title: CoilinChIP_input_rep2

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

institute: Yokohama City University

data_processing:
For biotinylation-DNA-seq and ChIP-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev), and reads were mapped to human genome GRCH38 using the Bowtie2 alignment tool (version 2.3.5.1) with the default settings. The mapped reads from each in situ biotinylation-seq dataset were subjected to count per million (CPM) normalization and then used for downstream analysis. IP/input enrichment per gene was calculated with R (v. 4.0.2) and its package rtracklayer (version 1.48.0) using the Ensembl GRCH38.92 gene annotation model.
For biotinylation-RNA-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev), and reads were mapped to Ensembl gene annotation of human genome GRCh38.p13 using hisat2 (version). Read counts were obtained using Rsubread (version 2.2.6). Differential gene expression analysis was performed using R (v. 4.0.2) package DESeq2 (v. 1.28.1). Genes with an adjusted P-value <0.01 and absolute log2 fold-change >0.5 were included in the downstream analysis.
Assembly: GRCH38 and Drosophila melanogastergenome build5.41 from NCBI
Supplementary files format and content: BigWig files include normalized count data obtained from methods shown above.

growth_protocol: HeLa and HEK293T cells  were cultured in Dulbecco’s modified Eagle’s medium (08458-45; Nacalai Tesque, Kyoto, Japan) with 10% foetal bovine serum and penicillin/streptomycin under 5% CO2 at 37 ºC.

extract_protocol:
For antibody-based in situ biotinylation-seq, HeLa cells cultured in 10 cm dish were fixed with 4% PFA and permeabilized with 0.5% Triton X-100. After blocking, cells were incubated with primary antibodies, and then incubated with HRP-labeled secondary antibodies. After washing, HRP-based in situ biotinylation was performed by incubating cells with biotinylation buffer. The cells were lysed in 1% SDS RIPA buffer and were sonicated for DNA fragmentation. The biotinylated chromatin was pulled-down using SoftLinkTM Soft Release Avidin Resin (Promega), and the chromatin DNA was purified.
For ChIP-seq, crosslinking was performed with 2 mM DSG and 1% formaldehyde. Crosslinked HEK293T cells were resuspended with hypotonic buffer and then resuspended with ChIP Lysis Buffer and subjected to mild sonication using Bioruptor Sonicator (Diagenode, Denville, NJ). The lysate was diluted and incubated with anti-Coilin antibodies (HPA027885; Atlas, Bromma, Sweden)-conjugated Protein G beads overnight at 4 ºC with rotation. The beads were washed once with low-salt buffer, once with high-salt buffer, once with LiCl buffer and twice with TE buffer. DNA–protein complexes were eluted, crosslinks were reversed, and then DNA was purified.
The sequence libraries for in situ biotinylation DNA-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina, San Diego, CA). The sequence libraries for in situ biotinylation RNA-seq were prepared using SMART-Seq Stranded Kit (Takara). The sequence libraries for ChIP-seq were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

tag: cell line


title: 20_56_mouse_CTR_bio_rep3

status: Public on Oct 01 2024

type: SRA

city: Heidelberg

first: Rebecca

middle: Emma

last: Wagner

address: Inf 280 im Neuenheimer Feld

department: Cell Biology and Tumor Biology

country: Germany

institute: DKFZ

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCm38mm10 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Assembly: Grcm38mm10
Supplementary files format and content: tab and delimited text file

molecule: total RNA

organism: Mus musculus

source_name: back skin

extract_protocol:
RNA was extracted with Trizol following manufacturer's instructions
For SRSF2 knock out mice and controls RNA sequencing libraries were prepared using TruSeq Stranded Total RNA Gold library prep kit. For SRSF2 P95H mutant mice and controls RNA sequencing libraries were prepared using stranded Total RNA prep with Ribo-zero plus kit.

treatment_protocol: mouse back skin was treated topically every other day for a given period of time with 4-hydroxy tamoxifen

tag: tissue

value: back skin

tag: genotype

value: ctr

value: Cre negative

tag: srsf2 ko/mut

value: SRSF2 KO

tag: tdtomato

value: wild type

tag: treatment

value: 4-hydroxy tamoxifen

tag: time

value: 10 days


title: repeat_93_140-8_ng-20-mJ-cm2-48-hr_R1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.0
Alignment was performed using STAR v2.7.10a
Gene counts were performed with qCount in the QuasR R package v1.34.0
Normalization was performed with DESeq2 v1.36.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated count matrix

molecule: polyA RNA

source_name: Dorsal skin, 20 mJ/cm2 48 hr

extract_protocol:
Total RNA was extracted using RNeasy Fibrous Tissue Kits (Qiagen Inc., cat #: 74704) according to the manufacturer’s instructions (with 700 µL of the mixed lysate transferred to a RNeasy Mini column and repeated until all lysate had been used). During the procedure, Qiagen’s On-Column RNase-free DNase was used to eliminate possible DNA contamination.
Library preparation for next-generation sequencing was conducted on randomized RNA samples using the TruSeq-stranded mRNA kit (Illumina, San Diego, California) according to the sample preparation guide. The input RNA for library preparation was 300 ng per sample. A dual index scheme was used to multiplex samples for sequencing, which were pooled and sequenced on high output flow cells using an Illumina NextSeq® 500. Single-end sequencing was performed with a read length of 75 bp. A sequencing depth ~40 million reads per sample was achieved.

value: Dorsal skin

value: 20 mJ/cm2

value: 48 hr


title: blood, CTR-39

city: Napoli

first: Aannamaria

last: Carissimo

address: via Pietro Castellino

department: IAC

country: Italy

institute: CNR Italy

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in
fastq file through bcl2fastq
Trimming and cleaning with Trim Galore (v0.6.2)
Alignment was performed with Bowtie (v1.2.2)
The counts were determined with SAMtools (v1.9)
Assembly: hg19 (release 75) - miRBase (release 21)
Supplementary files format and content: tab-delimited text files including raw counts

organism: Homo sapiens

source_name: BLOOD-CELLS

extract_protocol:
small RNAs was then extracted from PBMCs using the miRNeasy Kit (Qiagen, Germantown, MD, USA) according to the manufacturer′s instructions. 250 ng of total RNA was used for the construction of sequqncing libraries.
Libraries were prepared from 250 ng of total RNA using NEGEDIA smallRNAseq sequencing service (Next Generation Diagnostics srl) which included, library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 50 cycle strategy (Illumina Inc.).
NEGEDIA smallRNAseq

tag: cell type

value: BLOOD-CELLS

tag: condition

value: CTR


title: H3K27ac_PBS_rep1

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

country: USA

institute: University of California, San Diego

description: Regions_gained_by_MSUc_H3K27ac.txt & Regions_reduced_by_MSUc_H3K27ac.txt

library_source: genomic

data_processing:
RNA-Seq analysis  FASTQ sequencing files were mapped to the mm10 using STAR with default parameters. Biological and technical replicates were used in all experiments. Quantification of transcripts was performed using the analyzeRepeats.pl of HOMER with the following parameters -condenseGenes -count exons -noadj. Principal Component Analysis (PCA) and correlation analyses were obtained based on the Transcripts Per kilobase Million (TPM) on all genes of all samples and TPM for each transcript was calculated using the analyzeRepeats.pl tool of HOMER with the parameters -condenseGenes -count exons -tpm. Differential expression analysis was generated using getDiffExpression.pl tool of HOMER (Heinz et al. 2010) with default parameters: FDR <0.05 and log2fold change >1 or < (-1) for cells treated with PBS or MSUc and FDR <0.05 for treatment with other chemicals. Pathway analyses of differentially expressed genes were performed using Metascape (Zhou et al. 2019).    ChIP-Seq analysis  ChIP-Seq analysis was performed as described previously (Cobo, Tanaka, et al. 2022; Seidman et al. 2020). Briefly, ChIP-Seq peaks for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A replicates were obtained using HOMER with parameters –L 0 –C 0 –fdr 0.9 –minDist 200 –size 200. Only peaks with IDR <0.05 were considered for downstream analyses. The merged tag directories from all replicates from each experimental conditions were used for visualization in the UCSC Browser (Kent et al. 2002). Peaks were annotated with the nearest gene to analyse the overlap between conditions. For H3K27ac and H3K4me3 differential peaks, H3K27ac and H3K4me3 ChIP-Seq peaks were centred to regions of open chromatin using the annotatePeak.pl tool of HOMER an ATAC-Seq peak file of BMDM treated with PBS or MSUc. Differential peaks were calculated using the getDiffExpression.pl tool of HOMER with default parameters. A list of the IDR peaks for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L, DNMT3A, H3K27ac, H3K4me3 and H3K79me3 as well as the differential peaks after treatment with MSUc can be found in GEO under the accession number (GSE). To generate a histogram of the intensity of a given ChIP-Seq over a subset of differential peaks or regions using the annotatePeaks.pl tool of HOMER with the parameters -size 6000 -hist 25. To identify DNA motifs in differential peak or regions over background sequences, the findMotifGenome.pl tool of HOMER was used with default parameters and random genomic sequences as background (Heinz et al. 2010). In the figures, de novo motifs are displayed unless otherwise indicated.
In silico promoter analysis of differentially expressed genes was performed using the findMotifs.pl tool of Homer searching for motifs of length 8 and 10 and from -2000 to +500 bp relative to the TSS, using 4 threads.
Assembly: mm10
Supplementary files format and content: The list of Transcripts Per Million reads (TPM) and differential peak files are provided in fastq.gz

molecule: genomic DNA

source_name: Bone Marrow

growth_protocol: Flushed bone marrow from both femurs and tibias of C57BL/6, Tfeb-Tg, Bhlhe40-/- and Bhlhe41-/- mice were cultured in DMEM medium supplemented with 10% de-complemented FBS, Penicillin-Streptomycin 100 U/mL and 16 ng/mL of recombinant murine M-CSF (Peprotech, #315-02). Fresh M-CSF was added 72h after seeding. Ampkα1-/-  BMDM were generated as explained elsewhere (Wang et al. 2016). Briefly, bone marrows from 7-week-old to 8-week-old Ampkα1-/- and congenic WT mice were cultured in complete Roswell Park Memorial Institute (RPMI) media containing 10% fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 μg/mL) in the presence of 5 ng/mL of MCSF (R&D Systems).

