title: STAD-PKU-9-me

description: cfMeDIP-seq of homo sapiens: stomach cancer patient's plasma; Provided by Peking University First Affiliated Hospital.

data_processing:
Methylation data were trimmed by fastp (version 0.20.1).
Clean reads were firstly subjected to lambda genome alignment and then hg38 genome using bowtie2 (version 2.3.5.1) with “end-to-end” mode
Mapped reads were then de-duplicated by GATK MarkDuplicates (version 4.2.0)
Peak enrichment analysis was carried out by macs2 (version 2.2.6) with parameters: "-g hs -p 0.01 --nomodel --extsize 200 --call-summits".
Genome_build: hg38
Supplementary_files_format_and_content: CPM matrix table for every gene and every sample

extract_protocol:
cfDNA was extracted from 1-3 mL plasma using QIAamp MinElute ccfDNA Kit
End repair and A-tailing are done by Kapa Hyper Prep Kit. Adaptors are NEBNext Multiplex Oligos index. Methylated sequences are pull down and purified by MagMeDIP kit and Diagenode iPure Kit v2. MeDIP library is amplificated by Kapa HiFi Hotstart ReadyMix (Roche) in 14-16 cycles


title: Afra sub inhibitory 24h 4

status: Public on Sep 28 2023

type: SRA

city: Worcester

first: Scarlet

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

country: USA

institute: Worcester Polytechnic Institute

description:
Afra_sub_inh_4
GEO_featureCounts_table.txt

library_source: transcriptomic

data_processing:
Raw fastq files were demultiplexed using Cutadapt as in DOI 10.14806/ej.17.1.200.
Reads were aligned using BWA mem (DOI 10.1093/bioinformatics/btp324).
Reads aligned to genes were quantified using FeatureCounts (DOI 10.1093/bioinformatics/btt656).
Supplementary files format and content: GEO_featureCounts_table.txt is a tab-delimited text file that contains the output from running FeatureCounts on bam files generated from these fastq files. The FeatureCounts table can be used as input for DESeq2 for differential expression analysis.

molecule: total RNA

organism: Mycobacterium tuberculosis

growth_protocol: Bacteria were grown in Middlebrook 7H9 supplemented with OADC, 0.2% glycerol, 0.05% Tween 80, and 24 μg/mL pantothenate (7H9) at 37 °C and 200 rpm. Bacteria were grown to mid-log phase, then diluted to OD 0.1 and treatments were applied.

extract_protocol:
5 ml of culture from the 24 hour time-points or 20 ml of culture from the 4 hour time-points was pelleted at 4 degrees, snap-frozen in liquid nitrogen, and stored at -80 until RNA extractions were performed. Pellets were resuspended in 1 ml Trizol or equivalent generic reagent, disrupted with a Fastprep 5G (MP Bio) using tubes pre-filled with 600 mg 100 um zirconium beads, molecular grade (OPS Diagnostics) for two cycles of 40 seconds each at 9 m/s. RNA was then extracted and purified with a Direct-Zol Kit (Zymo) including on-column DNase digestion.
rRNA was depleted using a set of biotinylated oligos designed as described in DOI 10.1128/mBio.00010-20. Paired-end Illumina sequencing libraries were constructed as described in DOI 10.1128/mBio.02012-21

treatment_protocol: Artemisinin and plant extracts were dissolved in DMSO. The concentrations of plant extracts indicated refer to the dry leaf mass used to make the extract, not the mass of the extract itself.

tag: strain

tag: genotype

value: H37Rv deltaRD1 deltapanCD

tag: treatment

value: A. afra DCM extract from 1.25 mg leaf dry weight/mL (0.5X MIC)

tag: time


title: sample_41019081703793

city: Los Angeles

first: Matteo

last: Pellegrini

address: 405 Hilgard Avenue

institute: UCLA

description: Targeted Bisulfite Sequencing

library_source: genomic

data_processing:
The processing of bisulfite sequencing data was carried out using BSBolt (v1.5.0)
Demultiplexed FASTQ files were subjected to adapter removal using cutadapt (v4.1) and aligned to the GRCh38 reference genome using the BSBolt Align function.
PCR duplicates were removed using the samtools markdup function (v1.15) before calling methylation with BSBolt CallMethylation function.
Assembly: GRCh38
Supplementary files format and content: tab-delimeted text file includes methylation matrix for the 178 samples and 16,160 CpG sites

