title: 3xTG Control 4

description: Library name: Sample 4


title: 3xTG Control 6

status: Public on Jun 12 2025

type: SRA

city: Boston

first: Jae Joon

last: Choi

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description: Library name: Sample 6

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR aligner (STAR aligner options: --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --limitBAMsortRAM 40000000000).
Reads aligned to each genes were counted using htseq-count (default options, used mm10 gene annotation(.gtf) from NCBI RefSeq).
Assembly: mm10
Supplementary files format and content: htseq-count output file (.htseq). Tab-delimited files containing gene symbols and their supporting read counts.

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Mice were transcardially perfused with cold PBS 1x and the hippocampi were rapidly dissected and snap frozen. The total hippocampal RNA was extracted using Trizol reagent (Ambion 15596018) and purified using the Direct-zol RNA Mini Prep kit (Zymo Research, R2050) according to the manufacturer’s instructions. RNA integrity and concentration were assayed using an Agilent 2100 Bioanalyzer instrument. All RNA samples had a RIN>8.2.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified using Qubit fluorometer, Agilent TapeStation 2200, and RT–qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols. Uniquely indexed libraries were pooled and sequenced on an Illumina NextSeq 500 with paired-end 75-bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. Samples were pooled with multiple samples per lane and sequenced.

treatment_protocol: Control vs Lithium Orotate

tag: tissue

value: Hippocampus

tag: genotype

tag: treatment

value: Control


title: Stat1-GOF Splenic NK cells, IFN-a, biol rep 2

status: Public on Jun 13 2025

city: Bethesda

first: Kan

last: Jiang

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

description: Library name: gof.NK.IFNa_rep2

data_processing:
Sequence reads were trimmed with Cutadapt (v2.10), aligned to mouse genome (build mm10) using STAR (v2.5.4a, options: --outFilterType BySJout --outFilterMultimapNmax 200 -alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1,000,000 -alignMatesGapMax 1,000,000), bam files were created with SAMtools (v1.10) and transcript abundance quantified using subread (v2.0.2).
Assembly: mm10
Supplementary files format and content: CSV file is count per million (CPM) calculated using calcNormFactors(method = "TMM") and cpm(normalized.lib.sizes = TRUE) from the edgeR package.

molecule: total RNA

source_name: spleen

extract_protocol:
Cells were harvested and stored in Zymo Trizol Reagent until RNA isolation with Direct-zol RNA MicroPrep kit (Zymo Research, #R2062) per manufacturer’s instructions, with DNase I treatment
library preparation with QuantSeq 3′ mRNA-seq Library Prep kit FWD and SIRV + ERCC Spike-In Controls

treatment_protocol: Splenic NK cells (Live, NK1.1+NKp46+TCRb-B220-) were isolated by FACS on a FACSAria Fusion and then 8 × 104 cells were stimulated with 5000 U/ml of IFN-α in complete media (RPMI + 10% FCS + P/S/Q/NEAA) at 37°C for 2 hours or no cytokine for 30 min

value: spleen

tag: cell type

value: Natural Killer cells

value: IFN-a


title: 3xTG Control 1

description: Library name: Sample 1


title: mRNA_rep1_input_for_ribo_preQ1

status: Public on Jun 02 2025

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: Library name: Sample 39

data_processing:
Paired end reads for input mRNA were split by internal barcode sequence using Je demultiplex with options BPOS = BOTH BM = READ 1 LEN = 4:6 FORCE = true C = false 6. Barcode sequences are available on Github at https://github.com/ckatanski/Q_paper. The quality of reads were checked by fastqc v0.11.9131 and the reads were aligned to human hg38 genome (GRCh38.p13.genome.fa) by STAR 2.7.9a with the human annotation file (gencode.v39.annotation.gtf) from GENCODE database (https://www.gencodegenes.org). Then the expression levels were counted and collected by RSEM v1.3.3133/featureCounts. Low expressed genes were filtered by filterByExpr function with default parameters in edgeR v3.36.0135 and the CPM (Counts Per Million reads mapped) and TPM (Transcripts Per Million) of each gene were calculated. The TPM in visualization was the mean of the two replicates. Translation efficiency was calculated using DESeq2/EdgeR with raw reads count. For Ribo-seq, normalized RPF reads count were divided by input mRNA reads count to get translation efficiency. Codon usage of a gene or a group of genes was defined as the ratio of each amino acid within CDS region of a gene or a group of genes. The gene ontology (GO) analysis was performed using the Gene Ontology Resource (http://geneontology.org)136,137.Single end reads were obtained for RPF sequencing. Trimmomatic was used to remove NEBNext small library adaptors, primer dimers, and poly-G sequences and filter out low-quality reads from raw sequencing reads. Cutadapt was used to further trim adaptors from the sequencing reads. Reads less than 10 nt was removed during both adaptor trimming steps. The trimmed reads were first mapped to human rRNA, tRNA, and noncoding RNA combined reference (Homo_sapiens.GRCh38.ncrna.fa.gz, Ensembl) using bowtie2 saving the unmapped reads. The unmapped reads were then mapped to human hg38 genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa) using STAR with the human annotation file (Homo_sapiens.GRCh38.113.gtf) from Ensembl database (https://www.ensembl.org). The mapped bam files were then sorted and indexed using samtools. The resulted bam files were then analyzed using Ribo-TISH138. RPF sequence length distribution was obtained from Ribo-TISH output. Ribosome occupancy analysis was performed using CONCUR139. Translation efficiency analysis, codon usage analysis and gene ontology analysis were performed as polysome profiling data analysis.
Assembly: hg38
Supplementary files format and content: tab separated value (tsv) - indicates the total number of reads mapping to each mRNA gene in hg38

organism: Homo sapiens

growth_protocol: 2× 15-cm plates (5×106 cells/plate) of 0Q HEK293T cells per sample were seeded 24 hours before collection. PreQ1was added to 4 of the plates to 1 µM at the time of seeding cells and incubated for 24 hours. 4 plates of cells were also treated with 1µg/mlEmetine for 15 min to induce ribosome collision.

extract_protocol:
At the time of collection, 10-35% sucrose gradient was prepared in ultra-centrifuge tolerant tube (Seton) by combining 10% sucrose buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 10% sucrose, 0.1% protease inhibitor, 0.1% phosphatase inhibitor) with 35% sucrose buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 35% sucrose, 0.1% protease inhibitor, 0.1% phosphatase inhibitor)using Gradient Station (Biocomp). The sucrose gradient for all samples was stored in cold room (4 ºC) before use. Cells in 4× 15-cm plates were then treated with 1 µg/ml emetine (positive control) for 15 min followed by immediate wash with ice-cold 1× PBS buffer. Cells were immediately collected with 10 ml ice-cold 1× PBS and pelleted by centrifugation at 500× g for 5 min. Cells from 2× 15-cm plates were combined as one sample. 4× volumes of lysis buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 1% protease inhibitor, 1% phosphatase inhibitor) were added to the combined cell pellet and the cells were lysed on ice for 20 min with periodic perturbation (or rotating at 4 ºC). Supernatant lysate was collected after centrifugation at 16,000× g for 15 min. 4 µl Turbo DNase (ThermoFisher) was added to the lysate and incubated at room temperature for 15 min. Supernatant lysate was collected after centrifugation at 16,000× g for 15 min after DNase treatment to remove any debris. Total RNA concentration in the lysate was measured using the Qubit RNA HS Assay Kit (ThermoFisher, Q32852) after 20× dilution according to the manufacturer’s manual. Lysate containing 90 µg of total RNA from each sample was used and adjusted to 500 µl using the lysis buffer. 5 µl 100 mM CaCl2 was added to each sample to 1 mM final. 1 µl 100 U/µl Micrococcal Nuclease (Thermo Fisher, 88216) was added to each sample and mixed. RNA digestion was performed for 40 min at 25 °C before the reaction was terminated by adding 10 µl SUPERaseIn RNase inhibitor (ThermoFisher, AM2696). For Ribo-seq, lysate after RNase digestion (~516 µl) together with 8 ml sucrose cushion buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 0.1 % SUPERaseIn RNase inhibitor (ThermoFisher), 0.1% protease inhibitor, 0.1% phosphatase inhibitor) was loaded gently to the bottom of the 70.1 Ti ultracentrifuge tubes (Beckman Coulter, 355603). 1.5 ml 37.5% (1M) sucrose buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 37.5% sucrose, 0.1 % SUPERaseIn RNase inhibitor (ThermoFisher), 0.1% protease inhibitor, 0.1% phosphatase inhibitor) was loaded gently to the bottom of the tube using long blunt end needle. All the ultracentrifuge tubes were weighed and balanced. The tubes were then centrifuged at 65,000 rpm and 4 ºC under vacuum for 2.5 hours using ultracentrifuge (Beckman Coulter Optima L-100XP, 70.1 Ti rotor). After ultracentrifugation, the supernatant was removed, and the ribosome pellet was washed with 2 ml sucrose cushion buffer three times. 1 ml TRIzol reagent was directly added to the ribosome pellet and incubated at room temperature for 10 mins or until the ribosome pellet was completely dissolved. The TRIzol ribosome mixture was then transferred to microcentrifuge tubes and total RNA was extracted according to manufacturer’s manual. 5 µg RNA from each sample was loaded on 10% TBE-Urea gel for ribosome protected fragments extraction. For both monosome and disome protected fragments, gel region containing RNA from 15 to 40 nt and 50 to 80 nt was excised from the gel and transferred to microcentrifuge tubes. The gel slices were crushed into tiny pieces using pipet tips or disposable homogenizer pestle. 400 µl of RNA gel extraction buffer (300 mM NaOAc, pH 5.2, 1 mM EDTA, 0.25% SDS) was added to the gel pieces and flash-freeze by liquid nitrogen. The samples were then mixed end-to-end on a rotary mixer at room temperature for 12-20 hours. The RNA gel extraction buffer and gel pieces mixture was transferred to a 0.22-µm filter inserted into a 1.5-ml microcentrifuge tube (Corning Spin-X Centrifuge Tube Filters, 8160) using wide-bore tips. The samples were centrifuged at 10,000× g at 4 ºC for 1 min. The cleared elute was transferred to new microcentrifuge tubes. 3 µl of GlycoBlue and 500 µl isopropanol were added to each sample and thoroughly mixed followed by incubation in -20 °C freezer overnight. Samples were then centrifuged at 17,000 × g at 4 °C for 30 min to pellet the RNA. The RNA pellets were washed with 1 ml of 75% ethanol followed by centrifuge at 4 °C for 3 min. Supernatant was completely removed and RNA pellets were air-dried for 10 min at room temperature. RNA was resuspended in 41 µl H2O and the concentrations were measured using the Qubit RNA HS Assay Kit (ThermoFisher).
5 µl 10× T4 PNK buffer A and 5 µl T4 PNK (ThermoFisher, EK0032) were added to the RPF RNA from above (~40 µl) and mixed. The samples were incubated at 37 °C for 20 min. 6 µl 10 mM ATP, 1 µl 10× T4 PNK buffer A, and 3 µl T4 PNK were then added to each sample (~60 µl total) and mixed followed by incubation at 37 °C for 20 min. 120 µl RNA binding buffer and 270 µl 100% ethanol were added to each sample followed by RNA purification using RNA Clean & Concentrator-5 (Zymo, R1016). The purified RNA samples were then used for sequencing library construction using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300S) according to manufacturer’s manual. rRNA blocker oligos (Nanodigmbio 1002901) were added at the reverse transcription primer hybridization step during library construction to reduce rRNA reads. Sequencing libraries were sequenced on Illumina NextSeq system using single-end kit (Illumina, 20100995). mRNA inputlibraries for ribo-seq was constructed using MSR-seq (PMID: 35513407).
NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300S) and MSR-seq (PMID: 35513407)