extract_protocol:
It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB).
RNA-Seq library preparation  It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB). 500 ng-1 μg of RNA was incubated with Oligo d(T) magnetic beads (NEB, #S1419S) to enrich for poly-A tailed transcripts and then fragmented by incubating for 9 min at 94º in 2X Superscript III first-strand buffer containing 10 mM DTT (Invitrogen, #P2325). Reverse transcription (RT) of fragmented RNA was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and the solution of RNA-cDNA complexes was then added to a mix containing 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5 U/ml RNAseH (Enzymatics, #Y9220L), 1 μl of 10 U/ml DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween 20 and 1.05 μl of nuclease free water; and incubated at 16ºC overnight. Next day, the resulting DNA was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Health- care, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration. After two washes owith 80% etOH, air dry and eluted, the purified DNA was end-repaired by blunting followed by A-tailing and adapter ligation using NOVA (BIOO-NextFlex adapters. Libraries were amplified by PCR for 13 cycles using Solexa 1GA and Solexa 1GB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on NovaSeq SP100 (Illumina, San Diego, California).  ChIP-Seq library preparation  Chromatin immunoprecipitation (ChIP) was performed as described elsewhere (Seidman et al. 2020; Gosselin et al. 2017). Briefly, MDM or BMDM were fixed with 1% formaldehyde for H3K27ac, H3K4me3 and H3K79me3 or doubly fixed with 3 mM Disuccinimidyl-glutarate -DSG- (Proteochem, #C1104) in PBS for 30 min at room temperature and then with 1% formaldehyde (ThermoFisher, #28906) for 10 min at room temperature for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A. Fixation was then quenched upon adding glycine to final concentration of 125 mM. Cells were then washed with 0.01%Triton X-100:PBS, scraped and pelleted by centrifugation at 3000 rpm for 10 min at 4ºC and snap frozen for storage at -80ºC. For ChIP experiments, fixed cells were thawed and permeabilised in 1 mL of chilled buffer containing 10 mM HEPES/KOH pH7.9, 85 mM KCl, 1 mM EDTA, 0.2% IGEPAL CA-630 (Sigma-Aldrich, #I8896), 1X protease inhibitor cocktail (Sigma, #11836145001) and 1 mM PMSF for 10 min on ice. After that cells were spun down and lysed in 130 μl of either LB3 lysis buffer containing 10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail for H3K27ac, H3K4me3 and H3K79me3 or lysis buffer containing 20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Sodium Deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail and 1 mM PMSF. Chromatin was sheared by sonication in a 96 microTUBE Rack (Covaris, #500282) using a Covaris E220 for 25 cycles with the following settings: time, 60 s; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0. Sonicated lysates were spun down at 10,000 rpm for 10 min at 4ºC and one percent of the sonicated lysate was kept as ChIP input for analysis. In all buffers, DTT, protease inhibitor and PMSF were added freshly. Sonicated lysates were incubated with a mix consisting of Protein G Dynabeads (Invitrogen, #10003D) and TFEB antibody cocktail (Abcam, #ab2636 plus CST, #37785), TFE3 antibody cocktail (Abcam, #196681 plus Abcam, #93808), BHLHE40 (Novus Biologicals, #NBP100-1800), DOT1L (CST, #D1W4Z), DNMT3A cocktail (Abcam, #ab2850 plus Diagenode, #C15410085), H3K27ac (ActiveMotifs, #AB_2793305), H3K4me3 (Millipore, #04-745), or H3K79me3 (Diagenode, #C15410068),  was added to the sonicated material and incubated overnight on a rotator at 4ºC. Next day, immunocomplexes were placed on a magnet and bead complexes were washed with 100 μl of chilled buffers. For H3K27ac, H3K4me3 and H3K79me3 ChIP, beads were washed four times each with wash buffer I containing 20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, wash buffer III containing 10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA and twice with ice-cold TET containing 10 mM Tris/HClpH7.5, 1 mM EDTA, 0.2% Tween-20. For TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A ChIP beads were washed as it follows: 3 times lysis buffer, 6 times with wash buffer containing 10 mM Tris/HCl pH7.5, 250 mM LiCl, 1 mM EDTA, 0.7% Na-Deoxycholate and 1% NP-40 alternative; 3 times with TET buffer containing 10 mM Tris/HCl pH 8.0, 1 mM EDTA, 0.2% Tween 20; and 1 time with IDTE buffer containing 10 mM Tris/HCl pH 8.0 and 0.1 mM EDTA. Bead complexes were resuspended in 25 mL of TT buffer containing 10 mM Tris/HCl pH 8.0, 0.05% Tween 20. ChIP libraries for sequencing were prepared on beads using NEBNext Ultra II Library kit (NEB, #E7645L) by reducing 50% the reaction volume as previously described (Heinz et al. 2015; Sakai et al. 2019). Reverse crosslinking was performed by adding 33.5 μl of a mix containing 4 μl 10% SDS, 3 μl 0.5 M EDTA, 1.6 μl 0.2M EGTA, 1 μl 10 mg/ml Proteinase K (Biolabs, #P8107 S), 1 μl 10 mg/ml RNase A, 4.5 μl 5M NaCl and 18.4 μl nuclease free water and incubating at 55C for 1h followed by 75ºC for 30 min. After removing the dynabeads, libraries were cleaned by adding  2 μl of SpeadBeads in 124 μl of 20% PEG 8000/ 1.5M NaCl and washed twice with 100 μl of 80% etOH, air dry and eluted in 13 μl of buffer containing 10 mM Tris/HCl pH 8.0 and 0.05% Tween 20. Libraries were amplified by PC for 14 cycles using NEBNext Ultra II PCR master mix using Solexa 1GA and Solexa 1GB primers. After that, libraries were size selected 200-500 bp upon running in 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX) and sequenced using a NovaSeq SP100.

treatment_protocol: On day six after seeding, BMDM were scrapped out and plated one day prior treatment with Metformin (MP Biomedicals, #151691), 125 mM A769662 (Sigma, # SML2578), or since day 0 with 1 μM SGC0946 (Selleckchem, #S7079). BMDM were then treated with control PBS or 250 μg/mL of MSUc, calcium pyrophosphate dihydrate crystals, silica nanoparticles (Invivogen, #tlrl-sio-2), or aluminum hydroxide salt (Invivogen, #tlrl-aloh) at various timepoints as explained in the text and Figure legends.

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: WT

value: PBS


title: 94-20-mJ-cm2-48-hr_R1


title: CoilinChIP_input_rep1

country: Japan


title: 90-10-mJ-cm2-48-hr_R1

source_name: Dorsal skin, 10 mJ/cm2 48 hr

value: 10 mJ/cm2


title: H3K27ac_MSUc_rep1

value: MSUc


title: 89-10-mJ-cm2-48-hr_R1


title: CoilinChIP_rep2


title: 20_65_mouse_CTR_bio_rep1

value: back skin

value: ctr

value: heterozygous

value: 12 days


title: 91-20-mJ-cm2-48-hr_S43_R1_001


title: CoilinChIP_rep1


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 6month old male replicate 2

city: Vermillion

first: Mark

last: Bouska

state: SD

address: 414 E Clark St.

institute: Mark Bouska

data_processing:
Quality control (Fastqc)
Trim adapters and remove low quality sequences (Trimmomatic)
Alignment (Hisat2, Samtools)
Raw count table(Stringtie)
Normalized count tables and pairwise DE comparisons(DESeq2)
Assembly: Build index (GRCm39.106)(Hisat2)
Supplementary files format and content: Excel Files contain ensembl gene ID, gene, sample ID, raw read counts

source_name: Heart apex

extract_protocol: RNA was harvested using Rneasy Fibrous Tissue mini kit (Qiagen).  1ug was used for the construction of libraries using RNA TruSeq stranded mRNA Library prep kit.

value: Heart apex

tag: age

value: 6 months

tag: Sex

value: male

value: Cryab*R120G mutant

tag: strain background


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 6month old male replicate 3


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 6month old male replicate 1


title: input2

description: Peaks_gained_by_MSUc_DOT1L.txt & Peaks_reduced_by_MSUc_DOT1L.txt

value: input


title: 88-10-mJ-cm2-48-hr_R1

value: Dorsal skin

value: 48 hr


title: H3K27ac_MSUc_rep2

value: Bone Marrow


title: MAS98.12PR, Resistant, sample7

city: Oslo

first: Eivind Valen

last: Egeland

address: Ullernchausseen 70

department: Department of Tumor Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description: col S38 in raw_counts.txt

data_processing:
Fastq files were cropped to longest common read length, 75 bp, with Trimmomatic (v0.38).
Trimmed samples were aligned to grch38 with STAR (v2.7.8a), and transcript reference (GENECODE; v41) using default parameters.
Reads with better mapping to the mouse geneome (mm10) than grch38 were removed using XenoFilteR (v1.6)
Gene counts were retrieved with featureCounts from Subread.
Assembly: hg38
Supplementary files format and content: tab-delimited txt-file containes raw-counts from all Samples

source_name: triple negative breast cancer patient-derived xenograft

growth_protocol: Tumors were grown in Hsd: Athymic Nude-Foxn1nu

extract_protocol:
RNA was extracted with AllPrep DNA/RNA/miRNA Unviersal kit (Qiagen).
Libraries were prepared with Kapa RNA HyperPrep with dual index to generate cDNA, followed by Twist Human Comprehensive Exome for the mRNA capturing according to manufacturer's protocol. Amount of starting material 100 ng total RNA.

tag: paclitaxel sensitivity

value: Resistant

value: Untreated


title: input1

value: Bone Marrow-derived macrophages

value: WT


title: FVB.B6. 6month old male replicate 3


title: MAS98.12PR, Resistant, sample6

description: col S14 in raw_counts.txt

value: triple negative breast cancer patient-derived xenograft


title: 87-10-mJ-cm2-48-hr_S46_R1_001

value: 10 mJ/cm2


title: DOT1LChIP_PBS_rep3

value: PBS


title: FVB.B6. 6month old male replicate 2


title: 86-10-mJ-cm2-48-hr_S42_R1_001


title: MAS98.12PR, Resistant, sample5

description: col S59 in raw_counts.txt


title: DOT1LChIP_PBS_rep2


title: FVB.B6. 6month old male replicate 1


title: DOT1LChIP_PBS_rep1


title: MAS98.12PR, Resistant, sample4

description: col S57 in raw_counts.txt


title: 85-5-mJ-cm2-48-hr_R1

source_name: Dorsal skin, 5 mJ/cm2 48 hr

value: 5 mJ/cm2


title: DOT1LChIP_MSUc_rep3

value: MSUc


title: MAS98.12PR, Resistant, sample3

description: col S51 in raw_counts.txt


title: repeat_83_114-62_ng-5-mJ-cm2-48-hr_R1


title: DOT1LChIP_MSUc_rep2


title: MAS98.12PR, Resistant, sample2

description: col S48 in raw_counts.txt


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 3month old male replicate 2

value: Heart apex

value: 3 months


title: MAS98.12, Sensitive, sample3

description: col S62 in raw_counts.txt

value: Sensitive


title: DOT1LChIP_MSUc_rep1


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 3month old male replicate 1

value: male

value: Cryab*R120G mutant


title: 81-5-mJ-cm2-48-hr_S41_R1_001

value: Dorsal skin


title: 82-5-mJ-cm2-48-hr_S45_R1_001

value: 48 hr


title: FVB.B6. 3month old male replicate 3


title: FVB.B6. 3month old male replicate 2


title: MAS98.12, Sensitive, sample2

description: col S61 in raw_counts.txt


title: VehiclePBS_rep3

description: Treatment_of_macrophages_with_DOT1Li.txt

value: Bone Marrow


title: 80-Sham-48-hr_R1

source_name: Dorsal skin, Sham 48 hr

value: Sham


title: EH_2hr_TL_rep3

city: Baltimore

first: Nicolle

last: Rosa Mercado

state: MD

address: 725 N. Wolfe Street  714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
cutadapt  --minimum-length=20 -q 20,20
hisat-3n --base-change T,C --add-chrname --directional-mapping
samtools view
samtools sort
samtools index
Assembly: hg38
Supplementary files format and content: cB.csv

growth_protocol: HEK-293Ts were cultured in DMEM (ThermoFisher) supplemented with 10% fetal bovine serum (ThermoFisher) and kept in a 37ºC humidified incubator at 5% CO2.

extract_protocol:
RNAs were extracted using TRIzol according to manufacturer's instructions.10 µg of RNA were treated using 0.4 units of TURBO DNase (ThermoFisher) per microliter in 200 µL reactions  incubating samples at 37ºC for 30 minutes.  RNAs treated with TURBO DNase were recovered using RNA XP beads (Beckman). RNAs were then subjected to TimeLapse chemistry (Schofield et al. 2018) by incubating samples at 45ºC for 1 hour with 600 mM TFEA, 1 mM EDTA, 100 mM sodium acetate pH 5.2 and 10 mM sodium periodate and then reduced by incubating samples at 37ºC for 30 minutes with 100 mM DTT, 100 mM Tris pH 7.4, 10 mM EDTA and 1mM NaCl.
For 1hr treatments, libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina). For 2hr treatments, the SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian kit was used to prepare libraries.
TL-seq

treatment_protocol: For emetine treatments, cells were seeded at a density of 2x106 in 10 cm dishes 48 hours before the experiment. The day of the treatment, media was changed 2 hours before addition of translation inhibitors. Aqueous emetine from 100 µM stocks was added to treated cells at 1.8 µM for low doses and at 240 µM for high doses.

