title: ChIP-seq with H3K27ac Abs in NIH3T3+EV cells

value: H3K27ac (Abcam, catalog # ab4729)

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: NIH3T3 stably expressing EV (Empty Vector)


title: Fbxo2GAP_D36

status: Public on Jan 03 2024

type: SRA

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic single cell

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to genes by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted.
Assembly: mm10
Supplementary files format and content: Tab-separated UMI count matrix; Files: Exon_UMI_matrix.txt

molecule: total RNA

organism: Mus musculus

source_name: cochlea

extract_protocol:
After tissue dissociation, single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following SMART-MATQ protocol.

treatment_protocol: Animal were treated with tamoxifen at 3 weeks and cells were harvested at 5 weeks.

tag: tissue

value: cochlea

tag: genotype

tag: treatment

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: ChIP-seq with H3K27ac Abs in NIH3T3+BORIS cells

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

library_source: genomic

data_processing:
ChIP-seq, ATAC-seq, CAGE-seq data: single-end or paired-end reads were aligned either to the UCSC hg19 (human samples) or UCSC mm9 (mouse samples) genome using Bowtie version 2 under default parameters.
RNA-seq data: FASTQ files were either mapped to the UCSC mouse (build mm9) or human ((build hg19) reference genomes using STAR with default settings. Normalized gene counts and differentially expressed genes (DEG) were obtained with the R package DESeq2.
For ChIP-seq and ATAC-seq data, output BAM files were converted into bdg track files using MACS2
For CAGE-seq, ChIP-seq, ATAC-seq data, output BAM files were converted into bigwig files using bamCoverage option in deepTools 3.5.0 in order to display normilized coverage throughout the genome (in RPKM).
ChIP-seq and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
CAGE-seq clusters were called using MACS2  with parameters (--nomodel --shift -1)
bdg files were generated using  MACS2  with default settings.
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bdg, xlsx (differentially expressed genes (DEG) were obtained with the R package DESeq2), bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM))

molecule: genomic DNA

growth_protocol: DMEM (NIH3T3, 293T, MDA-MB-435, MCF7 cells), RPMI (K562, CH12cells), 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2. Stable NIH3T3, MDA-MB-435 and MCF7 clones were maintained under 150 mkg/ml of Hygromycin B.

extract_protocol:
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

tag: cell line

tag: cell type

value: Mouse immortalized embryonic fibroblast cell line

tag: chip antibody

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2

value: NIH3T3 stably expressing BORIS


title: AP301

city: Hangzhou

first: Jiucheng

last: Chen

state: Zhejiang

address: No.866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Endometrial tissue collected on day P+3 (3th day of progesterone management) of a hormone replacement therapy (HRT) cycle

library_source: transcriptomic

data_processing:
Use the fastp tool for quality control of sequencing data. Remove sequences with the following low-quality criteria: Sequences with unknown bases numbering 5 or more. Sequences with a length less than 75bp. Sequences with an average base quality value less than 15. The resulting data after this step is termed Clean Data.
Use the sortmerna tool to align the Clean Data against a ribosomal database. Exclude sequences that align to the ribosomal database. The data obtained after this step is termed de-rRNA Clean Data.
Use the STAR tool to align the de-rRNA Clean Data to the reference genome.
Use the RSeQC tool to assess the quality of the alignment results from STAR.
Use the featureCounts tool to quantify gene expression from the alignment results.
Use the edgeR tool for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited rawcount files for each samples
Supplementary files format and content: tab-delimited FPKM files for each samples

organism: Homo sapiens

source_name: endometrium tissue

growth_protocol: All endometrial biopsy samples were obtained with disposable uterine-cavity tissue-suction tubes (Runting), and all the collected samples were stored in All protect Tissue Reagent (QIAGEN). The samples were transported to our laboratory on ice packs and stored at -80°C before processing.

extract_protocol:
RNA was extracted from endometrial tissue using RNAprep Pure Tissue Kit (DP341; Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using a KAPA Stranded RNA-Seq Library Preparation Kit (KR0934, KAPA Biosystems), following the manufacturer’s instructions.

treatment_protocol: The estradiol administration of all patients was started from the second day of menstruation with 4 mg estradiol valerate (Progynova; Bayer, Leverkusen, Germany) per day. When endometrial thickness was at least 7 mm and endogenous progesterone level was less than 1.5 ng/ml, 90 mg progesterone sustained-release vaginal gel (Crinone; Merck-Serono, Darmstadt, Germany) was applied transvaginally per day. The initial day of progesterone administration was recognized as “P+0” and endometrial biopsies were respectively taken on days P+3, P+5, and P+7 for each patient by a dedicated physician.

value: endometrium tissue

tag: time

value: day P+3


title: tumor cell and BMDM spheroids day 10

city: Zurich

first: Florence

last: Vallelian

address: Rämistrasse 100

country: Switzerland

institute: University Hospital Zürich

data_processing:
Read Alignment using CellRanger (version 7.0.0)
Preprocessing, Dimensionality reduction, Clustering (separate processing of conditions), remove cluster identified as macrophages
Functional classification of tumor cell clusters by means of DGE and GSEA using the MSigDB_Hallmark_2020 database
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: .h5: output of cellRangerCount (raw and filtered bc_matrix)
Supplementary files format and content: .h5ad: processed data for tumor only spheroids, tumor cells of mixed spheroids, and macrophages of mixed spheroids

source_name: MC38-GFP & BMDM

growth_protocol: MC38-GFP cells were from L.Borsig and cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (P/S, Gibco), 1% non essential amino acids (NEAA, Gibco) and 1% sodium-pyruvate (Gibco). BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old C57BL/6J mice and passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dish in complete RPMI-1640 medium supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 with 300 μM heme-albumin or albumin (as vehicle/control). For inflammatory polarization, INFγ (10 ng/ml, PeproTech) or LPS (10 ng/ml, Sigma) was added on day 6 for 24 hours. The BM cells were harvested for analysis on day 7 from the temperature responsive cell culture plates after cooling to room temperature. Cells were washed in PBS and centrifuged (300 g, 10 min) before processing.5 x 104  MC38-GFP cells +/- BMDMs in 1-1 ratio were seeded in 800 μl tumor cell medium with M-CSF (100 ng/ml) in 24-well microwell Sphericalplate® 5D (Kugelmeiers). 800 μl fresh culture cell medium was added on day 2-3.We conducted multiplexed scRNA-seq experiments with tumor-only and mixed cell type spheroids collected on days 4, 8, and 10 after formation.

extract_protocol:
Spheroids were dissociated in 2 ml digestion medium (RPMI medium (Gibco) + 25 µg/ml Liberase ™ (Roche) + 40 µg/ml DNase I (Roche; 2000 U/ml) and incubated for 30-45 min in a water bath at 37°C with gentle shaking every 5 min. 4 ml PBS + 0.04% BSA was added to stop the digestion.
Single-cell suspensions were counted and transferred to 2 ml safe lock tubes and directly used for GEM generation following 10X Genomics protocol (CG000388 Demonstrated Protocol Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing Rev B) targeting a cell recovery rate of 10’000 cells.

value: MC38-GFP & BMDM


title: Fbxo2GAP_D35


title: FPKM.OSTXCTNP4

first: Jinyong

address: Jiefang Road 88

department: Department of Cardiology

institute: Second Afliated Hospital, Zhejiang University School of Medicine

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38, version 94 (https://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/) whole genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.0.4) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample.

source_name: Human aortic valve interstitial cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a cell sample was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Human aortic valve interstitial cells

value: WT

tag: media

value: Osteogenic differentiation medium supplemented with XCT790-loaded nanoparticles


title: Control CMO301

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-7.0.0)
Preprocessing: Filtering, normalization and log(x+1)-transformation, dimensionality reduction and UMAP
downstream analysis
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: *_sample_alignments.bam: demultiplexed raw data
Supplementary files format and content: .h5 output of CellRangerMulti
Supplementary files format and content: .h5ad containing processed data of the combined experiments

growth_protocol: MC38-GFP cells were from L.Borsig and cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (P/S, Gibco), 1% non essential amino acids (NEAA, Gibco) and 1% sodium-pyruvate (Gibco). BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old C57BL/6J mice and passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dish in complete RPMI-1640 medium supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 with 300 μM heme-albumin or albumin (as vehicle/control). For inflammatory polarization, INFγ (10 ng/ml, PeproTech) was added on day 6 for 24 hours. The BM cells were harvested for analysis on day 7 from the temperature responsive cell culture plates after cooling to room temperature. Cells were washed in PBS and centrifuged (300 g, 10 min) before processing. 5 x 104  MC38-GFP cells +/- BMDMs in 1-1 ratio were seeded in 800 μl tumor cell medium with M-CSF (100 ng/ml) in 24-well microwell Sphericalplate® 5D (Kugelmeiers). 800 μl fresh culture cell medium was added on day 2-3.

extract_protocol:
Spheroids were dissociated in 2 ml digestion medium (RPMI medium (Gibco) + 25 µg/ml Liberase ™ (Roche) + 40 µg/ml DNase I (Roche; 2000 U/ml) and incubated for 30-45 min in a water bath at 37°C with gentle shaking every 5 min. 4 ml PBS + 0.04% BSA was added to stop the digestion.
Cell Multiplexing Oligos (CMO) labels B301 - B305 (3’ CellPlex Kit Set A) were used to label the 5 samples. After labeling, cell suspensions were counted again and the 5 samples were pooled according to the pooling calculations in appendix of the labeling protocol (CG00391) in equivalent ratios. The pool was then directly used for GEM generation following 10X Genomics protocol (CG000388 Demonstrated Protocol Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing Rev B) targeting a cell recovery rate of 10’000 cells.


