: LRJZ7


title: LRJZ5

value: control


title: LRJZ3


title: LRJZ1


title: LRJZ2


title: 15-day old liver infect 2

city: Yangzhou

first: chen

last: qiaoguang

address: No.48 Wenchang East Road, Yangzhou

country: China

institute: College of Veterinary Medicine, Yangzhou University

data_processing:
Illumina Casava1.8 software used for basecalling
The raw reads obtained by sequencing contains low-quality reads with connectors. In order to ensure the quality of information analysis, rawreads must be processed to get cleanreads.
The clean reads of each sample was screened, and the sRNA within a certain length was selected for follow-up analysis.
Reference sequence alignment analysis
The expression levels of known and new miRNAs in each sample were counted, and transcripts per million clean tags (TPM)
Assembly: gallus_gallus_Ensembl_97
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
The liver samples aseptically collected from chickens were thoroughly rinsed in PBS and immediately frozen in liquid nitrogen. Then the liver samples were stored at −80°C until RNA extraction.Total RNA was prepared from individual liver samples using TRIzol Reagent according to the manufacturer's instruction. The small RNA libraries were prepared from a total of 2 μg total RNA isolated from each sample using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®
smallRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Histomonas meleagridis infect/control

value: 15-day old

value: infect

value: liver


title: 15-day old liver infect 3


title: ONP, day 30 post microbeads injection, rep7

city: Oxford

first: Amélie

middle: M

last: Julé

address: Roosevelt Drive, Headington

country: United Kingdom

institute: Kennedy Institute of Rheumatology (KIR)

data_processing:
Reads were aligned to NCBI build mm10 of the mouse genome (Mus musculus) using STAR aligner (version 2.6.1d)
Transcripts were quantified through a quasi-alignment approach using Salmon (version 0.14.2). Transcript-level counts were aggregated at the gene level and imported into R (version 4.1.0) using tximport.
Differential expression analyses and normalization (variance stabilization transformation) were performed with DESeq2 (version 1.34.0 or above). Additional transcript-level information was sourced from Ensembl release 94.
Assembly: mm10
Supplementary files format and content: CSV file of raw counts for all samples, filtered for genes expressed in at least one sample (non-zero read count)
Supplementary files format and content: CSV file of normalized data (VST normalization) for all samples, filtered for genes expressed in at least one sample (non-zero read count)

source_name: optic nerve proper

extract_protocol:
HA-tagged risobosomes were isolated using anti-HA antibody and magnetic beads separation. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). 3.95-37.4 ng of RNA were used to make libraries.
mRNA was extracted with oligo-dT beads, capturing poly(A) tails, and cDNA libraries were made with the Smart-Seq HT Ultra-low input RNA kit (Takara Biosciences)

treatment_protocol: ONH and ONP were micro-dissected from WT mice sacrificed at day 7 or day 30 following injection with microbeads in the eye. Dissection were performed on ice in chilled PBS. Tissue dissected from 4 distinct mice (2 males and 2 females) were pooled together to constitute one replicate.

value: B6J.129(Cg)-Rpl22tm1.1Psam/SjJ (The Jackson Laboratory, strain #029977) x B6.Cg-Tg (GFAP-Cre) 73.12Mvs/J (The Jackson Laboratory, strain #012886)

value: optic nerve proper

value: astrocyte

value: WT

value: microbeads injection


title: TPF-R3 control

type: RNA

city: Odense

first: Carlos

middle: Maria Lourenco

last: Alves

address: J.B. Winsløws vej 25 3.

country: Denmark

institute: SDU

description:
Gene expression data from TPFR control
CAlv-Ext-TRF-R3-ctrl-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on human transcriptome array 2.0 (HTA). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data analysis was conducted in Transcriptome Analysis Console (Thermo Fisher Scientific).

label: biotin

source_name: TPFR cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MPFR cells were cultured in phenol red-free Dulbecco’s modified Eagle medium (D-MEM)/F-12 (Gibco) supplemented with 1% heat-inactivated fetal bovine serum (FBS, Gibco), 2 mM glutamine (Gibco) and 6 ng/ml insulin (Sigma-Aldrich) supplemented with 200 nM CDK4/6i and 100 nM fulvestrant. TPFR cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 media without phenol red (Gibco, ThermoFisher Scientific, Waltham, MA, USA), supplemented with 5% FBS, 2 mmol/L glutamine, 8 µg /mlL insulin and 200 nM CDK4/6i and 100 nM fulvestrant.

extract_protocol: Total RNA was extracted and purified with RNeasy Mini kit (Qiagen) according to the manufacturer´s instructions.

treatment_protocol: MPFR and TPFR were established through long-term treatment with 100 nM fulvestrant and 200nM palbociclib over a period of 2-4 months.

tag: cell line background

value: T47D cells

value: TPFR cells


title: TPF-R3 RET

description:
Gene expression data from TPFR RET-siRNA
CAlv-Ext-TRF-R3-ret-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal

value: RET siRNA


title: TPF-R1 RET

description:
Gene expression data from TPFR RET-siRNA
CAlv-Ext-TRF-R1-ret-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: TPF-R2 control

description:
Gene expression data from TPFR control
CAlv-Ext-TRF-R2-ctrl-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: TPF-R2 RET

description:
Gene expression data from TPFR RET-siRNA
CAlv-Ext-TRF-R2-ret-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: ONP, day 30 post microbeads injection, rep5


title: MPF-R3 RET

description:
Gene expression data from MPFR RET-siRNA
CAlv-Ext-MPF-R3-ret-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal

source_name: MPFR cells

value: MCF-7 cells

value: MPFR cells


title: MPF-R2 RET

description:
Gene expression data from MPFR RET-siRNA
CAlv-Ext-MPF-R2-ret-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: 15-day old liver infect 1


title: ONP, day 30 post microbeads injection, rep6


title: TPF-R1 control

description:
Gene expression data from TPFR control
CAlv-Ext-TRF-R1-ctrl-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: ONP, day 30 post microbeads injection, rep3


title: 15-day old liver control 1


title: MPF-R2 control

description:
Gene expression data from MPFR control
CAlv-Ext-MPF-R2-ctrl-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: ONP, day 30 post microbeads injection, rep2


title: 15-day old liver control 3


title: LRJZ8

value: Rogdi -/-

value: male


title: 15-day old liver control 2


title: ONP, day 30 post microbeads injection, rep1


title: 10-day old liver infect 2

value: 10-day old


title: 10-day old liver infect 3


title: MPF-R1 RET

description:
Gene expression data from MPFR RET-siRNA
CAlv-Ext-MPF-R1-ret-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: ONP, day 7 post microbeads injection, rep4


title: 10-day old liver infect 1


title: ONP, day 30 post microbeads injection, rep4


title: MPF-R3 control

description:
Gene expression data from MPFR control
CAlv-Ext-MPF-R3-ctrl-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal

value: control


title: ONP, day 7 post microbeads injection, rep2


title: ONP, day 7 post microbeads injection, rep3


title: 10-day old liver control 1


title: ONP, day 7 post microbeads injection, rep1


title: MPF-R1 control

description:
Gene expression data from MPFR control
CAlv-Ext-MPF-R1-ctrl-HTA-2_0-a1.sst-rma-combined-dabg.chp Signal


title: ONH, day 30 post microbeads injection, rep5

source_name: optic nerve head

value: optic nerve head


title: ONH, day 30 post microbeads injection, rep7


title: Tet1+/+ Tdg+/+ ApcMin/+ .2

city: Philadelphia

first: Alfonso

last: Bellacosa

address: 333 Cottman Avenue

department: Cancer Signaling & Epigenetics

institute: Fox Chase Cancer Center

data_processing:
Raw sequence reads were aligned to the mouse genome (mm10) using the Tophat algorithm
 Cufflinks  was implemneted to assemble transcripts and estimate their abundance.
Cuffdiff was used to statistically assess expression changes in quantified genes in different conditions
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Sample ...