value: human embryonic kidney cells

value: 2hr 250 uM s4U

value: 2hr 240 uM emetine


title: VehiclePBS_rep2

value: Bone Marrow-derived macrophages

value: WT


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 3month old male replicate 3


title: VehiclePBS_rep1

value: PBS


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 1month old male replicate 3

value: 1 month


title: 79-Sham-48-hr_R1


title: EL_2hr_TL_rep3

value: 2hr 1.8uM emetine


title: FVB.B6. 3month old male replicate 1

value: Heart apex


title: VehicleMSUc_rep3

value: MSUc


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 1month old male replicate 2


title: UT_2hr_TL_rep3


title: 78-Sham-48-hr_R1


title: VehicleMSUc_rep2


title: FVB.B6.-Tg(Myh6-Cryab*R120G)134Rbns 1month old male replicate 1


title: EL_2hr_TL_rep2


title: VehicleMSUc_rep1


title: UT_2hr_TL_rep2


title: 84-5-mJ-cm2-48-hr_R1

value: 5 mJ/cm2


title: EH_2hr_TL_rep2


title: SGCPBS_rep3


title: FVB.B6. 1month old male replicate 2

value: male


title: 77-Sham-48-hr_S38_R1_001


title: FVB.B6. 1month old male replicate 3


title: 76-Sham-48-hr_S34_R1_001


title: 75-40-mJ-cm2-24-hr_R1

source_name: Dorsal skin, 40 mJ/cm2 24 hr

value: 40 mJ/cm2

value: 24 hr


title: 74-40-mJ-cm2-24-hr_R1

value: Dorsal skin


title: FVB.B6. 1month old male replicate 1


title: SGCPBS_rep2

value: Bone Marrow


title: 73-40-mJ-cm2-24-hr_S71_R1_001


title: EL_2hr_TL_rep1


title: SGCMSUc_rep3


title: 72-40-mJ-cm2-24-hr_S37_R1_001


title: UT_2hr_TL_rep1


title: RAW264.7 WT rep3

city: wuhan

first: wang

middle: li

last: ping

address: Jiefang Avenue, Jianghan District, Wuhan City, Hubei Province

country: China

institute: Department of Clinical Laboratory, Union Hospital, T ongji Medical College

data_processing:
Illumina NovaSeq 6000 used for basecalling.
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: RAW264.7 WT rep3

growth_protocol: RAW264.7 cells were plated in 6-well plates  and incubated with 140 mM of HFCS

extract_protocol:
Cells are captured, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: three replicate was HFCS treated for 18 hours.


title: RAW264.7 WT rep2

source_name: RAW264.7 WT rep2


title: EL_1hr_TL_rep3

value: 1hr 500 uM s4U

value: 1hr 1.8uM emetine


title: SGCMSUc_rep1


title: UT_1hr_TL_rep3

value: human embryonic kidney cells


title: RAW264.7 HFCS 140 mM rep3

source_name: RAW264.7 HFCS 170 mM rep3

value: HFCS 140 mM


title: repeat_69_3-20-mJ-cm2-24-hr_R1

source_name: Dorsal skin, 20 mJ/cm2 24 hr

value: 20 mJ/cm2


title: WT_PBS_rep2

description: Exposure_of_Bhlhe40KO_and_Bhlhe41KO_to_MSUc.txt

value: Bone Marrow-derived macrophages

value: WT


title: EL_1hr_TL_rep2


title: WT_PBS_rep1

value: PBS


title: RAW264.7 WT rep1

source_name: RAW264.7 WT rep1


title: 68-20-mJ-cm2-24-hr_S67_R1_001


title: EH_2hr_TL_rep1

value: 2hr 250 uM s4U

value: 2hr 240 uM emetine


title: 67-20-mJ-cm2-24-hr_S36_R1_001


title: WT_MSUc_rep2

value: MSUc


title: RAW264.7 HFCS 140 mM rep2

source_name: RAW264.7 HFCS 170 mM rep2


title: WT_MSUc_rep1


title: EL_1hr_control_rep1


title: UT_1hr_TL_rep2


title: LF

city: Hefe

first: sheng

last: zhang

state: Anhui Province

address: Shushan District

institute: anhui agriculture university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned against the S. marcescens FY Lactobacillus plantarum FY1.Then, genome and counted by StarSolo. Sequencing data was further analyzed using the Scanpy software.
We initially reduced dimensionality of the dataset using principal components analysis (PCA), retaining 20 principal components.
Subsequent steps, like low-dimensional UMAP visualization and cell clustering via Leiden algorithm, were based on the initial PCA.
Finally, Wilcoxon rank sum was used to analyze the difference between different cluster cells.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: tsv files include gene counts for each Sample

organism: Lactiplantibacillus plantarum

source_name: WT

extract_protocol:
Up to half a million cells were collected by centrifuging at 4000 rpm for 5 min at 4℃.The supernatant was removed and cell pellets were resuspended in 2 mL ice-cold 4% formaldehyde (Sigma, 47608) and incubated with shaking overnight at 4℃. The fixative was removed by centrifuging at 4000 rpm for 5 min at 4℃ and cells were washed twice by 1 mL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.1 U/mL Murine RNase inhibitor (Vazyme, R 301)). The supernatant was removed and cells were resuspended in 200 μL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.2 U/mL Murine RNase inhibitor (Vazyme, R 301)).
The cell suspensions were counted with a Moxi cell counter (ORFLO Technologies, Ketchum, Idaho) and diluted according to the manufacturer’s instructions to obtain 2000-4000 single-cell per sample. Random primers were added to amplify the full length of RNA, and the resulting cDNA fragment was added with adaptor. The microbeads with cell barcode, UMI, and the cDNA fragments linked to the adaptor were combined with the mixture of enzymes and extended in the microfluidic system to obtain the labeled cDNA chain. The beads were lysed and the cDNA was used as a template for PCR amplification. All products were pooled to construct a standard sequencing library.

tag: strain

value: Lactobacillus plantarum FY1

value: bacteria and larvae were co-cultured


title: UT_1hr_control_rep1


title: 66-20-mJ-cm2-24-hr_S32_R1_001


title: B41KO_PBS_rep2


title: SGCMSUc_rep2


title: 65_3-10-mJ-cm2-24-hr_R1

source_name: Dorsal skin, 10 mJ/cm2 24 hr

value: 10 mJ/cm2


title: 70-20-mJ-cm2-24-hr_R1

value: 24 hr


title: L

description: 10x Genomics

value: single cultivation


title: 71-40-mJ-cm2-24-hr_S33_R1_001

value: Dorsal skin

value: 40 mJ/cm2


title: B41KO_PBS_rep1

value: Bone Marrow


title: 64-10-mJ-cm2-24-hr_R1


title: B41KO_MSUc_rep2


title: UT_1hr_TL_rep1

value: human embryonic kidney cells

value: 1hr 500 uM s4U


title: RAW264.7 HFCS 140 mM rep1

source_name: RAW264.7 HFCS 170 mM rep1

value: HFCS 140 mM


title: Macrophages, UV-treated HSE, M2G, Rep3

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Sequences in FASTQ files were trimmed for adapter sequences and were aligned to the human genome hg19 using HISAT2.
Sam and bam files were sorted via Samtools.
Reads were counted by HTSeq-count.
Differential expression analysis (DEGs) was conducted in RStudio 2023.12.1 using the R Bioconductor package, DESeq2, version 1.40.2
Assembly: hg19
Supplementary files format and content: Normalized counts

source_name: Reconstructed human skin equivalent

growth_protocol: THP1 was maintained in RPMI 1640 medium (Nacalai Tesque) supplemented with 10% (v/v) FBS (Gibco) and 1% (v/v) antibiotic (Nacalai Tesque). Cells were incubated at 37°C with humidified 5% (v/v) CO2.

extract_protocol:
Harvested CD45+ cells underwent total RNA extraction with PicoPureTM RNA Isolation Kit (Applied Biosystems), according to the manufacturer's instructions. Total RNA was subjected to RNA-sequencing.
NexteraXT

treatment_protocol: For establishment of immunocompetent HSEs, NHDFs and THP-1 cells were co-cultured in fibrin hydrogel. HSEs were exposed to UVA irradiation with or without M2G treatment before UVA exposure.

value: Reconstructed human skin equivalent

value: macrophages

value: 3D culture with UVA and M2G treatment


title: 63-10-mJ-cm2-24-hr_S66_R1_001


title: B41KO_MSUc_rep1

source_name: Bone Marrow

value: Bone Marrow-derived macrophages


title: LF2

description: replicate=LF group biological replicate 2

data_processing:
For annotation, the genome of S. marcescens (GCF_013122155.1) and L. plantarum (GCF_032436005.1) was used as reference.
The significant differentially expressed genes were determined in different groups using the DESeq software, with the standards of P-value ≤0.05, and fold change |log2FC| ≥1.
KEGG B class database was used to classify the genes with significantly differential expression based on their functions using the tool Omicshare.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: txt files include gene count values for each Sample

source_name: Lactobacillus plantarum FY1

extract_protocol:
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1 ug of total RNA was used for the construction of sequencing libraries.
With Ribo-off rRNA Depletion Kit (Vazyme), the total bacterial RNA was subjected to rRNA removing to obtain mRNA.And then RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

value: WT


title: 62-10-mJ-cm2-24-hr_S35_R1_001


title: Macrophages, UV-treated HSE, M2G, Rep2


title: Macrophages, UV-treated HSE, M2G, Rep1


title: B40KO_PBS_rep2

value: PBS


title: L4

description: replicate=L group biological replicate 4

value: Lactobacillus plantarum FY1


title: 61-10-mJ-cm2-24-hr_S31_R1_001


title: 60-5-mJ-cm2-24-hr_R1

source_name: Dorsal skin, 5 mJ/cm2 24 hr

value: 5 mJ/cm2


title: B40KO_PBS_rep1


title: EL_1hr_TL_rep1

value: 1hr 1.8uM emetine


title: LF1

description: replicate=LF group biological replicate 1

value: bacteria and larvae were co-cultured


title: B40KO_MSUc_rep2

value: MSUc


title: Macrophages, UV-treated HSE, Rep3

description:
B_norRNA_HSETHP1UVVsHSETHP1.csv
C_norRNA_HSETHP1UVM2GVsHSETHP1UV.csv

value: 3D culture with UVA treatment


title: LF4

description: replicate=LF group biological replicate 4


title: LF3

description: replicate=LF group biological replicate 3


title: Macrophages, UV-treated HSE, Rep2


title: L2

description: replicate=L group biological replicate 2

value: single cultivation


title: B40KO_MSUc_rep1

value: Bone Marrow


title: 58-5-mJ-cm2-24-hr_S58_R1_001

value: Dorsal skin

value: 24 hr


title: ATAC_PBSrep2

description: ATAC-Seq used to annotate Histone marks ChIP-Seq


title: L1

description: replicate=L group biological replicate 1


title: Macrophages, UV-treated HSE, Rep1


title: 57-5-mJ-cm2-24-hr_S27_R1_001


title: ATAC_PBSrep1


title: 55-Sham-24-hr_R1

source_name: Dorsal skin, Sham 24 hr

value: Sham


title: ATAC_MSUcrep2


title: THP-1 cells, 2D culture, Rep3

source_name: cell line

value: cell line

value: monocytes

value: 2D culture


title: Ampka1WT_PBS_rep3

value: Bone Marrow-derived macrophages


title: 53-Sham-24-hr_S57_R1_001


title: L3

description: replicate=L group biological replicate 3

value: WT


title: 54-Sham-24-hr_R1


title: Ampka1WT_PBS_rep2

value: PBS


title: THP-1 cells, 2D culture, Rep1


title: THP-1 cells, 2D culture, Rep2


title: 52-Sham-24-hr_S26_R1_001


title: 59-5-mJ-cm2-24-hr_R1


title: Ampka1WT_PBS_rep1


title: Ampka1WT_MSUc_rep3


title: 50_S47-40-mJ-cm2-6-hr_R1

source_name: Dorsal skin, 40 mJ/cm2 6 hr

value: 40 mJ/cm2

value: 6 hr


title: p53 KO GCN2iB 4

city: Indianapolis

first: Ricardo

last: Cordova

state: IN

address: 635 Barnhill Drive, MS4067

institute: Indiana University School of Medicine

data_processing:
Barcodes and sequencing adapters were trimmed using TrimGalore
Reads were aligned to Human reference genome GRCh38 (ENSEMBL) using HISAT2 aligner
Mapped reads were assigned to annotated genomic features of GRCh38 using featureCounts
Differential expression analysis was carried out using DESeq2 package
Assembly: GRCh38 ENSEMBL
Supplementary files format and content: comma-separated values (csv) file shows the number of reads (unnormalized counts) mapped to each gene (shown as Ensembl ID) for all the samples

source_name: LNCaP

growth_protocol: LNCaP cells were cultured in phenol-free RPMI-1640 supplemented with 10% FBS. Cells were maintained at 37°C in a fully humidified atmosphere containing 5% CO2, used at early passage for experiments, and were tested to be free of mycoplasma contamination.