molecule: genomic DNA

organism: Homo sapiens

source_name: Buccal cells

extract_protocol:
DNA was extracted starting from 500µl following the protocol supplied by the manufacturer.
DNA libraries were prepared using the NEBNext UltraII library prep kit (New England Biolabs) and custom, pre-methylated Dual-Unique-Index adapters from Integrated DNA Technologies (IDT) were used for adapter ligation. Groups of 16 libraries, each carrying a different adapter, were pooled together, concentrated by drying with a SpeedVac system and used for targeted enrichment with custom made 5’-biotinylated oligos (IDT).

tag: age

tag: Sex

value: F

tag: cell type

value: Buccal cells


title: CRC-PKU-14-pico

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

country: China

institute: Tsinghua University

description: RNA-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital; Constructed by SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; Purpose: To explore novel plasma extracellular RNA biomarkers for cancer diagnosis

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.3a_modified) was used to map clean reads to the hg38 genome index built with the GENCODE v27 annotation
Duplicates in the aligned reads were removed using Picard Tools MarkDuplicates (version 2.20.0)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v27 annotation, transcripts with uncertain coding potential annotation extracted from mitranscriptome, circular RNA annotation from circBase, Promoter, enhancer and repeat regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: plasma

extract_protocol:
RNA was extracted from 1 mL of plasma using the Plasma/Serum Circulating RNA and Exosomal Purification kit (Norgen)
cell free RNA library is prepared using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian.

tag: gender

value: male

tag: Stage


title: sample_41019081703786

description: Targeted Bisulfite Sequencing

value: M


title: CRC-PKU-10-pico

value: female


title: Afra inhibitory 24h 2

description:
Afra_inh_2
GEO_featureCounts_table.txt

value: A. afra DCM extract from 2.5 mg leaf dry weight/mL (1X MIC)


title: sample_41019081703801

description: Targeted Bisulfite Sequencing


title: TDIMI281_seq_2

city: Ann Arbor

first: Logan

middle: Alexander

last: Walker

state: MI

address: 109 Zina Pitcher Pl, Lab 3838 (loganaw)

department: Biophysics

institute: University of Michigan, Ann Arbor

data_processing:
Picard tools and samtools preprocessing of FASTQ.
RNA-SeQC and RSeQC quality control processing.
Bowtie2 alignment to contaminating sequences.
STAR alignment to the genome.
Quantification with featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: TSV-formatted count matrix files

source_name: AML Patient Tissue Sample_trizol_testset

extract_protocol:
Either trizol extraction, norgen column extraction, or both, as described in the manuscript. All extractions followed manufacturer instructions.
The Illumina TruSeq library preparation kit was used following manufacturer recommendation