source_name: Colonic adenoma

growth_protocol: Mutant mice were appropriately crossed to generate experimental mice from four-genotype groups: Tet1-/- Tdg+/+ ApcMin/+; Tet1+/- TdgN151A/+ ApcMin/+ ; Tet1+/+ TdgN151A/+ ApcMin/+; and Tet1+/+ Tdg+/+ ApcMin/+.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen)
The sequencing libraries were constructed from 500 ng of total RNA using the TruSeq RNA Sample pre kit V2 (Illumina), following the manufacturer’s instructions. The fragment size and concentration of RNAseq libraries were determined using a 2100 Bioanalyzer (Agilent) and a Qubit instrument (LifeTech), respectively.  The libraries were loaded onto an Illumina HiSeq 2500 at 6-10 pM on the rapid mode for 1x75bp single-end read sequencing.  The fastq files were generated on the Illumina’s BaseSpace for further analysis. Sequence reads were aligned to mouse mm10 genome using Tophat2

treatment_protocol: Mice were sacrificed at 150-160 days, and colonic adenomas were dissected for RNA extraction

value: Colonic adenoma

value: Tet1+/+ Tdg+/+ ApcMin/+


title: Tet1+/+ Tdg+/+ ApcMin/+ .3


title: 10-day old liver control 2

value: liver


title: ONH, day 30 post microbeads injection, rep6

value: B6J.129(Cg)-Rpl22tm1.1Psam/SjJ (The Jackson Laboratory, strain #029977) x B6.Cg-Tg (GFAP-Cre) 73.12Mvs/J (The Jackson Laboratory, strain #012886)


title: 10-day old liver control 3


title: Tet1+/+ TdgN151A/+ ApcMin/+ .2

value: Tet1+/+ TdgN151A/+ ApcMin/+


title: ONH, day 30 post microbeads injection, rep3

value: astrocyte

value: WT


title: ONH, day 30 post microbeads injection, rep4

value: microbeads injection


title: ONH, day 7 post microbeads injection, rep4


title: Tet1+/+ TdgN151A/+ ApcMin/+ .3


title: ONH, day 30 post microbeads injection, rep2


title: Tet1+/- TdgN151A/+ ApcMin/+ .2

value: Tet1+/- TdgN151A/+ ApcMin/+


title: ONH, day 30 post microbeads injection, rep1


title: Tet1-/- Tdg+/+ ApcMin/+ .3

value: Tet1-/- Tdg+/+ ApcMin/+


title: ONH, day 7 post microbeads injection, rep2


title: ONH, day 7 post microbeads injection, rep3


title: ONH, day 7 post microbeads injection, rep1


title: Tet1+/- TdgN151A/+ ApcMin/+ .3


title: Tet1+/- TdgN151A/+ ApcMin/+ .1


title: Tet1-/- Tdg+/+ ApcMin/+ .2


title: Tet1+/+ Tdg+/+ ApcMin/+ .1


title: Tet1-/- Tdg+/+ ApcMin/+ .1


title: VS_OLD_WT_MIXED_C2.TOTAL1-3

first: Peter

last: Kilfeather

address: Biochemistry Building Phase II, South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
Reads were trimmed using trim galore with default settings
Alignment and quantification were performed using Salmon in mapping mode, using Gencode mm10 genome/transcriptome data as a reference
Read count extraction and normalization were performed using tximeta and DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: ventral midbrain

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: ventral midbrain

value: dopaminergic neurons

tag: region

value: VS

value: OLD

value: MIXED

tag: collection


title: VS_YOUNG_WT_MIXED_C2.TOTAL4-5

value: YOUNG


title: CON_1

city: Shijiazhuang

first: chu

last: chen

state: Hebei

address: 361 Zhongshan East Road

department: Department of Toxicology

institute: Hebei medical university

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: Male mice of the prefrontal cortex of the brain

growth_protocol: The mice normal eating and drinking. Male, C57BL/6 mice, at 5 weeks old, weight 17 ± 2 g. Before experiment, the animals were fed in the experimental room for 3 days to habituate to the environment of the laboratory. An ambient condition with temperature of 25 ± 2 ℃, relative humidity of 50 ± 2%, and photoperiod of 12 h was maintained throughout the study.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: The PS NPs via oral gavage once per day and for 6 months.  The mice were treated with water in control group.

value: the prefrontal cortex of the brain

value: gavage 0 mg/kg body weight PS NPs


title: TREAT_HIGH_2

value: gavage 50 mg/kg body weight PS NPs


title: TREAT_HIGH_1


title: CON_3


title: CON_2


title: Tet1+/+ TdgN151A/+ ApcMin/+ .1

value: Colonic adenoma


title: MB_OLD_WT_MIXED_C2.TOTAL1-5

value: MB


title: VS_OLD_WT_MIXED_C2.TOTAL4-5


title: MB_YOUNG_WT_MIXED_C2.TOTAL1-5


title: MB_OLD_WT_MIXED_C2.7


title: VS_YOUNG_WT_MIXED_C2.TOTAL1-3


title: VS_OLD_WT_MIXED_C2.5


title: RPF_P21_rep2

city: Guangzhou

first: Hongwei

last: Wang

state: Guangdong

address: No 7 Jinsui Rd, Research Building, Rm 301

department: Zhongshan Ophthalmic Center

institute: Sun Yat-Sen University

data_processing:
Illumina Casava1.82 were used for basecalling
Adapter was clipped using Cutadapt(v1.8.1) with options:-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -match-read-wildcards -m 6.Low-quality bases were trimmed using Sickle(v1.33) with options:-q 20.
The trimmed reads were filtered by their length with the ranges: [25, 35] for ribosome footprints, and [20, 125] for mRNA. The retaining reads mapped to the mouse rRNA or tRNA reference were further removed.
The remaining reads were then aligned to the mouse reference genome (GENCODE, NCBIM37) using Tophat2(v2.0.11). After each alignment, only uniquely mapped reads were assigned to the 5'UTR, CDS, 3'UTR  and the Exonic region of each gene using HTSeq(v0.6.1p1).
To avoid differences in library composition across samples, the raw count for each gene was normalized and transformed into the RPKM value (reads per kilobase per million mapped reads).
Genome_build: Genome Reference Consortium  NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample;gene IDs are ENSEMBL-Gene-IDS

extract_protocol:
Frozen retina tissues from 7 development times samples were lysed separately using 1 ml of mammalian lysis buffer (200 µl 5x Mammalian Polysome Buffer, 100 µl 10% Triton X-100, 10 µl DTT(100 mM), 10 µl DNase I (1U/µl), 2 µl Cycloheximide (50 mg/ml), 10 µl 10% NP-40 and 668 µl Nuclease-Free Water). After incubation for 20 min on ice, lysates were cleared by centrifugation at 10000 x g for 3 min at 4°C. Ribosomal RNA was depleted using the Ribo-Zero magnetic kit (Epicentre). Sequencing libraries of ribosome protected fragments were generated using ARTseqTM Ribosome Profiling Kit according to the manufacturer's instructions. Sequencing libraries of poly(A)+ RNA were generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina according to the manufacturer's instructions.
Sequencing libraries of ribosome protected fragments were generated using ARTseqTM Ribosome Profiling Kit (Epicentre, RPHMR12126) according to the manufacturer's instructions. And, sequencing libraries of poly(A)+ RNA were  generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina (Vazyme Biotech, NR601-01) according to the manufacturer's instructions.

tag: genotype/variation

value: wild type

value: postnatal days 21

value: Retina


title: RPF_P42_rep2

value: postnatal days 42


title: RPF_P42_rep1


title: RPF_P6_rep2

value: postnatal days 6


title: RPF_P6_rep1


title: RPF_P0_rep2

value: postnatal days 0


title: MB_OLD_WT_MIXED_C2.5

value: ventral midbrain

value: WT


title: DS_OLD_WT_MIXED_C2.5

value: dopaminergic neurons

value: DS


title: VS_OLD_WT_MIXED_C2.4

value: VS

value: OLD

value: MIXED


title: TREAT_HIGH_3

value: the prefrontal cortex of the brain


title: DS_OLD_WT_MIXED_C2.TOTAL4-5


title: DS_OLD_WT_MIXED_C2.4


title: RPF_P0_rep1


title: DS_YOUNG_WT_MIXED_C2.TOTAL4-5

value: YOUNG


title: DS_YOUNG_WT_MIXED_C2.TOTAL1-3


title: MB_OLD_WT_MIXED_C2.4


title: RNA_P42_rep2


title: VS_OLD_WT_MIXED_C2.2


title: RPF_E13.5_rep2

value: embryo days 13.5


title: RPF_E13.5_rep1


title: VS_OLD_WT_MIXED_C2.3


title: DS_OLD_WT_MIXED_C2.2


title: RPF_P21_rep1


title: MB_OLD_WT_MIXED_C2.2

value: MB


title: VS_OLD_WT_MIXED_C2.1


title: RNA_P6_rep2

value: wild type


title: RNA_P21_rep2

value: postnatal days 21


title: RNA_P21_rep1

value: Retina


title: RNA_P42_rep1

value: postnatal days 42


title: MB_OLD_WT_MIXED_C2.1


title: RNA_P6_rep1

value: postnatal days 6


title: MB_YOUNG_WT_MIXED_C2.6


title: RNA_P0_rep2

value: postnatal days 0


title: DS_YOUNG_WT_MIXED_C2.5

value: ventral midbrain


title: RNA_E13.5_rep2


title: RNA_P0_rep1


title: DS_OLD_WT_MIXED_C2.1

value: WT


title: VS_YOUNG_WT_MIXED_C2.5

value: dopaminergic neurons


title: RNA_E13.5_rep1


title: MB_YOUNG_WT_MIXED_C2.5


title: VS_YOUNG_WT_MIXED_C2.4


title: MB_OLD_WT_MIXED_C2.3


title: PC-3, TGH 2.5 µM treated-2

first: William

last: Oh

address: 1 Gustave Levy Place

data_processing:
Samples were run on an Illumina NextSeq as a single end run.
Counts were transformed into log2-TPM.
Assembly: hg19
Supplementary files format and content: log2_TPM_TGH.txt: tab-delimited text file includes log2-TPM in each gene for each sample

source_name: Prostate

growth_protocol: DMEM/F12+10% FBS

extract_protocol:
Tizol RNA extraction followed by Rneasy extraction kit
RNA quality was examined by Bioanalyzer nanochips and must have had a minimal RIN of 7. RNA sequencing was performed in the NextSeq core facility at Mount Sinai after in-house RNA library preparation with RiboMinus Eukaryote System v2 and Nextflex Rapid Directional RNA-seq kit.
Ribo-Zero

treatment_protocol: PC-3 cells were treated with DMSO control or TGH2.5uM for 24 hours before RNA was extracted.