extract_protocol:
Total RNA was extracted using RNeasy Plus Kit (Qiagen) according to the manufacturer’s instructions.
RNA quality control, library preparation, and NGS paired-end sequencing on the Illumina NovaSeq platform were performed by Azenta (South Plainfield, NJ).

treatment_protocol: LNCaP p53 KO cells were generated using CRISPR. LNCaP WT and p53 KO cells (350,000 cells) were plated in 6-well plates. Cells were allowed to attach for 1 day and were then treated with vehicle (DMSO) or 5 µM GCN2iB for 48 h.

value: LNCaP

value: Prostate Cancer

value: p53 KO


title: Ampka1WT_MSUc_rep2

value: MSUc


title: Macrophages, HSE, Rep3

description:
A_norRNA_HSETHP1VsTHP1.csv
B_norRNA_HSETHP1UVVsHSETHP1.csv

value: Reconstructed human skin equivalent

value: macrophages

value: 3D culture


title: p53 KO GCN2iB 2


title: 56-5-mJ-cm2-24-hr_S24_R1_001

value: Dorsal skin

value: 5 mJ/cm2

value: 24 hr


title: Macrophages, HSE, Rep2


title: 49-40-mJ-cm2-6-hr_R1


title: p53 KO GCN2iB 3


title: p53 KO GCN2iB 1


title: 48-40-mJ-cm2-6-hr_S49_R1_001


title: Ampka1KO_PBS_rep3

value: Bone Marrow


title: Macrophages, HSE, Rep1


title: 47-40-mJ-cm2-6-hr_S25_R1_001


title: ATAC_MSUcrep1


title: p53 KO Vehicle 3

value: Vehicle


title: 45_S11-20-mJ-cm2-6-hr_R1

source_name: Dorsal skin, 20 mJ/cm2 6 hr

value: 20 mJ/cm2


title: Ampka1KO_PBS_rep1

value: Bone Marrow-derived macrophages


title: Ampka1KO_MSUc_rep3


title: p53 KO Vehicle 2


title: Ampka1KO_PBS_rep2

value: PBS


title: Ampka1KO_MSUc_rep1


title: 42-20-mJ-cm2-6-hr_S72_R1_001


title: Ampka1WT_MSUc_rep1


title: RT10_4OHT_rep2

city: Illkirch

first: Stephane

middle: D

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

description:
spike: 4-sU labeled S2 RNA
SNVT213

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were preprocessed in order to remove adapter, poly A and low-q uality sequences (Phred quality score below 20). After this prep rocessing, reads shorter than 40 bases were discarded for further analy is. These preprocessing step s were performed using cutadapt version 1.10. Reads were mapp ed to rRNA seq uences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis.
Reads were mapped onto the mm10 and BDGP6 assembly of Mus musculus and Drosophilia melanogaster genome using STAR version 2.5.3a.
Gene expression quantiﬁcation was performed from uniquely aligned reads using htseq -count version 0.6.1 p 1, with annotations from Ensembl version 93 and “union” mode 1 . Only non-ambiguously assigned reads to a gene have been retained for further analyses.
Data were normalized using DesSEQ2 (version 1.16.1) size factors computed with the median-of-ratios method on Drosophilia melanogaster counts. Differential gene expression analysis was performed using DESeq2 version 1.16.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for all samples of mouse reads (mm10_counts.tsv)
Supplementary files format and content: tab-delimited text file includes raw count for all samples of drosophila reads (BDGP6_counts.tsv)
Supplementary files format and content: tab-delimited text file includes DeSEQ2 differential gene expression analysis (S21089_alldata.tsv)

growth_protocol: cells were cultured on plates coated with 0.1% gelatin solution in 1x PBS (Dutcher, Cat# P06-20410) using DMEM medium supplemented with 15% fetal calf serum ES-tested (ThermoFisher Scientific, Cat# 10270-106), 2 mM ʟ-glutamine (ThermoFisher Scientific, Cat# 25030-024), 0.1% β-mercaptoethanol (ThermoFisher Scientific, Cat# 31350-010), 100 UI/ml penicillin and 100 μg/ml streptomycin (ThermoFisher Scientific, Cat# 15140-122), 0.1 mM non-essential amino acids (ThermoFisher Scientific, Cat# 11140-035) and 1,500 U/ml leukemia inhibitory factor (home-made),  3 μM CHIR99021 (Axon Medchem, Cat# 1386) and 1 μM PD0325901 (Axon Medchem, Cat# 1408) were added freshly to the medium. Cells were grown at 37°C in a humidiﬁed, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted usingTri Reagent (Trizol), treated with Dnase. For 200 µg total mouse RNA, 25 µg labeled S2 total RNA and 25 µg non labeled yeast RNA. RNA was fragmented on a Covaris E220. Newly transcribed RNA fragments were purified o nµMACS columns using streptavidin magnetic beads after biotinylation uing biotin-HPDP.
P2616 : Total RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 1 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: 4-OHT to induce the deletion of the floxed alleles, 4-sU to label nascent RNA: cells were plated at day 0, treated with EthOH or 100 mM 4-OHT from day 0 to day 3, and labelled 5 minutes with 500 µM 4-sU at day 3.

value: mouse ES cells

value: 4-OHT, 4-sU


title: WT GCN2iB 2

value: LNCaP

value: WT


title: RT10_4OHT_rep1

description:
spike: 4-sU labeled S2 RNA
SNVT212


title: 41-20-mJ-cm2-6-hr_S21_R1_001

value: 6 hr


title: WT GCN2iB 3

value: Prostate Cancer


title: 51-Sham-24-hr_S23_R1_001

value: Sham


title: 44-20-mJ-cm2-6-hr_R1


title: 46-40-mJ-cm2-6-hr_S22_R1_001

value: 40 mJ/cm2


title: 40-10-mJ-cm2-6-hr_R1

source_name: Dorsal skin, 10 mJ/cm2 6 hr

value: 10 mJ/cm2


title: WT GCN2iB 1


title: E4421-T2215, Pembrolizumab(10mg/kg) + Tiragolumab(10mg/kg), rep2

city: Shanghai

first: Yongqiang

last: Shan

address: 367 Shengrong Rd, Pudong District

institute: Shanghai Henlius Biologics Co.,Ltd.

data_processing:
The quality of RNAseq raw data was checked by FastQC software. The adapter and low-quality sequences were trimmed by Trimmomatic software.
The reads were mapped to human (hg19) and mouse genome (mm10) by STAR software, the reads that prefer to map to the mouse genome were removed.
The reads were mapped to reference genes (ENSEMBL GRCh37.66) by Bowtie software, and the gene expression was calculated by MMSEQ software.
Assembly: ENSEMBL GRCh37.66
Supplementary files format and content: tab-delimited text files include log2(FPKM) values for each Sample

extract_protocol:
Tumor tissue RNA was purified using the Qiagen RNeasy kit (t#74106). Total RNA was quantified by NanodropTM 2000 spectrophotometer (Thermo Scientific) and qualified by LabChip GX Touch (Perkin Elmer). Only high-quality RNA (concentration > 100 ng/μL, 260/280 >= 2, 2.2 >= 260/230 >=2, RIN>7) were used for library construction.
Library construction was performed following the official guide of MGIEasy RNA Library Prep Set (MGI).

value: Undifferentiated colon carcinoma cell

value: HuGEMM human PD-1 and TIGIT double knock-in


title: RT10_vehicle_rep3

description:
spike: 4-sU labeled S2 RNA
SNVT210

value: Ethanol, 4-sU


title: E4421-T2215, Pembrolizumab(10mg/kg) + HLX53(10mg/kg), rep3

value: Pembrolizumab(10mg/kg) + HLX53(10mg/kg)


title: 43-20-mJ-cm2-6-hr_S48_R1_001

value: Dorsal skin


title: p53 KO Vehicle 4

value: p53 KO

value: Vehicle


title: 39-10-mJ-cm2-6-hr_R1


title: WT Vehicle 4


title: p53 KO Vehicle 1


title: Ampka1KO_MSUc_rep2

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: MSUc


title: RT10_vehicle_rep2

description:
spike: 4-sU labeled S2 RNA
SNVT209

value: mouse ES cells


title: E4421-T2215, Pembrolizumab(10mg/kg) + HLX53(10mg/kg), rep2


title: WT Vehicle 3

value: LNCaP

value: WT


title: 38-10-mJ-cm2-6-hr_S40_R1_001

value: 6 hr


title: E4421-T2215, Pembrolizumab(10mg/kg) + Tiragolumab(10mg/kg), rep3


title: WT GCN2iB 4

value: Prostate Cancer


title: E4421-T2215, Pembrolizumab(10mg/kg) + HLX53(10mg/kg), rep1


title: RT10_vehicle_rep1

description:
spike: 4-sU labeled S2 RNA
SNVT208


title: E4421-T2215, Pembrolizumab(10mg/kg) + Tiragolumab(10mg/kg), rep1


title: E4421-T2215, Serplulimab(10mg/kg) + Tiragolumab(10mg/kg), rep3


title: RT7 _4OHT_rep3

description:
spike: 4-sU labeled S2 RNA
SNVT207

value: 4-OHT, 4-sU


title: 37-10-mJ-cm2-6-hr_S30_R1_001

value: 10 mJ/cm2


title: 36-10-mJ-cm2-6-hr_S14_R1_001


title: WT Vehicle 1


title: RT7 _4OHT_rep2

description:
spike: 4-sU labeled S2 RNA
SNVT206


title: E4421-T2215, Serplulimab(10mg/kg) + Tiragolumab(10mg/kg), rep2

value: Undifferentiated colon carcinoma cell


title: WT Vehicle 2


title: Hela KO + W377A 3 (batch 2)

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

description: Hela KO + W377A 3

data_processing:
The raw data contains FASTQ files of 4 experimental conditions wild type (WT), empty vector (EV), and 2 mutation conditions W377A, Y112A. Each condition has three biological replicates. The quality of raw data is initially assessed using FastQC. Subsequently, Trim Galore is employed to eliminate any adapters from the raw data. Following this, Tophat is utilized with default settings to align and annotate sequences, utilizing the mouse reference genome obtained from Gencode version M31. Finally, splicing events are detected and analyzed using rMATS based on the Tophat alignment results. Five categories of splicing events are SE (skipped exon), RI (retained intron), MXE (mutually exclusive exons), A5SS (alternative 5’ splice site), and A3SS (alternative 3’ splice site). The FDR threshold was chosen to be 0.05.
Assembly: GRCm39
Supplementary files format and content: text file

source_name: Hela

growth_protocol: Hela cell line was maintained at 37 °C in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 1% Antibiotic-Antimycotic.

extract_protocol:
Total RNA was harvested using Rneasy kit(QIAGEN, 74106)
Library was prepared by Medgenome using Illumina TruSeq stranded mRNA kit.
RNA-seq for 40M paired reads (80M total) per sample

value: Hela


title: 33-5-mJ-cm2-6-hr_S39_R1_001

source_name: Dorsal skin, 5 mJ/cm2 6 hr

value: 5 mJ/cm2


title: 34-5-mJ-cm2-6-hr_R1


title: RT7 _4OHT_rep1

description:
spike: 4-sU labeled S2 RNA
SNVT205


title: E4421-T2215, Serplulimab(10mg/kg) + Tiragolumab(10mg/kg), rep1

value: HuGEMM human PD-1 and TIGIT double knock-in


title: E4421-T2215, HLX53(10mg/kg) + Serplulimab(10mg/kg), rep3

value: HLX53(10mg/kg) + Serplulimab(10mg/kg)


title: Hela KO + W377A 2 (batch 2)

description: Hela KO + W377A 2


title: 32-5-mJ-cm2-6-hr_S17_R1_001

value: Dorsal skin


title: E4421-T2215, HLX53(10mg/kg) + Serplulimab(10mg/kg), rep2


title: RT7_vehicle_rep3

description:
spike: 4-sU labeled S2 RNA
SNVT204

value: Ethanol, 4-sU


title: RT7_vehicle_rep1

description:
spike: 4-sU labeled S2 RNA
SNVT202


title: RT7_vehicle_rep2

description:
spike: 4-sU labeled S2 RNA
SNVT203


title: E4421-T2215, HLX53(10mg/kg) + Serplulimab(10mg/kg), rep1


title: Hela KO + Y112A 2 (batch 2)

description: Hela KO + Y112A 2


title: 31-5-mJ-cm2-6-hr_S13_R1_001


title: RRBS_HF_HF5

city: Rishon LeZiyyon

first: Noam

last: Meiri

address: 68 HaMakkabbim Road

country: Israel

institute: Aro, The Volcani Center

data_processing:
Trimming of Illumina adapters, as well as quality trimming, was performed with Trim Galore using the following options: --nextseq --non_directional –rrbs.
Assembly: Reads were mapped to the rat genome
Supplementary files format and content: Bedgraph files were created with Bismark v. 0-22-3, bowtie mode.