tag: tissue

value: AML Patient Tissue Sample

tag: groupid


title: CRC-PKU-13-pico


title: sample_41019081703758

description: Targeted Bisulfite Sequencing


title: sample_41019081703748

description: Targeted Bisulfite Sequencing


title: STAD-PKU-8-me


title: Afra sub inhibitory 24h 3

description:
Afra_sub_inh_3
GEO_featureCounts_table.txt


title: STAD-PKU-7-me


title: Afra sub inhibitory 24h 2

description:
Afra_sub_inh_2
GEO_featureCounts_table.txt


title: TDIMI281_seq_1


title: sample_41019081703747

description: Targeted Bisulfite Sequencing


title: M1

city: Guangzhou

first: Zixin

last: Chen

state: Guangdong

address: No. 106, Zhongshan Second Road

department: Guangdong Cardiovascular Institute Medical Research Center

institute: Guangdong Provincial People's Hospital

data_processing:
library strategy: m6A-REF-seq
FastQC software was used for raw fastq quanlity control. fastp software (v0.20.0) was used to trim adaptor and remove low quality reads.
According to the principles of single base m6A sequencing (ref: Zhang Z, Chen LQ, Zhao YL, Yang CG, Roundtree IA, Zhang Z, Ren J, Xie W, He C, Luo GZ. Single-base mapping of m6A by an antibody-independent method. Sci Adv. 2019 Jul 3;5(7):eaax0250), the m6A-REF-seq clean reads was mapped to the Trinity assembled transcriptome with hisat2 software (v2.4.2).
Using read coverage count (10) and decreasing ratio (0.1) as cutoffs, the m6A ratio was assined to each m6A site by REF - IVT.
Assembly: assembled with Trinity; unigene.fasta.gz
Supplementary files format and content: read count and m6A ratio in excel format

organism: Dugesia japonica

source_name: Trunk

extract_protocol:
10-20 planarians were cut and separated into head, trunk, and tail, then mixed to extract total RNA, and then enriched mRNA by polyT for library construction
m6A-REF-seq

value: Trunk

tag: time point

value: MazF


title: Afra inhibitory 24h 3

description:
Afra_inh_3
GEO_featureCounts_table.txt


title: TDIMI283_seq_1

source_name: AML Patient Tissue Sample_column_testset


title: TDIMI280_seq_2


title: Afra sub inhibitory 24h 1

description:
Afra_sub_inh_1
GEO_featureCounts_table.txt


title: STAD-PKU-5-me


title: sample_41019081703739

description: Targeted Bisulfite Sequencing


title: STAD-PKU-3-me


title: STAD-PKU-38-me


title: sample_41019081703718

description: Targeted Bisulfite Sequencing


title: No drug 24h 2

description:
No_drug_24h_2
GEO_featureCounts_table.txt


title: TDIMI277_seq_1


title: No drug 24h 3

description:
No_drug_24h_3
GEO_featureCounts_table.txt


title: TDIMI277_seq_2


title: STAD-PKU-4-me


title: sample_41019081703717

description: Targeted Bisulfite Sequencing


title: STAD-PKU-37-me


title: No drug 24h 1

description:
No_drug_24h_1
GEO_featureCounts_table.txt


title: TDIMI276_seq_1


title: STAD-PKU-36-me


title: sample_41019081703738

description: Targeted Bisulfite Sequencing


title: artemisinin lethal 4h 3

description:
Artemisinin_lethal_4hs_3
GEO_featureCounts_table.txt

value: 150 ug/mL artemisinin (2X MIC)


title: sample_41019081703639

description: Targeted Bisulfite Sequencing


title: TDIMI275_seq_1


title: TDIMI275_seq_2


title: sample_41019081703689

description: Targeted Bisulfite Sequencing


title: sample_41019081703636

description: Targeted Bisulfite Sequencing


title: STAD-PKU-35-me


title: STAD-PKU-34-me


title: TDIMI280_seq_1


title: No drug 24h 4

description:
No_drug_24h_4
GEO_featureCounts_table.txt


title: artemisinin lethal 4h 2

description:
Artemisinin_lethal_4hs_2
GEO_featureCounts_table.txt


title: sample_41019081703616

description: Targeted Bisulfite Sequencing


title: STAD-PKU-33-me


title: artemisinin lethal 4h 4

description:
Artemisinin_lethal_4hs_4
GEO_featureCounts_table.txt


title: TDIMI273_seq_1


title: sample_41019081703595

description: Targeted Bisulfite Sequencing


title: TDIMI272_seq_1


title: STAD-PKU-32-me


title: Annua lethal 4h 3

description:
Annua_lethal_4hs_3
GEO_featureCounts_table.txt

value: A. annua DCM extract from 9 mg leaf dry weight/mL (2X MIC)


title: STAD-PKU-31-me


title: Annua lethal 4h 4

description:
Annua_lethal_4hs_4
GEO_featureCounts_table.txt


title: sample_41019081703546

description: Targeted Bisulfite Sequencing


title: sample_41019081703582

description: Targeted Bisulfite Sequencing


title: STAD-PKU-30-me


title: TDIMI269_seq_1


title: STAD-PKU-2-me


title: STAD-PKU-29-me


title: Afra lethal 4h 4

description:
Afra_lethal_4hs_4
GEO_featureCounts_table.txt

value: A. afra DCM extract from 5 mg leaf dry weight/mL (2X MIC)