title: ChIP-seq with H3K4me3 Abs in NIH3T3+EV cells

value: H3K4me3 (Abcam, catalog # ab8580)


title: Fbxo2GAP_D34


title: Fbxo2GAP_D41


title: ChIP-seq with H3K4me3 Abs in NIH3T3+BORIS cells


title: tumor cell and BMDM spheroids day 8


title: FPKM.OSTXCTNP3


title: ChIP-seq with H2AZ Abs in NIH3T3+BORIS cells

value: H2A.Z (Abcam, catalog # ab4174)


title: AP302


title: FPKM.OSTXCTNP2


title: Interferon gamma CMO302

value: BMDM:Interferon gamma


title: Fbxo2GAP_D32


title: FPKM.OSTXCTNP1


title: Fbxo2GAP_D33


title: FPKM.OST4

value: Osteogenic differentiation medium


title: ChIP-seq with H2AZ Abs in mutant CH12+BORIS cells

value: Mouse B lymphoma cell

value: Ectopic expression of BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: mutant CH12 expressing BORIS


title: tumor cell and BMDM spheroids day 4


title: ChIP-seq with H2AZ Abs in NIH3T3+EV cells

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: NIH3T3 stably expressing EV (Empty Vector)


title: tumor cell spheroids day 10


title: tumor cell spheroids day 8


title: tumor cell spheroids day 4


title: Fbxo2GAP_D27

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: ChIP-seq with H2AZ Abs in mutant CH12 cells

value: CRISPR editing to create a homozygous deletion of ZF9-11 in CTCF gene

value: mutant CH12


title: FPKM.OST3


title: FPKM.OST2


title: LPS-treated BMDM + MC38-GFP spheroids (24h)

description:
combined_spheroids_day1_processed.h5ad
macrophages_processed.h5ad
combined_raw_feature_bc_matrix.h5

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger-6.1.2)
Preprocessing: Filtering, normalization and log(x+1)-transformation, dimensionality reduction and UMAP
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: .h5 output of CellRangerMulti
Supplementary files format and content: .h5ad containing processed data of the combined experiments

growth_protocol: MC38-GFP cells were from L.Borsig and cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (P/S, Gibco), 1% non essential amino acids (NEAA, Gibco) and 1% sodium-pyruvate (Gibco). BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old C57BL/6J mice and passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dish in complete RPMI-1640 medium supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 with 300 μM heme-albumin or albumin (as vehicle/control). For inflammatory polarization, INFγ (10 ng/ml, PeproTech) or LPS (10 ng/ml, Sigma) was added on day 6 for 24 hours. The BM cells were harvested for analysis on day 7 from the temperature responsive cell culture plates after cooling to room temperature. Cells were washed in PBS and centrifuged (300 g, 10 min) before processing. 5 x 104 MC38-GFP cells +/- BMDMs in 1-1 ratio were seeded in 800 μl tumor cell medium with M-CSF (100 ng/ml) in 24-well microwell Sphericalplate® 5D (Kugelmeiers).

extract_protocol:
Spheroids were dissociated in 2 ml digestion medium (RPMI medium (Gibco) + 25 µg/ml Liberase ™ (Roche) + 40 µg/ml DNase I (Roche; 2000 U/ml) and incubated for 30-45 min in a water bath at 37°C with gentle shaking every 5 min. 4 ml PBS + 0.04% BSA was added to stop the digestion.
Single-cell suspensions were multiplexed and then used for GEM generation following the 10X Genomics protocol (CG000388 Demonstrated Protocol Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing Rev B) targeting a cell recovery rate of 10’000 cells. GEM generation and library preparation were performed according to the 10X Genomics protocol (CG000388).

value: MC38-GFP & BMDM

value: LPS


title: ChIP-seq with H2AZ Abs in CH12 cells

value: wild type


title: FPKM.OST1

value: Human aortic valve interstitial cells

value: WT


title: Fbxo2GAP_D26


title: interferon-treated BMDM + MC38-GFP spheroids (24h)

value: Interferon


title: FPKM.NC4

value: Growth medium


title: Fbxo2GAP_D25


title: HepG2 cells, siControl, Benzopyrene treatment

city: Jung-gu

first: Min

last: Kim

state: Seoul

address: 30, Pildong-ro 1-gil

country: South Korea

institute: Dongguk university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using NextSeq 500/550, SE 75bp
Assembly: mm10
Supplementary files format and content: tab-delimited test file includes raw counts for each sample
Supplementary files format and content: tab-delimited test file includes RPLM value for each sample

source_name: Liver

growth_protocol: HepG2 cells were maintained in MEM suppelmented with 10% fetal bovine serum and 1% antibiotics in humidfied atmosphere with 5% CO2 and 37`C

extract_protocol:
RNA was extracted using Rneasy mini plus kit(quiagen). 2 ug of total RNS was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD following manufacturer`s protocols.

treatment_protocol: Cells were seeded and transfected with siCYP1A1 or siCYP1B1 for 24 h.

value: Liver

value: Carcinoma

value: siControl+Benzopyrene


title: Fbxo2GAP_D30


title: FPKM.NC3


title: heme/LPS-treated BMDM + MC38-GFP spheroids (24h)

value: Heme + LPS


title: HepG2 cells, siCyp1B1, Benzopyrene treatment


title: Fbxo2GAP_D22


title: ChIP-seq with H2AZ Abs in CH12+BORIS cells

value: Mouse B lymphoma cell

value: H2A.Z (Abcam, catalog # ab4174)

value: Ectopic expression of BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: wild type CH12 expressing BORIS


title: Fbxo2GAP_D29

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: FPKM.NC2


title: Fbxo2GAP_D21


title: heme/interferon-treated BMDM + MC38-GFP spheroids (24h)

value: MC38-GFP & BMDM

value: Heme + Interferon


title: HepG2 cells, siCyp1A1, Benzopyrene treatment


title: RNA-Seq shNC3_3

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
RNA-seq reads were aligned to human genome (hg38) by TopHat version 2.1.0 with default parameter. Aligned reads in bam file were sorted by genomic coordinate by samtools.
Gene differential expression (DE) analysis was conducted by Cuffdiff version 2.2.1
Assembly: hg38
Supplementary files format and content: tab delimated file containing gene expression for each gene in each sample

growth_protocol: Human neuroblastoma cells SH-SY5Y (ATCC) were purchased from ATCC and cultured in Eagle's Minimum Essential Medium (EMEM) (Corning) and Ham’s F12 medium (Corning) (1:1, v:v) supplemented with 15% v/v fetal bovine serum (FBS) at 37℃ and 5% carbon dioxide (CO2).

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Ambion). About 1 million cells were lysed in 1 mL of TRIzol followed by the addition of 0.2 mL (5:1 ratio) of chloroform. Samples were then centrifuged at 12,000 g for 15 min at 4℃. The top layer was transferred to a tube and the RNA was precipitated in 100% isopropanol (1:1 ratio), 3 M sodium acetate (10:1 ratio), and 4 μL of glycogen (5 mg/mL) for an hour at -20℃. The samples were then centrifuged at 15,000 RPM for 20 min at 4℃ and washed twice with 1 mL of 75% ethanol.
RNA was isolated as described above. About 1 μg of total RNA was sent to Admera Health for library construction. The NEBNext Poly(A) mRNA Magnetic Isolation Module was used to isolate intact poly(A)+ RNA followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. Library concentration was measured by qPCR, and library quality was evaluated by Tapestation High Sensitivity D1000 ScreenTapes (Agilent Technologies, CA, USA). Equimolar pooling of libraries was performed based on qPCR values.

treatment_protocol: shRNA oligos (shNC and shTDP-43) synthesized from Integrated DNA Technologies (IDT) were annealed and inserted into linearized lentiviral vector pLVX-U6-shRNA1 (Genprice, #PVT2302) using BamH I and EcoR I. The shRNA constructs were then used for lentivirus production. 293T packaging cells were seeded at 5x106 cells per 10 cm tissue culture plate the day before transfection. 1.3 pmol of psPAX2 (Addgene, #12260), 0.72 pmol of pMD2.G (Addgene, #12259), and 1.64 pmol of lentiviral plasmid were co-transfected into 293T cells using polyethylenimine MW 25000 (PEI 25K, Polyscience, #23966-100) at a ratio of 1:3 (w:w). Virus-containing medium was harvested 48 and 72 hr post-transfection and passed through a 0.45 μm PES filter (VWR, #76211-008). The virus was then concentrated 100-fold with Lenti-X concentrator (TaKaRa, #631231). Virus infection was performed by adding 20 μL of lentivirus to ~800,000 SH-SY5Y cells (MOI: 1:3) in a 6-well plate. TDP-43 stable knockdown cells were selected by Puromycin at a concentration of 2 μg/mL for 2 weeks and maintained in medium with 1 μg/mL of Puromycin for long-term use.

value: Neuroblastoma


title: Fbxo2GAP_D20


title: heme-treated BMDM + MC38-GFP spheroids (24h)

value: Heme


title: RNA-Seq shNC3_1


title: Ghost Matrigel Plugs

description:
combined_matrigel_plugs_preprocessed.h5ad
combined_matrigel_plugs_analysed.h5ad

data_processing:
Read alignment using CellRangerCount (cellranger-6.1.2)
Preprocessing: Filtering, normalization and log(x+1)-transformation, dimensionality reduction and UMAP
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: .h5 containing output of CellRangerCount (raw and filtered)
Supplementary files format and content: .h5ad containing processed data of the combined experiments

source_name: macrophages

extract_protocol:
Excized matrigel plugs were mechanically disrupted, placed in pyruvate-free DMEM with 1.2 mM calcium chloride dihydrate and 1 mg/mL collagenase IV (Stemcell), and incubated on a shaker at 37°C for 60 min. Cells were passed through a 70 µm cell strainer and RBCs were lysed with 1x RBC Lysis Buffer (BioLegend). The samples were then washed, centrifuged (450 g, 5 min, 4°C), and resuspended in 1% FBS in PBS for flow cytometry measurement or in 0.1% bovine serum albumin (BSA) in 2 mM EDTA PBS for macrophage isolation and transcriptome analysis. Anti-rat IgG Dynabeads (Invitrogen) were washed and incubated with rat anti-mouse F4/80 IgG2a antibodies (BD Biosciences) and CD11b IgG2b antibodies (BioLegend) at a ratio of 3.33 µg of antibody per 50 µl of Dynabeads. Single-cell suspensions from matrigel plugs were incubated with anti-F4/80-coated and anti-CD11b coated Dynabeads on a shaker at 4°C for 30 minutes. After incubation, positive selection of Dynabead-bound single-cell suspensions was performed on a DynaMag magnet (Invitrogen) with three washing steps, as instructed by the manufacturer.
GEM generation and library preparation were performed according to the 10X Genomics protocol (CG000388)

treatment_protocol: 350 µl of matrigel mixture was injected subcutaneously into the flanks of anesthetized C57BL/6J mice using a 24-G needle. Seven days later, the mice were euthanized, and plugs were collected for downstream analysis.