value: Prostate

value: TGH


title: PC-3, TGH 2.5 µM treated-3


title: PC-3, TGH 2.5 µM treated-1


title: DS_YOUNG_WT_MIXED_C2.4

value: DS


title: PC-3, DMSO-2

value: DMSO


title: PC-3, DMSO-3


title: DS_YOUNG_WT_MIXED_C2.3

value: MIXED


title: MB_YOUNG_WT_MIXED_C2.4

value: YOUNG


title: PC-3, DMSO-1


title: DS_YOUNG_WT_MIXED_C2.2


title: VS_YOUNG_WT_MIXED_C2.2

value: VS


title: CutAndRun.AN3CA.Empty_Vector.SMARCC1

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For Cut and Run libraries, the CutRunTools pipeline (Zhu et al. 2020) was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

growth_protocol: AN3CA cells were maintained in EMEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Epicypher's CUT&RUN protocol was followed to extract nuclei and probe chromatin localization.
Epicypher's CUT&RUN protocol was followed to construct libraries. Size distribution of libraries was determined using TapeStation D1000

value: human endometrial carcinoma

tag: chip antibody

value: SMARCC1 (CST, #11956S)

value: AN3CA cells expressing Empty Vector Control


title: CutAndRun.AN3CA.Empty_Vector.SMARCA4

value: SMARCA4 (CST, #49360S)


title: CutAndRun.AN3CA.Empty_Vector.H3K27ac


title: VS_YOUNG_WT_MIXED_C2.1


title: MB_YOUNG_WT_MIXED_C2.2

value: MB


title: MB_OLD_OVX_FEMALE_C1.TOTAL

value: OLD

value: OVX

value: FEMALE


title: DS_YOUNG_WT_MIXED_C2.1

value: ventral midbrain

value: WT


title: CutAndRun.AN3CA.ARID1B_WT.SMARCA4

value: AN3CA cells expressing ARID1B WT


title: CutAndRun.AN3CA.Empty_Vector.HA_Rep2


title: CutAndRun.AN3CA.Empty_Vector.HA_Rep1


title: MB_OLD_WT_FEMALE_C1.TOTAL

value: dopaminergic neurons


title: MB_YOUNG_WT_MIXED_C2.1


title: CutAndRun.AN3CA.ARID1B_WT.HA


title: MB_OLD_OVX_MALE_C1.TOTAL

value: MALE


title: CutAndRun.AN3CA.ARID1B_S320_G327del.SMARCA4

value: AN3CA cells expressing ARID1B S320_G327del disease mutant


title: CutAndRun.AN3CA.ARID1B_S320_G327del.HA


title: MB_OLD_WT_MALE_C1.TOTAL


title: CutAndRun.AN3CA.ARID1B_S320_G327del.H3K27ac


title: MB_YOUNG_WT_FEMALE_C1.TOTAL


title: MB_YOUNG_WT_MIXED_C2.3

value: MIXED


title: CutAndRun.AN3CA.ARID1B_Block9del.SMARCA4

value: AN3CA cells expressing ARID1B Block 9 inframe deletion mutant


title: CutAndRun.AN3CA.ARID1B_Block9del.H3K27ac


title: MB_YOUNG_OVX_MALE_C1.TOTAL

value: YOUNG


title: MB_YOUNG_WT_MALE_C1.TOTAL


title: MB_OLD_WT_FEMALE_C1.4


title: MB_YOUNG_OVX_FEMALE_C1.TOTAL


title: CutAndRun.AN3CA.ARID1B_Block13del.HA

value: human endometrial carcinoma

value: AN3CA cells expressing ARID1B Block 13 inframe deletion mutant


title: MB_OLD_OVX_FEMALE_C1.4


title: MB_OLD_OVX_FEMALE_C1.3


title: CutAndRun.AN3CA.ARID1B_Block13del.SMARCA4


title: CutAndRun.AN3CA.ARID1B_WT.H3K27ac


title: CutAndRun.AN3CA.ARID1B_Block13del.H3K27ac


title: MB_OLD_OVX_FEMALE_C1.2


title: CutAndRun.AN3CA.ARID1B_A457_G461del.HA

value: AN3CA cells expressing ARID1B A457_G461 disease mutant


title: CutAndRun.AN3CA.ARID1B_A457_G461del.SMARCA4

value: SMARCA4 (CST, #49360S)


title: MB_OLD_WT_FEMALE_C1.3

value: MB


title: MB_OLD_OVX_FEMALE_C1.1

value: OLD


title: CutAndRun.AN3CA.ARID1A_dIDR1.HA

value: AN3CA cells expressing ARID1A delIDR1 truncation mutant


title: MB_OLD_WT_FEMALE_C1.2

value: FEMALE


title: MB_OLD_WT_FEMALE_C1.1

value: ventral midbrain


title: MB_OLD_OVX_MALE_C1.4

value: OVX


title: CutAndRun.AN3CA.ARID1A_Y42S.SMARCA4

value: AN3CA cells expressing ARID1A 42YS mutant


title: CutAndRun.AN3CA.ARID1A_Y42S.H3K27ac


title: MB_OLD_WT_MALE_C1.4

value: dopaminergic neurons

value: WT


title: CutAndRun.AN3CA.ARID1A_Y42S.HA


title: MB_OLD_OVX_MALE_C1.3

value: MALE


title: CutAndRun.AN3CA.ARID1A_WT.HA

value: AN3CA cells expressing ARID1A WT


title: CutAndRun.AN3CA.ARID1A_DBDmut.HA

value: AN3CA cells expressing ARID1A DBDmut mutant


title: MB_OLD_WT_MALE_C1.3


title: MB_OLD_WT_MALE_C1.2


title: MB_OLD_OVX_MALE_C1.2


title: MB_OLD_OVX_MALE_C1.1


title: CutAndRun.AN3CA.ARID1B_A457_G461del.H3K27ac


title: CutAndRun.AN3CA.ARID1A_AQGscramC1C2.H3K27ac

value: AN3CA cells expressing ARID1A AQG scramble mutant


title: MB_OLD_WT_MALE_C1.1


title: CutAndRun.AN3CA.ARID1A_AQGscramC1C2.SMARCA4

value: human endometrial carcinoma


title: MB_YOUNG_WT_FEMALE_C1.4

value: YOUNG


title: CD34, GATA1, rep1

city: Chicago

first: Megan

last: McNerney

state: IL

address: 5128 Knapp Center for Biomedical Discovery 900 East 57th Street

department: Dept. of Pathology and Dept. of Pediatrics, Hematology/Oncology

institute: University of Chicago

data_processing:
CUT&RUN reads were trimmed in order to filter out illumina adaptor sequences using Cutadapt (version 4.2.0) and the final base had a quality score > 30
paired-end reads were aligned to the UCSC hg19 genome using bwa (version 0.7.17). Only uniquely mapped reads with at most two mismatches were retained. Duplicated reads were removed using samtools (version 1.16.1)
deepTools(version 3.5.1) was used to create coverage file in bigWig format. Scores represent normalized to fragments (reads) per kilobase per million (RPKM) at a given genomic coordinate
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.1, with input control, narrowPeak files were generated using the default MACS2 settings
Consensus peaks between two biological replicates were called using irreproducible discovery rate (IDR) threshold of < 0.05
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

source_name: primary CD34+ peripheral blood mononuclear HSPC

growth_protocol: Primary CD34+ cells were grown in StemSpan SFEMII media (STEMCELL Technologies 09655) supplemented with 1X StemSpan CC110 cytokine cocktail (Stemcell Technologies 02697).