tag: cell line


title: 3xTG Control 3

description: Library name: Sample 3


title: Stat1-GOF Splenic NK cells, no cytokine, biol rep 1

description: Library name: gof.NK.nc_rep1

value: no cytokine


title: WT Splenic NK cells, no cytokine, biol rep 2

description: Library name: wt.NK.nc_rep2

value: WT


title: mRNA_rep2_input_for_ribo_0Q

description: Library name: Sample 38


title: mRNA_rep2_input_for_ribo_preQ1

description: Library name: Sample 40


title: RPF_rep2_preQ1

description: Library name: Sample 34


title: mRNA_rep1_input_for_ribo_0Q

description: Library name: Sample 37


title: RPF_rep2_EME

description: Library name: Sample 36


title: 3xTG LiO 8

description: Library name: Sample 17

value: LiO


title: RPF_rep1_EME

description: Library name: Sample 35


title: 3xTG LiO 6

description: Library name: Sample 15


title: RPF_rep1_0Q

description: Library name: Sample 31


title: RPF_rep2_0Q

description: Library name: Sample 32


title: tRNA_rep1_preQ1_plus_PNK

description: Library name: Sample 28

data_processing:
Starting from index demultiplexed fastq data, paired end reads were split by internal barcode sequence using Je demultiplex with options BPOS = BOTH BM = READ 1 LEN = 4:6 FORCE = true C = false 6. Barcode sequences are available on Github at https://github.com/ckatanski/Q paper.
Next read 2 files were used to map with bowtie2 (PMID:22388286) with the following parameters: -q -p 10 –local ––no-unal. Reads were mapped to curated list of non-redundant tRNA mature genes with tRNAScane score > 40 from hg19. Bowtie2 output sam files were converted to bam files, then sorted using samtools.
Next IGV was used to collapse reads into 1 nt window. IGV output.wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/Q paper).
The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools (PMID:19505943) to sum all reads that mapped to each gene.
Related custom scripts were used to divide reads based on which 10 nt window the 3′end mapped to for each tRNA; this is for fragment analysis. Data were visualized with custom R scripts. All custom scripts are available on GitHub (https://github.com/ckatanski/CHRIS-seq). R script for the present analysis is available on Github (https://github.com/ckatanski/PreQ1).
Assembly: hg19
Supplementary files format and content: tab separated value (tsv) - indicates the total number of reads mapping to each tRNA gene in hg19

extract_protocol:
Total RNA was used to construct libraries for tRNA sequencing as previously described for multiplex small RNA-seq (MSR-seq). tRNA libraries: Briefly, total RNA was deacylated with a modified beta-elimination protocolwhereinsodium periodate was omitted, buthigh pH sodium tetra boratewas used to deacylated tRNA. tRNAs were ligated to a biotinylated hairpin oligo with a barcode and Illumina sequencing primer binding sites overnight. Reaction conditions were overnight at 16° C in a 50 μl ligation solution with the following final concentration: 15% PEG 8000, 1× NEB T4 RNA ligase I buffer, 50 μM ATP, 5% DMSO, 1 mM hexaamine cobalt (III) chloride, 0.8 μM barcode ligation oligo, and 1 U/μl NEB T4 RNA ligase I. After ligation, 50 μl of 100 mM EDTA were added to each sample to inactivate the ligase. The samples were then combined and 8 μl of ThermoFisher Streptavidin MyOne C1 Dynabeads per sample. The biotinylated samples were allowed to bind the beads for 15 min. After binding, the beads were magnetized, the supernatant was removed, and the samples were washed once with a high salt Tween wash buffer (1 M NaCl, 0.1% Tween 20, and 20 mM Tris–HCl, pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris–HCl, pH 7.4). At this point, beads frommultiple samples were combine into a single tube. After combining, the sample was divided in two; one portion was demethylated with AlkB the other was untreated. For AlkB treatment, three stock solutions are made fresh immediately before reaction: L-ascorbic acid 200 mM, 2-ketoglutarate 3 mM, and ammonium iron sulfate 5 mM. The final reaction mixture contained 2 mM L-ascorbic acid, 1 mM 2-ketoglutarate, 0.3 mM ammonium iron sulfate, 100 mM KCl, 50 mM MES pH 6, 50 ng/μL BSA, 4 μM wild-type AlkB, and 4 μM AlkB-D135S. About 50 μL of the reaction mixture was added to 5 –20 μL of decanted streptavidin bead slurry after ligation, immobilization, and washing. The reaction continued for 30 min at 37 °C. Following the reaction, beads were washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.4). Following AlkB treatment, both the treated and untreated samples were used for reverse transcription. The RT reaction was done with Superscript IV at 55° C for 10 min, then further incubated at 37 °C overnight. Beads were then resuspended into 50 μl of RNase H master mix containing 0.4 U/μl RNaseH (NEB) and 1× NEB RNase H buffer and incubated at 37° Cfor15 min, then washed. Unextended hairpin-oligo was blocked by addition of 10 μl of 250 mM freshly prepared sodium periodate, 0.5 M sodium acetate, pH 5 were added to the RNase H digested sample and incubated at room temperature for 30 min. Afterwards, ribose was added to a final concentration of 167 mM to quench excess periodate at room temperature for 5 min. Beads were resuspended into 50 μl of a ligation master mix with the following components: 2 U/μl T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 2 μM second ligation oligo, 25% PEG 8000, 50 μM ATP, 7.5% DMSO and 1 mM hexaamine cobalt chloride. After incubation at room temperature overnight (> 12 h), the reaction was diluted with 50 μl water to reduce viscosity, washed once with high salt wash buffer and once with low salt wash buffer, and then resuspended in water. These beads were used as template for PCR reaction to make libraries for sequencing.
MSR-seq (PMID: 35513407)


title: tRNA_rep2_preQ1_plus_PNK

description: Library name: Sample 29


title: tRNA_rep2_0Q_plus_PNK

description: Library name: Sample 26


title: tRNA_rep3_0Q_plus_PNK

description: Library name: Sample 27


title: tRNA_rep3_preQ1_minus_PNK

description: Library name: Sample 24


title: tRNA_rep1_0Q_plus_PNK

description: Library name: Sample 25


title: tRNA_rep2_preQ1_minus_PNK

description: Library name: Sample 23


title: tRNA_rep1_preQ1_minus_PNK

description: Library name: Sample 22


title: 3xTG Control 2

description: Library name: Sample 2


title: tRNA_rep3_0Q_minus_PNK

description: Library name: Sample 21


title: tRNA_rep1_0Q_minus_PNK

description: Library name: Sample 19


title: tRNA_rep2_plus_preQ1_plus_4u8C

description: Library name: Sample 18


title: tRNA_rep2_0Q_minus_PNK

description: Library name: Sample 20


title: tRNA_rep2_minus_preQ1_minus_4u8C

description: Library name: Sample 14


title: tRNA_rep1_plus_preQ1_plus_4u8C

description: Library name: Sample 17


title: tRNA_rep1_plus_preQ1_minus_4u8C

description: Library name: Sample 15


title: tRNA_rep2_plus_preQ1_minus_4u8C

description: Library name: Sample 16


title: RPF_rep1_preQ1

description: Library name: Sample 33


title: tRNA_rep1_minus_preQ1_minus_4u8C

description: Library name: Sample 13


title: tRNA_rep2_100nM_preQ1_plus_100nM_Q

description: Library name: Sample 11

source_name: BMDC

value: BMDC


title: tRNA_rep3_100nM_preQ1_plus_100nM_Q

description: Library name: Sample 12


title: tRNA_rep1_100nM_preQ1_plus_100nM_Q

description: Library name: Sample 10


title: tRNA_rep1_100nM_preQ1

description: Library name: Sample 7


title: tRNA_rep3_100nM_preQ1

description: Library name: Sample 9


title: tRNA_rep3_preQ1_plus_PNK

description: Library name: Sample 30


title: tRNA_rep3_100nM_Q

description: Library name: Sample 6


title: tRNA_rep1_no_treatment_control_0Q

description: Library name: Sample 1


title: tRNA_rep2_100nM_Q

description: Library name: Sample 5


title: tRNA_rep2_100nM_preQ1

description: Library name: Sample 8


title: tRNA_rep1_100nM_Q

description: Library name: Sample 4


title: tRNA_rep3_no_treatment_control_0Q

description: Library name: Sample 3


title: tRNA_stool_plusDM_plusIO4

data_processing:
MSR-seq reads were mapped to a reference genome composed of bacterial 5S rRNA sequences
Reference sequences for 5S rRNA were downloaded from the 5S rRNA database (http://combio.pl/rrna/)17. Sequences were combined from Bacteria (n=7291), Archaea (n=319), Eukaryota (n=2861), mitochondria (n=110), and plastids (n=838). Full lineages were assigned to each reference using the ETE3 NCBITaxa toolkit in python.
From here, tRNA reference genomes were retrieved from gtRNAdB for microbes from the most abundant class taxon: Lachnoclostridium_phytofermentans_ISDg, Erysipelothrix_rhusiopathiae_SY1027, Carnobacterium_maltaromaticum, Faecalibacterium_prausnitzii, Bacteroides_dorei, Bifidobacterium_longum_subsp_longum_BBMN68, Clostridium_beijerinckii, Roseburia_intestinalis_XB6B4, Ruminococcus_bromii_L2-63. These reference tRNA genomes were combine into a single reference fasta and tRNA-seq reads were mapped to this combine reference. Further analysis was performed with custom R scripts available on github/ckatanski/PreQ1.
Assembly: 5S rRNA database (http://combio.pl/rrna/), gtRNAdB
Supplementary files format and content: tab separated value (tsv) - indicates read pileup, mutation rate, deletion, insertion rates, etc at each base along each tRNA gene
Supplementary files format and content: tab separated value (tsv) - indicates the total number of reads mapping to each tRNA gene
Library strategy: MSR-seq (PMID: 35513407)

source_name: Stool

extract_protocol: RNA was extracted from human stool samples and prepared for MSR-seq. Samples were deacylated without beta-elimination to detect charging. After the first ligation reaction, samples were split in two, one aliquot treated with AlkB demethylase and the other untreated. Both of those samples were again split, one set of aliquots were treated with sodium periodate, the other set of aliquots untreated. These 4 samples were then usedin reverse transcription and followed the usual MSR-seq protocol.

value: Stool


title: mRNA_preQ1_polysome_rep1

data_processing:
Paired end reads were split by by internal barcode sequence using Je demultiplex with options BPOS = BOTH BM = READ 1 LEN = 4:6 FORCE = true C = false 6. Barcode sequences are available on Github at https://github.com/ckatanski/Q paper.
The quality of reads were checked by fastqc and the reads were aligned to human hg38 genome (GRCh38.p13.genome.fa) by STAR with the annotation file gencode.v39.annotation.gtf from GENCODE database (https://www.gencodegenes.org)
Then the expression levels were counted and collected by RSEM.
genome build/assembly: hg38
processed data files format and content: comma separated value (csv) - indicates expression level of each gene generated by RSEM
Library strategy: MSR-seq (PMID: 35513407)

growth_protocol: 4× 15-cm plates (5×106 cells/plate) of 0Q HEK293T cells per sample were seeded 3 days before collection. PreQ1 was added to half of the plates to 1 µM final at the time of seeding cells and incubated for 3 days.