tag: sample type

value: Ghost Matrigel Plugs

value: macrophages


title: Erythrocyte Matrigel Plugs

value: Erythrocyte Matrigel Plugs


title: OST3_FPKM

value: Human aortic valve interstitial cells

value: WT

value: Osteogenic differentiation medium


title: Fbxo2GAP_D19


title: Fbxo2GAP_D18


title: OST2_FPKM


title: RNA-Seq shT2_3


title: OST1_FPKM


title: Fbxo2GAP_D17


title: NC2_FPKM

value: Growth medium


title: RNA-Seq shT2_1


title: IL10KO_D77_Anti-p40 [FRI18]

city: San Diego

first: Jun

last: Yin

state: California

address: 4245 Sorrento Valley Blvd. I

department: Computational Biology and Data Science

institute: Ferring Research Institute

description:
FRI18
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt

data_processing:
Raw sequencing reads were processed using cutadapt v3.7 to remove adapter remnants.
Trimmed reads were then aligned using STAR aligner version 2.7.8a to human genome version 38 using Ensembl gene annotation version 88.
Quantification was performed based on RSEM v1.3.3 for raw read counts and Transcript Per Million (TPM) values.
Estimated read counts from RSEM were compared using the R Bioconductor package DESeq2 version 1.30.1 using Wald test.
Genes with Benjamini-Hochberg–corrected P value <0.05 and Fold Change ≥2 or ≤0.5 were selected as significantly differentially expressed genes.
Assembly: mm10/Ensembl 88
Supplementary files format and content: Counts matrix (tab separated text)
Supplementary files format and content: TPM matrix (tab separated text)

extract_protocol:
RNA was extracted using RNeasy kit from Qiagen (#74106) according to the manufacturer’s guidelines and used for RNA-seq.
mRNA library was prepared using a poly A enrichment method

value: distal colon

value: IL10 knockout


title: Fbxo2GAP_D15


title: IL10KO_D77_Anti-p40 [FRI17]

description:
FRI17
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: Fbxo2GAP_D16


title: RNA-Seq shNC3_2


title: Fbxo2GAP_D14


title: Fbxo2GAP_D13


title: IL10KO_D77_Anti-p40 [FRI16]

description:
FRI16
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: Macrophage_normoxicCM_replicate1

city: Minneapolis

first: Elizabeth

middle: W

last: Bradley

state: Minnesota

address: 2001 6th St SE

department: Department of Orthopedic surgery

institute: University of Minnesota

description: 10x Genomics

data_processing:
The 10× Genomics Cell Ranger software (version 6.0.0) was used to process the raw scRNA-seq data in accordance with the guidelines specified by the manufacturer. Cell Ranger software (2020-A, 10× GenomicsCell Ranger Count v7.0.1) was used to demultiplex the raw base call (BCL) files produced by the Illumina NovaSeq 6000 sequencer.
Cell Ranger was used to count the unique molecular identifiers (UMI) and barcodes and align fastq files to the human reference genome (GRCh38).
We then used R software (4.2.2) with the Seurat package (4.3.0) (29) to conduct quality assurance and subsequent studies on the feature-barcode matrices created by Cell Ranger. The study was filtered to exclude cells with outlier status, aberrant gene detection rates (<500 and >5,000), and high mitochondrial transcript level (>8%), a sign of cellular stress. Possible doublets were also excluded from the data using doubletFinder for subsequent analysis.
The remaining cells were then normalized, and a set of 2000 highly variable genes were selected based on a variance stabilizing transformation (‘vst’). Next, the data was scaled to account for technical variability in the data and used for principal component analysis (PCA) to reduce the dimensionality of the data.
Using Seurat's "FindNeighbors" and "FindClusters" functions, cells were then organized into an ideal number of clusters for de novo cell type discovery. Then, using uniform manifold approximation and projection (UMAP), a non-linear dimensional reduction was carried out, enabling for the identification and visualization of different cell clusters. Then, clusters over expressing “TAGLN”, “SERPINE1”, “TPM1”, “FN1” and “IGFBP7” genes (e.g., MSC contaminants) were removed, and the remaining data were normalized. After variable feature identification, the data were used for integrated analysis.  The 'VlnPlot' and'FeaturePlot'functions of Seurat were used to construct gene expression plots
Assembly: GRCh38
Supplementary files format and content: Tab separated value files
Supplementary files format and content: Matrix files

source_name: Bone marrow

extract_protocol:
Macrophages were generated from MACS sorted cells by culturing isolated CD14+/CD11B+ cells at a density of 0.26x106 per cm2 in α-Minimal Essential Medium supplemented with 50 ng/ml recombinant human macrophage-colony stimulating factor (M-CSF) (R&D Systems, 416-ML) at atmospheric oxygen tension at 37C. Cells were maintained in culture and supplemented with M-CSF for 7 days or until adherent. Macrophages were stimulated with 20 ng/ml IFN-γ and cultured cells at 2% O2 for 24 hours. IFN-γ-containing medium was then replaced with human MSC-conditioned media and macrophages were maintained at 2% O2 for 24 hours in MSC-conditioned media. Cells were then rinsed with PBS and incubated Macrophage Detachment Solution (Sigma Millipore, #41330) for 35 minutes to remove cells from plastic. Cells were counted and pelleted at 1000 rpm for 5 minutes. Dead cells were cleared from the cell suspension utilizing the Dead Cell Removal Kit (Miltenyi, #130-090-101) as per the manufacturer’s instructions. Macrophages were suspended at a density of 700-1200 cells/μl in MEM with 10% FBS. Cell viability was assessed using a Luna Cell Counter to ensure greater than 75% viability before proceeding to scRNA-Seq.
The libraries were prepared with Chromium Single cell 3′ Reagent v3 Kits (10× Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Each single-cell suspension was mixed with primers, enzymes, and the gel beads containing barcode information, and then loaded on a Chromium Single Cell Controller (10× Genomics) to generate single-cell gel beads in emulsions (GEMs). Each gel bead was bonded to one cell and encased within oil surfactant. After generating the GEMs, reverse transcription was performed using barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with an appropriate number of cycles and thermal conditions that depended on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, ligated to an index adaptor, and subjected to library amplification. Quality of amplified cDNA was assessed using an Agilent Bioanalyzer prior to high-throughput sequencing. Following quality control, the cDNA libraries were sequenced on an Illumina NovaSeq 6000 sequencer

value: Bone marrow

tag: cell subtype

value: Cd11b+Cd14+ cells

value: Macrophages

value: normoxia


title: NC3_FPKM


title: IL10KO_D77_Vehicle [FRI15]

description:
FRI15
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt

value: vehicle


title: NC1_FPKM


title: IL10KO_D77_Anti-p40 [FRI20]

description:
FRI20
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: DRIP-Seq shNC3_1

data_processing:
DRIP-seq, hMe-Seal, ATAC-seq reads were first aligned to human genome sequence (hg38) by Bowtie 2 version 2.4.4 with default parameter.
Aligned reads in bam file were sorted by genomic coordinate by samtools.
Peaks for DRIP-seq and hMe-Seal libraries were identified by MACS2 version 2.2.6 with their corresponding input bam file
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Briefly, for each replicate, about 2-3 million cells were harvested for nucleic acid isolation. Nucleic acids were extracted from the cells by SDS/proteinase K treatment followed by phenol-chloroform extraction using MaXtract High Density Tubes (Qiagen) and ethanol precipitation. Nucleic acids were fragmented with a group of restriction enzymes (BsrGI, EcoRI, HindIII, SspI, XbaI, 30 unit each). Digested nucleic acids were recovered by phenol-chloroform extraction. 6 μg of fragmented nucleic acids were treated with RNase H for 6 hr as negative control. 6 μg of digested DNA and RNase H-treated DNA were immunoprecipitated with 8 μL of DNA-RNA structure-specific S9.6 antibody (Millipore) overnight at 4℃. 40 ul of protein G beads (Invitrogen) were used to pull down the DNA:RNA hybrid at 4℃ for 2 hr. The beads were washed twice. DNA-RNA hybrids were eluted in 0.5% SDS and cleaned up by phenol-chloroform extraction. Immunoprecipitated DNA-RNA hybrids were quantified by Qubit (Thermo Fisher Scientific). 10 ng of DNA was then subjected to library construction.
For DRIP-seq, immunoprecipitated DNA was first sonicated into small fragments (~100-500 bp) using Covaris Focused-Ultrasonicator Me220. Fragmented ends of DRIPed-DNA and 5hmC-DNA were blunted, 5′ phosphorylated and 3’ A-tailed by NEBNext Ultra II End Prep Enzyme Mix following the manufacturer’s instruction (New England Biolabs, E7645L). Adaptor was ligated to the DNA with optimized working concentration and USER enzyme was used for U excision to yield adaptor-ligated double-strand DNA followed by cleanup and size selection with AMPure XP bead. The adaptor-ligated DNA was PCR-amplified using barcoded PCR primers (New England Biolabs, E7335L, E7500L). After AMPure XP bead purification, Qubit quantification, the size and quality of the libraries was assessed by 2100 Bioanalyzer system.  Libraries were sent to Admera Health for sequencing with Illumina.

treatment_protocol: shRNA oligos (shNC3 and shT2) synthesized from Integrated DNA Technologies (IDT) were annealed and inserted into linearized lentiviral vector pLVX-U6-shRNA1 (Genprice, #PVT2302) using BamH I and EcoR I. The shRNA constructs were then used for lentivirus production. 293T packaging cells were seeded at 5x106 cells per 10 cm tissue culture plate the day before transfection. 1.3 pmol of psPAX2 (Addgene, #12260), 0.72 pmol of pMD2.G (Addgene, #12259), and 1.64 pmol of lentiviral plasmid were co-transfected into 293T cells using polyethylenimine MW 25000 (PEI 25K, Polyscience, #23966-100) at a ratio of 1:3 (w:w). Virus-containing medium was harvested 48 and 72 hr post-transfection and passed through a 0.45 μm PES filter (VWR, #76211-008). The virus was then concentrated 100-fold with Lenti-X concentrator (TaKaRa, #631231). Virus infection was performed by adding 20 μL of lentivirus to ~800,000 SH-SY5Y cells (MOI: 1:3) in a 6-well plate. TDP-43 stable knockdown cells were selected by Puromycin at a concentration of 2 μg/mL for 2 weeks and maintained in medium with 1 μg/mL of Puromycin for long-term use.