organism: Rattus norvegicus

source_name: hypothalamic Arc

growth_protocol: Generation F0: Male rats were supplied to Bar-Ilan University on PND 21. At arrival, rats were randomly split into two groups based on their diet—a chow group or a HF group—and housed in pairs. The animals were habituated to the animal house cage for 5 days (acclimation) to minimize the degree of stress after transportation. On PND 90-100, each male was mated with one naïve (chow-fed) female in her cage.

extract_protocol:
Total DNA was isolated from the hypothalamic Arc using TriReagent
RRBS libraries were prepared using a Zymo-Seq RRBS Library Kit

treatment_protocol: Generation F1: Litter size was adjusted randomly (per sex) on PND 2 to a maximum of 8. From PND 35, the rats were subjected to diet challenge.  Paternal chow diet-fed pups and paternal HF diet-fed pups were switched to HF until PND70 at which time they were sacrifised and their Arc extracted..

value: hypothalamic Arc

value: Paternal HF


title: E4421-T2215, Tiragolumab(10mg/kg), rep3


title: 30_S35-Sham-6-hr_R1

source_name: Dorsal skin, Sham 6 hr

value: Sham


title: Hela KO + Y112A 1 (batch 2)

description: Hela KO + Y112A 1


title: RRBS_HF_HF3


title: Hela KO + WT 3 (batch 2)

description: Hela KO + WT 3


title: 35-5-mJ-cm2-6-hr_R1


title: E4421-T2215, Tiragolumab(10mg/kg), rep2


title: Hela KO + WT 2 (batch 2)

description: Hela KO + WT 2


title: E4421-T2215, Tiragolumab(10mg/kg), rep1


title: 28-Sham-6-hr_S29_R1_001


title: Hela KO + Y112A 3 (batch 2)

description: Hela KO + Y112A 3


title: RRBS_HF_HF2


title: E4421-T2215, HLX53(10mg/kg), rep3


title: RRBS_HF_HF1


title: E4421-T2215, HLX53(10mg/kg), rep2


title: 27-Sham-6-hr_S16_R1_001


title: Hela KO + WT 1 (batch 2)

description: Hela KO + WT 1


title: 26-Sham-6-hr_S12_R1_001


title: R54-prot

city: Paris

first: Jennifer

last: Bordenave

address: 1 avenue Claude Vellefaux

institute: INSERM

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R54.Ac
R54barcodes.tsv.gz
R54features.tsv.gz
R54matrix.mtx.gz

library_source: other

data_processing:
fastq files were generated using cellranger 7.0.0 mkfastq
matrix filles were generated using cellranger 7.0.0 count function, with hg38 reference transcriptome and the Antibody-Derived Tags detailed in ADT_details_README.txt, with 10000 cells as expected-cells number
Cellranger V7.0.0 count and aggr functions to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Assembly: hg38
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz

molecule: protein

growth_protocol: Bone marrow mononuclear cells were obtainded using Ficoll for gradient centrifugation technology from bone marrow patients.

extract_protocol:
Bone marrow mononuclear cells sorted from 4 donors, 7 recipients of group 1 and 3 recipients of group 2. Single cells were encapsulated in Gel-Beads-in Emulsion (GEMs) using the 10X Controller with a Chromium Nest GEM Single Cell 5' Reagent Kits v2 (Dual Index)
The CITE-seq protocol described by Stoeckius et al was used to generate an antibody-derived tag (ADT) sequencing library and a 5' gene expression library (CG000330_ChromiumNextGEMSingleCell5_v2_CellSurfaceProtein_UserGuide_RevF.pdf)
CITE-seq

value: Bone Marrow

value: Bone marrow mononuclear cell

tag: sample id

tag: bone marrow mononuclear cells sorted from

value: Recipient of group 1


title: 25-40-mJ-cm2-0-hr_R1

source_name: Dorsal skin, 40 mJ/cm2 0 hr

value: 40 mJ/cm2

value: 0 hr


title: E4421-T2215, HLX53(10mg/kg), rep1


title: RRBS_C_HF4

value: Paternal C


title: E4421-T2215, Serplulimab(10mg/kg), rep3


title: RRBS_C_HF5


title: R35-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R35.Ac
R35barcodes.tsv.gz
R35features.tsv.gz
R35matrix.mtx.gz


title: RRBS_HF_HF4


title: RRBS_C_HF3


title: E4421-T2215, Serplulimab(10mg/kg), rep2


title: 23-40-mJ-cm2-0-hr_S28_R1_001


title: R35-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R35.ARN
R35barcodes.tsv.gz
R35features.tsv.gz
R35matrix.mtx.gz


title: 29-Sham-6-hr_R1

value: 6 hr


title: E4421-T2215, Serplulimab(10mg/kg), rep1

value: Undifferentiated colon carcinoma cell


title: RRBS_C_HF2


title: R21-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R21.Ac
R21barcodes.tsv.gz
R21features.tsv.gz
R21matrix.mtx.gz


title: E4421-T2215, Pembrolizumab(10mg/kg), rep3


title: RRBS_C_HF1


title: 21-40-mJ-cm2-0-hr_S11_R1_001


title: 22-40-mJ-cm2-0-hr_S15_R1_001


title: R21-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R21.ARN
R21barcodes.tsv.gz
R21features.tsv.gz
R21matrix.mtx.gz


title: CG4, H3k27ac, ChIP

first: 敏溪

last: 方

address: 杭师大仓前

institute: 浙江大学

data_processing:
Pair-end sequencing was performed on Illumina platform (San Diego, CA)
Data were processed further with MACS version 2.1.0 peak calling software to identify regions enriched in IP over Input samples.
HOMER  was used to detect the de novo motif and the matched known motifs of Myt1 peaks.
Assembly: Rn6
Supplementary files format and content: bigwig

extract_protocol:
CG4 cells were cross-linked with 1% paraformaldehyde at RT and chromatin was sheared to fragment of 150-400 bp with a Scientz-IID sonicator. 10% of the sheared chromatin sample were removed as the input group.
Library construction and sequencing of Chip-seq were performed by Novogene Co., Ltd. (Beijing, China).go, CA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Rat oligodendrocyte precursor

tag: chip antibody


title: repeat_20_2-20-mJ-cm2-0-hr_R1

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.0
Alignment was performed using STAR v2.7.10a
Gene counts were performed with qCount in the QuasR R package v1.34.0
Normalization was performed with DESeq2 v1.36.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated count matrix

source_name: Dorsal skin, 20 mJ/cm2 0 hr

extract_protocol:
Total RNA was extracted using RNeasy Fibrous Tissue Kits (Qiagen Inc., cat #: 74704) according to the manufacturer’s instructions (with 700 µL of the mixed lysate transferred to a RNeasy Mini column and repeated until all lysate had been used). During the procedure, Qiagen’s On-Column RNase-free DNase was used to eliminate possible DNA contamination.
Library preparation for next-generation sequencing was conducted on randomized RNA samples using the TruSeq-stranded mRNA kit (Illumina, San Diego, California) according to the sample preparation guide. The input RNA for library preparation was 300 ng per sample. A dual index scheme was used to multiplex samples for sequencing, which were pooled and sequenced on high output flow cells using an Illumina NextSeq® 500. Single-end sequencing was performed with a read length of 75 bp. A sequencing depth ~40 million reads per sample was achieved.

value: 20 mJ/cm2


title: R12-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R12.Ac
R12barcodes.tsv.gz
R12features.tsv.gz
R12matrix.mtx.gz


title: E4421-T2215, Pembrolizumab(10mg/kg), rep2

tag: cell line

value: HuGEMM human PD-1 and TIGIT double knock-in


title: 19-20-mJ-cm2-0-hr_R1

tag: tissue


title: CG4, H3k9ac, ChIP


title: 24_2-40-mJ-cm2-0-hr_R1


title: Hela KO + W377A 1 (batch 2)

description: Hela KO + W377A 1

value: Hela


title: E4421-T2215, Pembrolizumab(10mg/kg), rep1

tag: genotype


title: R12-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R12.ARN
R12barcodes.tsv.gz
R12features.tsv.gz
R12matrix.mtx.gz


title: 18-20-mJ-cm2-0-hr_S19_R1_001

value: Dorsal skin


title: R54-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R54.ARN
R54barcodes.tsv.gz
R54features.tsv.gz
R54matrix.mtx.gz


title: CG4, input


title: CG4, MYT1, ChIP


title: R7-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R7.Ac
R7barcodes.tsv.gz
R7features.tsv.gz
R7matrix.mtx.gz


title: E4421-T2215, Vehicle, rep2

value: Vehicle


title: R7-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R7.ARN
R7barcodes.tsv.gz
R7features.tsv.gz
R7matrix.mtx.gz


title: CG4, MYT1, input


title: E4421-T2215, Vehicle, rep1


title: 16-20-mJ-cm2-0-hr_S4_R1_001


title: DB-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
DB.Ac
DBbarcodes.tsv.gz
DBfeatures.tsv.gz
DBmatrix.mtx.gz

value: DB

value: Donor


title: E4421-T2106, HLX53(10mg/kg) + Serplulimab(10mg/kg), rep3

value: HLX53(10mg/kg) + Serplulimab(10mg/kg)


title: 17-20-mJ-cm2-0-hr_S10_R1_001


title: 15-10-mJ-cm2-0-hr_R1

source_name: Dorsal skin, 10 mJ/cm2 0 hr

value: 10 mJ/cm2


title: DA-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
DA.Ac
DAbarcodes.tsv.gz
DAfeatures.tsv.gz
DAmatrix.mtx.gz

value: Bone Marrow

value: Bone marrow mononuclear cell

value: DA


title: 13-10-mJ-cm2-0-hr_S18_R1_001

value: 0 hr


title: E4421-T2106, HLX53(10mg/kg) + Serplulimab(10mg/kg), rep1


title: 2102EP-C1.sh6A+6B.3

city: Urbana

first: Doha

last: Shokry

state: Illinois

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois Urbana-Champaign

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p14 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (³|2.0|-fold and £1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Assembly: human genome assembly NCBI GRCh38.p14
Supplementary files format and content: tab-delimited text files includeTMM normalized log counts per million (log CPM) values for each Sample …

source_name: testis

growth_protocol: Cells were treated with 0.5 µM Cisplatin for 6hrs, 1 µM GSK-J4 for 3 days, or combination of both drugs, and then assessed for cell proliferation by CellTiter-Glo (Promega).