extract_protocol:
On the day of collection, 5%-50% sucrose gradient was prepared in ultra-centrifuge tolerant tube by combining 5% sucrose buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 5% sucrose, 100 µg/ml CHX, 1% protease inhibitor, 1% RNase inhibitor) with 50% sucrose buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 50% sucrose, 100 µg/ml CHX, 1% protease inhibitor, 1% RNase inhibitor)  using Gradient Station (Biocomp). The sucrose gradient for all samples was stored in cold room (4 ºC) before use. Cells were then treated with 100 µg/ml cycloheximide (CHX) in complete medium for 7 min at 37 ºC followed by immediate wash with ice-cold PBS buffer containing 100 µg/ml CHX twice. The cells were collected in 5 ml ice-cold PBS buffer containing 100 µg/ml CHX and pelleted by centrifugation at 500× g for 5 min. Cells from 4× 15-cm plates were combined as one sample. 4× volumes of lysis buffer (20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 µg/ml CHX, 1% protease inhibitor, 1% RNase inhibitor) was added to the combined cell pellet and the cells were lysed on ice for 20 min with periodic perturbation (or rotating at 4 ºC). Supernatant lysate of each sample was collected after centrifugation at 16,000× g for 15 min. 4 µl Turbo DNase was added to the lysate and incubated at room temperature for 15 min. The lysate samples were centrifuged at 16,000× g for 15 min after DNase treatment to remove any debris. OD260 of each lysate sample was measured using Nanodrop. The OD260 values of all samples were adjusted to the same using lysis buffer. 20 µl of the lysate was saved for Western blot validation. 1/5 of the lysate was saved as the input and the total RNA was extracted using TRIzol reagent. All the sucrose gradient tubes were weighed and balanced and 500 µl gradient solution was slowly removed from the top before loading. Equal amount (~500 µl) of the 4/5 lysate were slowly and horizontally added to the top of the gradient while gently rotating the tube. The gradient tubes were then centrifuged at 28,000 rpm and 4 ºC under vacuum for 3 hours using ultracentrifuge (Beckman Coulter Optima L-100XP, SW28.1 rotor). The sucrose gradient fractions (30 fractions, 590 µl each) were collected automatically using Sucrose Gradient and fraction collector (Gilson). All fractions were flash frozen using liquid nitrogen before RNA extraction and Western blot validation. 400 µl aliquot from disome and above (polysome) fractions were used to extract total RNA. Total RNA from these fractions were combined for polysome associated tRNA sequencing and polysome mRNA extraction and sequencing.
Polysome mRNA sequencing libraries were constructed using MSR-seq. Briefly, 400ng input and polysome polyA+ RNA was fragmented at 94 ºC for 3 min using Magnesium fragmentation buffer (NEB, E6150S) to get ~300 nt fragment RNA. Fragment RNA larger than 200 nt was then purified using RNA clean and concentrator kit and eluted in 8 µl sterile H2O. 1 μl T4 PNK buffer and 1 µl 10 U/μl T4 PNK (NEB M0201L) were added to the fragment RNA and incubated at 37°C for 30 min. T4 PNK was inactivated by incubation at 75 °C for 10 minutes followed by immediately incubation on ice. The entire reaction mixture (~10 μl) was used as the RNA input for MSR-seq.


title: tRNA_stool_plusDM_minusIO4


title: mRNA_0Q_polysome_rep2


title: mRNA_preQ1_polysome_rep2


title: mRNA_0Q_polysome_rep1


title: mRNA_preQ1_input_rep2


title: mRNA_preQ1_input_rep1


title: mRNA_0Q_input_rep2


title: mRNA_0Q_input_rep1


title: tRNA_rep2_plusDM_100Q

data_processing:
Starting from index demultiplexed fastq data, paired end reads were split by internal barcode sequence using Je demultiplex with options BPOS = BOTH BM = READ 1 LEN = 4:6 FORCE = true C = false 6. Barcode sequences are available on Github at https://github.com/ckatanski/Q paper.
Next read 2 files were used to map with bowtie2 (PMID:22388286) with the following parameters: -q -p 10 –local ––no-unal. Reads were mapped to curated list of non-redundant tRNA mature genes with tRNAScane score > 40 from hg19. Bowtie2 output sam files were converted to bam files, then sorted using samtools.
Next IGV was used to collapse reads into 1 nt window. IGV output.wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/Q paper).
The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools (PMID:19505943) to sum all reads that mapped to each gene.
Related custom scripts were used to divide reads based on which 10 nt window the 3′end mapped to for each tRNA; this is for fragment analysis. Data were visualized with custom R scripts. All custom scripts are available on GitHub (https://github.com/ckatanski/CHRIS-seq). R script for the present analysis is available on Github (https://github.com/ckatanski/PreQ1).
genome build/assembly: hg19
processed data files format and content: tab separated value (tsv) - indicates read pileup, mutation rate, deletion, insertion rates, etc at each base along each tRNA gene  in hg19
processed data files format and content: tab separated value (tsv) - indicates the total number of reads mapping to each tRNA gene in hg19
Library strategy: MSR-seq (PMID: 35513407)

extract_protocol: Total RNA was used to construct libraries for tRNA sequencing as previously described for multiplex small RNA-seq (MSR-seq) (PMID: 35513407). tRNA libraries: Briefly, total RNA was deacylated with a modified beta-elimination protocol  wherein  sodium periodate was omitted, but  high pH sodium tetra borate  was used to deacylated tRNA. tRNAs were ligated to a biotinylated hairpin oligo with a barcode and Illumina sequencing primer binding sites overnight. Reaction conditions were overnight at 16° C in a 50 μl ligation solution with the following final concentration: 15% PEG 8000, 1× NEB T4 RNA ligase I buffer, 50 μM ATP, 5% DMSO, 1 mM hexaamine cobalt (III) chloride, 0.8 μM barcode ligation oligo, and 1 U/μl NEB T4 RNA ligase I. After ligation, 50 μl of 100 mM EDTA were added to each sample to inactivate the ligase. The samples were then combined and 8 μl of ThermoFisher Streptavidin MyOne C1 Dynabeads per sample. The biotinylated samples were allowed to bind the beads for 15 min. After binding, the beads were magnetized, the supernatant was removed, and the samples were washed once with a high salt Tween wash buffer (1 M NaCl, 0.1% Tween 20, and 20 mM Tris–HCl, pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris–HCl, pH 7.4). At this point, beads from  multiple samples were combine into a single tube. After combining, the sample was divided in two; one portion was demethylated with AlkB the other was untreated. For AlkB treatment, three stock solutions are made fresh immediately before reaction: L-ascorbic acid 200 mM, 2-ketoglutarate 3 mM, and ammonium iron sulfate 5 mM. The final reaction mixture contained 2 mM L-ascorbic acid, 1 mM 2-ketoglutarate, 0.3 mM ammonium iron sulfate, 100 mM KCl, 50 mM MES pH 6, 50 ng/μL BSA, 4 μM wild-type AlkB, and 4 μM AlkB-D135S. About 50 μL of the reaction mixture was added to 5 –20 μL of decanted streptavidin bead slurry after ligation, immobilization, and washing. The reaction continued for 30 min at 37 °C. Following the reaction, beads were washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.4). Following AlkB treatment, both the treated and untreated samples were used for reverse transcription. The RT reaction was done with Superscript IV at 55° C for 10 min, then further incubated at 37 °C overnight. Beads were then resuspended into 50 μl of RNase H master mix containing 0.4 U/μl RNaseH (NEB) and 1× NEB RNase H buffer and incubated at 37° Cfor15 min, then washed. Unextended hairpin-oligo was blocked by addition of 10 μl of 250 mM freshly prepared sodium periodate, 0.5 M sodium acetate, pH 5 were added to the RNase H digested sample and incubated at room temperature for 30 min. Afterwards, ribose was added to a final concentration of 167 mM to quench excess periodate at room temperature for 5 min. Beads were resuspended into 50 μl of a ligation master mix with the following components: 2 U/μl T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 2 μM second ligation oligo, 25% PEG 8000, 50 μM ATP, 7.5% DMSO and 1 mM hexaamine cobalt chloride. After incubation at room temperature overnight (> 12 h), the reaction was diluted with 50 μl water to reduce viscosity, washed once with high salt wash buffer and once with low salt wash buffer, and then resuspended in water. These beads were used as template for PCR reaction to make libraries for sequencing.


title: tRNA_rep1_plusDM_100Q


title: tRNA_rep2_no_treatment_control_0Q

description: Library name: Sample 2


title: tRNA_rep2_plusDM_preQ1


title: tRNA_rep1_plusDM_preQ1


title: tRNA_rep2_plusDM_preQ1+10nMQ


title: tRNA_rep1_plusDM_preQ1+1nMQ


title: tRNA_rep1_plusDM_preQ1+10nMQ


title: tRNA_stool_minusDM_minusIO4


title: tRNA_rep1_plusDM_0Q


title: tRNA_rep2_minusDM_100Q


title: tRNA_rep2_minusDM_preQ1


title: tRNA_rep2_plusDM_0Q


title: tRNA_rep1_minusDM_preQ1+10nMQ


title: tRNA_stool_minusDM_plusIO4


title: tRNA_rep1_minusDM_100Q


title: tRNA_rep2_minusDM_0Q


title: tRNA_rep2_minusDM_preQ1+1nMQ


title: tRNA_rep1_minusDM_0Q


title: tRNA_rep1_minusDM_preQ1+1nMQ


title: tRNA_rep2_minusDM_preQ1+10nMQ


title: tRNA_rep2_plusDM_preQ1+1nMQ


title: Donor1, cocultured, day 7, RNA-seq

status: Public on May 22 2025

city: Minneapolis

first: Pedram

last: Motallebnejad

state: MN

address: 421 Washington Ave SE

institute: University of Minnesota

data_processing:
Fastq files were mapped to the human genome (hg38) using STAR, and raw counts were obtained with HT-seq.
Genes expressed in at least 3 samples with counts per million (CPM)>1 were retained for analysis (14790 genes).
Filtered genes underwent TMM normalization for PCA and clustering in R. EdgeR identified differentially expressed genes (DEGs) at day 7 vs unstimulated, with differential expression criterion of |log2(fold change)| > 1 and adjusted P value < 0.05.
Assembly: hg38
Supplementary files format and content: Comma-separated value (csv) file includes raw counts for all genes and each sample

source_name: Peripheral Blood

growth_protocol: K562 cells expressing mb-4-1BBL and mb-IL-21 (referred to as feeder cells, mb stands for membrane-bound) were cultured in RPMI 1640 Medium containing 10% fetal bovine serum. Feeder cells were irradiated at 10,000 rads, cryopreserved and thawed for co-culture with NK cells. Peripheral blood mononuclear cells (PBMCs) were extracted from leukocyte reduction system chambers using Ficoll-Paque Premium (Cytiva). NK cell enrichment was carried out with the EasySep Human NK Cell Enrichment Kit. NK cells were cultured overnight in B0 medium supplemented with 100 U/mL of IL-2 (R&D Systems) for recovery. B0 medium is a 2:1 (vol:vol) mixture of DMEM with 4.5 g/L glucose, L-glutamine, and sodium pyruvate (Gibco) and Ham’s F12 Medium (Corning) supplemented with 20 µM 2-mercaptoethanol (Gibco), 50 µM ethanolamine (Sigma), 10 µg/mL ascorbic acid (Sigma), 1.6 ng/mL sodium selenite (Sigma), 100 U/mL penicillin/streptomycin (Gibco), and 20% heat-inactivated human AB serum (Valley Biomedical).

extract_protocol:
Total RNA from collected samples was purified using the Qiagen™ RNeasy Mini Kit.
The Illumina TruSeq® Stranded mRNA Sample Prep Kit protocol was employed to isolate poly-A containing mRNA molecules and generate sequence libraries. Pooled libraries were sequenced using the Illumina HiSeq 2500 at the University of Minnesota Genomics Center.

treatment_protocol: Enriched NK cells from PBMCs were cultured in media containing IL-2 overnight. Subsequently, NK cells were co-cultured with irradiated feeder cells at 2×105 cells/mL and 4×105 cells/mL, respectively, in B0 media with IL-2 supplementation for 7 days (Figure 1A). Samples were collected right after enrichment (unstimulated) and 7 days after co-culture initiation (day 7) for RNA-seq and ATAC-seq.