title: Fbxo2GAP_D12

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: IL10KO_D77_Vehicle [FRI14]

description:
FRI14
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: IL10KO_D77_Anti-p40 [FRI19]

description:
FRI19
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: FPKM.NC1


title: Macrophage_hypoxicCM+IL4_replicate1

description: 10x Genomics

value: hypoxia


title: Fbxo2GAP_D11


title: DRIP-Seq shT2_3

value: Neuroblastoma


title: IL10KO_D77_Vehicle [FRI13]

description:
FRI13
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: Macrophage_hypoxicCM_replicate1

description: 10x Genomics


title: RNA-Seq shT2_2


title: DRIP-Seq shNC3_3


title: Fbxo2GAP_D10


title: DRIP-Seq shT2_2


title: DRIP-Seq shNC3_2


title: IL10KO_D77_Vehicle [FRI12]

description:
FRI12
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: Macrophage_hypoxicCM+1D11_replicate1

description: 10x Genomics


title: postThaw_t0,-inh,-RBC,RT,rep1

city: Montreal

first: Martine

last: Tetreault

state: QC

address: 900 Rue Saint-Denis

country: Canada

institute: CRCHUM

data_processing:
The raw paired-end fastq files were aligned to the hg19 with STAR aligner (v2.6.1b)
The raw gene expression was obtained with Feature Counts (v2.0.1) for all samples
Assembly: hg19
Supplementary files format and content: tab-delimited text file, includes raw counts for each Sample

source_name: peripheral blood mononucleated cells

growth_protocol: For time post thaw experiments, cryopreserved PBMC cell vials were thawed briefly in a 37℃ water bath, rinsed with pure FBS, and quantified for plating at a concentration of 1 million cells in 1ml of RPMI media with 10% FBS. After the specified time in vitro, cells were harvested.

extract_protocol:
RNA was purified with the RNeasy mini kit (Qiagen) and quantified using a BioPhotometer plus model 6132 (Eppendorf).
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare mRNA sequencing libraries, according to manufacturer’s instructions.

value: peripheral blood mononucleated cells

tag: ID

tag: age

tag: Sex

value: M

tag: inhibitor

value: n

tag: rbc

tag: temperature

value: RT


title: Fbxo2GAP_D09


title: TDP43KD_2_merged

data_processing:
Micro-C reads were first aligned to human genome (hg38) using HiC-Pro
AllvalidPairs files were then converted to hic format using hicpro2juicebox.sh and then converted to cool format using hic2cool
Differential interaction analysis was performed by diffHiC using 50 kb resolution and FDR<0.05 was used to define significant changed interaction
Assembly: hg38
Supplementary files format and content: differential analysis of interaction
Library strategy: micro-C-Seq

extract_protocol: Micro-C was performed as previously described (Krietenstein et al., 2020). 1 million cells per replicate were resuspended in 200 μL cold PBS with 1x BSA (NEB, #B9000S) and incubated on ice for 20 min. Cells were spun down at 5,000 g for 5 min and washed with 500 μL buffer MB#1 (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1x cOmplete Protease Inhibitor Cocktail EDTA-free (Sigma-Aldrich, 11836170001)). Cells were spun down at 5,000 g for 5 min and resuspended in 200 μL buffer MB#1. MNase (Wortington Biochem, LS004798) digestion efficiency was tested to determine an optimal concentration to yield mono-nucleosomal fragments. Chromatin was digested with 5-20 U MNase, and the reaction was stopped by adding EGTA (BIOWORLD, #40520008-1) (1.5 mM final) and incubating at 65℃ for 10 min. After centrifugation, chromatin was washed once with 500 μL 1x NEBuffer 2.1 (NEB, #B7202S) and resuspended in 45 μl 1x NEBuffer 2.1. Samples were incubated with 5 μL rSAP (NEB, #M0203) at 37℃ for 45 min and then incubated 65℃ for 5 min to stop the reaction. 40 μL pre-mix (5 μL 10x NEBuffer 2.1, 2 μL 100 mM ATP (Thermo Fisher, #R0441), 3 μL 100 mM DTT, 30 μL H2O), 8 μL Large Klenow Fragment (NEB, #M0210L) and 2 μL T4 PNK (NEB, #M0201L) were added to the samples and incubated at 37℃ for 15 min. 100 μL pre-mix (25 μL 0.4 mM Biotin-dATP (Invitrogen, #19524016), 25 μL 0.4 mM Biotin-dCTP (Invitrogen, #19518018), 2 μL 10 mM dGTP and 10 mM dTTP (NEB, #N0446S), 10 μL 10x T4 DNA Ligase Reaction Buffer (NEB, #B0202S), 0.5 μL 200x BSA, 38.5 μL H2O) were added to the samples and incubated at 25℃ for 45 min. 12 μL 0.5 M EDTA (Invitrogen, #15575038)  were added and incubated at 65℃ for 20 min to stop the reaction. The chromatin was spun down at 10,000 g and washed once with 500 μL 1x Ligase Reaction Buffer (1x NEB Ligase buffer, 1x BSA, 12500 U T4 Ligase (NEB, #M0202L)). The pellet was resuspended in 2500 μL 1x Ligation Reaction Buffer and rotated at room temperature for 2.5-3 hr. The chromatin was spun down, resuspended in 200 μL 1x NEBuffer 1 (NEB, #B7001S) and 200 U Exonuclease III (NEB, #M0206S), and incubated at 37℃ for 5 min. 25 μL proteinase K (25mg/mL in TE with 50% glycerol) and 25 μL 10% SDS were added to the samples and incubated at 65℃ overnight. The DNA was purified by phenol/chloroform followed by a second purification using DNA Clean & Concentrator Kit (Zymo, #D4013). The DNA was run on a 1.5% agarose gel. The DNA around 300 bp was extracted with Zymoclean Gel DNA Recovery Kit (Zymo, #D4002) and resolved in 50 μL H2O. The DNA was captured by 5 μL of Dynabeads MyOne Streptavidin C1 beads (Invitrogen, #65002) in a final 300 μL volume of 1x TBW (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl). The samples were rotated at room temperature for 20 min, washed twice with 300 μL 1x TBW, and suspended in 50 μL TE buffer. The DNA attached to the beads was blunted, 5′ phosphorylated, 3’ A-tailed and adaptor-ligated following the manufacturer’s instruction. The samples were washed twice with 300 μL 1x TBW and once with 0.1x TE buffer. The beads were resuspended in 20 μL 0.1x TE. The adaptor-ligated DNA was PCR-amplified using barcoded PCR primers (NEB, #E7335L, #E7500L) following the manufacturer’s instruction. After AMPure XP bead (1:1 raio, v/v) purification, Qubit quantification, the size and quality of the libraries was assessed by 2100 Bioanalyzer system. Libraries were sent to Admera Health for sequencing with Illumina. Equimolar pooling of libraries was performed, and 8-12 samples were pooled in one lane. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 740 M total reads per lane (370 M in each direction).

value: TDP-43 knockdown


title: DRIP-Seq shT2_1


title: IL10KO_D77_Vehicle [FRI11]

description:
FRI11
gene.results.merged.FR.count.txt
gene.results.merged.FR.tpm.txt
IL10KO_D77_Anti-p40_vs_IL10KO_D77_Vehicle_GeneDEreformated.txt


title: postThaw_t24,-inh,-RBC,RT,rep3


title: Fbxo2GAP_D08


title: IL10ko_C13_30mpk [GI45]

source_name: distal colon

value: compound 13 10mg/kg


title: Fbxo2GAP_D07


title: TDP43KD_1_merged


title: control_1_merged

value: control


title: postThaw_t2,-inh,-RBC,RT,rep3


title: IL10ko_C13_10mpk [GI44]

value: distal colon

value: IL10 knockout


title: t0,+inh,+RBC,4C,rep2

value: y


title: postThaw_t0,-inh,-RBC,RT,rep3


title: IL10ko_C13_10mpk [GI43]


title: control_2_merged


title: Fbxo2GAP_D06


title: t0,-inh,+RBC,4C,rep2


title: Fbxo2GAP_D04


title: Fbxo2GAP_D05


title: [RNA-Seq] shTDP43_3


title: IL10ko_C13_10mpk [GI41]


title: IL10ko_C13_10mpk [GI42]


title: [RNA-Seq] shTDP43_2


title: t0,+inh,-RBC,4C,rep2


title: [RNA-Seq] shTDP43_1


title: Fbxo2GAP_D02


title: t0,-inh,-RBC,4C,rep2


title: IL10ko_C13_10mpk [GI38]


title: Fbxo2GAP_D03


title: t0,+inh,+RBC,RT,rep2


title: [RNA-Seq] shNC_3


title: Fbxo2GAP_D01


title: [RNA-Seq] shNC_2


title: IL10ko_C13_10mpk [GI37]


title: Fbxo2GAP_C96


title: t0,-inh,+RBC,RT,rep2


title: IL10ko_C13_30mpk [GI35]

value: compound 13 30mg/kg


title: Fbxo2GAP_C95


title: [RNA-Seq] shNC_1


title: t0,+inh,-RBC,RT,rep2


title: IL10ko_C13_30mpk [GI33]


title: Input_SH_DRIP


title: t0,-inh,-RBC,RT,rep2


title: DRIP_shTDP43_RH


title: IL10ko_C13_30mpk [GI34]


title: IL10ko_C13_30mpk [GI32]


title: t0,-inh,+RBC,4C,rep1


title: IL10ko_C13_10mpk [GI39]


title: t0,+inh,+RBC,4C,rep1


title: DRIP_shTDP43_3


title: Fbxo2GAP_C92


title: Fbxo2GAP_C93


title: t0,+inh,-RBC,4C,rep1


title: Fbxo2GAP_C91


title: DRIP_shTDP43_1


title: IL10ko_C13_30mpk [GI30]


title: postThaw_t24,-inh,-RBC,RT,rep2

value: F


title: IL10ko_C13_30mpk [GI31]


title: DRIP_shNC_RH


title: IL10ko_C13_30mpk [GI29]


title: t0,-inh,-RBC,4C,rep1


title: Fbxo2GAP_C94


title: Fbxo2GAP_C89


title: DRIP_shNC_3


title: postThaw_t2,-inh,-RBC,RT,rep2


title: IL10ko_C13_30mpk [GI28]


title: IL10ko_C13_30mpk [GI25]