extract_protocol:
5x10E5 cells were harvested from CD34+ HSPCs expanded for 48 hours post-thawing and bound to ConA-coating beads by rotation for 10 minutes at room temperature. Cells were permeabilized (20 mM HEPES pH 7.5, 150 mM NaCL, 0.5 mM Sperimidine, Roche Complete EDTA free 5892953001, 0.05% w/v digitonin) and incubated overnight at 4°C with anti-CUX1 (PUC) 1:50, anti-SMARCA4 (Cell Signaling, 49360s) 1:100, or anti-GATA1 (Abcam, ab181544) 1:100 antibodies. Protein A/G-MNase beads were added and placed on a tube rotator for 1 hour at 4°C. MNAse bound DNA was cleaved and released by adding 1X pA-MNAse mix containing CaCl2 at 0°C for 30 minutes, STOP buffer was added and CUT&RUN fragments were released by incubating for 30 minutes at 37°C.
Library end repair, ligation, and amplification were performed using the Ovation Ultralow System V2 kit (Tecan Genomics Inc. 0344NB-32) and amplified by PCR with the following parameters: 1 cycle of 72°C  2 minutes, 95°C  3 minutes, followed by 13 cycles of 98°C  20 seconds, 65°C  30 seconds, 72°C  30 seconds, and a final extension at 72°C  for 1 min.  Libraries were cleaned up using MinElute PCR purification kit (Qiagen) and a left-sided size selection using SPRI beads (Beckman Coulter B23317). Final libraries were analyzed by Bioanalyzer (Agilent) prior to sequencing.

value: GATA1 (Abcam, #ab181544)


title: MB_YOUNG_WT_FEMALE_C1.3


title: CD34, SMARCA4, rep2

value: primary CD34+ peripheral blood mononuclear HSPC

value: SMARCA4 (Cell Signaling, #49360s)


title: CD34, GATA1, rep2


title: CD34, SMARCA4, rep1


title: MB_YOUNG_OVX_FEMALE_C1.3

value: MB


title: CD34, CUX1, rep2

value: CUX1 (PUC, Poconos)


title: CD34, CUX1, rep1


title: MB_YOUNG_WT_FEMALE_C1.1

value: FEMALE


title: MB_YOUNG_OVX_FEMALE_C1.1

value: ventral midbrain


title: MB_YOUNG_WT_FEMALE_C1.2


title: CD34, CUX1_KO, rep2

data_processing:
For both K562 and human CD34+ HSPC ATAC-seq analysis, sequenced samples were trimmed using Cutadapt (version 4.2.0) in order to filter out illumina sequencing adaptors
Paired-end ATAC-seq reads were aligned to the UCSC hg19 genome using bwa (version 0.7.17). Only uniquely mapped reads with at most two mismatches were retained. Duplicated reads and mitochondrial reads were removed using samtools (version 1.16.1)
deepTools(version 3.5.1) was used to create ATAC-seq coverage file in bigWig format. Scores represent normalized to fragments (reads) per kilobase per million (RPKM) at a given genomic coordinate.
Peaks were called using MACS2 (version 2.1.0) with “ --nomodel,  -- shift -75, and  -- extsize 150 ” options, with the significance cut-off p-value <=0.1. NarrowPeak files were generated using the default MACS2 settings
Consensus peaks between two biological replicates were called using irreproducible discovery rate (IDR) threshold of < 0.05
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: K562 cells were grown in RPMI 1640 media (Gibco 61870127) supplemented with 10% FBS and 1X Antibiotic-Antimycotic (Gibco 15240062), at 37 °C and 5% CO2.  Primary CD34+ cells were grown in StemSpan SFEMII media (STEMCELL Technologies 09655) supplemented with 1X StemSpan CC110 cytokine cocktail (Stemcell Technologies 02697), at 37 °C and 5% CO2.

extract_protocol:
For all experiments, K562 cells were harvested from cultures at ~60% confluency and primary CD34+ HSPCs were harvested 48 hours post transfection. For both K562 and primary CD34+ HSPCs, 50,000 cells were lysed using the following buffer: 10 mM Tris-HCL, pH 7.4, 10 mM NaCL, 3 mM MgCl2, and 0.1% IGEPAL CA-630. Cells were transposed using a 1X concentration of Nextera Tn5 Transposase (Illumina) for 30 minutes at 37 °C with shaking at 500 rpm. Following transposition, DNA was purified using the MinElute PCR Purification Kit (Qiagen).
DNA was amplified for 5 initial cycles using the custom Nextera barcoded PCR primers with the following parameters: 1 cycle of 72 °C for 5 minutes and 98 °C for 30 seconds, followed by 5 cycles of 98 °C for 10 seconds, 63 °C for 30 seconds, and 72 °C for 1 min. Following the initial 5 cycles of PCR, the additional number of cycles needed was determined by qPCR as previously described. Following the additional PCR cycles, DNA was obtained using the MinElute PCR Purification Kit and analyzed by Bioanalyzer (Agilent) prior to sequencing.

tag: condition

value: CRISPR gCUX1


title: CD34, CUX1_KO, rep1


title: CutAndRun.AN3CA.ARID1A_CBR.HA

value: AN3CA cells expressing ARID1A CBR truncation mutant


title: MB_YOUNG_WT_MALE_C1.4

value: dopaminergic neurons


title: CD34, CTRL, rep2

value: CRISPR gHPRT (CTRL)


title: MB_YOUNG_OVX_MALE_C1.4

value: OVX

value: MALE


title: CutAndRun.AN3CA.ARID1A_AQGscramC1C2.HA


title: ATACseq.AN3CA.ARID1B_Block9del.Rep2

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
Output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
Assembly: hg19
Supplementary files format and content: bigWig, broadPeak

extract_protocol:
Genomic DNA containging tagmented regions was purified using Qiagen's Minelute DNA purification Kit
Tagmented DNA was amplified from genomic DNA via PCR using custom primers. A total of 7 cycles were run to prevent overamplification.

value: AN3CA cells expressing empty vector control


title: MB_YOUNG_WT_MALE_C1.3

value: WT


title: MB_YOUNG_OVX_FEMALE_C1.4


title: CD34, CTRL, rep1


title: MB_YOUNG_OVX_MALE_C1.2


title: ATACseq.AN3CA.ARID1B_Block9del.Rep1

value: human endometrial carcinoma


title: ATACseq.AN3CA.ARID1B_Block13del.Rep2


title: MB_YOUNG_OVX_FEMALE_C1.2

value: YOUNG


title: MB_YOUNG_WT_MALE_C1.2


title: MB_YOUNG_OVX_MALE_C1.1


title: MB_YOUNG_WT_MALE_C1.1


title: ATACseq.AN3CA.ARID1B_Block13del.Rep1


title: ATACseq.AN3CA.ARID1B_A457_G461del.Rep2


title: ATACseq.AN3CA.ARID1A_Y42S.Rep2


title: ATACseq.AN3CA.ARID1B_A457_G461del.Rep1


title: Liver-cKO-3, input

city: Xi'an

first: Xiang

address: Changle west road #169

institute: the Fourth Military Medical University

data_processing:
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: For MeRIP-seq, xlsx files contain each peak of associated genes; for RNA-seq ,xlsx files include FPKM values for each Sample.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure (Meyer et al., 2012) with slight modifications. Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

value: 8 weeks

value: Mettl3 cKO

value: male

value: liver


title: Liver-cKO-2, input


title: ATACseq.AN3CA.ARID1A_Y42S.Rep1


title: ATACseq.AN3CA.ARID1A_AQGscramC1C2.Rep2


title: Liver-cKO-3, IP


title: Liver-cKO-1, IP


title: RNAseq.AN3CA.ARID1B_Block9del.Rep2

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw gene count values for each sample

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 for RNA-seq were prepared using NEB Next mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: AN3CA cells expressing ARID1B Block9 deletion mutant

tag: time


title: Liver-cKO-1, input


title: MB_YOUNG_OVX_MALE_C1.3

value: MB


title: RNAseq.AN3CA.ARID1B_Block13del.Rep2

value: AN3CA cells expressing ARID1B Block13 deletion mutant


title: RNAseq.AN3CA.ARID1B_Block9del.Rep1


title: Liver-WT-3, input

value: wild type


title: Liver-WT-3, IP


title: Liver-WT-2, input


title: RNAseq.AN3CA.ARID1B_A457_G461del.Rep2

value: AN3CA cells expressing ARID1B A457_G461del mutant


title: Liver-WT-2, IP


title: RNAseq.AN3CA.ARID1B_Block13del.Rep1


title: RNAseq.AN3CA.ARID1B_A457_G461del.Rep1


title: RNAseq.AN3CA.ARID1A_Y42S.Rep2

value: AN3CA cells expressing ARID1A 42YS mutant


title: RNAseq.AN3CA.ARID1A_Y42S.Rep1


title: RNAseq.AN3CA.ARID1A_AQGscramC1C2.Rep1

value: AN3CA cells expressing ARID1A AQG scramble mutant


title: RNAseq.AN3CA.ARID1A_AQGscramC1C2.Rep2


title: Liver-WT-1, IP


title: EHTs, DMSO 1

city: Enschede

first: Carla

last: Cofiño Fabrés

address: Drienerlolaan 5

country: Netherlands

institute: University of Twente

data_processing:
Trimming of the reads and alignment was performed with seq2science (v0.4.0, https://doi.org/10.5281/zenodo.4451349).
Fastp (v0.20.1) trimmed the low quality 3’ ends and Salmon (v1.3.0) quant aligned the reads to the GRCh38.p13 genome from Ensembl
tximeta (v1.4.3) was used to generate the gene expression matrix.
Assembly: GRCh38.p13 (Ensembl)
Supplementary files format and content: "hg38-counts.tsv" contains the raw gene counts

source_name: Engineered Heart Tissues

extract_protocol:
RNA was isolated from EHTs 24 hours after treatment using the Nucleospin mini kit (Macherey-nagel, 740955.250)
Libraries were generated from 200 ng RNA using the KAPA-RNA HyperPrep kit with RiboErase (Roche) to remove ribosomal RNA (ie, rRNA depleted total RNA), according to manufacturer’s instructions. Library amplification was performed with 11 cycles.
Libraries were multiplexed and sequenced on NextSeq500 Illumina to generate 38bp PE reads.