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
The libraries were sequenced on a HiSeq 4000 using HiSeq 4000 sequencing kit version 1. according to the manufacturer’s instructions.

value: testis

value: 2102EP-C1 Cisplatin resistant testicular cancer cell line

value: Cisplatin resistant testicular cancer


title: 2102EP-C1.sh6A+6B Cisplatin.2

value: sh6A+6B Cisplatin


title: DB-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
DB.ARN
DBbarcodes.tsv.gz
DBfeatures.tsv.gz
DBmatrix.mtx.gz

source_name: Bone Marrow


title: 2102EP-C1.sh6A+6B Cisplatin.3


title: E4421-T2215, Vehicle, rep3

value: Undifferentiated colon carcinoma cell


title: R50-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R50.Ac
R50barcodes.tsv.gz
R50features.tsv.gz
R50matrix.mtx.gz

value: Recipient of group 2


title: 11-10-mJ-cm2-0-hr_S3_R1_001

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

institute: Government of Canada


title: 14_2-10-mJ-cm2-0-hr_R1


title: 12-10-mJ-cm2-0-hr_S7_R1_001


title: DA-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
DA.ARN
DAbarcodes.tsv.gz
DAfeatures.tsv.gz
DAmatrix.mtx.gz


title: E4421-T2106, HLX53(5mg/kg) + Serplulimab(10mg/kg), rep3

value: HuGEMM human PD-1 and TIGIT double knock-in

value: HLX53(5mg/kg) + Serplulimab(10mg/kg)


title: E4421-T2106, HLX53(10mg/kg) + Serplulimab(10mg/kg), rep2


title: E4421-T2106, HLX53(5mg/kg) + Serplulimab(10mg/kg), rep2


title: R50-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R50.ARN
R50barcodes.tsv.gz
R50features.tsv.gz
R50matrix.mtx.gz


title: E4421-T2106, HLX53(5mg/kg) + Serplulimab(10mg/kg), rep1


title: R36-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R36.Ac
R36barcodes.tsv.gz
R36features.tsv.gz
R36matrix.mtx.gz

value: Recipient of group 1


title: 2102EP-C1.sh6A+6B.2


title: 10-5-mJ-cm2-0-hr_R1

source_name: Dorsal skin, 5 mJ/cm2 0 hr

value: Dorsal skin

value: 5 mJ/cm2


title: 2102EP-C1.pLKO1 Cisplatin.3

value: Cisplatin


title: R36-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R36.ARN
R36barcodes.tsv.gz
R36features.tsv.gz
R36matrix.mtx.gz


title: E4421-T2106, Serplulimab(10mg/kg), rep3


title: 9-5-mJ-cm2-0-hr_R1


title: 2102EP-C1.sh6A+6B.1


title: E4421-T2106, Serplulimab(10mg/kg), rep2


title: 8-5-mJ-cm2-0-hr_S9_R1_001


title: 2102EP-C1.sh6A+6B Cisplatin.1


title: 2102EP-C1.pLKO1 Cisplatin.2


title: R33-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R33.Ac
R33barcodes.tsv.gz
R33features.tsv.gz
R33matrix.mtx.gz


title: 2102EP-C1.pLKO1 Cisplatin.1


title: E4421-T2106, Serplulimab(10mg/kg), rep1


title: E4421-T2106, HLX53(10mg/kg), rep3


title: 2102EP-C1.pLKO1.3

value: Control


title: 6-5-mJ-cm2-0-hr_S2_R1_001


title: 7-5-mJ-cm2-0-hr_S6_R1_001


title: R33-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R33.ARN
R33barcodes.tsv.gz
R33features.tsv.gz
R33matrix.mtx.gz

value: Bone Marrow


title: R28-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R28.Ac
R28barcodes.tsv.gz
R28features.tsv.gz
R28matrix.mtx.gz

value: Bone marrow mononuclear cell


title: 2102EP-C1.pLKO1.2


title: 5-Sham-0-hr_R1

source_name: Dorsal skin, Sham 0 hr

value: Sham


title: E4421-T2106, HLX53(10mg/kg), rep2


title: E4421-T2106, HLX53(10mg/kg), rep1


title: R14-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
R14.Ac
R14barcodes.tsv.gz
R14features.tsv.gz
R14matrix.mtx.gz


title: 2102EP-C1.Combination.3

value: Combination


title: 4-Sham-0-hr_R1

value: 0 hr


title: R28-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R28.ARN
R28barcodes.tsv.gz
R28features.tsv.gz
R28matrix.mtx.gz


title: 2102EP-C1.pLKO1.1

value: testis

value: 2102EP-C1 Cisplatin resistant testicular cancer cell line


title: E4421-T2106, Pembrolizumab(10mg/kg) + Tiragolumab(10mg/kg), rep3


title: 3-Sham-0-hr_S8_R1_001


title: R14-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
R14.ARN
R14barcodes.tsv.gz
R14features.tsv.gz
R14matrix.mtx.gz


title: 2102EP-C1.Combination.2

value: Cisplatin resistant testicular cancer


title: E4421-T2106, Pembrolizumab(10mg/kg) + Tiragolumab(10mg/kg), rep2

value: Undifferentiated colon carcinoma cell


title: 2-Sham-0-hr_S5_R1_001


title: D9-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
D9.Ac
D9barcodes.tsv.gz
D9features.tsv.gz
D9matrix.mtx.gz

value: Donor


title: E4421-T2106, Pembrolizumab(10mg/kg) + Tiragolumab(10mg/kg), rep1

value: HuGEMM human PD-1 and TIGIT double knock-in


title: 2102EP-C1.Combination.1


title: D9-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
D9.ARN
D9barcodes.tsv.gz
D9features.tsv.gz
D9matrix.mtx.gz


title: KEC, HNF1B-KO, rep3

first: Marco

last: PONTOGLIO

state: Choisir votre état

address: Inserm U1016, 24 rue du Faubourg Saint-Jacques

department: Growth and Signalling

institute: Inserm

description: RSEM counts

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using  STAR version=2.7.6.a
Reads counts per genes were computed with RSEM v1.3.1
Assembly: mm10
Supplementary files format and content: Reads counts by sample done by RSEM

source_name: KEC

growth_protocol: KEC cells were grown in DMEM, 10% fetal bovine serum and 1% penicillin/streptomycin at 37C with 5% CO2.

extract_protocol:
Cells were collected in TRIzol and RNA was extracted following the manufacturer’s instructions.
Libraries were prepared from 250 ng of total RNA per sample using the Stranded mRNA Prep kit (Illumina).

value: KEC

value: Kidney epithelial cells

tag: cell cycle_stage

value: Asynchronous


title: D7-prot

description:
ADT: read1 file contains cell bracode and UMI; read2 file contains Antibody Derived Tag reads
D7.Ac
D7barcodes.tsv.gz
D7features.tsv.gz
D7matrix.mtx.gz


title: E4421-T2106, Vehicle, rep3

value: Vehicle


title: 2102EP-C1.GSK-J4.3


title: 1-Sham-0-hr_S1_R1_001

value: Dorsal skin


title: 2102EP-C1.GSK-J4.2


title: KEC, HNF1B-KO, rep2

description: RSEM counts


title: E4421-T2106, Vehicle, rep1


title: D7-GEX

description:
GEX (5'mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
D7.ARN
D7barcodes.tsv.gz
D7features.tsv.gz
D7matrix.mtx.gz


title: E4421-T2106, Vehicle, rep2


title: 2102EP-C1.Cisplatin.3

value: Cisplatin


title: 20_00198_LI_SING,Control, scRNAseq

city: Chuncheon

first: HEO

last: YEONJEONG

address: 70, Bangsong-gil

country: South Korea

institute: Kangwon National University Hospital

description: 10x Genomics

data_processing:
Barcoded processing, gene coungting were made using the Cell Ranger software v6.0.2. 10x Genomics) software. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Feature-barcode matrices were then processed in R (v4.0.3) using the Seurat package (v 3.2.2).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Immune cells from peripheral blood were isolated by Ficoll density gradient centrifugation protocol. And after two rounds of PBS washing, cell counting was performed.
Library was performed according to the manufacter's instructions (Chromium Next GEM single cell 3' v3.1 protocol, 10x genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into

value: Blood

value: PBMC

tag: group

value: Control


title: 2102EP-C1.GSK-J4.1

tag: treatment


title: 20_00197_LI_SING,COPD, scRNAseq

description: 10x Genomics

value: COPD


title: 2102EP-C1.Cisplatin.2


title: KEC, WT, rep2

description: RSEM counts

value: WT


title: Intestinalepithelialcells, Git2-knockout mice, rep2

city: shanghai

first: huijuan

last: le

address: kongjiang road

department: School of Medicine

institute: Shanghai Jiaotong University

data_processing:
Raw data was cleaned by SOAPnuke.
Clean data was mapped by HISAT.
Clean reads were mapped to GRCm39 using Bowtie2.
Read count normalization was performed using RSEM.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

source_name: intestine

extract_protocol:
RNA was harvested using Pure Yield RNA Midi-prep kit (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
mRNA was harvested using oligodT, then cut and synthesized into cDNA.

value: intestine

value: Intestinalepithelialcells (IEC)

value: Git2 knockdown


title: KEC, HNF1B-KO, rep1

description: RSEM counts


title: KEC, WT, rep1

description: RSEM counts


title: 2102EP-C1.VC.3

value: testis

value: 2102EP-C1 Cisplatin resistant testicular cancer cell line

value: Cisplatin resistant testicular cancer


title: Intestinalepithelialcells, wild type mice, rep3


title: KEC, Mit NAQC,TOP1, rep2

description:
BamCoverage of WT_Mit_NAQC_TOP1_2
Mit_Naqc_TOP1_2_bamCoverage_CPM.bigwig

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with 2 replicates (each replicate was sequenced in two sessions: set1 + set2 )
bams files from set1 and set2 were pooled with samtools merge
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize = 1
Supplementary files format and content: Peaks were called using using  GEM version 3.4 http://cgs.csail.mit.edu/gem/, narrowPeak format

growth_protocol: KECs (kidney epithelial cells) were grown in DMEM, 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
DNAs from ChIP or Input were de-crosslinked and extracted with the IPure kit v2 (Diagenode).
Libraries were prepared from 1ng of immunoprecipitated DNA or Inputs with the MicroPlex v2 kit (Diagenode), according to manufacturer's instructions.

treatment_protocol:
Mitotic cells were obtained with a thymidine block (2mM 24h) followed by an incubation in 5uM STLC (S-trityl-L-cysteine) for 8-14 h
The HNF1β-knockout KEC cell line was created by CRISPR/Cas9 targeting of HNF1b's exon 1.

value: KEC

value: Mitosis

value: TOP1 (ABclonal custom made rabbit polyclonal)


title: 20_00194_LI_SING,COPD, scRNAseq

description: 10x Genomics


title: 2102EP-C1.Cisplatin.1


title: 20_00195_LI_SING,COPD, scRNAseq

description: 10x Genomics


title: 20_00193_LI_SING,Control, scRNAseq

description: 10x Genomics


title: 2102EP-C1.VC.2


title: Intestinalepithelialcells, Git2-knockout mice, rep1


title: Intestinalepithelialcells, wild type mice, rep2


title: KEC, Mit NAQC,TOP1, rep1

description:
BamCoverage of WT_Mit_NAQC_TOP1_1
Mit_Naqc_TOP1_1_bamCoverage_CPM.bigwig
BamCoverage pool of WT_Mit_NAQC_TOP1_1, WT_Mit_NAQC_TOP1_2
Mit_Naqc_TOP1_pool_bamCoverage_CPM.bigwig

value: Kidney epithelial cells


title: 2102EP-C1.VC.1


title: Intestinalepithelialcells, wild type mice, rep1


title: Intestinalepithelialcells, Git2-knockout mice, rep3


title: 20_00196_LI_SING,COPD, scRNAseq

description: 10x Genomics


title: 20_00265_LI_SING,COPD, scRNAseq

description: 10x Genomics


title: KEC HNF1b-KO, Mit NAQC,TOP1, rep2

description:
BamCoverage of KO_Mit_NAQC_TOP1_2
KO_Mit_NAQC_TOP1_ChIP_1_sorted_bamCoverage_CPM.bigwig


title: KEC, WT, rep3

description: RSEM counts

value: Asynchronous


title: KEC HNF1b-KO, Mit NAQC,TOP1, rep1

description:
BamCoverage of KO_Mit_NAQC_TOP1_1
KO_Mit_NAQC_TOP1_ChIP_1_sorted_bamCoverage_CPM.bigwig
BamCoverage pool of KO_Mit_NAQC_TOP1_1, KO_Mit_NAQC_TOP1_2
KO_Mit_NAQC_TOP1_ChIP_pool_sorted_bamCoverage_CPM.bigwig


title: NT2/D1-A4.Combination.3

value: NT2/D1-A4 Cisplatin resistant testicular cancer cell line

value: Combination


title: 20_00264_LI_SING,Control, scRNAseq

description: 10x Genomics

value: Blood

value: PBMC


title: NT2/D1-A4.Combination.2


title: KEC HNF1b-KO, Mit NAQC, Inp

description:
BamCoverage of KO_Mit_NAQC_Input
KO_Mit_NAQC_Inp_sorted_bamCoverage_CPM.bigwig


title: 20_00266_LI_SING,Control, scRNAseq

description: 10x Genomics

value: Control


title: NT2/D1-A4.Combination.1


title: KEC, Mit NAQC, Inp1

description:
BamCoverage of Mit_Naqc_INPUT_1
Mit_Naqc_INPUT_1_bamCoverage_CPM.bigwig

value: WT


title: NT2/D1-A4.GSK-J4.3


title: p35KO_rep3

city: Hangzhou

first: Shudi

last: Zhao

address: Yuhangtang Road No.866

institute: Zhejiang University

data_processing:
Raw data was cleaned by Trim Galore (Version 0.6.6) with the parameters "-q 25 --phred33 --length 36 -e 0.1 --stringency 5", and maped to silkworm genome using HISAT2 (Version 2.2.1). The resulted SAM file was transformed to BAM file and sorted by SAMtools (Version 1.12). Mapped reads at the exons of each gene were counted via featureCounts, which is a part of the Subread (Version 2.0.1).
Assembly: SilkBase November 2016
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Bombyx mori

source_name: BmN cells

extract_protocol:
BmN cells (1e6) with indicated treatments were harvested and total RNA of the cells was extracted using Trizol.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the instructions.