title: DRIP_shNC_2


title: Fbxo2GAP_C87


title: Fbxo2GAP_C88


title: t0,+inh,+RBC,RT,rep1


title: DRIP_shNC_1


title: Adult Urothelium Replicate 4

city: Columbus

first: Xin

last: Wang

state: OH

address: 700 Children's Dr,

department: The Kidney and Urinary Tract Center

institute: Nationwide Children's hosptial

description: FACS enriched Krt5-tdT-positive bladder urothelial cells

data_processing:
Demultiplexed FASTQ files were utilized for a comprehensive analysis pipeline encompassing data normalization, differential gene expression detection, and functional enrichment. We obtained the mm10 mouse genome and its corresponding reference gene set from UCSC. Adapter sequences were removed, and high-quality filtered reads were generated using Trim Galore v0.6.6.
Tophat v2.1.2 was used to map these high-quality reads to the mm10 genome. Successfully mapping reads were sorted, and unique mapped reads was retained by SAMtools v1.15. Quantification of reads per gene was performed by Htseq-count v0.12.4 with a union gene region parameter. EdgeR_3.42.4 was used to identify differentially expressed genes (DEGs). We filtered out any gene that is sparsely quantified in samples with loose criteria, i.e., a total count less than five across all samples, and more than two sample with cpm greater than 0.5. Then, quantile normalization method was used to eliminate or minimize technical variability. Principal component analysis (PCA) was used as an unsupervised dimensionality for gene abundance levels across samples.
We defined DEGs as those with a fold change greater than 1.5 and an adjusted P value smaller than 0.05. Gene ontology (GO) analysis for the functional enrichments of up-regulated and down-regulated genes was performed by clusterProfiler_4.8.2. A Chi-square test was used to test for statistically enriched pathways and an FDR of < =0.05 was used as the significance threshold to detect enriched molecular functions, biological processes, and cellular components. Finally, transcription factors and their activities were predicted and estimated by decoupleR 2.5.3. For data visualization, we mainly used a series of R packages such as "ggplot2", "enrichplot", “pheamap” to create heatmaps, volcano plots, bar plots and venn diagrams.
Assembly: mm10
Supplementary files format and content: Ensembl gene ID, Count

source_name: bladder

growth_protocol: Animals were maintained in accordance to Public Health Service Animal Welfare Assurance no. A3544-01 and Institutional Animal Care and Use Committee no. AR16-00058.

extract_protocol:
Cells were sorted directly into the Takara SMART-Seq HT lysis buffer containing RNase Inhibitor + 3’ SMART-Seq CDS Primer II A (SMART-Seq® HT Kit, Takara Bio USA, Ann Arbor, MI). Samples were immediately frozen on dry ice, stored at -80ºC, then transported to The Ohio State University Comprehensive Cancer Center NextGen Sequencing Shared Resource facility.
lcRNAseq libraries were generated using the Takara SMART-Seq HT Kit, Nextera XT DNA Library Preparation and Nextera XT Index kits (Illumina, Inc., San Diego, CA). Samples were evaluated using a High Sensitivity DNA Bioanalyzer and Tapestation HS-DNA1000 Bioanalyzer (Agilent), and Qubit (ThermoFisher).
Sequencing was performed using a NovaSeq6000 SP 200 cycle (≤2x100bp) flow cell.

treatment_protocol: The Adult cohort received tamoxifen (75mg/kg body weight in corn oil, via ip) at postnatal day 35, and were euthanized at postnatal day 42. The Neonate cohort received tamoxifen (75mg/kg body weight in corn oil, via ip) at postnatal day 5, and were euthanized at postnatal day 7. Bladders were harvested in ice cold 1X PBS, everted with blunt forceps, and incubated with Dispase II (2.5 mg/mL, Sigma-Aldrich, St. Louis, MO) in 1X PBS/50mM HEPES for 1 hour at 37ºC. Urothelium was scraped, disaggregated in TrypLE Express (Sigma-Aldrich, St. Louis, MO), then passed through a 70 µm strainer. Red blood cells were lysed using Ammonium-Chloride-Potassium (ACK; Thermofisher, Waltham, MA) lysis solution, and cells were resuspended in 1X PBS containing 2% Fetal Bovine Serum (FBS, Thermofisher, Waltham, MA). The BD Influx System (BD Biosciences, San Jose, CA, USA) was used to sort 300 tdTK5

value: bladder

value: bladder urothelium Krt5 cell

tag: strain background

value: Adult (Tamoxifen (ip) at postnatal day 35, euthanized at postnatal day 42)


title: IL10ko_Veh [GI24]

tag: tissue

value: vehicle


title: postThaw_t0,-inh,-RBC,RT,rep2


title: Fbxo2GAP_C86

value: cochlea

tag: genotype

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: [ATAC-Seq] shTDP43_3

data_processing:
DRIP-seq, hMe-Seal, ATAC-seq reads were first aligned to human genome sequence (hg38) by Bowtie 2 version 2.4.4 with default parameter.
Aligned reads in bam file were sorted by genomic coordinate by samtools.
ATAC-seq reads in each TE were counted and normalized, TE with average reads over 5 in either shNC and shTDP43 were considered as activated TE and were reported
Assembly: hg38
Supplementary files format and content: tab delimated file containing normalized ATAC-seq reads in each activated TE, average reads count in shNC and shTDP43 and logFC

extract_protocol: 5x104-1x105 cells were used for ATAC-seq following the manufacturer's instructions (Active Motif, 53150). Cells were lysed with 100 μL of ATAC Lysis Buffer. Accessible DNA region in nuclei was then probed with Tn5 Transposase that inserts sequencing adapters into open regions. The tagged DNA was cleaved, purified, PCR-amplified and sequenced.

value: Neuroblastoma


title: IL10ko_Veh [GI22]

tag: treatment


title: t0,-inh,+RBC,RT,rep1

value: peripheral blood mononucleated cells

value: M

value: n


title: DRIP_shTDP43_2

tag: cell line

value: TDP-43 knockdown


title: [ATAC-Seq] shTDP43_2

tag: cell type


title: Fbxo2GAP_C84

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to genes by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted.
Assembly: mm10
Supplementary files format and content: Tab-separated UMI count matrix; Files: Exon_UMI_matrix.txt

extract_protocol:
After tissue dissociation, single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following SMART-MATQ protocol.


title: Fbxo2GAP_C90


title: IL10ko_Veh [GI20]


title: Fbxo2GAP_C85


title: IL10ko_Veh [GI21]


title: postThaw_t24,-inh,-RBC,RT,rep1

value: RT


title: [ATAC-Seq] shTDP43_1


title: Fbxo2GAP_C83


title: t0,+inh,-RBC,RT,rep1


title: IL10ko_Veh [GI19]

value: distal colon


title: postThaw_t2,-inh,-RBC,RT,rep1


title: Fbxo2GAP_C81


title: [ATAC-Seq] shNC_3

value: control


title: [ATAC-Seq] shNC_1


title: EGFP(R96W)+Arg-tRNA_Trp(CCA)_tRNA_rep3

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Paired end reads were split by by internal barcode sequence using Je demultiplex with options BPOS = BOTH BM = READ 1 LEN = 4:6 FORCE = true C = false 6. Barcode sequences are available on Github at https://github.com/ckatanski/Q paper.
The quality of reads were checked by fastqc and the reads were aligned to a curated hg38 tRNA reference including 5 mc-tRNA sequences by bowtie2 with options -q -p 10 --local --no-unal.
The aligned reads were used to determine RNA sequence abundance using custom python script.
RNA modifications were detected based on aligned reads using samtools sort feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads. All custom scripts are available on GitHub (https://github.com/ckatanski/CHRIS-seq).
Assembly: Curated hg38 tRNA reference with 5 mc-tRNA sequences included
Supplementary files format and content: tab separated value (tsv) - indicates expression level of tRNA calculated with all reads (*.tsv)
Supplementary files format and content: tab separated value (tsv) - indicates read coverage and mutation rate of each position on each tRNA calculated with all reads (*.sam.tsv)
Supplementary files format and content: tab separated value (tsv) - indicates expression level of tRNA calculated with only full-length reads (*_60_200_.tsv)
Supplementary files format and content: tab separated value (tsv) - indicates read coverage and mutation rate of each position on each tRNA calculated with only full-length reads (*_60_200_.sam.tsv)
Library strategy: MSR-seq (PMID: 35513407)

growth_protocol: HEK293 cells were authenticated and tested negative for mycoplasma. HEK293 cells were cultured at 37°C with 5% CO2 in Dulbecco’s Modified Eagle’s (DMEM) high-glucose medium (Cytiva Cat. SH30022.01) supplemented with 10% heat-inactivated fetal bovine serum and 100U/ml Penicillin-Streptomycin.

extract_protocol:
MSR-seq experiments were performed on 3 independent replicates from HEK293 cells overexpressing the mistranslation reporters with and without cognate mc-tRNAs. HEK293 cells were sorted on the FACSAria Fusion 5-18 cell sorter for mCherry+, i.e., successfully transfected, cell populations 48 h post-transfection. Total RNAs were extracted from sorted cells with TRIzolTM reagent (Invitrogen Cat. 15596026). 1 µg of total RNA per sample was used as input for MSR-seq library construct.
Libraries for tRNAs were constructed as previously described for multiplex small RNA-seq (MSR-seq) (PMID: 35513407).

treatment_protocol: Cells were seeded 6-well plates one day before transfection and reached 50-70% confluent on the day of transfection. Plasmids used for transfection were prepared with PureYieldTM plasmid Miniprep/Midiprep systems (Promega Cat. A1222/A2492) and ethanol precipitated. Transfections were performed using LipofectamineTM 3000 (InvitrogenTM Cat. L3000015) and following the manufacture’s protocol.

value: wt

value: Transfected with EGFP(R96W)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Trp(CCA) on a single plasmid


title: IL10ko_Veh [GI15]

value: IL10 knockout


title: Fbxo2GAP_C80


title: IL10ko_Veh [GI16]


title: Fbxo2GAP_C79


title: EGFP(R96W)+Arg-tRNA_Trp(CCA)_tRNA_rep2


title: shTDP43_3

data_processing:
DRIP-seq, hMe-Seal, ATAC-seq reads were first aligned to human genome sequence (hg38) by Bowtie 2 version 2.4.4 with default parameter.
Aligned reads in bam file were sorted by genomic coordinate by samtools.
Peaks for DRIP-seq and hMe-Seal libraries were identified by MACS2 version 2.2.6 with their corresponding input bam file
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: 5hmC-Seal-seq

extract_protocol:
hMe-Seal was performed as previously described[2]. About 2 millions of cells were lysed in lysis buffer (100 mM Tris-HCl pH 8.0, 5 mM EDTA, 200 mM NaCl, 0.2% SDS) with addition of proteinase K at 55℃ overnight. gDNA was then extracted by phenol-chloroform extraction followed by ethanol precipitation. 5 μg of gDNA was sonicated into small fragments (~100-500 bp) using Covaris Focused-Ultrasonicator Me220. Fragmented gDNA was treated with β-glucosyltransferase (β-GT, New England BioLabs) in the presence of UDP-6-N3-Glu (Jena Bioscience) to selectively label 5hmC into N3-5-gmC. After AMPure XP bead (Beckman Coulter) purification, N3-5-gmC was further labeled with disulfide DBCO biotin (Click Chemistry Tools) to install biotin. DNA was purified with AMPure XP bead and pulled down with 50 μL of Dynabeads MyOne Streptavidin C1 beads (Invitrogen). 5hmC-fragments were released from the beads by adding Dithiothreitol (DTT), purified with AMPure XP bead and quantified by Qubit. 5 ng of 5hmC-DNA was subjected to library construction.
For DRIP-seq, immunoprecipitated DNA was first sonicated into small fragments (~100-500 bp) using Covaris Focused-Ultrasonicator Me220. Fragmented ends of DRIPed-DNA and 5hmC-DNA were blunted, 5′ phosphorylated and 3’ A-tailed by NEBNext Ultra II End Prep Enzyme Mix following the manufacturer’s instruction (New England Biolabs, E7645L). Adaptor was ligated to the DNA with optimized working concentration and USER enzyme was used for U excision to yield adaptor-ligated double-strand DNA followed by cleanup and size selection with AMPure XP bead. The adaptor-ligated DNA was PCR-amplified using barcoded PCR primers (New England Biolabs, E7335L, E7500L). After AMPure XP bead purification, Qubit quantification, the size and quality of the libraries was assessed by 2100 Bioanalyzer system.  Libraries were sent to Admera Health for sequencing with Illumina.