value: Engineered Heart Tissues

value: hiPSC-Cardiomyocytes

tag: timepoint

value: 24h after treatment

value: DMSO


title: EHTs, DMSO 3


title: EHTs, DOXO 3

value: Doxorubicin


title: EHTs, DOXO 2


title: EHTs, DOXO 1


title: ATACseq.AN3CA.ARID1A_AQGscramC1C2.Rep1

value: human endometrial carcinoma

value: AN3CA cells expressing empty vector control


title: Liver-cKO-2, IP

last: Zhang

value: 8 weeks

value: Mettl3 cKO


title: Zebrafish_BC6

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: Zv82
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Danio rerio

extract_protocol:
Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. They were dissociated in papain, followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors.
Single cell libraries were generated using the Chromium 3’ V3 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single cells were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single cell RNA sequecning (10X Genomics)

value: Retina

value: Retinal neurons


title: Zebrafish_BC7


title: Zebrafish_BC8


title: Zebrafish_BC5


title: EHTs, AMR 1

value: Amrubicin


title: EHTs, ACLA 3

value: Aclarubicin


title: EHTs, AMR 2


title: Zebrafish_BC4


title: EHTs, ACLA 1


title: EHTs, AMR 3


title: Liver-WT-1, input

value: wild type

value: male

value: liver


title: HS6

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were generated through kallisto bustools (https://www.kallistobus.tools/)
The following command was applied to the fastq files of each sample: kallisto bus -x 10xv2 -o 10xv2 -i hg38.repeat_masked.gene.trans.exon.cds *R*fastq.gz
Each resulting bus file was corrected: bustools correct -w 737K-august-2016.txt -o output.correct.bus output.bus
Each corrected bus file was sorted: bustools sort -o output.correct.sort.bus output.correct.bus
Aggregation of reads: bustools count -o human_transcript_to_gene.tsv -e matrix.ec -t transcripts.txt --genecounts output.correct.sort.bus
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin, HS, scRNAseq

extract_protocol:
Skin samples were received in the form of excised surgical tissue from HS surgical intervention or excess mammoplasty tissue. Samples were weighed and proceessed into a single cell preparation using the Whole Skin Dissociation Kit. Samples were resuspended in CryoStor Cyropreservation mefia and frozen immediately at -80 degrees. Cryopreserved cells were shipped to collaborators at the AbbVie Bioresearch Centre (MA, USA). Once thawed, live single CD45+ cells were sorted into 500ul PBS/0.5% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: tissue

value: excised surgical tissue from seton intervention

tag: disease state

value: HS

value: 51 years old


title: Zebrafish_BC3

source_name: Retina


title: Zebrafish_BC1


title: EHTs, DMSO 2

value: Engineered Heart Tissues

value: hiPSC-Cardiomyocytes

value: 24h after treatment

value: DMSO


title: HS5

description: 10x Genomics

value: 23 years old


title: Zebrafish_BC2


title: Con2

description: 10x Genomics

source_name: Skin, Healthy, scRNAseq

value: Skin from mammoplasty surgey

value: Healthy

value: 41 years old


title: Con3

description: 10x Genomics

value: 24 years old


title: K562, H3K27ac, CUX1 KO, rep1

data_processing:
ChIP-seq reads were trimmed in order to filter out illumina adaptor sequences using Cutadapt (version 4.2.0) and the final base had a quality score > 30
single-end ChIP-seq reads were aligned to the UCSC hg19 genome using bwa (version 0.7.17). Only uniquely mapped reads with at most two mismatches were retained. Duplicated reads were removed using samtools (version 1.16.1)
deepTools (version 3.5.1) was used to create ChIP-seq coverage file in bigWig format. Scores represent normalized to fragments (reads) per kilobase per million (RPKM) at a given genomic coordinate.
Peaks were called using MACS v2.1.0 with the significance cut-off p-value <=0.1, with input control, narrowPeak files were generated using the default MACS2 settings
Consensus peaks between two biological replicates were called using irreproducible discovery rate (IDR) threshold of < 0.05
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: K562 cells were grown in RPMI 1640 media (Gibco 61870127) supplemented with 10% FBS and 1X Antibiotic-Antimycotic (Gibco 15240062).

extract_protocol:
Chromatin was fixed from 100x106 gHPRT and gCUX1 transfected K562 cells using 1% formaldehyde for 10 minutes at room temperature and stopped by the addition of 0.125 M glycine. For SMARCA4 ChIP, protein cross linking was performed first.  Cells were washed 3 times with 1X PBS at room temperature. 10 mL of PBS/MgCl2 were added to the cells after final PBS wash. 80 uL of 0.25M DSG-disuccinimidyl glutarate (Thermo Fischer 20593) was added and incubated for 45 minutes at room temperature. Cells were washed 3 times with 1X PBS and followed by DNA crosslinking with 1% formaldehyde as described above. Fixed chromatin was then sonicated (Bioruptor) for 10 minutes in 30 seconds on/off pulses two times for a total of 20 minutes, with vortexing in between.
DNA was purified using a PCR purification kit (Qiagen). Libraries were prepped using the Ovation Ultralow Library Kit Tecan Genomics Inc (0344NB-32) and size selected using SPRIselect beads (Beckman Coulter B23317)

value: human myeloid leukemia

value: H3K27ac(Abcam, #ab4729)

value: CRISPR gCUX1


title: Con1

description: 10x Genomics

value: 58 years old


title: K562, H3K27ac, CTRL, rep1

value: CRISPR gHPRT (CTRL)


title: K562, H3K27ac, CTRL, rep2


title: K562, SMARCA4, CUX1 KO, rep2

value: SMARCA4 (Abcam, #ab110641)


title: HS3

description: 10x Genomics

value: tissue

value: excised surgical tissue from seton intervention

value: HS

value: 62 years old


title: K562, SMARCA4, CUX1 KO, rep1


title: HS4

description: 10x Genomics

value: 31 years old


title: K562, SMARCA4, CTRL, rep2


title: HS2

description: 10x Genomics

value: 43 years old


title: EHTs, ACLA 2

value: Engineered Heart Tissues

value: hiPSC-Cardiomyocytes

value: 24h after treatment

value: Aclarubicin


title: K562, CUX1, rep1

value: CUX1 (PUC, Poconos)


title: K562, SMARCA4, CTRL, rep1

value: human myeloid leukemia


title: ATACseq.AN3CA.Empty.Vector.Rep3

value: human endometrial carcinoma

tag: genotype

value: AN3CA cells expressing empty vector control


title: ATACseq.AN3CA.Empty.Vector.Rep1


title: ATACseq.AN3CA.Empty.Vector.Rep2


title: K562, CUX1, rep2


title: K562, CUX1_KO, rep1

value: CRISPR gCUX1


title: HS1

description: 10x Genomics

tag: tissue

value: 22 years old


title: ATACseq.AN3CA.ARID1B.WT.Rep1

tag: cell type

value: AN3CA cells expressing ARID1B wild-type


title: K562, CTRL, rep2

value: CRISPR gHPRT (CTRL)


title: K562, H3K27ac, CUX1 KO, rep2

value: H3K27ac(Abcam, #ab4729)


title: ATACseq.AN3CA.ARID1B.WT.Rep2


title: K562, CTRL, rep1


title: ATACseq.AN3CA.Empty.Vector.Rep4


title: neg-2

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

country: Japan

institute: University of Tokyo

data_processing:
Crude readings were subjected to quality control checks, after which the clean readings were aligned to the human genome reference sequences (Hg19/GRCh37). The aligned reads were mapped and quantified using CLC Genomics Workbench software v7.5
Supplementary_files_format_and_content: Excel file that has total read counts, TPM, CPM, and RPKM of all genes in all cells

source_name: untreated control AGS cells

growth_protocol: AGS cells were cultured in Ham F-12 medium supplemented with 10% FBS

extract_protocol:
RNAs were extracted by Rneasy Mini kit
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed  by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation  reactions into a single step that greatly increases the efficiency of the library preparation process.  Adapter-ligated fragments are then PCR amplified and gel purified.
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn  of surface-bound oligos complementary to the library adapters. Each fragment is then amplified  into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the  templates are ready for sequencing.