value: BmN cells


title: NT2/D1-A4.GSK-J4.2


title: p35KO_rep2


title: KEC, Mit NAQC, HNF1b, rep1

description:
BamCoverage pool of Mit_Naqc_HNF1_1, Mit_Naqc_HNF1_2
Mit_Naqc_HNF1_pool_bamCoverage_CPM.bigwig
Peaks pool of Mit_Naqc_HNF1_1, Mit_Naqc_HNF1_2
gem_Mit_Naqc_HNF1_pool_all_bams.GPS_events.narrowPeak

value: HNF1b (ABclonal custom made rabbit polyclonal)


title: p35KO_rep1


title: 20_00263_LI_SING,Control, scRNAseq

description: 10x Genomics


title: hr5KO_rep2


title: NT2/D1-A4.GSK-J4.1


title: 20_00267_LI_SING,Control, scRNAseq

description: 10x Genomics


title: 20_00262_LI_SING,Control, scRNAseq

description: 10x Genomics


title: hr3KO_rep1


title: 20_00270_LI_SING,COPD, scRNAseq

description: 10x Genomics

value: COPD


title: KEC, Mit AQC, HNF1b, rep2

description:
BamCoverage pool of Mit_Aqc_HNF1_1, Mit_Aqc_HNF1_2
Mit_Aqc_HNF1_pool_bamCoverage_CPM.bigwig
Peaks pool of Mit_Aqc_HNF1_1, Mit_Aqc_HNF1_2
gem_Mit_Aqc_HNF1_pool_all_bams.GPS_events.narrowPeak

value: HNF1b (ABclonal custom rabbit polyclonal)


title: KEC, Mit AQC, Inp1

description:
BamCoverage of Mit_Aqc_INPUT_1
Mit_Aqc_INPUT_1_bamCoverage_CPM.bigwig


title: 20_00271_LI_SING,COPD, scRNAseq

description: 10x Genomics


title: NT2/D1-A4.Cisplatin.3

value: testis

value: Cisplatin


title: KEC, Mit AQC, HNF1b, rep1

value: KEC


title: NT2/D1-A4.Cisplatin.1

value: Cisplatin resistant testicular cancer


title: hr2KO_rep1


title: KEC, Asy NAQC, Inp1

description:
BamCoverage of Asy_Naqc_INPUT_1
Asy_Naqc_INPUT_1_bamCoverage_CPM.bigwig


title: hr2KO_rep2


title: NKG2D/Dap10-CD3z rep3

city: London

first: John

last: Maher

address: Great Maze Pond

country: United Kingdom

institute: King's College London

data_processing:
Quality of the sequencing data was studied by the package fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Transcript levels were quantified using Salmon (v. 1.9.0) against a decoy-aware transcriptome generated from the GENCODE reference assembly (v. 41) of the human genome.
Assembly: GRCh38
Supplementary files format and content: tab-separated text files generated by salmon, indicating transccript id, length, effective length, TPMs and number of reads

source_name: T-cells

growth_protocol: Retrovirus transduced CAR T-cells were expanded in RPMI + 5% human serum containing interleukin-2 (100U/mL)

extract_protocol:
Nucleic acid extractionwas performed by Genewiz (Genomics from Azenta Life Sciences).
Sample QC, library preparation and sequencing were performed by Genewiz (Genomics from Azenta Life Sciences). Paired-end sequencing was performed on the Illumina NovaSeq, with a 2x150bp configuration and an estimated 20 million paired-end reads per sample.

treatment_protocol: Non-tissue culture-treated 24-well plates were coated with 0.1 ug/mL of rhMICA in PBS. The next day, PBS was removed and 2x105 CAR T-cells were added per well in 1mL of R5 medium. After 24h, T cells were harvested into 15 mL Falcon tubes, washed with 5 mL of PBS, and centrifuged at 800 g for 10 minutes. Cells were then re-suspended into an appropriate volume of and counted using the LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems) (1:2 dilution with Trypan Blue) for determination of cell count and viability. A total of 1x106 T cells per construct were aliquoted and centrifuged at 800 g for 10 minutes. Pellets were stored at -20C until shipment for RNA sequencing.

tag: donor id

value: T-cells

value: NKG2D/Dap10-CD3z expressing

value: MICA activation


title: 20_00269_LI_SING ,COPD, scRNAseq

description: 10x Genomics

tag: cell type


title: NT2/D1-A4.VC.3

value: NT2/D1-A4 Cisplatin resistant testicular cancer cell line


title: KEC, Mit NAQC, HNF1b, rep2

value: Kidney epithelial cells

value: Mitosis


title: hr1KO_rep2


title: hr3KO_rep2


title: KEC, Asy NAQC, HNF1b, rep1

description:
BamCoverage pool of Asy_Naqc_HNF1_1, Asy_Naqc_HNF1_2
Asy_Naqc_HNF1_pool_bamCoverage_CPM.bigwig
Peaks pool of Asy_Naqc_HNF1_1, Asy_Naqc_HNF1_2
gem_Asy_Naqc_HNF1_pool_all_bams.GPS_events.narrowPeak

value: Asynchronous


title: NT2/D1-A4.VC.1

value: Control


title: hr1KO_rep1


title: NKG2D/Dap10-CD3z rep1


title: brobcKO_rep2


title: KEC, Asy AQC, Inp1

description:
BamCoverage of Asy_Aqc_INPUT_1
Asy_Aqc_INPUT_1_bamCoverage_CPM.bigwig

value: WT


title: NT2/D1-A4.Cisplatin.2


title: NT2/D1-A4.VC.2


title: KEC, Asy NAQC, HNF1b, rep2


title: hr5KO_rep1

value: BmN cells


title: NKG2D-CD3z/Dap10 rep3

value: NKG2D-CD3z/Dap10 expressing


title: retapamulin-treated, biol rep2

city: San Francisco

first: Brianna

middle: Lynn

last: Bibel

department: Cellular and Molecular Pharmacology

institute: Brianna Bibel

description: mitoribosome-protected footprints

data_processing:
Reads were trimmed to remove ligated 3’ linker (TAGACAGATCGGAAGAGCACACGTCTGAA) with Cutadapt
Reads without linker were discarded and the unique molecular identifier (UMI) was then extracted from remaining reads using a custom script. UMIs consisted of 5 random nucleotides at the 3’ end ligated as part of the 3’ linker
Trimmed reads were filtered after alignment using bowtie1 to human rRNA (allowing 1 internal and 1 5’ mismatch) and human tRNA (allowing 1 internal, 1 5’, and 3 3’ mismatches). Remaining reads were aligned to the GRCh38 human reference genome from GENCODE using STAR 2.7.3. For mitoRP samples with mouse spike-ins, the M17 mouse reference genome from GENCODE was merged with the human genome. STAR mismatch parameters for mitoRP and cytoRP: --outFilterMismatchNoverReadLmax 0.07 and --outFilterMismatchNmax 3. STAR parameters for RNA-seq: default
PCR duplicates were identified by their UMI and removed using a custom script
Read coverage for mitochondrial mRNA mapping mitoRP reads was transformed to A-site density using a custom script. Offsets from the 3’ end of 33:[-15], 34:[-16], 35:[-17], 36:[-17], 37:[-18], 38:[-19], 39:[-20] were used.
Coverage across each codon was calculated by summing the read counts across the three sub codon positions and counts were normalized to reads per million mitochondrial mRNA-mapped reads (rpm)
Pause scores were calculated as the fold-change over the mean of rpm-normalized values in a 21-codon sliding window
Assembly: hg38
Supplementary files format and content: *CodonCoverageEach_*.rpm.bedGraph files were made as described above, with the 4th column being codon rpm values. Plus (P) and minus (M) strand files are both given. Only read lengths given in the file name are included.
Supplementary files format and content: *CodonCoverageEach_*.rpm_pauseScorefold_win21.bedGraph files were made as described above, with the 4th column being pause scores. Plus (P) and minus (M) strand files are both given. Only read lengths given in the file name are included.

molecule: other

source_name: Freestyle 293-F

growth_protocol: Cell culture and treatment FreeStyleTM 293-F cells (HEK293 cells adapted for serum-free suspension culture) were grown in suspension culture at 37°C, 5% CO2, with orbital shaking (115 rpm) in unmodified FreeStyleTM 293 Expression Medium (Gibco) in the absence of antibiotics. Cell cultures were diluted to 2 x 10^6  viable cells/mL and 50 mL portions were transferred into 125 mL flasks before use.

extract_protocol:
Mitoribosome footprint isolation: Mitoribosome footprints were prepared as described in Soto et al., 2022 with modifications. Each 10 x 10^6 cell pellet of frozen cells was resuspended in 900 μL of mito-RP lysis buffer (10mM Tris pH 7.5; 50mM NH4Cl, 20mM MgCl2, 0.25% lauryl maltoside, 10mM DTT, 1X EDTA-free protease inhibitor cocktail (Pierce) containing antibiotic or DMSO at the same concentration as in the pre-treatment) and incubated for 10 min on ice. It was then homogenized via 15 strokes of a Dounce homogenizer and centrifuged for 1 min @ 1000 x g. The supernatant was transferred to new tubes and a 25 μL portion of each was flash frozen in liquid nitrogen for total RNA sequencing. RNase If (NEB) was added to each supernatant for a final concentration of 7.25 U/μL to produce mitoribosome footprints. Samples were incubated for 30 minutes at room temperature without rotation. 80 U of SUPERaseInTM RNase Inhibitor (Invitrogen) was then added per 450 μL of digested lysate to prevent overdigestion and the digested lysate was clarified by centrifugation in a benchtop microcentrifuge @ 10,000 RPM, 5 min, 4°C. Clarified lysates were then transferred to a 10-50% linear sucrose gradient (prepared in mito-RP lysis buffer without lauryl maltoside & protease inhibitor, using a BioComp GradientMasterTM) and centrifuged for 3 h @ 4°C, SW41Ti rotor. Fractions were collected with a BioComp Piston Gradient FractionatorTM and portions corresponding to mitomonosomes (identified based on UV 260 trace and confirmed via western blot for MRPL12 and MRPS18B) were frozen @ -80°C in 3 volumes of TRIzolTM LS (Invitrogen). Footprints were then isolated using a Direct-zolTM RNA kit (Zymo) and subsequently concentrated using a RNA Clean and Concentrator-5 kit (Zymo). RNA was then size-selected by running a 15% TBE-Urea gel and extracting fragments between 28 and 40 nt in length, corresponding to mitoribosome-protected footprints.
Sequencing library preparation: Libraries were prepared from the extracted footprint RNA as described2–5 with modifications. Briefly, extracted RNA was desalted using a RNA Clean and Concentrator-5 kit (Zymo), then dephosphorylated with T4 PNK (NEB) and ligated to a preadenylated oligonucleotide linker (NI-816: 5’-/5Phos/NNNNNTAGACAGATCGGAAGAGCACACGTCTGAA/3ddC/-3’) using T4 RNA Ligase 2 truncated KQ (NEB). Unligated linker was depleted by treatment with yeast 5’-deadenylase (NEB) and RecJ exonuclease (Lucigen/Epicenter), and the linker-ligated footprints were then purified via a Oligo Clean and Concentrator kit (Zymo). The ligation products were then reverse transcribed using Protoscript II reverse transcriptase (NEB) and NI-802 primer (5’-/5Phos/ NNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC-3’). The RNA template was then hydrolyzed with NaOH. The reverse transcription products were desalted and concentrated with an Oligo Clean & Concentrator kit (Zymo), followed by gel purification via a 15% TBE-Urea PAGE gel. Extracted cDNA was then circularized using CircLigase II (Lucigen). Circular DNA was quantified via qPCR, then amplified via PCR with the forward primer NI-798 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ and a unique reverse indexing primer (containing a unique 6 nucleotide barcode) for each sample. PCR products were then purified via a DNA Clean & Concentrator 5 column (Zymo) followed by gel purification via an 8% non-denaturing TBE PAGE gel. Extracted DNA was then quantified and checked for quality with a BioAnalyzer (Agilent).
Mitoribosome profiling

treatment_protocol: To each portion of 2 x 10^6 cells, DMSO or antibiotic was added to a final concentration of 1% DMSO, 300 μM (97 μg/mL) chloramphenicol (CHL), 300 μM (101 μg/mL) linezolid (LZD), or 100 μM (155 μg/mL) retapamulin (RET). Samples were placed back into the incubator for 5 minutes before collecting cells via fast vacuum filtration through a 0.8 μM filter. The collected cells were then quickly scraped off the filter and plunged into liquid nitrogen. The frozen cells were stored at -80°C until use.