title: IL10ko_Veh [GI13]


title: Fbxo2GAP_C78


title: shTDP43_1


title: shTDP43_2


title: Fbxo2GAP_C76


title: Fbxo2GAP_C77


title: Control [GI7]

value: WT


title: EGFP(R96W)_tRNA_rep2

value: Transfected with EGFP(R96W)-mCherry mistranslation reporter


title: Control [GI8]


title: EGFP(R96W)_tRNA_rep3


title: t0,-inh,-RBC,RT,rep1


title: IL10ko_Veh [GI18]


title: shNC_3


title: EGFP(R96W)_tRNA_rep1


title: [ATAC-Seq] shNC_2


title: Fbxo2GAP_C82


title: Fbxo2GAP_C75


title: shNC_2


title: Control [GI6]


title: EGFP(R96H)+Arg-tRNA_His(GUG)_tRNA_rep3

value: Transfected with EGFP(R96H)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_His(GUG) on a single plasmid


title: IL10ko_Veh [GI14]

value: vehicle


title: Input


title: EGFP(R96W)+Arg-tRNA_Trp(CCA)_tRNA_rep1


title: shNC_1


title: Fbxo2GAP_C73

value: cochlea


title: Fbxo2GAP_C74

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Control [GI5]


title: EGFP(R96H)+Arg-tRNA_His(GUG)_tRNA_rep2


title: Control [GI4]


title: EGFP(R96H)+Arg-tRNA_His(GUG)_tRNA_rep1


title: P3_miRNA

city: kunming

first: guanjian

last: Li

address: 519 Kunzhou Road

institute: Yunnan Cancer Hospital

data_processing:
Quality control: For RNA-seq, The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. For miRNA-seq, Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. Q20, Q30, and GC-content of the raw datas were calculated.
Genomic alignment and quantification: For RNA-seq, Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz. For miRNA-seq, miRBase20.0 was used as reference, software mirDeep_star_v38 was used to obtain the potential miRNA and the miRNA counts. MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
DESeq2 (v1.26.0) was applied for the detection of differentially expressed genes (DEGs), lncRNAs, and miRNAs between tumor and non-tumor samples. The limma R package (3.40.6) was used for circRNAs and all DEGs, lncRNAs, and miRNAs were screened with a P-value of ≤ 0.05 and fold change (FC) of ≥ 2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count or FPKM values for each Sample

source_name: adjacent lung tissue

growth_protocol: Samples were collected from the Department of Thoracic Surgery I of Yunnan Cancer Hospital (the Third Affiliated Hospital of Kunming Medical University)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
For RNA-seq: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.  For miRNA-seq: The entire 3 μg total RNA of each sample was divided into aliquots and a small RNA (sRNA) library prepared. The NEBNext Multiplex sRNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) was applied to generate the sequencing library. The index code was added to assign a sequence to every specimen. TruSeq SR Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA) was applied to cluster index-coded specimens. The libraries were sequenced on an Illumina Hiseq 2500 machine to generate the 50 bp single-end reads.

treatment_protocol: Biospecimens were collected from 3 patients who were recently diagnosed with lung adenocarcinoma, underwent surgical resection and did not receive any prior treatment for their disease, including chemotherapy or radiotherapy. Each specimen was collected within 30 min after operation, cleaned with sterile towel, immediately transferred into sterile freezing vials and immersed in liquid nitrogen, then stored at −80 °C until use.

value: adjacent lung tissue

value: Female

tag: Stage

value: IIIb

tag: tnm

tag: smoke

value: NO


title: Fbxo2GAP_C71


title: Control [GI3]


title: P2_miRNA

value: Ia


title: EGFP(R96H)_tRNA_rep3

value: Transfected with EGFP(R96H)-mCherry mistranslation reporter


title: Fbxo2GAP_C70


title: P1_miRNA


title: Control [GI2]

value: distal colon


title: Fbxo2GAP_C69


title: Control [GI1]


title: EGFP(R96H)_tRNA_rep2


title: Fbxo2GAP_C68


title: Ca3_miRNA

source_name: Lung adenocarcinoma tissue

value: Lung adenocarcinoma tissue


title: Ca2_miRNA


title: Fbxo2GAP_C67


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_WashOffDox, rep2

data_processing:
ChIP-seq, ATAC-seq, CAGE-seq data: single-end or paired-end reads were aligned either to the UCSC hg19 (human samples) or UCSC mm9 (mouse samples) genome using Bowtie version 2 under default parameters.
RNA-seq data: FASTQ files were either mapped to the UCSC mouse (build mm9) or human ((build hg19) reference genomes using STAR with default settings. Normalized gene counts and differentially expressed genes (DEG) were obtained with the R package DESeq2.
For ChIP-seq and ATAC-seq data, output BAM files were converted into bdg track files using MACS2
For CAGE-seq, ChIP-seq, ATAC-seq data, output BAM files were converted into bigwig files using bamCoverage option in deepTools 3.5.0 in order to display normilized coverage throughout the genome (in RPKM).
ChIP-seq and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
CAGE-seq clusters were called using MACS2  with parameters (--nomodel --shift -1)
bdg files were generated using  MACS2  with default settings.
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bdg, xlsx (differentially expressed genes (DEG) were obtained with the R package DESeq2), bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM))

extract_protocol:
ChIP-seq protocol: 2x10^6 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

treatment_protocol: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days. After Dox treatment, the media was replaced with regular media (without dox). The cells were allowed to grow for additional 5 days (washing off Dox).

value: Mouse immortalized embryonic fibroblast cell line

tag: chip antibody

value: WashOffDox

value: NIH3T3 stably transfected with dox-inducible pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: Ca1_miRNA


title: EGFP(R96C)+Arg-tRNA_Cys(GCA)_tRNA_rep3

value: wt

value: Transfected with EGFP(R96C)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Cys(GCA) on a single plasmid


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_Dox, rep2

treatment_protocol: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days.

value: Dox


title: EGFP(R96C)+Arg-tRNA_Cys(GCA)_tRNA_rep2


title: Fbxo2GAP_C66


title: Hemin-IL-10-Stattic-2

city: Beijing

first: Weihua

last: Wu

address: No.10 Xitoutiao, You'anmenWai, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: Capital Medical University

data_processing:
The original image data file obtained by high-throughput sequencing (such as NGS) is converted into raw data of sequencing sequence through CASAVA base calling analysis, and the results are stored in FASTQ (fq for short) file format.
Make statistics on filtered Clean Reads, including data volume statistics, base content distribution statistics, and base quality distribution statistics
We use StringTie (M, 2015) to reconstruct transcripts of each sample, and then use cuffmerge (al Cole Trapnell, 2010) to integrate the reconstruction information of all samples, then use cuffcompare to compare with the reference annotation information, and then select transcripts with class code types of 'u', 'i', 'o', 'j', and define them as new transcripts.
In this analysis, Bowtie2 is used to compare clean reads to the reference gene sequence after adding the new transcript (different from the reference genome, the reference gene sequence contains the base sequence of all transcripts), and then RSEM (B, ug 4) is used to calculate the expression level of genes and transcripts, and subsequent analysis is carried out.
Assembly: We use HISAT to compare clean reads to the reference genome. The full name of HISAT is Hierarchical Indexing for Spliced Alignment of Transcripts, which is developed by Johns Hopkins University. It replaces the Bowtie/TopHat program and can quickly compare RNA Seq reading with genome. HISAT is used in combination with StringTie. Compared with Cufflinks and other programs, StringTie achieves more complete and accurate gene reconstruction and better predicts the expression level when analyzing simulated and real data sets. At the same time, HISAT is very accurate in the comparison of reads across two or more exons.
Supplementary files format and content: The FPKM values and functional annotations of genes in single sample

source_name: Brain

extract_protocol:
RNA is extracted from the sample by standard extraction method, and then the RNA sample is subject to strict quality control. The quality control standards mainly include the total amount of RNA, purity (whether there is DNA or protein contamination) and integrity. Qubit RNA HS is used to control the total amount and purity of RNA; The 2100 RNA Nano/Pico kit is used for quality control of RNA integrity.
The library construction process is as follows: RNA template chain is reverse transcribed into cDNA. The second strand is synthesized and added to dUTP connector. A is added to the end, sequencing connector is added to both ends. PCR amplification and SPRI purification are performed.
After the construction of the library, the preliminary quantification is carried out first, the library is diluted, and then the Agilent 2100 DNA 1000 kit is used to detect the distribution of library fragments. The  concentration of the library is accurately quantified by qRT-PCR to ensure the quality of the library. Finally, the target region library of double chain is denatured, cyclized and digested to obtain single stranded circular DNA. Single stranded circular DNA is amplified by RCA (Rolling Circle Amplification) to obtain DNA nanospheres (DNB, DNA Nano Ball). After the construction of the library, Qubit is used for quantitative quality control. After the library is qualified, computer sequencing is carried out.

value: Brain

value: Primary cells

value: Oligodendrocyte progenitor cells

value: Wild-type

value: Hemin (50 μM)-IL-10 (10 ng/mL)-Stattic (2.5 μM)

tag: time


title: Hemin-IL-10-Stattic-3


title: Fbxo2GAP_C65

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: RNA-seq in NIH3T3_pBIG_EV cells_with_WashOffDox, rep2

value: NIH3T3 stably transfected with dox-inducible pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_NoDox, rep2

treatment_protocol: The cells were cultured in the absence of doxycycline (noDox), under regular culturing conditions.