value: Peripheral Blood

value: Primary cells

value: Natural Killer Cells

value: Cocultured with feeder cells


title: 14H020 [re-analysis]

status: Public on Apr 23 2025

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: reanalysis of GSM1636925

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters for samples sequenced using stranded libraries.
Strand orientation is reverse for stranded samples, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

source_name: Heparinised blood

extract_protocol:
TruSeq RNA Stranded Sample Preparation (Illumina)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: Bone marrow

value: acute myeloid leukemia

tag: strand orientation

value: reverse


title: Sp5cVM3_FPKM

status: Public on Mar 12 2025

city: Harbin

first: Qingling

last: Zhai

state: Heilongjiang

address: No. 23, Youzheng Street, Nangang District

department: Neurology

country: China

institute: Harbin medical university

description:
Library name: Sample22
Sp5cVM3_FPKM

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adapter sequence/low-quality sequence using CLC genomic workbench (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to GRCm38/mm10 using CLC genomic workbench (parameters- mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic workbench.
Assembly: mm10
Supplementary files format and content: processed data.xls with FPKM

source_name: Vestibular Nuclei

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

value: Spinal Trigeminal Nucleus Causals

value: brain tissue

value: paired-end

value: NTG (10 mg/kg, i.p.) and kainic acid (12.5 mM, 0.10 ml, tympanic membrane), every other day for 9 days (total 5 injections each).


title: Donor3, cocultured, day 7, RNA-seq


title: Sp5cVM2_FPKM

description:
Library name: Sample21
Sp5cVM2_FPKM


title: Sp5cVM1_FPKM

description:
Library name: Sample20
Sp5cVM1_FPKM


title: Sp5cVEH4_FPKM

description:
Library name: Sample19
Sp5cVEH4_FPKM

value: Vehicle (saline), intraperitoneal (i.p.), every other day for 9 days (total 5 injections)


title: 14H023 [re-analysis]

description: reanalysis of GSM1636926

source_name: Bone marrow

value: Blood


title: Sp5cVEH3_FPKM

description:
Library name: Sample18
Sp5cVEH3_FPKM


title: tRNA_rep1_minusDM_preQ1


title: Sp5cM4_FPKM

description:
Library name: Sample15
Sp5cM4_FPKM

value: NTG (nitroglycerin), 10 mg/kg, intraperitoneal (i.p.), every other day for 9 days (total 5 injections)


title: Sp5cM2_FPKM

description:
Library name: Sample13
Sp5cM2_FPKM


title: Sp5cVEH2_FPKM

description:
Library name: Sample17
Sp5cVEH2_FPKM


title: Sp5cM3_FPKM

description:
Library name: Sample14
Sp5cM3_FPKM


title: Sp5cVEH1_FPKM

description:
Library name: Sample16
Sp5cVEH1_FPKM


title: Sp5cM1_FPKM

description:
Library name: Sample12
Sp5cM1_FPKM


title: VNVEH3_FPKM

description:
Library name: Sample7
VNVEH3_FPKM

source_name: Spinal Trigeminal Nucleus Causals

value: Vestibular Nuclei


title: VNVEH4_FPKM

description:
Library name: Sample8
VNVEH4_FPKM


title: VNVM3_FPKM

description:
Library name: Sample11
VNVM3_FPKM


title: sorted B-cells, scRNA-seq from individual patient WM47

status: Public on May 02 2025

city: New York

first: Gareth

last: Morgan

address: 550 1st Avenue

institute: NYU Langone Health

description:
Library name: WM47-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence

library_source: transcriptomic single cell

data_processing:
ATAC-seq objects were generated from fragment files using ArchR, includng QC, data normalization, batch correction, and identification of single-cell transcription factor motif deviations via chromVAR
Gene expression count matrices were generated using cellranger v5 and processed in R using Seurat v4, including QC, library integration, data normalization, and clustering. Gene expression objects were subsequently integrated into ArchR-derived ATAC-seq objects.
Assembly: Human hg38
Supplementary files format and content: filtered cellrnager outputs (barcodes, features, matrix)
Supplementary files format and content: ATAC-seq fragment files

molecule: nuclear RNA

source_name: bone marrow

extract_protocol:
B-cells were flow sorted from bone marrow by first sorting live cells using Dapi-, and then selecting for B-cells which were CD14-/CD3-/CD19+.
Libraries were pooled as per 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (CG000365 - Rev C).

value: bone marrow

value: B-cell

value: MYD88 mutated

tag: disease state

value: Waldenstrom macroglobulinemia

tag: subtype

value: MBC-like

tag: batch

tag: sampleID


title: VNVM2_FPKM

description:
Library name: Sample10
VNVM2_FPKM


title: VNM1_FPKM

description:
Library name: Sample1
VNM1_FPKM


title: VNVM1_FPKM

description:
Library name: Sample9
VNVM1_FPKM


title: VNVEH2_FPKM

description:
Library name: Sample6
VNVEH2_FPKM


title: VNM3_FPKM

description:
Library name: Sample3
VNM3_FPKM


title: VNVEH1_FPKM

description:
Library name: Sample5
VNVEH1_FPKM


title: bulkRNA_Psat1KO_rep2

status: Public on Dec 18 2024

data_processing:
Adapter sequences were removed using trimgalore/0.6.6
Sequence reads(R1) were aligned to reference genome using TopHat 2.1.1 with default setting
Gene expression values, measured in reads per kilobase exon per million mapped reads (RPKM), were computed using Partek Genomic Suite 7.21.119
Differential gene expression analysis was conducted through ANOVA (Partek Genomic Suite), applying fold change criteria of 1.5 and a significance cutoff of P < 0.05
Assembly: mm10
Supplementary files format and content: Excel  files containing gene symbol, log2(RPKM+0.001)ANOVA, p-value, qvalue, ratio, fold change, fold change description

source_name: hindlimb muscles

growth_protocol: Ham's-F10, Horse Serum 10%, 1% Penicillin/Streptomycin, 2.5 ng/mL bFGF

extract_protocol:
RNA was extracted using Trizol. 500ng of RNA was used for the construction of library preparation
NEBNext Ultra II RNA library preparation kit for Illumina
RNA-seq using NEBNext Ultra II RNA library preparation kit for Illumina

value: hindlimb muscles

value: primary cells

value: myoblasts

value: Pax7 CRE+/-;Psat1fl/fl


title: VNM2_FPKM

description:
Library name: Sample2
VNM2_FPKM


title: bulkRNA_Psat1KO_rep1


title: bulkRNA_Psat1KO_rep3


title: bulkRNA_CTRL_rep3

value: Pax7+/+; Psat1fl/fl


title: bulkRNA_CTRL_rep1

value: Pax7 +/+; Psat1fl/fl


title: bulkRNA_CTRL_rep2


title: CUTRUN_Psat1KO_IgG_rep2

description: CUT&RUN

library_source: genomic

data_processing:
Paired end reads were processed with CutRunTools/20200629 tools
the adapter sequences and low-quality reads were removed with Trimmomatic/0.36
Sequence reads were aligned to reference genome using bowtie/2-2.3.4.3 with default parameters
Duplicate reads were marked using Picard/2.22.2
Assembly: mm10
Supplementary files format and content: Excel files including gene_name, transcript_id, strand
Library strategy: Cut&Run

molecule: genomic DNA

growth_protocol: Ham's-F10, Horse Serum 10%, 1% Penicillin/Streptomycin, 2.5ng/mL bFGF

extract_protocol:
cells were harvested and immediately processed for Concavanalin A and H3K27me3/IgG antibody binding
NEBNext® UltraTM II DNA Library Prep Kit for Illumina
Cut&Run using NEBNext® UltraTM II DNA Library Prep Kit for Illumina


title: CUTRUN_Psat1KO_IgG_rep1

description: CUT&RUN


title: CUTRUN_Psat1KO_H3K27me3_rep2

description: CUT&RUN


title: CUTRUN_Psat1KO_H3K27me3_rep1

description: CUT&RUN


title: CUTRUN_CTRL_IgG_rep2

description: CUT&RUN


title: 5hmC_Psat1KO_rep2

data_processing:
Adapter sequences were removed using trimgalore/0.6.7
Sequence reads(R1) were aligned to reference genome using Bowtie/1.3.1, allowing two mismatches
Uniquely mapped and non-redundant reads were used for peak calling using MACS 1.4.2,with parameter: --nomodel -p 1.0e-05
Assembly: mm10
Supplementary files format and content: Excel files, containing gene_name, transcript_id, strand
Library strategy: 5hmC-IP

extract_protocol:
genomic DNA was extracted from Ctrl and Psat1cKO myoblasts, sonicated with ME220 AFA Focused Ultrasonicator (Covaris) for 15 cycles of 30 sec on and 30 sec off to generate fragments of ~300 bp average size. 5ug DNA was used for 5hmC-IP. 10% of DNA was used as Input
IDT xGen ssDNA&Low-Input DNA library Prep kit
5hmC-IP sequencing using IDT xGen ssDNA&Low-Input DNA library Prep kit


title: VNM4_FPKM

description:
Library name: Sample4
VNM4_FPKM

value: brain tissue

value: paired-end


title: CUTRUN_CTRL_H3K27me3_rep2

description: CUT&RUN


title: 5hmC_Psat1KO_rep1


title: CUTRUN_CTRL_IgG_rep1

description: CUT&RUN


title: CUTRUN_CTRL_H3K27me3_rep1

description: CUT&RUN


title: 5hmC_Psat1KO_input_rep2


title: 5hmC_Psat1KO_input_rep1


title: 5hmC_CTRL_rep1


title: 5hmC_CTRL_input_rep1


title: 3 days post injury (dpi) RNA_Psat1KO_rep4

data_processing:
Sequence reads were aligned to reference genome using HISAT version 2.2.1 with default parameters
Aligned reads were quantifed using Sailfish
Aligned reads were annotated in R using org.Mm.eg.bd version 3.15.0
Differential expression analysis was performed using DESeq2 version 4.2.0
Genes were filtered by foldchange of 2 and ajdusted pvalue smaller that 0.05
Assembly: mm10
Supplementary files format and content: Excel files containing gene name, baseMean, log2FC, lfcSE, stat, pvalue, padj

source_name: Tibialis Anterior/Extensor Digitorum Longus (TA/EDL)

growth_protocol: Mice Ctrl and Psat1iKO

extract_protocol:
TA/EDL sample collection 3 dpi and MuSCs sorting by FACS
NEBNext Ultra II RNA library Preparation kit for Illumina
RNA-seq using NEBNext Ultra II RNA library Preparation kit for Illumina

treatment_protocol: Muscle injury in TA/EDL with Notexin 2mg/mL

value: Muscle stem cell (MuSC)

tag: time


title: 5hmC_CTRL_input_rep2


title: 3 days post injury (dpi) RNA_Psat1KO_rep3

value: Tibialis Anterior/Extensor Digitorum Longus (TA/EDL)


title: 3 days post injury (dpi) RNA_Psat1KO_rep1


title: 3 days post injury (dpi) RNA_CTRL_rep4

value: Ctrl


title: 3 days post injury (dpi) RNA_CTRL_rep2


title: iCD_hMES_6 (RNAseq)

status: Public on Sep 03 2024

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 6
CAT73_hMES

data_processing:
FastQC (version 0.11.9; BaseSpace Labs, Illumina) and MultiQC 23were used to evaluate the quality of raw read fastq data files.
We applied quality trimming using trimmomatic 24 (v0.30).
Reads were mapped against Homo sapiens reference genome using STAR software (v2.5.2) (Dobin et al., 2013).
Raw counts were tallied after assigning reads to genes using FeatureCounts from subread software (v. 2.8.2) (Liao et al., 2019) on the CCDS collection of annotated human transcripts summarized at the gene level
Differential expression (DE) analysis was conducted using DESeq2 package using the Wald test and an Approximate Posterior Estimation for the Generalized Linear Model (apeglm) approach to check the DE genes between conditions. Gender and age of each patient were used as covariates in the model.
Assembly: hg38 (Ensembl release 78, Homo_sapiens.GRCh38.dna.primary_assembly)
Supplementary files format and content: supplementary excel file includes DESeq2 normalized read counts for all CCDS annotated hg38