title: TDIMI268_seq_1


title: TDIMI270_seq_1


title: STAD-PKU-28-me


title: Afra lethal 4h 3

description:
Afra_lethal_4hs_3
GEO_featureCounts_table.txt


title: Annua lethal 4h 1

description:
Annua_lethal_4hs_1
GEO_featureCounts_table.txt


title: TDIMI274_seq_1


title: sample_41019081703424

description: Targeted Bisulfite Sequencing


title: sample_41019081703543

description: Targeted Bisulfite Sequencing


title: sample_41019081703513

description: Targeted Bisulfite Sequencing


title: TDIMI267_seq_1


title: sample_41019081703418

description: Targeted Bisulfite Sequencing


title: Afra lethal 4h 2

description:
Afra_lethal_4hs_2
GEO_featureCounts_table.txt


title: Annua lethal 4h 2

description:
Annua_lethal_4hs_2
GEO_featureCounts_table.txt


title: STAD-PKU-27-me

description: cfMeDIP-seq of homo sapiens: stomach cancer patient's plasma; Provided by Peking University First Affiliated Hospital.


title: artemisinin lethal 4h 1

description:
Artemisinin_lethal_4hs_1
GEO_featureCounts_table.txt


title: TDIMI271_seq_1


title: sample_41019081703410

description: Targeted Bisulfite Sequencing


title: TDIMI266_seq_1


title: STAD-PKU-26-me


title: Afra lethal 4h 1

description:
Afra_lethal_4hs_1
GEO_featureCounts_table.txt


title: sample_41019081703403

description: Targeted Bisulfite Sequencing


title: TDIMI265_seq_1


title: No drug 4h 4

description:
No_drug_4h_4
GEO_featureCounts_table.txt


title: sample_41019081702945

description: Targeted Bisulfite Sequencing


title: No drug 4h 2

description:
No_drug_4h_2
GEO_featureCounts_table.txt


title: TDIMI163_seq_2


title: sample_41019081702858

description: Targeted Bisulfite Sequencing


title: TDIMI163_seq_1


title: No drug 4h 3

description:
No_drug_4h_3
GEO_featureCounts_table.txt


title: STAD-PKU-24-me


title: STAD-PKU-23-me


title: STAD-PKU-21-me


title: STAD-PKU-22-me


title: sample_41019081702819

description: Targeted Bisulfite Sequencing


title: TDIMI162_seq_2


title: sample_41019081702820

description: Targeted Bisulfite Sequencing


title: No drug 4h 1

description:
No_drug_4h_1
GEO_featureCounts_table.txt


title: Drosophila melanogaster S2 cells sRNA-seq r1

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
sRNA-seq; small RNA mapping in H.vulgare cells; Experiment SD136
D.melanogaster-S2cells-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Drosophila melanogaster

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.


title: sample_41019081702818

description: Targeted Bisulfite Sequencing


title: STAD-PKU-1-me


title: STAD-PKU-25-me


title: TDIMI264_seq_1


title: sample_Turk.C42

description: Targeted Bisulfite Sequencing


title: Drosophila melanogaster S2 cells csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in H.vulgare cells; Experiment SD135
D.melanogaster-S2cells-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: csRNA-Seq


title: TDIMI162_seq_1


title: TDIMI161_seq_1


title: sample_Turk.C40

description: Targeted Bisulfite Sequencing


title: STAD-PKU-18-me


title: TDIMI160_seq_2


title: STAD-PKU-19-me


title: Positive_2

city: Urbana

first: Thomas

last: Gaj

state: IL

address: 1406 W. Green St.