value: NoDox


title: EGFP(R96C)_tRNA_rep3

value: Transfected with EGFP(R96C)-mCherry mistranslation reporter


title: EGFP(R96C)+Arg-tRNA_Cys(GCA)_tRNA_rep1


title: Hemin-IL-10-Stattic-1


title: Fbxo2GAP_C63


title: EGFP(R96C)_tRNA_rep2


title: Fbxo2GAP_C62


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_WashOffDox, rep1


title: EGFP(R96H)_tRNA_rep1

value: Transfected with EGFP(R96H)-mCherry mistranslation reporter


title: Hemin-IL-10-2

value: Hemin (50 μM)-IL-10 (10 ng/mL)


title: Fbxo2GAP_C61


title: EGFP(R96C)_tRNA_rep1


title: Hemin-IL-10-3


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_Dox, rep1

value: Mouse immortalized embryonic fibroblast cell line


title: EGFP(R96Q)+Arg-tRNA_Gln(CUG)_tRNA_rep3

value: Transfected with EGFP(R96Q)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Gln(CUG) on a single plasmid


title: Hemin-IL-10-1


title: Fbxo2GAP_C60


title: RNA-seq in NIH3T3_pBIG_EV cells_with_NoDox, rep2


title: Hemin-3

value: Hemin (50 μM)


title: RNA-seq in NIH3T3_pBIG_BORIS cells_with_NoDox, rep1

value: NIH3T3 stably transfected with dox-inducible pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: EGFP(R96Q)+Arg-tRNA_Gln(CUG)_tRNA_rep2

value: wt


title: Fbxo2GAP_C59


title: RNA-seq in NIH3T3_pBIG_EV cells_with_WashOffDox, rep1

value: WashOffDox


title: EGFP(R96Q)+Arg-tRNA_Gln(CUG)_tRNA_rep1


title: Fbxo2GAP_C64


title: RNA-seq in NIH3T3_pBIG_EV cells_with_Dox, rep2

value: Dox


title: Hemin-2

value: Brain

value: Primary cells

value: Oligodendrocyte progenitor cells


title: RNA-seq in NIH3T3_pBIG_EV cells_with_Dox, rep1


title: EGFP(R96Q)_tRNA_rep3

value: Transfected with EGFP(R96Q)-mCherry mistranslation reporter


title: Fbxo2GAP_C58

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Hemin-1

value: Wild-type


title: RNA-seq in NIH3T3_pBIG_EV cells_with_NoDox, rep1

value: NoDox

value: NIH3T3 stably transfected with dox-inducible pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: Fbxo2GAP_C57


title: EGFP(R96Q)_tRNA_rep2


title: EGFP(R96Q)_tRNA_rep1


title: Veh-3

value: Veh (DMSO)


title: Fbxo2GAP_C55


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with WashOff DOX

value: Mouse immortalized embryonic fibroblast cell line

value: BORIS custom-made mouse monoclonal (characterized in  PMID:21659515)

value: WashOff DOX


title: Veh-2


title: Veh-1


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX

value: DOX

value: NIH3T3 stably transfected with dox-inducible pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: EGFP(R65)+Ser-tRNA_Arg(CCG)_tRNA_rep3

value: wt

value: Transfected with EGFP(R65)-mCherry mistranslation reporter together with mc-tRNA Ser-tRNA_Arg(CCG) on a single plasmid


title: Fbxo2GAP_C54


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_EV cells_Treated with DOX


title: EGFP(R65)+Ser-tRNA_Arg(CCG)_tRNA_rep2


title: MOLM14,input,DMSO_2

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
ChIP-seq reads were aligned to UCSC hg37 using BWA 0.7.10-r789 with all default parameters
ChIP broad peaks were identified using MACS v2.1 with all default parameters
BW files were created using wigToBigWig from ucsc tool directory
Assembly: hg37
Supplementary files format and content: bw, broadpeak

extract_protocol:
Cells were fixed in 1% paraformaldehyde for 10 min. After quenching, cells were lysed in 1% SDS buffer and ultrasonicated (qSonica).
ChIP-Seq libraries were prepared by Genewiz/Azenta using their standard protocols for Illumina sequencing.

value: human blood

value: DMSO


title: MOLM14,input,AC220_2


title: EGFP(R65)_tRNA_rep3

value: Transfected with EGFP(R65)-mCherry mistranslation reporter


title: Fbxo2GAP_C52


title: ChIP-seq with BORIS Abs in NIH3T3+pBIGi_BORIS cells_Treated with no DOX

value: no DOX


title: CD3 cells, Combo_T

city: Los Angeles

first: Tian-hao

last: Zhang

state: CA

address: 650 Charles E Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

description: 10x Genomics

data_processing:
Raw data files were processed by Cell Ranger (version 3.1.0), which aligned raw reads to mm10 reference genome and provided transcript count matrices using Emsembl version 93. Scanpy (Version 1.6.0) was used to normalize, scale, select variable features and perform differential gene expression anlaysis. Poor quality and doublet cells were removed based on either detected genes (with < 200 or > 9000), total UMIs (<1000 or > 100000 counts), or reads aligned to mitochondrial genome (>20). A total of 18170 cells remains for 4 samples. Top 4,000 variable genes were selected for dimension reduction. Principal component analysis (PCA) was performed on the scaled data, and The first 50 principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) visualization and cell clustering using the Louvain algorithm. Differential gene expression was performed between clusters using t-test_overestim_var method.
Assembly: mm10, release 93
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: lung

extract_protocol:
Cells were stained with Zombie-NIR LIVE/DEAD stain and CD45 antibody for 20 min a 4oC. Viable leukocytes were sorted using BD Biosceinces Aria II cell sorter with 100-mm nozzle.
The 10X Genomics platform (10X Genomics, Pleasanton, CA) was utilized for assessing single-cell transcriptomic. In brief, sorted immune cells were loaded into 10X Genomics Chromium microfluidic chips with 3’ v3 chemistry to generate single-cell gelbead emulsions (GEMs).

treatment_protocol: FVB mice were purchased from Charles River Laboratories. Tumor cells were implanted in 7-9-week-old mice subcutaneously at optimal doses. Tumor length and width were measured by caliper and the volume calculated by the equation: 0.4*length*width^2. Mice bearing ~50mm^3 tumors were randomized and treated with control, IT CCL21-DC (1x10^6 cells), IP 200 μg of anti- PD-1 antibody (BioXcell, Clone RMP1-14) or combination.

tag: disease state

value: lung cancer

value: lung

tag: strain

value: FVB

value: PD1 and DC combination


title: EGFP(R65)+Ser-tRNA_Arg(CCG)_tRNA_rep1


title: Fbxo2GAP_C51

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: MOLM14,input,AC220_1


title: EGFP(R65)_tRNA_rep2


title: CD3 cells, Ctl_T

description: 10x Genomics

value: control


title: MOLM14,input,DMSO_1


title: Fbxo2GAP_C50


title: CD45 cells, Combo

description: 10x Genomics


title: Fbxo2GAP_C56


title: MOLM14,H3K27me3 ChIP,AC220_2


title: Fbxo2GAP_C49


title: CD45 cells, 21DC

description: 10x Genomics

value: IT CCL21-DC (1x10^6 cells)


title: Fbxo2GAP_C48


title: CD45 cells, PD1

description: 10x Genomics

value: IP 200 μg of anti-PD-1 antibody


title: MOLM14,H3K27me3 ChIP,AC220_1


title: EGFP(R96W)+Arg-tRNA_Trp(CCA)_mRNA_rep2

data_processing:
Paired end reads were mapped to human hg38 genome by STAR with the annotation file gencode.v26.annotation.gtf from GENCODE database (https://www.gencodegenes.org) and with options --limitBAMsortRAM 62425435837 --outSAMattributes NH HI AS nM NM MD jM jI XS --outFilterMultimapNmax 50 --outFilterMismatchNmax 15 --outSJfilterDistToOtherSJmin 10 0 5 10 --alignIntronMin 15 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 15 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts --twopassMode Basic --outSAMstrandField intronMotif.
Uniqule mapped reads were extracted by samtools view with options -bS -q 255 -f 0x2, and then sorted and indexed with samtools.
Uniquely mapped reads were counted by featureCounts with options --verbose -s 1 -B -C -p -t exon -g gene_id --extraAttributes gene_type.
Assembly: hg38
Supplementary files format and content: comma separated value (csv) - indicates expression level of each gene

extract_protocol:
RNA-seq experiments were performed on 3 independent replicates from HEK293 cells overexpressing the mistranslation reporters with and without cognate mc-tRNAs. HEK293 cells were sorted on the FACSAria Fusion 5-18 cell sorter for mCherry+, i.e., successfully transfected, cell populations 48 h post-transfection. Total RNAs were extracted from sorted cells with TRIzolTM reagent (Invitrogen Cat. 15596026). 1 µg of total RNA per sample was used as input for RNA-seq library construct. Total RNA samples were polyA-selected to enrich mature mRNA species.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ based mRNA-SEQ library protocol (Illumina). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).

treatment_protocol: Cells were seeded on 6-well plates one day before transfection and reached 50-70% confluent on the day of transfection. Plasmids used for transfection were prepared with PureYieldTM plasmid Miniprep/Midiprep systems (Promega Cat. A1222/A2492) and ethanol precipitated. Transfections were performed using LipofectamineTM 3000 (InvitrogenTM Cat. L3000015) and following the manufacture’s protocol.