growth_protocol: Patients with CD, active and inactive, and controls were recruited at Joan XXIII Hospital (Tarragona, Spain) and Vall d’Hebron University Hospital (Barcelona, Spain) according to Helsinki’s statements. All participants gave their informed consent, and the study was reviewed and approved by the ethics and research committees of the respective hospitals (references CEIM 177/2018; CEIM 41p/2015; PR(CS)383/2021). Donors were classified as those in relapse (active) or in remission (inactive) following the Crohn’s Disease Activity Index (CDAI) criteria and also based on biological and clinical parameters such as high-sensitivity C-reactive protein (hsCRP) and fecal calprotectin levels. Endoscopic evaluation was performed in 80% of the patients, with complete correspondence with the clinical classification obtained by CDAI.2. Samples of visceral (VAT, mesenteric origin) AT and subcutaneous tissue (SAT) were obtained from patients with inactive CD (n=7) and from patients without CD (control group) (n=7) undergoing non-acute surgical interventions such as hernia or cholecystectomy, in a scheduled routine surgery. Samples of mesenteric perilesional (81% ileum, 5% colon and 14% ileocolon) “wrapping” VAT (creeping fat origin) (n=7) were obtained from patients with active CD scheduled for surgery for symptomatic complications or failure of medical therapy. All tissue samples were aseptically collected. Clinical data, anthropometric, demographic, and biochemical variables of the cohort are shown in Table 1. Groups were matched by body mass index (BMI), gender and age.

extract_protocol:
Total RNA was extracted from from ASCs (100,000 cells/well) using TRIzol reagent (Roche, Basel, Switzerland). and further purified/DNase treated with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA concentration was determined by absorbance at 260 nm, and purity was estimated with a Nanodrop spectrophotometer (Nanodrop Technologies Inc., Wilmington, DE). Integrity was assed with Bioanalyzer Nano6000 assy with RIN values above 7.0.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer's protocol adapted with beads on a Sciclene NGS liquid handling robot (Calliper, PerkinElmer) with 200 ng of total RNA used as input.Final libraries were qualified using Bioanalyzer DNA 1000  (Agilent, Santa Clara, CA) and quantified by qPCR using the KAPA Library Quantification Kit KK4835 (Roche, Basel, Switzerland) prior to sequencing. Libraries were sequenced 1 x 51+8+8 bp to at least 24 million reads per sample on the Illumina HiSeq2500 platform with v4 SBS reagents

treatment_protocol: Tissue samples were first washed with PBS to remove any traces of blood, and when needed, the parts damaged by the extraction were removed with a scalpel. The tissue was then treated with 0.1% collagenase with PBS and 1% BSA for 90 minutes at 37°C under gentle agitation. The digested samples were centrifuged at 300G at 24°C for 5 minutes to obtain a phase separation, with the mature adipocytes at the top, and the vascular stroma in the pellet, consisting of stem cells, macrophage cells, endothelial cells, blood cells, etc. Mature adipocytes were stored, and another wash and centrifugation was performed to isolate the stem cells (ASCs). The pellet resulting from this last centrifugation step was resuspended with DG maintenance medium (DMEM / F12 in 10% fetal bovine serum (FBS)), seeded in a T75 flask and left to grow for seven days in an incubator at 37°C. (Dubois et al. 2008).DNA for methylation assays was extracted from cells at passage 3 whereas RNA for transcriptomic profiling was estracted from cells at passage 4. Adipose tissue (VAT)-derived macrophages (ATMs) were also isolated from the stromal vascular fraction of AT biopsies as described.

tag: tissue type

value: Mesenteric fat, associated to healthy intestine

value: visceral adipose tissue

value: Adipose tissue derived stem cells

tag: disease status

value: Inactive Crohn’s Disease

tag: gender

value: Female

tag: individual

tag: age

tag: hospital

value: VH

tag: tnf treatment

value: untreated

tag: bmi


title: iCD_hMES_4 (RNAseq)

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 4
CAT68_hMES

tag: tissue


title: iCD_hMES_5 (RNAseq)

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 5
CAT71_hMES

tag: cell type


title: iCD_hMES_3 (RNAseq)

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 3
CAT66_hMES


title: iCD_hMES_2 (RNAseq)

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 2
CAT65_hMES


title: iCD_hMES_1 (RNAseq)

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 1
CAT64_hMES

value: Male


title: aCD_hMES_7 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 7
CAT78_hMES

value: Active Crohn’s Disease

value: treated


title: aCD_hMES_6 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 6
CAT77_hMES


title: aCD_hMES_5 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 5
CAT76_hMES


title: aCD_hMES_4 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 4
CAT75_hMES


title: aCD_CF_7 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 7
CAT86_CF

value: Creeping fat, associated to inflamed intestine


title: aCD_hMES_1 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 1
CAT17_hMES


title: aCD_CF_6 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 6
CAT84_CF


title: aCD_hMES_2 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 2
CAT53_hMES


title: aCD_CF_5 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 5
CAT80_CF


title: aCD_hMES_3 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), healthy mesenteric fat (hMES), replicate 3
CAT74_hMES


title: aCD_CF_4 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 4
CAT77_CF


title: 3 days post injury (dpi) RNA_Psat1KO_rep2

tag: cell line

value: primary cells

tag: genotype


title: C_hMES_5 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 5
AT205_VAT

value: Healthy


title: 5hmC_CTRL_rep2

value: hindlimb muscles

value: myoblasts

value: Pax7 +/+; Psat1fl/fl


title: aCD_CF_1 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 1
CAT59_CF


title: iCD_hMES_7 (RNAseq)

description:
Human adipocytic stem cells (hASCs), inactive Crohn’s disease (iCD), healthy mesenteric fat (hMES), replicate 7
CAT82_hMES


title: 3 days post injury (dpi) RNA_CTRL_rep1

value: Tibialis Anterior/Extensor Digitorum Longus (TA/EDL)

value: Muscle stem cell (MuSC)

value: Ctrl


title: aCD_CF_3 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 3
CAT76_CF

value: visceral adipose tissue

value: Adipose tissue derived stem cells


title: C_hMES_6 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 6
AT211_VAT

value: Mesenteric fat, associated to healthy intestine


title: C_hMES_7 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 7
AT261_VAT


title: aCD_CF_2 (RNAseq)

description:
Human adipocytic stem cells (hASCs), active Crohn’s disease (aCD), creeping fat (CF), replicate 2
CAT69_CF

value: Female

value: VH


title: 3 days post injury (dpi) RNA_CTRL_rep3


title: C_hMES_2 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 2
AT102_VAT

value: untreated


title: C_hMES_4 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 4
AT193_VAT


title: C_hMES_1 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 1
AT99_VAT

value: Male


title: C_hMES_3 (RNAseq)

description:
Human adipocytic stem cells (hASCs), healthy control (C), healthy mesenteric fat (hMES), replicate 3
AT180_VAT


title: Py8119_Ribotag_Tumor_Ctl_1_Input

status: Public on Aug 08 2024

first: Jan

middle: K

last: Kitajewski

state: IL

address: 909 S. Wolcott Ave. MC 901

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

data_processing:
Raw reads (fastq) were aligned with the mouse genome (mm10) using STAR (version 2.7.4a).
The same files were processed to obtain raw counts by FeatureCounts (version 2.0.1)
Differential gene expression analysis was performed using a design formula in DESeq2 (design = ~condition) and changes in gene expression were assessed by Log-fold changes (LFC).
Assembly: Human Genome (ENSEMBL/GRCh38); Mouse Genome (UCSC/mm10)
Supplementary files format and content: Raw count files (.txt) were generated using FeatureCounts (v1.5.2) ; Normalized count files (.csv) were generated by DESeq2.

source_name: Homogenate

growth_protocol: Py8119 tumor cells were implanted into the left fifth mammary fat pad of female C57BL/6J mice

extract_protocol:
After the mice were euthanized, tumors were rapidly resected and snap frozen in liquid nitrogen. Samples were stored at -80oC until polysome immunoprecipitation. To isolate actively translating mRNA from endothelial cell polysomes, the tumor tissue was pulverized with a mortar and pestle in liquid nitrogen and suspended in RNA tissue lysis buffer [50mM Tris pH 7.5 (Invitrogen), 100mM KCl (Invitrogen), 15mM MgCl2 (Invitrogen), 100μg of  cycloheximide (Sigma Aldrich), 1% Triton X-100 (Fisher Sci), 1mM DTT (Sigma Aldrich), 7.5μL/mL Protector RNA (Roche), 12μL/mL Turbo DNAse (Thermofisher), 10μL/mL Halt Protease Inhbitor (Thermofisher), RNAse-Free H2O (Fisher Sci)]. The mixture was transferred to a glass Dounce homogenizer on ice and then lysed with 10 strokes of pestle A followed by an additional 10 strokes with pestle B. The lysed mixture was transferred to an ice-cold microcentrifuge tube and spun at 16000x G for 10mins at 4oC. The supernatant was aspirated and 100μL was set aside for input analysis. The remainder of the supernatant was added to Dynabeads (Thermofisher) conjugated to anti-HA antibodies (Abcam) and rocked on ice for 2hrs. The beads were separated by magnetic separation, washed twice with wash buffer, and then eluted using TRIzol (Thermofisher). The mRNA was isolated using a TRIzol Microprep Kit (Zymo Research) and eluted into 13μL of RNAse free H2O. Prior to submitting the samples for sequencing, RNA quality and concentration was assessed using an Agilent TapeStation 4200. Sequencing was performed on the NovaSeq 6000 (SP flow cell, 100bp single reads)
RNA quality and concentration was assessed using an Agilent TapeStation 4200. Sequencing was performed on the NovaSeq 6000 (SP flow cell, 100bp single reads)

treatment_protocol: Once tumors reached ~30mm3, mice were randomized and then injected intravenously through the retro-orbital sinus with either 25mg/kg of 6-3-A6 antibody or control mouse IgG (Jackson ImmunoResearch) twice weekly for 10 days.