department: Bioengineering

institute: University of Illinois Urbana-Champaign

data_processing:
Sequenced reads were pseudo-aligned to NCBI’s Mus musculus Annotation Release 109 transcripts  using Salmon (v1.5.2) and the GRCm39 genome as the decoy sequence and with the following options: --seqBias --gcBias  --numBootstraps=30 --validateMappings --recoverOrphans.
The transcript-levels counts were then read into R (v.4.2.2) and gene-level counts were calculated using the "lengthScaledTPM" method from the tximport package (v1.26.1)
Assembly: GRCm39, NCBI Annotation Release 109
Supplementary files format and content: Gaj_rawCounts_2023-02-07.txt : gene level annotations and counts in tab-delimited text format

organism: Mus musculus

source_name: Originally isolated from brain tissue

growth_protocol: Cells were maintained in DMEM with 10% FBS and 1% anti-anti at 37 C for 48 hr after transfection, at which point they were harvested.

extract_protocol:
RNA was extracted from Neuro2A cells using the PureLink RNA Mini Kit (Invitrogen) and converted to complementary DNA (cDNA) using the iScript cDNA Synthesis Kit (Bio-Rad).
RNA-seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche). The libraries were pooled; quantitated by qPCR and sequenced on two SP lanes for 101 cycles from one end of the fragments on a NovaSeq 6000 with V1.5 sequencing kits. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: Cells were transfected with plasmids encoding the CRISPR effector protein, with either a mATXN2-targeting crRNA or a non-targeting crRNA, via transient transfection.

value: Originally isolated from brain tissue

tag: cell line

value: Neuro2A cells

value: Mouse neuroblasts

value: Wild-type

value: Positive Control (Ataxin-2-targeting ASO)


title: TDIMI160_seq_1


title: Positive_3


title: sample_Turk.C39

description: Targeted Bisulfite Sequencing

value: F


title: sample_Turk.C37

description: Targeted Bisulfite Sequencing

value: Buccal cells


title: STAD-PKU-16-me


title: TDIMI159_seq_2


title: Negative_3

value: Untransfected Negative Control


title: sample_Turk.C33

description: Targeted Bisulfite Sequencing


title: TDIMI158_seq_1


title: STAD-PKU-13-me

value: male


title: TDIMI159_seq_1


title: TDIMI157_seq_1


title: TDIMI156_seq_1


title: Positive_1


title: sample_Turk.C31

description: Targeted Bisulfite Sequencing


title: Negative_2


title: STAD-PKU-17-me


title: STAD-PKU-15-me

value: female


title: Negative_1


title: sample_Turk.C32

description: Targeted Bisulfite Sequencing


title: Cas711_G10_2


title: Cas711_G10_3


title: STAD-PKU-11-me


title: STAD-PKU-12-me


title: TDIMI155_seq_1


title: sample_Turk.C28

description: Targeted Bisulfite Sequencing


title: sample_Turk.C26

description: Targeted Bisulfite Sequencing

value: M


title: TDIMI154_seq_2

value: AML Patient Tissue Sample


title: NC-PKU-mix9-me

description: cfMeDIP-seq of homo sapiens: healthy donor's plasma; Provided by Peking University First Affiliated Hospital.

value: No stage (healthy donor)