value: Transfected with EGFP(R96W)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Trp(CCA) on a single plasmid


title: Fbxo2GAP_C53


title: MOLM14,H3K27me3 ChIP,DMSO_1


title: EGFP(R96W)+Arg-tRNA_Trp(CCA)_mRNA_rep1


title: EGFP(R96W)_mRNA_rep3

value: Transfected with EGFP(R96W)-mCherry mistranslation reporter


title: CD45 cells, Ctl

description: 10x Genomics


title: Fbxo2GAP_C45


title: P3

value: adjacent lung tissue

tag: age

tag: Sex

value: Female

value: IIIb

value: NO


title: Fbxo2GAP_C46


title: EGFP(R65)_tRNA_rep1

value: wt

value: Transfected with EGFP(R65)-mCherry mistranslation reporter


title: P2

value: Ia


title: E11.5 limb bud, ZRS(LacZ/+), enhancer-capture HiC

city: Irvine

first: Evgeny

last: Kvon

address: McGaugh Hall

institute: University of California, Irvine

description: ecHi-C LZ-LB

data_processing:
Ligated reads were trimmed using DpnII restriction recognition sites and mapped to the DpnII-digested reference genome (mm10) using HiCUP (Wingett et al. 2015), followed by quality filtering and deduplication. For each tissue, the ecHi-C experiment produced, on average, 20 million unique on-target paired-end reads, resulting in a total of 200 million valid read pairs
Next, all DpnII fragments overlapping with the same bait region were merged into a single fragment in silico. Subsequently, the rest of the DpnII fragments were merged based on the size distribution of the pooled fragments that overlapped with bait regions. The mean fragment size of pooled fragments is ~3,000 bp. Significant interactions were called by CHiCAGO (score > 5) with default setting (Cairns et al. 2016; Freire-Pritchett et al. 2021) using combined replicates from HiCUP pipeline, by using the design file with the following parameters: --minFragLen=300 --maxFragLen=20000 --binsize=20000 --maxLBrownEst=3000000 --removeAdjacent=FALSE. We removed significant interactions that didn’t have valid ditag reads on neighboring fragments to avoid spurious interaction spikes (Schoenfelder et al. 2015). Regions >2 Mb from the bait regions were excluded from the analysis.
Assembly: mm10
Supplementary files format and content: bed

source_name: limb bud

extract_protocol:
E11.5 embryos were collected for dissection using approved institutional protocols. Tissue from multiple embryos was pooled together in the same collection tube, and at least two separate collection tubes were collected for each tissue for biological replication.
Tissues were incubated with collagenase (Gibco) in a thermomixer at 37 ℃ until the cells were dissociated, about 10 to 20 min. The single-cell solution was fixed by adding formaldehyde (Sigma-Aldrich) to a final concentration of 2% at RT for 10 min as described previously. Ice-cold glycine solution was added to a final concentration of 200 mM to quench crosslinking. Cells were then resuspended in cold lysis buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100 and 1X protease inhibitor cocktail (Thermo Scientific)) and incubated on ice for 15 min. Nuclei pellets were obtained by centrifuge at 750 g for 5 min at 4 ℃, followed by snap-freezing and storage at -80 ℃. Frozen nuclei pellets (2-6 million) were thawed on ice, followed by adding SDS and Triton X-100 to remove non-crosslinked proteins and sequester SDS, and digested using DpnII (NBE) overnight at 37 ℃. The ends of restriction fragments were labeled with biotinylated dCTP and ligated at room temperature for 4 hours. After de-crosslinking and precipitation, ligated products were sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, treatment time: 180 s in total) to an average fragment size of 200bp. The ligated sheared 3C libraries (10-12 ug for each replicate) were pulled down using Streptavidin Dynabeads (Thermo Scientific) to get rid of unligated fragments, followed by end repair, adaptor ligation and library amplification according to modified Agilent SureSelectXT protocol. The ecHi-C library was created by performing a target-enrichment protocol using capture RNA probes according to Agilent SureSelect XT protocol with an input amount of 750 ng of Hi-C library per sample.
Following hybridization to the RNA oligo library, each ecHi-C library was amplified using 13 cycles and post amplification libraries were size selected at 200-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were sequenced (paired-end 100 or 150 bp) using Illumina NovaSeq 6000 to enrich enhancer-centric interactions yielding a total of 1 billion unique paired-end reads.

value: limb bud

tag: developmental stage


title: P1


title: EGFP(R96W)_mRNA_rep2


title: EGFP(R96W)+Arg-tRNA_Trp(CCA)_mRNA_rep3


title: EGFP(R96W)_mRNA_rep1


title: Fbxo2GAP_C44

first: Chenghang

institute: Baylor College of Medicine


title: E11.5 forebrain, wildtype, RNA-seq rep2

data_processing:
Paired-end reads were mapped to the reference genome (mm10) using STAR software with default parameters (Dobin et al. 2013) and were counted on RefSeq genes by HTSeq (Putri et al. 2022). Differential gene expression analysis was performed using DEseq2 (Love, Huber, and Anders 2014). Genes with adjusted p-value < 0.05 were considered differentially expressed.
Supplementary files format and content: (RNA-seq) counts

source_name: forebrain

extract_protocol:
E11.5 embryos were collected for dissection using approved institutional protocols. Dissected tissues were immediately submerged in RNAprotect Tissue Reagent (Qiagen) and stored at -80 ℃. Multiple samples from the same tissue and genotype were pooled to at least 1 million cells in total for each of the two replicates.
RNA isolation, preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China).

value: forebrain

value: wildtype


title: E11.5 forebrain, hs267-853 knockout, RNA-seq rep1

value: hs267-853 knockout


title: Fbxo2GAP_C43

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: MOLM14,H3K27me3 ChIP,DMSO_2

value: human blood

value: DMSO


title: Fbxo2GAP_C42


title: EGFP(R96H)+Arg-tRNA_His(GUG)_mRNA_rep3

value: Transfected with EGFP(R96H)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_His(GUG) on a single plasmid


title: Ca3

value: Lung adenocarcinoma tissue


title: E11.5 forebrain, hs267-853 knockout, RNA-seq rep2


title: Fbxo2GAP_C47


title: Fbxo2GAP_C41


title: E11.5 forebrain, wildtype, RNA-seq rep1


title: EGFP(R96H)_mRNA_rep3

value: Transfected with EGFP(R96H)-mCherry mistranslation reporter


title: E11.5 midbrain, wildtype, RNA-seq rep1

source_name: midbrain

value: midbrain


title: Fbxo2GAP_C39

source_name: cochlea


title: EGFP(R96H)+Arg-tRNA_His(GUG)_mRNA_rep1


title: Ca1

value: Female


title: EGFP(R96H)_mRNA_rep2


title: Mnase_brm-1_IP2

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.   MNase-seq data analyses were performed according to published methods86 with some modifications. In brief, raw reads were processed with cutadapt (version 3.4, -m 10) to remove adaptors. Secondly, the processed reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 with default settings78. Thirdly, the nucleosome positions were determined by applying the improved nucleosome-positioning algorithm iNPS with default settings87. And then, the smoothed bigwig files across biological replicates were generated by using ‘dpos’ function in DANPOS388. Finally, MNase-seq data among samples were normalized by applying quantile normalization methods to normalize occupancy with ‘wiq’ function in DANPOS3.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.05, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Assembly: TAIR10
Supplementary files format and content: bigwig files

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 14h light/10h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
About 2 ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Novaseq was used for high-throughput sequencing of the ChIP-seq library.  The MNase assays were carried out as described previously85 with minor modifications. Approximately 0.4g of seedlings were used per sample. For MNase treatment, the prepared nuclei were resuspended in prewarmed MNase digestion buffer (20 mM Tris-HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2), followed by the addition of 0.5 units of MNase (Takara, Cat. No. 2910A,) and incubation (10 min at 37◦C with periodic agitation). Finally, the mono-nucleosome DNA was isolated from 2% agarose gels and quantified by the Qubit dsDNA HS assay kit (ThermoFisher, Cat. No. Q32851).

value: Seedling

value: 14-day-old,short day


title: E11.5 midbrain, wildtype, RNA-seq rep2


title: EGFP(R96H)_mRNA_rep1

value: wt


title: Mnase_brm-1_IP1


title: Mnase_bcl7ab_IP2


title: EGFP(R96H)+Arg-tRNA_His(GUG)_mRNA_rep2


title: Fbxo2GAP_C38

city: Houston

last: Zong

address: 1 Baylor Plaza


title: E11.5 midbrain, hs654 knockout, RNA-seq rep2

value: hs654 knockout


title: Fbxo2GAP_C36


title: EGFP(R96C)+Arg-tRNA_Cys(GCA)_mRNA_rep3

value: Transfected with EGFP(R96C)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Cys(GCA) on a single plasmid


title: Ca2

value: Ia

value: NO


title: E11.5 forebrain, wildtype, enhancer-capture HiC rep1

description: FB.ibed

data_processing:
Ligated reads were trimmed using DpnII restriction recognition sites and mapped to the DpnII-digested reference genome (mm10) using HiCUP (Wingett et al. 2015), followed by quality filtering and deduplication. For each tissue, the ecHi-C experiment produced, on average, 20 million unique on-target paired-end reads, resulting in a total of 200 million valid read pairs
Next, all DpnII fragments overlapping with the same bait region were merged into a single fragment in silico. Subsequently, the rest of the DpnII fragments were merged based on the size distribution of the pooled fragments that overlapped with bait regions. The mean fragment size of pooled fragments is ~3,000 bp. Significant interactions were called by CHiCAGO (score > 5) with default setting (Cairns et al. 2016; Freire-Pritchett et al. 2021) using combined replicates from HiCUP pipeline, by using the design file with the following parameters: --minFragLen=300 --maxFragLen=20000 --binsize=20000 --maxLBrownEst=3000000 --removeAdjacent=FALSE. We removed significant interactions that didn’t have valid ditag reads on neighboring fragments to avoid spurious interaction spikes (Schoenfelder et al. 2015). Regions >2 Mb from the bait regions were excluded from the analysis.
Supplementary files format and content: (capture hic) iBED

value: forebrain


title: EGFP(R96C)+Arg-tRNA_Cys(GCA)_mRNA_rep2


title: EGFP(R96C)+Arg-tRNA_Cys(GCA)_mRNA_rep1


title: Fbxo2GAP_C37

value: cochlea


title: Mnase_WT_IP2


title: E11.5 forebrain, wildtype, enhancer-capture HiC rep2

description: FB.ibed


title: Mnase_bcl7ab_IP1


title: E11.5 midbrain, wildtype, enhancer-capture HiC rep1

description: MB.ibed


title: Fbxo2GAP_C34

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Fbxo2GAP_C33


title: Mnase_WT_IP1


title: E11.5 midbrain, wildtype, enhancer-capture HiC rep2

description: MB.ibed


title: ChIP-seq_BRM-GFP brm-1 bcl7ab_Drosophila

tag: antibody

value: GFP (ab290, abcam)


title: EGFP(R96C)_mRNA_rep3

value: Transfected with EGFP(R96C)-mCherry mistranslation reporter


title: Fbxo2GAP_C32


title: Fbxo2GAP_C30


title: E11.5 midbrain, hs654 knockout, RNA-seq rep1


title: Fbxo2GAP_C35


title: Fbxo2GAP_C29


title: EGFP(R96Q)+Arg-tRNA_Gln(CUG)_mRNA_rep3

value: Transfected with EGFP(R96Q)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Gln(CUG) on a single plasmid