tag: strain

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

value: 3 weeks old

value: Homogenate

tag: treatment

value: Control IgG

tag: treatment harvest_time

value: 10 days after treatment


title: eGFP, multi, ncATAC-seq

status: Public on Jul 26 2024

city: Lausanne

first: Johannes

last: Graeff

address: Station 19

department: SV

country: Switzerland

institute: EPFL

description: 10X Multiomic

library_source: genomic single cell

data_processing:
Single nuclei multimodal analysis. snRNA-seq and snATAC-seq libraries were processed with CellRanger-arc software (v. 2.0.0)
Reads were aligned to a custom Mouse reference genome built from the mm10 genome and combined with the pVLX lentiviral vector carrying either eGFP, CBP, KAT5.
Fasta and gtf used to generate the custom reference genomes with Cellranger-arc mkfaskq are provided as supplementary files.
Assembly: mm10_full_P244_eGFPmyc_masked.fa: fasta sequences of mm10 including the pVLX lentiviral vector carrying eGFP.
Assembly: mm10_full_P244_eGFPmyc.gtf: genomic annotations of mm10 including the pVLX lentiviral vector carrying eGFP.
Assembly: mm10_full_P246_CBPmyc_masked.fa: fasta sequences of mm10 including the pVLX lentiviral vector carrying CBP.
Assembly: mm10_full_P246_CBPmyc.gtf: genomic annotations of mm10 including the pVLX lentiviral vector carrying CBP.
Assembly: mm10_full_P245_KAT5myc.gtf: fasta sequences of mm10 including the pVLX lentiviral vector carrying KAT5.
Assembly: mm10_full_P245_KAT5myc.gtf:  genomic annotations of mm10 including the pVLX lentiviral vector carrying KAT5.
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, atac_fragments.tsv,  per_barcode_metrics.csv
Supplementary files format and content: meta_detailedCellTypes_eGFP_CBP_KAT5.csv.gz: comma-separated table reporting the main cell-types and excitatory neurons subtypes associated to each individual cell

source_name: Brain Lateral Amygdala

extract_protocol:
Frozen tissue was homogenized in 100 µL homogenization buffer NP+ (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris⋅HCl, pH 7.4; plus 1 mM DTT, 1X protease inhibitor 50X, 1 U/uL RiboLock RNAse inhibitor, 0.1% NP-40, in H20), filtered through a 40 µm cell strainer and washed with 500 µL homogenization buffer (no NP-40). Samples were centrifuged at 1000g for 8 min at 4 °C. The pellet was resuspended in 210 µL homogenization buffer (no NP-40), and 290 µL of 50% Iodixanol solution (Iodixanol 60%, IDM 1X, 1 mM DTT, 1X protease inhibitor 50X, 1 U/uL RiboLock RNAse inhibitor) was added. Nuclei suspension was transferred to a tube (ref:344090, Beckman), completed with a layer of 100 µL homogenization buffer (no NP-40) and centrifuged at 10000g for 22 min at 4 °C using SW 55 Ti rotor, Optima XL-80K ultracentrifuge. Pellet was resuspended in 100 µL of permeabilization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, pH 7.4; plus 1 mM DTT, 1X protease inhibitor 50X, 1 U/uL RiboLock RNAse inhibitor, 0,01%  Tween, 0,001% Digitonin, 0,01% NP-40, 0,5% BSA, in H20)  for 2 min at 4 °C, 500 µL of wash buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris⋅HCl, pH 7.4; plus 1 mM DTT, 1X protease inhibitor 50X, 1 U/uL RiboLock RNAse inhibitor, 0,5% BSA, in H20) were added and samples were centrifuged at 1000g for 10 min at 4 °C. Pellets were resuspended in diluted nuclei buffer (see Chromium nuclei isolation kit, 10X Genomics) and filtered through a 40 µm Flowmi strainer. Final sample concentrations were eGFP: 4040 nuclei/uL, CBP: 3645 nuclei/uL, KAT5: 2925 nuclei/uL. Samples were immediately processed for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

value: Brain Lateral Amygdala

value: 6-12 weeks old


title: KAT5, multi, ncATAC-seq

description: 10X Multiomic

value: KAT5 construct:pCMV6-KAT5-Myc-DKK (ref:MR223769, Origene)


title: CBP, multi, ncATAC-seq

description: 10X Multiomic

value: CBP construct:pRc/RSV-m CBP-HA (ref:16701, Addgene)


title: CBP, multi, snRNAseq

description: 10X Multiomic


title: eGFP, multi, snRNAseq

description: 10X Multiomic


title: In vivo setup, 12hr post-hCG administration, replicate 2

status: Public on Jul 08 2024

city: Goettingen

first: Sarah Mae

last: Penir

address: Am Fassberg 11

department: Department of Meiosis

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
Count matrices were converted to FASTQ files using the cellranger software (version 3.0.2, 10X Genomics).
Assembly: GRCm38
Supplementary files format and content: Cell ranger mapping output is provided.

source_name: Follicle

extract_protocol:
The follicles were isolated 0, 3, 6, 9, and 12 hrs post-hCG addition.
The single-cell suspensions were processed using the 10X Genomics Chromium Single Cell System and the Chromium Single Cell 3’ v3 Reagent Kits following the manufacturer’s instructions.

value: Follicle

tag: background strain


title: In vivo setup, 12hr post-hCG administration, replicate 1


title: In vitro setup, 12hr post-hCG administration, replicate 1


title: In vitro setup, 12hr post-hCG administration, replicate 3


title: In vivo setup, 12hr post-hCG administration, replicate 3


title: In vitro setup, 9hr post-hCG administration, replicate 3


title: In vitro setup, 12hr post-hCG administration, replicate 2


title: In vitro setup, 9hr post-hCG administration, replicate 1


title: In vitro setup, 9hr post-hCG administration, replicate 2


title: In vivo setup, 9hr post-hCG administration, replicate 1


title: KAT5, multi, ncRNAseq

description: 10X Multiomic


title: In vitro setup, 3hr post-hCG administration, replicate 1


title: In vivo setup, 9hr post-hCG administration, replicate 2


title: In vivo setup, 9hr post-hCG administration, replicate 3


title: In vitro setup, 6hr post-hCG administration, replicate 3


title: In vivo setup, 6hr post-hCG administration, replicate 2


title: In vitro setup, 6hr post-hCG administration, replicate 2


title: In vitro setup, 6hr post-hCG administration, replicate 1


title: In vivo setup, 6hr post-hCG administration, replicate 1


title: In vivo setup, 0hr post-hCG administration, replicate 3


title: In vitro setup, 3hr post-hCG administration, replicate 3


title: In vivo setup, 6hr post-hCG administration, replicate 3


title: In vitro setup, 0hr post-hCG administration, replicate 2


title: In vitro setup, 0hr post-hCG administration, replicate 3


title: In vivo setup, 3hr post-hCG administration, replicate 3


title: In vivo setup, 3hr post-hCG administration, replicate 2


title: BMDM_WT_IMQ12h_rep1

status: Public on Apr 17 2024

data_processing:
Sequencing data were generated with an Illumina Novaseq6000 system.  The FastQ files were produced by processing raw sequencing data using bcl2fastq (v2.20.0)
Subsequently, paired end sequence reads were processed with Partek Flow version 10.0.22.1204 (Partek Inc.)The trimmed reads were mapped onto mouse genome mm10 using STAR 2.7.8a as implemented in Partek Flow with default settings
Quantification was done using the Partek Flow “quantify to annotation model (Partek E/M)” and the Ensembl transcript release 101
The gene counts were used for differential gene expression was assessed using DESeq2 (v1.42.0), or normalized, generated FPKM (fragments per kilobase millions) and conducted ANOVA analyses
Assembly: mm10
Supplementary files format and content: Deseq2_metadata.xlsx, bulkRNA_rawcounts.txt

source_name: BMDM

extract_protocol:
Tri Reagent (Sigma-Aldrich) was used followed by column-based purification with RNA Clean & Concentrator-5 Kit (Zymo Research).
NEBNext Poly(A) mRNA Magnetic Isolation kit (New England BioLabs) was used to generate cDNA libraries. Picogreen dsDNA quantitation assay (Thermo Fisher Scientific) was used to measure the cDNA concentration; cDNA was diluted to 3 nM, cDNA libraries were pooled together

value: BMDM

value: Imiquimod 12h


title: BMDM_WT_IMQ12h_rep6


title: BMDM_WT_IMQ12h_rep4


title: BMDM_WT_IMQ12h_rep3


title: BMDM_WT_rep3


title: BMDM_WT_IMQ12h_rep5


title: BMDM_WT_rep5


title: In vitro setup, 3hr post-hCG administration, replicate 2


title: BMDM_WT_rep6


title: P664

status: Public on Nov 09 2023

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.3). Reads were mapped to GRCh38.89 (Ensembl) using STAR (v. 2.5.3a) (Dobin et al., 2013). The STAR parameters used were: --runThreadN 24 --sjdbOverhang 99 --genomeDir ref_ensembl_GRCh38_89/star_index --sjdbGTFtagExonParentGene gene_id --sjdbGTFfile ref_ensembl_GRCh38_89/Homo_sapiens.GRCh38.89.gtf --outSAMtype BAM Unsorted SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts. Ensembl genes with at least 10 counts in 25% of samples were filtered for the analysis. Normalization and differential expression analysis were performed using R (v. 4.0.3) package DESeq2 (v. 1.30.1) (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID to HUGO gene names (Durinck 2009), and gene set enrichment analysis was done using R (v. 4.0.3) package FGSEA (v. 1.16.0).
Assembly: GRCh38.89(Ensembl)
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample post filtering

source_name: Placenta

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer. All samples had a RIN above 7.0.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina).

value: Placenta

value: Asian

tag: disease

value: Severe Preeclampsia


title: BMDM_WT_rep4


title: BMDM_WT_IMQ12h_rep2


title: P1_756

value: Non-hypertensive control

value: Female


title: P1_2699

value: European

value: Male


title: P1_2703

value: African


title: In vitro setup, 0hr post-hCG administration, replicate 1


title: P7_2190


title: S2_fibrotic_1

status: Public on Mar 20 2024

city: Rochester

first: Yuanhang

last: Liu

address: 200 1ST ST SW

institute: Mayo Clinic

description: FFPE spatial transcriptomics

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_iamge.jpg: image of tissue and spots
Supplementary files format and content: scalefators_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of the tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of the tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: spatial enrichment in csv format

source_name: liver

growth_protocol: Age-matched and sex-matched mice were selected for experiments. HK2fl/fl mice were generated by Dr. Nissim Hay and provided by Dr. Michael Simons. We crossed HK2fl/fl with PDGFRBcreERT2 (The Jackson Laboratory B6.Cg-Tg(Pdgfrb-cre/ERT2)6096Rha/J) mice to obtain PDGFRBcreERT2/Hk2fl/fl mice

extract_protocol:
Visium Technology Platform from 10x Genomics was utilized. FFPE liver sections were positioned on the capture areas of the Visium Spatial Gene Expression Slide (10x Genomics, PN-1000185) and stained with hematoxylin and eosin following manufacturer’s protocol.  Liver sections were then imaged using a Huron TissueScope LE slide scanner
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Gene Expression Slides & Reagent kit according to manufacturer's instructions

treatment_protocol: Intraperitoneal administration of tamoxifen (75 mg/kg/day) for 5 consecutive days was used to activate Cre-ERT2 and induce HSCs-specific deletion of Hk2 gene (HK2ΔHSC). There was a 2-week waiting period after the last tamoxifen injection prior to any experimentation. Liver fibrosis was induced by intraperitoneal injection of carbon tetrachloride (CCl4, 1 μL/g of body weight, Sigma-Aldrich #319961) twice a week for 4 or 6 weeks.