treatment_protocol: AGS cells were incubated with bacteria for 4 hours

value: gastric cell line

value: AGS

tag: treatment

value: untreated


title: ATACseq.AN3CA.ARID1B.S320_G327del.Rep1

value: AN3CA cells expressing ARID1B mutant M2 (S320_G327del)


title: neg-1


title: ATACseq.AN3CA.ARID1A.delIDR1.Rep2

value: AN3CA cells expressing ARID1A delIDR1 truncation mutant


title: ATACseq.AN3CA.ARID1A.delIDR1.Rep1


title: Nc-2

source_name: Neisseria-treated AGS cells

value: Neisseria


title: ATACseq.AN3CA.ARID1A.WT.Rep2

value: AN3CA cells expressing ARID1A wild-type


title: Hp-3

source_name: Helicobacter-treated AGS cells

value: Helicobacter


title: ATACseq.AN3CA.ARID1A.WT.Rep1


title: K562, CUX1_KO, rep2


title: Hp-2


title: Fn-3

source_name: Fusobacterium-treated AGS cells

value: Fusobacterium


title: CutAndRun.AN3CA.ARID1B_Block9del.HA

value: AN3CA cells expressing ARID1B Block 9 inframe deletion mutant


title: ATACseq.AN3CA.ARID1A.FUS.Rep2

value: human endometrial carcinoma

value: AN3CA cells expressing ARID1A FUS IDR hybrid mutant


title: ATACseq.AN3CA.ARID1A.DDX4.Rep2

value: AN3CA cells expressing ARID1A DDX4 IDR hybrid mutant


title: Fn-2


title: ATACseq.AN3CA.ARID1A.FUS.Rep1


title: ATACseq.AN3CA.ARID1B.S320_G327del.Rep2


title: ATACseq.AN3CA.ARID1A.DDX4.Rep1


title: ATACseq.AN3CA.ARID1A.DBDmut.Rep2

value: AN3CA cells expressing ARID1A DBDmut ARID domain mutant


title: OC2 RNAseq

city: Harbin

first: Can

last: Wei

address: Baojian Road

department: Department of Pathophysiology

institute: Harbin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome using HISAT2(2.1.0)
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Homo sapiens ensemb release101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: tumor tissue of oral cavity carcinomas

extract_protocol:
Tissues were frozen on dry ice, and RNA was harvested using Trizol reagent.
After the total RNA was extracted from the sample, the ribosomal RNA was removed to retain all coding RNA and ncRNA. The obtained RNA was randomly broken into short fragments, and then the first strand of cDNA was synthesized with six base random primers using the fragmented RNA as the template; Then, buffer, dNTPs (dUTP instead of dTTP), RNase H and DNA polymerase I were added to synthesize the second strand of cDNA, which was purified by QiaQuick PCR kit and eluted with EB buffer, repaired at the end, added base A and adapter, and then degraded the second strand by UNG (Uracil-N-Glycosylase) enzyme. Agarose gel electrophoresis was used for fragment size selection and PCR amplification.

value: oral mucosa

value: tumor tissue of oral cavity carcinomas

value: high and middle differentiated


title: OC3 RNAseq


title: OC1 RNAseq


title: ATACseq.AN3CA.ARID1A.CBR.Rep2

value: AN3CA cells expressing ARID1A CBR truncation mutant


title: ATACseq.AN3CA.ARID1A.CBR.Rep1


title: OP3 RNAseq

source_name: paracancerous tissue of oral cavity carcinomas


title: OP3 Riboseq

description: Ribosome profiling sequencing

data_processing:
Library strategy: Ribosome profiling sequencing
Data filter:remove Ribosomal RNA, tRNA, snoRNA, snRNA, miRNA through blast to GenBank and Rfam database
Sequenced reads mapped to reference genome whole genome using bowtie2(2.2.8) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
calculates the number of reads of Ribo-seq level in ORF region of coding gene and converts it into FPKM value using Rsem software(v1.3.3)
Genome_build: Homo sapiens ensemb release101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Ribosome nascent peptide chain complex was treated with low concentration RNase to degrade RNA fragments without ribosome coverage, and then ribosomes were removed
RNA libraries were prepared for sequencing using standard Illumina protocols

value: paracancerous tissue of oral cavity carcinomas


title: CutAndTag.AN3CA.Empty.Vector.SMARCC1.Rep2

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For Cut and Tag libraries, the CutRunTools pipeline (Zhu et al. 2020) was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Epicypher's CUT&Tag protocol was followed to extract nuclei and probe chromatin localization.
Epicypher's CUT&Tag protocol was followed to ampllification of tagmented DNA from genomic DNA, 14 PCR cycles were run, followed by purification of DNA using AMPure beads (1.3X). Size distribution of libraries was determined using TapeStation D1000

value: SMARCC1 (CST, #11956S)

value: AN3CA cells expressing empty vector control


title: Nc-3

value: gastric cell line

value: AGS


title: ATACseq.AN3CA.ARID1A.DBDmut.Rep1


title: CutAndTag.AN3CA.Empty.Vector.SMARCC1


title: OC3 Riboseq

description: Ribosome profiling sequencing


title: CutAndTag.AN3CA.Empty.Vector.SMARCA4.Rep2

value: SMARCA4 (CST, #49360S)


title: OC2 Riboseq

description: Ribosome profiling sequencing


title: CutAndTag.AN3CA.Empty.Vector.SMARCA4


title: OC1 Riboseq

description: Ribosome profiling sequencing


title: CutAndTag.AN3CA.Empty.Vector.H3K27ac.Rep2


title: skeletal muscle of ACS SD rats, ACS,18h_3

city: NanNing

first: He

last: Ling

state: Guangxi

address: NO. 6 ShuangYong Road

institute: the First Affiliated Hospital of Guangxi Medical University

data_processing:
Seqtk was used to remove rRNA reads, adaptors and poor quality reads (length < 25 or Q20>0.01).
Clean reads were mapped to rnor 6.0 genome by Hisat2 v2.0.4 (Pertea M et al., 2016) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of gene expression was calculated by Stringtie v1.3.0 (Pertea M et al., 2016).
Assembly: rnor 6.0
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

organism: Rattus norvegicus

source_name: skeletal muscle of ACS SD rats, ACS,18h

growth_protocol: These rats were fed with standard food and water, and they adapted to the environment before use

extract_protocol:
rRNA was eliminated by using VAHTS Ribo-off rRNA Depletion Kit(Human/Mouse/Rat) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Acute osteofascial compartment syndrome was induce by percutaneously ligate the skin on the knee joint of rats with low-elastic band. The circumference of the band loop was 1/2 of the circumference of the ligation site.

tag: strain

value: Sprague-Dawley

value: Flexor digitorum longus on hind limbs

value: WT

value: ACS


title: CutAndTag.AN3CA.Empty.Vector.H3K27ac

value: human endometrial carcinoma


title: skeletal muscle of ACS SD rats, ACS,18h_2


title: OP2 RNAseq


title: skeletal muscle of SD rats, Control,0h_3

source_name: skeletal muscle of SD rats, Control,0h


title: skeletal muscle of ACS SD rats, ACS,18h_1


title: CutAndTag.AN3CA.ARID1A.delIDR1.SMARCA4

value: AN3CA cells expressing ARID1A delIDR1 truncation mutant


title: CutAndTag.AN3CA.ARID1A.delIDR1.H3K27ac


title: CutAndTag.AN3CA.ARID1A.WT.SMARCC1

value: AN3CA cells expressing ARID1A wild-type


title: CutAndTag.AN3CA.ARID1A.delIDR1.SMARCC1


title: skeletal muscle of SD rats, Control,0h_2


title: skeletal muscle of SD rats, Control,0h_1


title: CutAndTag.AN3CA.ARID1A.WT.SMARCA4


title: CutAndTag.AN3CA.ARID1A.FUS.SMARCC1

value: AN3CA cells expressing ARID1A FUS IDR hybrid mutant


title: CCIB_4

city: Pittsburgh

first: Vijay

last: Yechoor

state: PA

address: 200 Lothrop street,

department: Vascular Medicine Institute

institute: University of Pittsburgh

data_processing:
quality control and removal of adaptor sequences
reads were alighned using HISAT2
gene expression was estimated using FPKM (fragments per kilobase of transcript sequence per millions base pairs sequenced
differential gene expression analysis was done using DESeq2 R package
Supplementary_files_format_and_content: Excel sheet with
Supplementary_files_format_and_content: Heatmap_annotation

source_name: Insulinoma cell line

growth_protocol: INS1 cells were cultured in RPMI-1640 medium containing 11mM glucose, 10% fetal bovine serum, 10mM Hepes, 2mM L-glutamine, 1mM sodium pyruvate, and 0.05mM 2-mercaptoethanol.