value: Freestyle 293-F

value: Human embryonic kidney

value: 100 uM retapamulin


title: NKG2D-CD3z/Dap10 rep1


title: KEC, Asy AQC, HNF1b, rep2

description:
BamCoverage pool of Asy_Aqc_HNF1_1, Asy_Aqc_HNF1_2
Asy_Aqc_HNF1_pool_bamCoverage_CPM.bigwig
Peaks pool of Asy_Aqc_HNF1_1, Asy_Aqc_HNF1_2
gem_Asy_Aqc_HNF1_pool_all_bams.GPS_events.narrowPeak

value: HNF1b (ABclonal custom made rabbit polyclonal)


title: retapamulin-treated, biol rep1

description: mitoribosome-protected footprints


title: broaKO_rep2


title: brobcKO_rep1


title: NKG2D-CD3z rep3

value: NKG2D-CD3z expressing


title: KEC, Asy AQC, HNF1b, rep1

value: KEC


title: linezolid-treated, biol rep4

description: mitoribosome-protected footprints

value: 300 uM linezolid


title: broaKO_rep1


title: NKG2D-CD3z rep2

value: T-cells


title: mRNA_BmGATA_V_rep3

data_processing:
Raw data was cleaned by Trim Galore (Version 0.6.6) with the parameters "-q 25 --phred33 --length 36 -e 0.1 --stringency 5". For RNA-seq, cleaned data was maped to silkworm genome using HISAT2 (Version 2.2.1). The resulted SAM file was transformed to BAM file and sorted by SAMtools (Version 1.12). Mapped reads at the exons of each gene were counted via featureCounts, which is a part of the Subread (Version 2.0.1). For ChIP-seq, cleaned data was maped using Bowtie 2 (Version 2.4.4). Afterwards, the resulted SAM files were converted into BAM format using SAMtools (Version 1.12), and MACS2 (Version 2.2.7.1) was adopted for peaks calling with the parameters "-p 0.1 -f BAMPE -g 4.6e8".
Assembly: SilkBase November 2016
Supplementary files format and content: tab-delimited narrowPeak files includes narrow peaks for each ChIP-seq sample
Supplementary files format and content: tab-delimited text files includes raw counts for each RNA-seq sample

extract_protocol:
For RNA-seq, BmN cells (1e6) with indicated treatments were harvested and total RNA of the cells was extracted using Trizol. For ChIP-seq, cells were collected and cross-linked with 1% formaldehyde for 10 min at 25˚C. The reaction was then quenched by addition of glycine to a final concentration of 125 mM. Afterwards, cells were lysed and chromatin was obtained on ice. Chromatin was sheared to a mean fragment size of 200-500 base pairs. The samples were immunoprecipitated by anti-HA antibody (Abcam, 9110).
For RNA-seq, a total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the instructions. For ChIP-seq, sequencing libraries were generated using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) following the instructions.

value: BmNPV infection


title: linezolid-treated, biol rep3

description: mitoribosome-protected footprints


title: NKG2D-CD3z rep1

value: MICA activation


title: RGCs of  WT mice (P21) 2

city: Beijing

first: Tao

last: Huang

state: Beijing

address: Dong Da Jie No.8

institute: The Fifth Medical Center of Chinese PLA General Hospital

data_processing:
All raw sequencing reads were quality checked with FastQC (v0.11.9), and leading bases were trimmed from the reads with Trimmomatic (v0.39) as appropriate.
Quality-checked reads were mapped to the GRCm38/mm10 mouse reference genome with splice-aware aligner HISAT2 (v2.2.1).
featureCounts (Subread v2.0.3) was used to estimate the expression counts of the genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Retina

extract_protocol:
Total RNA was isolated using TRIzol® Reagent following the manufacturer's protocol. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Retina

value: retinal ganglion cells

tag: facs type

value: Thy1.2 positive

value: developmental control


title: NKG2D/Dap10-CD3z rep2

value: NKG2D/Dap10-CD3z expressing


title: linezolid-treated, biol rep2, tech rep 2

description: mitoribosome-protected footprints


title: mRNA_BmGATA_V_rep2

value: BmN cells


title: RGCs of  WT mice (P14) 3

tag: age

value: WT


title: RGCs of  WT mice (P21) 1


title: mRNA_BmGATA_V_rep1


title: RGCs of  WT mice (P14) 2


title: linezolid-treated, biol rep1, tech rep 2

description: mitoribosome-protected footprints

value: Freestyle 293-F


title: NKG2D / Dap10-12 rep2

value: NKG2D / Dap10-12 expressing


title: NKG2D / Dap10-12 rep3


title: linezolid-treated, biol rep2, tech rep 1

description: mitoribosome-protected footprints

value: Human embryonic kidney


title: NKG2D / Dap10-12 rep1


title: RGCs of  WT mice (P1) 3


title: NKG2D rep3

value: NKG2D over-expressing


title: mRNA_BmGATA_Mock_rep2

value: Mock


title: mRNA_BmGATA_Mock_rep1


title: linezolid-treated, biol rep1, tech rep 1

description: mitoribosome-protected footprints


title: RGCs of  WT mice (P1) 2


title: chloramphenicol-treated, biol rep3

description: mitoribosome-protected footprints

value: 300 uM chloramphenicol


title: ChIP_BmGATA_V


title: RGCs of  WT mice (P1) 1


title: NKG2D rep1


title: ChIP_BmGATA_Mock


title: miR-324_null_4

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

institute: Newcastle University

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the mouse GRCh38 (release 92) transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Mouse GRCh38 (release 92)

source_name: rib cartilage

extract_protocol:
RNA was extracted from the cells using trizol/mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.
The sequencing library was prepared using the NEB_low_input_RNA kit following the manufacturer’s protocol. Barcoding was with the NEBNext_Multiplex Oligos for Illumina_(96 Unique Dual Index Primer Pairs)

treatment_protocol: None. Tissue was processed as decribed and RNA directly isolated.

value: rib cartilage

value: chondrocyte


title: Untransduced rep3

value: T-cells


title: chloramphenicol-treated, biol rep2, tech rep 1

description: mitoribosome-protected footprints


title: mRNA_BmGATA_Mock_rep3


title: nrpd1_3,replicate3,sRNA-seq

first: Ling

middle: Tong

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
Adapters and low-quality reads were removed and 18-30 bp long clean reads were mapped without mismatches on the tomato reference genome (ITAG 4.0) (Tomato Genome, 2012) using bowtie.
Then all reads mapping to tRNAs, snRNAs, rRNAs, or snoRNAs were removed according to the ncRNA annotation information of the tomato.
Mapped reads from three biological replicates were pooled together and remapped to the tomato reference genome using the ShortStack software v3.8.5 (--mismatches 0 --mmap f) to annotate and quantify sRNA.
Assembly: SL4.0
Supplementary files format and content: ShortStack output

organism: Solanum lycopersicum

source_name: 21 DAF embryo

growth_protocol: The tomato cultivar S. lycopersicum L. cv. Micro-Tom was grown in a climate-controlled chamber under a 16-h light/26°C and 8-h dark/22°C cycle with a light intensity of 100~200 μmol m-2 s-1.

extract_protocol:
Total RNAs were isolated from tomato embryos of 21 DAF using TRIzol reagent (Invitrogen, 15596026).
Libraries for sRNA-seq were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (NEB E7300L).

value: 21 DAF embryo

tag: cultivar

value: Micro-Tom

value: SlNRPD1 knockout


title: nrpd1_2,replicate2,sRNA-seq


title: Untransduced rep2

value: MICA activation


title: miR-324_null_2


title: Untransduced rep1


title: miR-324_null_3


title: nrpd1_1,replicate1,sRNA-seq


title: RGCs of  WT mice (P14) 1

value: Retina

value: retinal ganglion cells

value: Thy1.2 positive

value: developmental control


title: chloramphenicol-treated, biol rep1

description: mitoribosome-protected footprints

value: Freestyle 293-F


title: chloramphenicol-treated, biol rep4

description: mitoribosome-protected footprints


title: miR-324_null_1


title: con_rep4

city: Shijiazhuang

first: Yuchen

last: Wang

state: Hebei

address: No.12, Jiankang Road

institute: The Fourth Hospital of Hebei Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample

source_name: Human esophageal squamous cell carcinoma tissues

growth_protocol: All patients underwent thorough evaluation according to the stringent criteria established by the AJCC (American Joint Committee on Cancer) and UICC (Union for International Cancer Control).   The eighth edition of UICC's TNM staging for esophageal cancer was meticulously applied.   Specifically: 1.   R0 resection of esophageal cancer was skillfully performed.   2.   Only patients with the thoracic ESCC subtype were included.   3.   An expertly administered preoperative neoadjuvant chemotherapy regimen was utilized.   4.   Patients with abnormal heart, lung, liver, or kidney function, as well as those with unremarkable blood routine test results rendering them unsuitable for neoadjuvant chemotherapy and surgical intervention, were excluded from the study.   In total, eight esophageal cancer specimens were collected from eight patients who had undergone radical resection.   Immediately after collection, all tissue samples were gently washed with physiological saline at 4℃, rapidly snap-frozen in liquid nitrogen, and stored at -80℃ for subsequent processing.   Clinical data from the patients were meticulously collected and organized.   Subsequently, patients were stratified into two groups based on postoperative pathology: those with a CAP (College of American Pathologists) score of 0-1 were designated as the experimental group (Responder), while patients with a CAP score of 3, matched to the experimental group in terms of clinical staging (cTNM), were categorized into the control group (Non-responder).

extract_protocol:
Total RNA was extracted from tissues using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The human Esophageal Carcinoma cell lines KYSE-150, TE-1 and TE-12, and human esophageal normal cells (Het-1A) were maintained in RPMI Medium 1640 (C11875500BT, Gibco) supplemented with 10% fetal bovine serum (FBS) (10270-106, Gibco) at 37°C in a humidified atmosphere containing 5% CO2 and 95% air. For maintenance, 800,000 cells were seeded into 10ml of complete media every 3–4 d in 10-cm plates. Inhibition treatment involved the LY294002, a phosphoinositide 3-kinase (PI3K) inhibitor (HY-10108, MedChemExpress, 20 μmol/L), over a 24-hour period. Following this treatment, cells were subsequently harvested for protein extraction. The backbones pcDNA3.1 vector were purchased from TsingkeBiotechnologyCo., Ltd (Beijing, China). Plasmid constructs were generated via Gibson Assembly® Master Mix – Assembly (E2611, NEB) according to Gibson Assembly® Protocol (E5510, NEB).

value: Not sensitive to chemotherapy


title: NKG2D rep2


title: con_rep3

value: Human esophageal squamous cell carcinoma tissues


title: DMSO-treated, biol rep2

description: mitoribosome-protected footprints

value: Human embryonic kidney

value: 1% DMSO


title: DMSO-treated, biol rep4

description: mitoribosome-protected footprints


title: WT2,replicate2,sRNA-seq

value: WT