value: liver

tag: Sex

value: male

value: 5 months


title: P1_2326


title: P7_1853


title: BMDM_WT_rep2


title: BMDM_WT_rep1

description: original runid: 230710_0776 & 230710_0777


title: P7_2634


title: In vivo setup, 0hr post-hCG administration, replicate 2


title: P7_2511


title: S4_fibrotic_2

description: FFPE spatial transcriptomics

tag: age


title: S3_fibrotic with intervention

description: FFPE spatial transcriptomics


title: P1_2013


title: P1_1973


title: P1447


title: P1410


title: P1205


title: P1230


title: P1516


title: S1_healthy

description: FFPE spatial transcriptomics

value: olive oil


title: P1043


title: P829


title: P1178


title: P7_1362


title: P1_1154


title: P1_1651


title: P1120


title: disome HFHS, rep 1

status: Public on Oct 23 2023

first: David

last: Gatfield

address: Genopode building

department: Center for Integrative Genomics

institute: University of Lausanne

data_processing:
reads where trimmed from adapter sequence using cutadapt (version: 3.5; options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30) and quality filtered using faion: 0.0.14; options: -Q33 -q 30 -p 90)
UMIs were extracted from each read with UMItools (options: extract --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode –error-correct-cell).
Reads where size-selected for single ribosome (monosomes; size 26 to 35; disomes; size 45 to 70). To estimate rRNA and tRNA contamination, reads were mapped to human and mouse rRNA and mouse tRNA databases using bowtie2 (options: -p 2 -L 15 -k 20 --trim5 2). Reads that failed to map to these, where then mapped to the mouse transcript database (Ensembl database v. 100).
Assembly: Ensembl transcript v100
Supplementary files format and content: Samples SGA files: tab delimited file reporting transcript ID, sample type, position, strand and read counts of predicted ribosome A sites.
Supplementary files format and content: cdsCounts.csv.gz: comma separated file with the following columns: Gene ID, transcript ID, read counts for each Monosome & Disome sample
Supplementary files format and content: codonCount_Monosome.dat.gz: tab delimited file with the following columns: Gene ID, transcript ID, codon position, read counts for each sample
Library strategy: Disome-seq

source_name: Liver

extract_protocol:
Liver pieces from control diet-fed or High-Fat-High-Sugar (HFHS) WT mice were collected and flash-frozen in liquid nitrogen. Using 200mg of frozen livers, lysates and ribosome footprints were generated by RNase I digestion and purified according to Janich etal. (2015) with minor modifications. Briefly, 10 μg of RNA was separated and excised from a 15% urea-polyacrylamide gel (30nt or 60nt footprints -monosomes or disomes respectively). From the gel slices, RNA was extracted overnight at 4 °C on a rotating wheel before precipitation in isopropanol during 3h at -20 °C
RNA3’-end repair was carried out with 2 U/μl of T4 PNK (Lucigen) prior to a 2h adaptor ligation at 25°C using 1.5 μl of ligase mix (0.33 U/μL of T4 RNA Ligase 1 (NEB), 6.66 U/μl of T4 RNA Ligase 2 Deletion Mutant (Lucigen) and 1.33 U/μL of riboguard (Lucigen)) and 1 uL of a 20 μM 5’-adenylated DNA adaptor (containing sample barcode and a 8N unique molecular identifiers (UMIs)). Adaptor removal was carried out by treating individual libraries with 2.7 U/μl of 5’deadenylase (NEB) and 1.8U/μL of RecJf exonuclease (NEB) for 1h at 30°C and 1h at 37°C. Using Zymo Clean & Concentrator columns, samples were purified and pooled . Ribosomal RNA was depleted according to siTools Biotech rRNA depletion kit specifications with a custom-made riboPOOL. The clean-up step was done using Zymo Clean & Concentrator columns

value: Liver

value: WT

value: High Fat High Sugar


title: disome HFHS, rep 3


title: disome Chow, rep 3

value: Chow Diet


title: disome Chow, rep 2


title: disome Chow, rep 1


title: monosome HFHS, rep 3

data_processing:
reads where trimmed from adapter sequence using cutadapt (version: 3.5; options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30) and quality filtered using faion: 0.0.14; options: -Q33 -q 30 -p 90)
UMIs were extracted from each read with UMItools (options: extract --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode –error-correct-cell).
Reads where size-selected for single ribosome (monosomes; size 26 to 35; disomes; size 45 to 70). To estimate rRNA and tRNA contamination, reads were mapped to human and mouse rRNA and mouse tRNA databases using bowtie2 (options: -p 2 -L 15 -k 20 --trim5 2). Reads that failed to map to these, where then mapped to the mouse transcript database (Ensembl database v. 100).
Assembly: Ensembl transcript v100
Supplementary files format and content: Samples SGA files: tab delimited file reporting transcript ID, sample type, position, strand and read counts of predicted ribosome A sites.
Supplementary files format and content: cdsCounts.csv.gz: comma separated file with the following columns: Gene ID, transcript ID, read counts for each Monosome & Disome sample
Supplementary files format and content: codonCount_Monosome.dat.gz: tab delimited file with the following columns: Gene ID, transcript ID, codon position, read counts for each sample
Library strategy: Ribo-Seq


title: P1_1748


title: monosome Chow, rep 3


title: monosome HFHS, rep 2


title: monosome Chow, rep 1


title: monosome Chow, rep 2


title: monosome HFHS, rep 1


title: HB13hpf_rep2_ATAC

status: Public on Sep 27 2023

city: Aurora

first: Charles

last: Sagerstrom

state: CO

address: 12801 East 17th Avenue

department: Pediatrics

institute: University of Colorado Medical School

description:
10x Genomics multiomic, ATAC-seq
hindbrain 13hpf rep2
HB13hpf_rep2.clustered.RDS

data_processing:
Generated cell feature counts for each single cell RNAseq library using cellranger arc  count --reference=GRCz11
single cell RNAseq feature and ATACseq feature data generated using Signac/Seurat Read10X_h5 and SeuratFromMatrixh5 functions using GRCz11.v99.EnsDb annotation
filtered Seurat object to select cells with nCount_ATAC>1000 & nCount_RNA >500  & percent.mitchondrial <5% & nucleosome_signal<2 & TSS.enrichment>1
generated ATAC peaks with Signac CallPeaks function using macs2 and used in CreateChromatinAssay with name "peaks"
processed filtered Seurat object using Seurat SCTransform, RunPCA, FindTopFeatures, RunTFIDF, RunSVD, FindMultiModalNeighbors(reduction.list=list("pca","lsi"),dims.list=list(1:50,2:50),FindClusters(various resolutions) and RunUMAP(reduction="pca",dims=1:50)
Assembly: GRCz11
Supplementary files format and content: h5 files are Hierarchical Data Formats files of cellranger_arc count matrix output
Supplementary files format and content: tsv.gz files are gzipped tab delimited bed files of atac fragments
Supplementary files format and content: RDS files are R file containing SeuratObject

organism: Danio rerio

source_name: dissected hindbrain region

growth_protocol: Zebrafish embryos were generated by natural spawnings and grown under standard conditions

extract_protocol:
Tissue was collected in 1XPBS, dissociated by repeated pipetting through a p1000 tip, and centrifuged at 4℃ at 400G for 5 minutes followed by resuspension of the pellet in 500 μl of protease (10 mg/ml BI protease (Sigma, P5380), 125 U/ml DNase, 2.5 mM EDTA in PBS) for 15minutes on ice. Samples were centrifuged at 4℃ at 400G for 5 minutes, resuspended in 1ml HBSS + FBS (2%), filtered through a 20 μm cell strainer (pluriSelect, KL-071912), recentrifuged at 4℃ at 400G for 5 minutes, resuspended in 500 μl of HBSS + FBS (2%) and again filtered through a 20 μm cell strainer. Following centrifugation at 4℃ at 400G for 5 minutes, the cells were resuspended in 200 μl PBS. For nuclei isolation, we followed the 10X Genomics recommended protocol with minor modifications. The dissociated cells were centrifuged at 900G at 4℃ for 5 minutes, resuspended in 100 μl of 0.1X lysis buffer (1 mM Tris-HCl pH7.4, 1 mM NaCl, 0.3 mM MgCl2, 0.1% BSA, 0.01 % Tween-20, 0.01 % NP40, 0.001 % Digitonin (Invitrogen, BN2006), 0.1 mM DTT, 0.1 U/μl RNase inhibitor, in nuclease-free water) and incubated on ice for 5 min. Samples were then washed three times by centrifugation at 4℃ at 900G for 10 min and resuspension in 1 ml of chilled wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1 % Tween-20, 1 mM DTT, 1 U/μl RNase inhibitor in nuclease-free water). Finally, nuclei were counted and resuspended in 1X nuclei buffer (provided in the 10x Genomics Single Cell Multiome ATAC Kit A; 1 mM DTT, 1 U/μl RNase inhibitor in nuclease free water) at a final concentration of approximately 2,000-3,000 nuclei/μl for sequencing on the 10X scMultiome platform.
10x Genomics Single Cell Multiome ATAC Kit A was used with the standard protocol
Targets of 100,000 reads each GEX and ATAC per cell and  >= 2,000 cells per sample.

treatment_protocol: 10hpf and 16hpf samples were left untreated. One 13hpf sample was left untreated, the other 13hpf sample was treated with 5uM DEAB (4-Diethylaminobenzaldehyde) from 4hpf until 13hpf.

value: dissected hindbrain region

value: wildtype(TU line obtained from ZIRC stockcenter)

value: untreated


title: HB13hpf_rep2_GEX

description:
10x Genomics multiomic, RNA-seq
hindbrain 13hpf rep2
HB13hpf_rep2.clustered.RDS


title: BEAS2B with 500 ug/ml Dibifree

status: Public on Oct 17 2023

city: Taipei

first: Tzu-Yi

last: Huang

address: No. 155, Sec. 2, Linong St. Beitou Dist.

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Trimmomatic (v.0.38) for the data clearance
HISAT2 performs clean reads and reference genome alignment. HISAT2 is an alignment tool based on HISAT and Bowtie2 that provides fast and accurate alignment results.
Used featureCounts (v1.6.3) to calculate the number of sequence mappings  and organized the gene expression in each sample.
Standardization will be done by TPM (Transcript Per Million) method
Assembly: GRCh38
Supplementary files format and content: Raw reads will filtered by Timmomatic to obtain  Clean reads

growth_protocol: BEAS2B cells were grown in RPMI medium containing 10% FBS, supplemented with 1% NEAA, penicillin/streptomycin, and L-glucose.

extract_protocol:
Total RNA was extracted by the RNeasy Mini Kit and frozen at -80℃
The cDNA library generates two sequence data (R1 and R2) files for the cDNA sequence annotation and quality control through Illumina Paired-End sequencing technology. Before sequenced the raw data, Trimmomatic (v.0.38) was used to remove low-quality reads and artificially added adapter to obtain high-quality information (clean reads).
KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland)

treatment_protocol: 1×106 cells were seeded on 10-cm petri dish and incubated overnight at 37oC. On the next day, cells were washed by PBS before treated with 66.67 or 500 µg/ml of Virofree for another 4 h.

value: epithelial cell line

value: 500 ug/ml Dibifree


title: mCRPC_19-048H2_LIVER_L_LOWER

status: Public on Sep 19 2023

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC liver L lower metastasis

extract_protocol:
Total RNA was isolated using RNA STAT-60 (Tel-Test). The isolated RNA was then purified with Qiagen RNeasy Kit (Qiagen Inc.) according to the manufacturer’s protocol utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: CRPC metastasis

value: prostate cancer


title: mCRPC_16-071I2_LUNG

source_name: CRPC lung metastasis


title: mCRPC_17-043K1_PELVIC_PERITONEAL

source_name: CRPC pelvic peritoneal metastasis


title: mCRPC_17-043I1_LN

source_name: CRPC lymph node (LN) metastasis


title: mCRPC_17-043J1_PERIRECTAL_OMENTAL

source_name: CRPC perirectal omental metastasis


title: mCRPC_16-071H10_LIVER

source_name: CRPC liver metastasis


title: mCRPC_19-045H2_LIVER_R_LOWER

source_name: CRPC liver R lower metastasis


title: mCRPC_17-042H2_BONE

source_name: CRPC bone metastasis


title: mCRPC_18-039I2_LIVER


title: mCRPC_19-045J2_LIVER_L_UPPER

source_name: CRPC liver L upper metastasis


title: mCRPC_19-028H2_LIVER


title: mCRPC_19-045M7_R_PELVIC_LN

source_name: CRPC R pelvic lymph node (LN) metastasis


title: BEAS2B with PBS control

value: PBS


title: mCRPC_19-029K2_PARIAORTIC

source_name: CRPC pariaortic metastasis


title: mCRPC_19-029M1_ANTERIOR_SPINAL

source_name: CRPC anterior spinal metastasis


title: mCRPC_19-028I2_LIVER


title: mCRPC_18-123K3_LIVER


title: mCRPC_19-026M2_ADRENAL

source_name: CRPC adrenal metastasis


title: mCRPC_18-123I7_LIVER


title: mCRPC_18-123G3_ADRENAL


title: mCRPC_18-115H1_LN


title: mCRPC_18-039G3_ADRENAL


title: mCRPC_13-099J2_LUNG


title: mCRPC_13-099H7_LIVER


title: mCRPC_18-112H2_LIVER


title: RNA-CHMP2B-+-+-veh-S3_B2

status: Public on Aug 10 2023

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

data_processing:
Quality control with FastQC v0.11.5 and MutiQC v1.9
Pre-processing with Cutadapt v1.18 to remove adapter residues, reads with low quality, and reads excessively short after trimming (-q = 30, --pair-filter = any, min_length= "20")
Removal of residual rRNA annotated in SILVA v119.1 with BBDuk v38.22, minimum covered fraction = 0.5, kmer size = 31
Mapping with STAR v2.6.1d (1-pass)
StringTie v2.0 assembly and annotation extension (min tpm=1, min fpkm=1)
Gene quantification with featureCounts (subread v1.6.3), min overlap = 90 nt, min fraction overlap = 90%, fragment non-chimeric mapping, both reads ends in pair aligned. Merged GENCODE v33 and FANTOM-CAT annotations were provided, see supplementary file gencode_fantomcat.v1.02.genes_transcripts_exons.gtf.gz.
Assembly: hg38