extract_protocol:
RNA was isolated using Direct-zol RNA miniprep by Zymo Research according to manufacturer instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were pre-treated with I-BET762 (500nM) or vehicle control (VC) for 48h followed by addition of cytokine cocktail (CC) of IL-1β (10 ng/ml), IFN-y (100 ng/ml) and TNF-α (25ng/ml) for another 8h in presence of the I-BET or VC

value: Cytokine cocktail+I-BET762


title: CutAndTag.AN3CA.ARID1A.WT.H3K27ac


title: OP2 Riboseq

description: Ribosome profiling sequencing

value: oral mucosa

value: high and middle differentiated


title: CCVC_3

value: Cytokine cocktail+ Vehicle control


title: CCIB_3


title: CutAndTag.AN3CA.ARID1A.FUS.SMARCA4


title: CutAndTag.AN3CA.ARID1A.FUS.H3K27ac


title: CCVC_5


title: CCVC_1


title: IB_4


title: CutAndTag.AN3CA.ARID1A.DDX4.SMARCC1

value: SMARCC1 (CST, #11956S)

value: AN3CA cells expressing ARID1A DDX4 IDR hybrid mutant


title: CutAndTag.AN3CA.ARID1A.DDX4.SMARCA4


title: IB_3


title: CutAndTag.AN3CA.ARID1A.DDX4.H3K27ac


title: IB_2


title: VC_4

value: Vehicle control


title: CutAndTag.AN3CA.ARID1A.DDX4.ARID1A.HA


title: CutAndTag.AN3CA.ARID1A.DBDmut.SMARCC1

value: AN3CA cells expressing ARID1A DBDmut ARID domain mutant


title: VC_2


title: CCIB_5


title: CutAndTag.AN3CA.ARID1A.DBDmut.SMARCA4

value: SMARCA4 (CST, #49360S)


title: VC_1


title: CutAndTag.AN3CA.ARID1A.CBR.SMARCC1

value: AN3CA cells expressing ARID1A CBR truncation mutant


title: CutAndTag.AN3CA.ARID1A.CBR.SMARCA4


title: parn1_prg1

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore. Sequences were then collapsed and transformed into fasta files using cutsom shell scripts.
Reads were aligned to contaminating RNAs (rRNAs, tRNAs, snRNAs…) using Bowtie. Reads that failed to align were aligned to the genome using Bowtie.
Aligned reads were normalized and assigned to genomic features using custom shell scripts. Alignments were converted to BigWig files using UCSC Tools.
Downstream analysis was preformed using R/Python/IGV.
Assembly: WormBase WS279
Supplementary files format and content: Unique fasta file of collapsed reads

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 C on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached day 1 adulthood.

extract_protocol:
60,000 L1 larvae were plated to 150 mm NGM plates supplemented with 2 mL of concentrated OP50 food. Approximately 64 hours after plating L1 larvae, day 1 adults with eggs were collected from plates using M9 solution. Harvested animals were washed twice with M9 and once with water. Animals were then suspended in TRI Reagent solution (Sigma) and frozen at -80°C until RNA extraction was performed. To extract RNAs animals suspended in TRI Reagent solution were thawed and lysed using a Bead Mill (Thermo Fisher Scientific). Bromo-chloropropane (Sigma) was added to the lysed worms and centrifuged at 12,000 x g for 15 minutes. Following centrifugation, the aqueous phase was pipetted to an equal volume of cold isopropanol and placed at -20°C for 1 hour to precipitate RNAs. RNAs were pelleted by centrifugation at 20,000 x g for 15 minutes at 4°C. Total RNAs were washed with 75% EtOH twice and suspended in RNAse free water. Small RNAs were enriched from total RNAs using the MirVana miRNA isolation kit according (Thermo Fisher Scientific).
Small RNAs were treated with RNA phosphatase PIR-1 to remove gamma and beta phosphates from the 5' triphosphorylated RNAs (50). Monophosphorylated RNAs were ligated to 3' adapters ( rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/, IDT) using T4 RNA ligase 2 in 25% PEG 8000 (NEB) at 15 C overnight. A 5' adapter (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT) was then ligated to RNAs to the product using T4 RNA ligase 1 (NEB) for 4 hours at 15 C. Ligated products were reverse transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific) to convert RNA to cDNA libraries. cDNA libraries were amplified by PCR and subsequently sequenced on an Illumina Novaseq platform (SP2 x 50 bp) at the OSU Comprehensive Cancer Center genomics core.

value: whole animal


title: parn1_prg1_ligation

value: PRG-1 IP / ligation


title: CutAndTag.AN3CA.ARID1A.CBR.H3K27ac


title: parn1_prg1_input

value: PRG-1 IP input


title: RNAseq.AN3CA.Empty.Vector.Rep4

value: human endometrial carcinoma

value: AN3CA cells expressing empty vector control


title: wt_prg1_ligation


title: parn1_prg1_IP

value: PRG-1 IP


title: RNAseq.AN3CA.Empty.Vector.Rep3


title: CutAndTag.AN3CA.ARID1A.FUS.ARID1A.HA

value: AN3CA cells expressing ARID1A FUS IDR hybrid mutant


title: wildtype_prg1_IP


title: wildtype_prg1_input


title: RNAseq.AN3CA.Empty.Vector.Rep1


title: RNAseq.AN3CA.Empty.Vector.Rep2


title: PDX20, Vehicle-treated

city: New York

institute: Icahn School of Medicine at Mount Sinai

description: H20, M20

data_processing:
Samples were run on an Illumina NextSeq as a single end run.
Assembly: hg19, mm10
Supplementary files format and content: count_human.txt: tab-delimited text file includes counts in each gene for human part of each sample
Supplementary files format and content: count_mouse.txt: tab-delimited text file includes counts in each gene for mouse part of each sample

organism:
Homo sapiens
Mus musculus

source_name: tumor

growth_protocol: The animal protocol was approved by Mount Sinai Institutional Animal Care and Use Committee (IACUC) (#2018-0064). The PC3 xenograft study was performed by a contractor company OXM Bio (Murray, UT). Aythmic nude mice were purchased through Jackson Laboratory (Strain 002019 52 Male NU/J Homozygous, Male). Mice were fed Teklad irradiated (sterilized) mouse diet and bedded with Teklad irradiated (sterilized) corncob bedding from Envigo (Indianapolis, IN). Mice were housed in Optimice carousel sterile quarters with filtered air supply in disposable cages from Animal Care Systems, Inc. (Centennial, CO). On the day of implantation, PC3 cells were resuspended in 50:50 RPMI (no supplementation): Matrigel at a concentration of 3 x 107 cells / mL. A volume of 100uL was injected into each hind flank of each animal (a total of 3 x 106 cells per injection).

extract_protocol:
At the end of the study, all mice were humanly euthanized. Half of the tumors were harvested in 10% formalin for histological analysis and the other half were snap frozen in liquid nitrogen for RNA extraction. PC3 xenograft RNA was extracted using Automated Robotic System using Beckman's Agencourt RNA dv Advance tissue kit at qPCR core facility at Mount Sinai.
RNA quality was examined by Bioanalyzer nanochips and must have had a minimal RIN of 7. RNA sequencing was performed in the NextSeq core facility at Mount Sinai after in-house RNA library preparation with RiboMinus Eukaryote System v2 and Nextflex Rapid Directional RNA-seq kit.
Ribo-Zero

treatment_protocol: Tumor volumes were monitored, and mice were stratified and placed into 2 treatment groups of 10 mice. One group was treated with vehicle control (7.5% NMP, 7.5% Solutol HS15, 30% PEG400, and 55% Saline), and one group was treated with TGH. Treatments were administered by daily I.P. injection (100 µL volumes) at a dose of 150mg/kg in the vehicle.  Animal weights and tumor volumes were measured.