source_name: hiPSC-derived microglia

growth_protocol: hiPSC-derived microglia were generated according to a modified protocol (Haenseler et al., 2017; McQuade et al., 2018; van Wilgenburg et al., 2013). Aggrewell 800 24-well plates (Stem Cell Technologies, 34811) were prepared by rinsing with Anti-Adherent Rinsing Solution (Stem Cell Technologies, 07010), then plate centrifugation, followed by a single wash of PBS. hiPSCs were collected using Accutase (Thermo Fisher Scientific, A1110501), and approximately 3x10^6 hiPSCs were plated per Aggrewell. Microglia induction of hiPSCs was initiated via embryoid bodies (EBs) in E8 media, supplemented with 50 ng/ml BMP4 (120-05ET), 50 ng/ml VEGF (Peprotech, 100-20A) and 20 ng/ml SCF (Thermo Fisher Scientific, PEP-0860), to direct differentiation towards mesoderm and hematopoiesis production. Following, EBs were harvested and macrophage precursor cell (MPC) producing factories were established in X-VIVO 15 (Lonza, BE02-060Q), with 1% Glutamax (Thermo Fisher Scientific, 35050061), 0.1% Pen/Strep (Sigma, P0781-100ML), supplemented with 100 ng/ml M-CSF (Peprotech, 300-25) and 25 ng/ml IL-3 (Cell Guidance System, GFH80-100), to ensure myeloid production. Factories were cultured and supplemented with 5-10 ml media every week for at least four weeks, before MPCs were harvested for terminal microglia differentiation. MPCs were harvested through a cell strainer, then plated with a seeding density of 100 000 cells/cm2 in pre-coated Corning Cellbind cell culture dishes (Sigma, CLS3294-210EA) in Advanced DMEM/F12 (Thermo Fisher Scientific, 12634010), 1% Glutamax (Thermo Fisher Scientific, 35050061), 0.1% Pen/Strep (Sigma Aldrich, P0781-100ML), 1% N2 (Thermo Fisher Scientific, 17502048), supplemented with 100 ng/ml IL-34 (Peprotech, 200-34) and 10 ng/ml GM-CSF (Peprotech, 300-03). Mature microglia-like cells were generated within two weeks, with two media changes each week, before harvesting for analyses.

extract_protocol:
RNeasy® Plus Micro Kit (Qiagen, 74004) according to the manufacturer’s protocol.
Library preparation and sequencing by BGI Hong Kong with DNBseq
TotalRNA-seq paired-end 2x100 nt, stranded

value: Wild-type for rs63750652 (no variant)

tag: batch

value: Batch 2

tag: disease state

value: healthy


title: mCRPC_19-048I1_PERIAORTIC_LN

source_name: CRPC periaortic lymph node (LN) metastasis

value: male


title: RNA-CHMP2B-+-+-veh-S2_B2


title: RNA-CHMP2B-+-+-veh-S1_B2


title: RNA-CHMP2B-+--veh-S1_B2

value: G>C rs63750652 - Heterozygous FTD3 cell line

value: diseased


title: RNA-CHMP2B-+-+-veh-S3_B1

value: Batch 1


title: RNA-CHMP2B----veh-S1_B1

value: G>C rs63750652 - Homozygous FTD3 cell line


title: RNA-CHMP2B----veh-S3_B1


title: RNA-CHMP2B-+--veh-S2_B2


title: RNA-CHMP2B-+--veh-S3_B2


title: RNA-CHMP2B-+-+LPS-S2_B1


title: RNA-CHMP2B-+-+LPS-S3_B1


title: RNA-CHMP2B-+--LPS-S3_B1


title: mCRPC_19-026H3_LIVER


title: RNA-CHMP2B-+-+LPS-S1_B1


title: RNA-CHMP2B----LPS-S1_B1


title: RNA-CHMP2B-+--LPS-S2_B1


title: RNA-CHMP2B-+--LPS-S1_B1


title: RNA-CHMP2B-+-+TNFalfa-S3_B1


title: RNA-CHMP2B----LPS-S3_B1


title: RNA-CHMP2B----LPS-S2_B1


title: RNA-CHMP2B-+-+TNFalfa-S2_B1


title: RNA-CHMP2B-+-+TNFalfa-S1_B1


title: RNA-CHMP2B-+--TNFalfa-S2_B1


title: RNA-CHMP2B-+--TNFalfa-S3_B1


title: RNA-CHMP2B----TNFalfa-S3_B1


title: RNA-CHMP2B----TNFalfa-S1_B1


title: RNA-CHMP2B----TNFalfa-S2_B1


title: HB13hpf_DEAB_ATAC

status: Public on Aug 08 2023

description: 10x Genomics multiomic, ATAC-seq

value: treated with 5uM DEAB (4-Diethylaminobenzaldehyde) from 4hpf until 13hpf.


title: HB16hpf_ATAC

description: 10x Genomics multiomic, ATAC-seq

value: dissected hindbrain region


title: RNA-CHMP2B-+-+-veh-S1_B1


title: RNA-CHMP2B----veh-S2_B1


title: HB16hpf_GEX

description: 10x Genomics multiomic, RNA-seq

value: wildtype(TU line obtained from ZIRC stockcenter)


title: E10hpf_ATAC

description: 10x Genomics multiomic, ATAC-seq

source_name: whole embryo

value: whole embryo

value: untreated


title: E10hpf_GEX

description: 10x Genomics multiomic, RNA-seq


title: HB13hpf_GEX

description: 10x Genomics multiomic, RNA-seq

source_name: dissected hindbrain region


title: HB13hpf_ATAC

description: 10x Genomics multiomic, ATAC-seq


title: Indel-seq DIvA_4OHT_RNaseH1OE

status: Public on Jul 03 2023

first: Jaewon

last: Min

state: New York

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology (in the Institute for Cancer Genetics)

institute: Columbia University

data_processing:
The demultiplexing, barcoded processing
Assembly: hg19
Supplementary files format and content: bed
Supplementary files format and content: mcool
Library strategy: Indel-seq

growth_protocol: U2OS cells were cultured in high-glucose DMEM supplemented with 10% FBS

extract_protocol:
gDNA extraction,Qiagen PureGene
Libraries were contructed using Indel-seq and Hi-C protocol

value: Cancer Cell line

value: WT

value: 4OHT, RNaseH1 OE


title: HI-C DIvA_4OHT

data_processing:
The demultiplexing, barcoded processing
Assembly: hg19
Supplementary files format and content: bed
Supplementary files format and content: mcool


title: Indel-seq DIvA_4OHT_eV

value: 4OHT, empty vector


title: Indel-seq DIvA_4OHT_amanitin

value: 4OHT, amanitin


title: Indel-seq DIvA_4OHT_4


title: Indel-seq U2OS_Cas9WT

value: TRIM37 gRNAs


title: Indel-seq U2OS_Cas9H840A


title: Indel-seq DIvA_4OHT_siBLM

value: 4OHT, siBLM


title: Indel-seq DIvA_4OHT_siLuc_3

value: 4OHT, siLuc


title: Indel-seq U2OS_Cas9D10A


title: RNA-CHMP2B-+--TNFalfa-S1_B1

value: G>C rs63750652 - Heterozygous FTD3 cell line


title: HB13hpf_DEAB_GEX

description: 10x Genomics multiomic, RNA-seq


title: Indel-seq DIvA_4OHT_siLuc_2


title: Indel-seq DIvA_4OHT_siRAD51

value: 4OHT, siRAD51


title: Indel-seq DIvA_4OHT_siPARI

value: 4OHT, siPARI


title: Indel-seq DIvA_4OHT_siLuc


title: Indel-seq DIvA_4OHT_NU7441_2


title: Indel-seq DIvA_4OHT_CK666

value: 4OHT, CK666


title: Indel-seq DIvA_4OHT_2


title: Indel-seq DIvA_mock_2

value: mock


title: HI-C DIvA_mock

value: mock/DMSO


title: Indel-seq DIvA_4OHT_1


title: Indel-seq DIvA_4OHT_NU7441_1


title: S8: MIX1444 day 3 (codon optimized)

status: Public on Feb 22 2023

description: MIX1444 day 3 (codon optimized)

data_processing:
QC with FastQC and trimmomatic
PCR bias reduction with Bbmap (first 7 bases of reads)
Mapping with segemehl
Identification of potential novel ncRNA with ANNOgesic + custom script
Expression analysis with featureCounts
Genome_build: (proprieatary genome sequence, part of bioproject)
Supplementary_files_format_and_content: DESeq2 normalized expressions

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: B. subtilis strain 168 ΔspoIIAC ΔamyE Δapr ΔnprE ΔsrfAC was maintained on LBPG medium at room temperature and not placed at 4 C. Two different substrains were generated, one with a codon-optimized α-amylase JE1 sequence (prsA+je1zyn), and one with the wild-type sequence (prsA+je1). The genomic sequences for both substrains were retrieved in a separate experiment by Novozymes A/S. If not indicated otherwise, strains were cultivated at 37 C in erythromycin (1 µg/ml)-supplemented triptone-yeast (TY) medium when appropriate. The bacterial enzyme production fermentations were conducted in duplicates in custom Novozymes made 5L tanks.

extract_protocol:
Samples were harvested by mixing 5 ml cell culture with 5 ml 100% ethanol, immediately storing on dry ice before transferring to -80°C. RNA was isolated using phenol-chloroform extraction.
Bacterial RNA library preparation was prepared from rRNA-depleted total RNA as described in https://doi.org/10.1002/cpnc.55
Single-end sequencing on an Illumina NextSeq 500. The read lengths were 76 bp.

tag: experimental group

value: codon optimized


title: 17-CL1_shCTL_0hpi_2

status: Public on Mar 23 2023

city: DURHAM

first: ANKIT

last: GUPTA

address: TW 111 ALEXANDER DRIVE

department: RDBL

institute: NIEHS

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

source_name: 17-CL1 cells

growth_protocol: Mouse 17-CL1 cells were cultured in DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The 17-CL1 cells were cultured at 37ºC and in 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA from 17-CL1 shCTL and shTUT4/7 knowckdown cells were used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

treatment_protocol: Cells were infected with 10 M.O.I. of MHV for different timepoints

value: shCTL

value: Non-infected with mouse hepatitis virus

tag: viral strain

tag: duration

value: 0 hours


title: Indel-seq DIvA_mock_1

tag: cell type

value: Cancer Cell line

tag: cell line

value: WT


title: 17-CL1_shCTL_0hpi_1

tag: genotype


title: S5: MIX1441 day 3 (control)

description: MIX1441 day 3 (control)

value: control


title: S4: MIX1444 day 1 (codon optimized)

description: MIX1444 day 1 (codon optimized)


title: Indel-seq DIvA_4OHT_MIRIN

value: 4OHT, MIRIN


title: S3: MIX1443 day 1 (codon optimized)

description: MIX1443 day 1 (codon optimized)