value: tumor

value: Vehicle-treated


title: RNAseq.AN3CA.ARID1B.WT.Rep1

value: AN3CA cells expressing ARID1B wild-type


title: CSF1 stimulated Input sgRNAs

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

description:
This sample represents the sgRNAs used to transduce cells with for the CSF1 stimulated dextran uptake screen
CSF1stim.count.txt

library_source: other

data_processing:
20 base sgRNA reads were trimmed using Cutadapt 2.3, where 20bp sequence flanked by cgaaacaccg...gttttagagc was identifed from all fastq files. Cutadapt arguments= -g cgaaacaccg...gttttagagc, -o, --minimum-length 15, --discard-untrimmed, -e 0.2, --cores=8
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9. arguments= count, -l BrieGuideLibwithNonTarg.csv, --sample-label, --fastq, -n, --unmapped-to-file, --pdf-report
We used the MAGeCK test command to identify enriched sgRNAs within the high and low populations. Arguments= test, -k, -c low, -t high, -n, --control-sgrna nontargets.txt --keep-tmp --pdf-reports
Assembly: Brie Library
Supplementary files format and content: .txt and .csv files contain the data files used to process the data.  The BrieGuideLibwithNonTarg.csv file contains the Brie library file used by MAGeCK to map the trimmed reads back to the library.  The readmapping step generated the "CSF1stim.count.txt" and "unstim.count.txt" files used for the MAGeCK test functions.  The MAGeCK test step used one of the count tables and the "nontargets.txt" file to identify sgRNAs enriched in the low and high fluroescence populations.  The MAGeCK test output includes the "CSF1_dexuptake_highlow.gene_summary.txt" and "unstim_dexuptake.gene_summary.txt" files.  The MAGeCK out files were used to identify genes regulating  dextran uptake.
Library strategy: CRISPR screen

molecule: other

organism: synthetic construct

source_name: Plasmid DNA used to make lentivirus

growth_protocol: BMDM were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.
The parameters for how the library sequenced - chip: 75 high fidelity read

treatment_protocol: Primary Macrophages expressing Cas9-GFP were transduced with the Brie Library at low multiplicity of infection (MOI) (0.3) to achieve 50 fold representation of each sgRNA in the Brie Mouse library.  After 48 h, transduced cells were selected with 5 ug/ml puromycin for 2 days and cultured another 8 before sorting.  To identify genes regulating dextran uptake, cells were starved of CSF1 overnight in DMEM plus 10% FBS.  Then, cells were exposed to 300 ug/ml 40 kDa fluorescent dextran for 15 minutes in the presence or absence of CSF1.  Cells were then sorted based on their ability to internalize dextran using a BD FACs jazz flow cytometer.  We sorted the top (high fluorescence) and bottom (low fluorescence) quintiles based on dextran fluorescence and sequenced both samples to idenfity sgRNAs enriched in each sample.


title: RNAseq.AN3CA.ARID1B.S320_G327del.Rep2

value: AN3CA cells expressing ARID1B mutant M2 (S320_G327del)


title: PDX19, Vehicle-treated

description: H19, M19


title: RNAseq.AN3CA.ARID1B.S320_G327del.Rep1


title: PDX16, Vehicle-treated

description: H16, M16


title: RNAseq.AN3CA.ARID1A.delIDR1.Rep1

value: AN3CA cells expressing ARID1A delIDR1 truncation mutant


title: RNAseq.AN3CA.ARID1A.delIDR1.Rep2


title: CutAndTag.AN3CA.ARID1A.DBDmut.H3K27ac


title: RNAseq.AN3CA.ARID1A.WT.Rep2

value: AN3CA cells expressing ARID1A wild-type


title: PDX14, Vehicle-treated

description: H14, M14


title: RNAseq.AN3CA.ARID1A.FUS.Rep1


title: RNAseq.AN3CA.ARID1A.FUS.Rep2


title: PDX13, Vehicle-treated

description: H13, M13


title: RNAseq.AN3CA.ARID1A.DDX4.Rep2

value: AN3CA cells expressing ARID1A DDX4 IDR hybrid mutant


title: RNAseq.AN3CA.ARID1A.DDX4.Rep1


title: PDX11, Vehicle-treated

description: H11, M11


title: PDX07, TGH-treated

description: H07, M07

value: TGH-treated


title: RNAseq.AN3CA.ARID1B.WT.Rep2


title: RNAseq.AN3CA.ARID1A.DBDmut.Rep2

value: AN3CA cells expressing ARID1A DBDmut ARID domain mutant


title: PDX09, TGH-treated

description: H09, M09


title: PDX06, TGH-treated

description: H06, M06


title: Unstimulated Input sgRNAs

description:
This sample represents the sgRNAs used to transduce cells with for the unstimulated dextran uptake screen
Unstim.count.txt


title: PDX12, Vehicle-treated

description: H12, M12


title: PDX10, TGH-treated

description: H10, M10


title: PDX05, TGH-treated

description: H05, M05


title: PDX18, Vehicle-treated

description: H18, M18


title: RNAseq.AN3CA.ARID1A.CBR.Rep2

value: AN3CA cells expressing ARID1A CBR truncation mutant


title: RNAseq.AN3CA.ARID1A.CBR.Rep1


title: MEF2Ai 3

first: Adriana

last: Forero

address: 460 W 12th Ave

data_processing:
Both the genome sequence (fasta) and gene transfer files (gtf) for human were obtained using iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Raw RNaseq data (Fastq files) were demultiplexed and checked for quality (FastQC, version 0.11.3).
Ribosomal RNA was digitally removed using Bowtie2 (version 2.3.4). Sufficient host reads (greater than twenty million per sample) were mapped to the human genome (GRCh37) using STAR (version 2.5.3a) and converted into gene counts with HTSeq (version 0.6.1).
rior to statistical analysis, gene counts were filtered with a cutoff of a mean of ten or greater across all samples using R statistical programming language (version 3.4.3) and ‘edgeR’ (version 3.20.9). Gene counts were normalized using voom and statistical analysis for differential expression was carried out in using ‘limma’ (version 3.34.8) in R.
Assembly: GRCm37
Supplementary files format and content: Tab delimited text file of counts and normalised counts.

growth_protocol: Human cardiomyocyte cell lines (AC16) (Millipore) and derivates were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 12.5% FBS, 2mM Glutamine, 100 U/ml Penicillin and 100 mg/ml Streptomycin and maintained at 37°C in 5% CO2.

extract_protocol:
AC16 cells transfected with negative control or MEF2A-targeting siRNA were seeded in 24-well plates at a density of 2 x 105 cells/well (n = 3 per treatment). Total RNA was extracted using the NucleoSpin RNA extraction kit (Macherey-Nagel) as indicated by manufacturer.
RNA integrity was assessed in a 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Kit. Fluorometric quantification of total RNA was performed using the Qubit RNA BR assay kit (Invitrogen). cDNA libraries were synthesized using the TruSeq Stranded mRNA Library Prep Kit and sequenced using the Ilumina NextSeq 500 sequencer. Library preparation, QC, and sequencing was carried out by Seattle Genomics (http://www.seattlegenomics.com).

treatment_protocol:
Non-targeted (H1), IRF3, STING, cGAS, IFI16 and DDX41-deficient AC16 cells were generated by CRISPR-Cas9 technologies
Transduced cells were enriched using antibiotic selection. BJ/tert human fibroblasts were cultured in DMEM supplemented with 10% FBS, 2mM Glutamine, 100 U/ml Penicillin and 100 mg/ml Streptomycin and maintained at 37°C in 5% CO2.

value: cardiomyocytes

tag: time (hours)


title: PDX15, Vehicle-treated

description: H15, M15


title: PDX03, TGH-treated

description: H03, M03


title: PDX02, TGH-treated

description: H02, M02


title: PDX01, TGH-treated

description: H01, M01


title: MEF2Ai 2

tag: cell line


title: RNAseq.AN3CA.ARID1A.WT.Rep1


title: MEF2Ai 1


title: Mock 3

value: Mock


title: RNAseq.AN3CA.ARID1A.DBDmut.Rep1


title: Mock 2


title: Mock 1


title: CRA_WB_96

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Mass General Brigham

data_processing:
Alignment and QC was done using the COMPSRA (Li et al. 2020) pipeline, which is similar to BCBio.
miRNAs with less than five mapped reads in at least 50% of subjects were removed prior to analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file with log normalized counts of miRNA x Sample, including sample batch.

source_name: whole blood

extract_protocol:
Total RNA was isolated from archival whole blood samples using the miRNeasy kit (Qiagen, Germantown, MD) according to the manufacturer's instructions
Blockers for miRs 451a, 486-5p, and 92a were added prior to library construction. Small RNA-seq libraries were prepared using the NEXTFLEX Small RNA-Seq Kit v3. First, adapters were ligated to the 3′ and 5′ ends of the RNA. Reverse transcription was then carried out to generate cDNA from the ligated RNA.
Detailed information is available in LaBelle et al, J Mol Diagnostics, 2021

value: whole blood

tag: age

tag: height (cm)

tag: batch

tag: ics use_prior_year

value: yes

tag: Sex

value: M


title: PDX04, TGH-treated

description: H04, M04


title: CRA_WB_99

value: no


title: CRA_WB_94

value: F


title: CRA_WB_97


title: CRA_WB_98


title: CRA_WB_95