title: Cas711_NTG_3


title: STAD-PKU-10-me


title: sample_Turk.C34

description: Targeted Bisulfite Sequencing


title: sample_Turk.C24

description: Targeted Bisulfite Sequencing


title: TDIMI154_seq_1


title: Cas711_NTG_2


title: NC-PKU-mix8-me


title: Cas711_G10_1


title: TDIMI153_seq_2


title: sample_Turk.C23

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix7-me


title: NC-PKU-mix6-me


title: sample_Turk.C21

description: Targeted Bisulfite Sequencing


title: TDIMI152_seq_1


title: TDIMI153_seq_1


title: sample_Turk.C18

description: Targeted Bisulfite Sequencing


title: TDIMI151_seq_2


title: sample_Turk.C17

description: Targeted Bisulfite Sequencing


title: N2V7_G10_3


title: NC-PKU-mix5-me


title: N2V7_G10_2


title: TDIMI151_seq_1


title: NC-PKU-mix3-me


title: NC-PKU-mix4-me


title: TDIMI150_seq_3


title: N2V7_G10_1


title: Cas711_NTG_1


title: sample_Turk.C16

description: Targeted Bisulfite Sequencing


title: N2V7_NTG_3


title: TDIMI150_seq_2


title: sample_Turk.C14

description: Targeted Bisulfite Sequencing


title: N2V7_NTG_1


title: NC-PKU-mix2-me


title: sample_Turk.C13

description: Targeted Bisulfite Sequencing


title: sample_Turk.C12

description: Targeted Bisulfite Sequencing


title: sample_Turk.C11

description: Targeted Bisulfite Sequencing


title: TDIMI148_seq_2


title: WTRx_G10_3


title: sample_Turk.C09

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix28-me


title: NC-PKU-mix27-me


title: NC-PKU-mix29-me


title: sample_Turk.C05

description: Targeted Bisulfite Sequencing


title: WTRx_G10_1


title: WTRx_NTG_2


title: NC-PKU-mix30-me


title: N2V7_NTG_2


title: sample_Turk.C04

description: Targeted Bisulfite Sequencing


title: TDIMI147_seq_2


title: WTRx_NTG_3


title: NC-PKU-mix25-me


title: TDIMI148_seq_1


title: sample_Turk.C02

description: Targeted Bisulfite Sequencing


title: WTRx_G10_2


title: TDIMI146_seq_1


title: NC-PKU-mix26-me


title: TDIMI150_seq_1


title: NC-PKU-mix24-me


title: TDIMI147_seq_1


title: TDIMI144_seq_1


title: WTRx_NTG_1


title: sample_Turk.C01

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix23-me


title: TDIMI142_seq_1


title: 4T1 cells, TREX1 KO-ICB_3

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

description:
TREX1 KO-ICB_3
TREX1_KO_invivoMouse1.xlsx

data_processing:
Data were quantified as transcripts per million (TPM) using kallisto
Assembly: GRCm38
Supplementary files format and content: Excel file includes TPM values for each sample

molecule: polyA RNA

source_name: Mammary tumor

extract_protocol:
Total RNA from control and TREX1-deficient 4T1 tumors was extracted using a Total RNA Kit I (Omega Bio-tek). RNA from three different tumors per treatment group was extracted according to the kit manufacturer’s instructions. After confirming the RNA quality, RNA-seq was performed by Novogene.
Poly-A RNA libraries for RNA-seq were prepared by Novogene company

treatment_protocol: ICB = 200 ug anti-PD1 + 100 ug anti-CTLA4 on 3x weekly for 1 week; IgG = Matched isotype controls

value: Mammary tumor

value: TREX1 KO

value: ICB


title: TDIMI141_seq_1


title: NC-PKU-mix21-me


title: NC-PKU-mix22-me


title: 4T1 cells, TREX1 KO-IgG_3

description:
TREX1 KO-IgG_3
TREX1_KO_invivoMouse1.xlsx

value: IgG


title: TDIMI140_seq_1


title: sample_Turk.9

description: Targeted Bisulfite Sequencing


title: 4T1 cells, TREX1 KO-IgG_1

description:
TREX1 KO-IgG_1
TREX1_KO_invivoMouse1.xlsx


title: sample_Turk.8R

description: Targeted Bisulfite Sequencing


title: 4T1 cells, TREX1 KO-IgG_2

description:
TREX1 KO-IgG_2
TREX1_KO_invivoMouse1.xlsx


title: TDIMI139_seq_1


title: sample_Turk.81

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix20-me


title: NC-PKU-mix1-me


title: 4T1 cells, TREX1 KO-ICB_2

description:
TREX1 KO-ICB_2
TREX1_KO_invivoMouse1.xlsx


title: TDIMI138_seq_1


title: 4T1 cells, TREX1 KO-ICB_1

description:
TREX1 KO-ICB_1
TREX1_KO_invivoMouse1.xlsx


title: 4T1 cells, CTRL-ICB_3

description:
CTRL-ICB_3
TREX1_KO_invivoMouse1.xlsx

value: CTRL


title: sample_Turk.80

description: Targeted Bisulfite Sequencing


title: sample_Turk.8

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix17-me


title: sample_Turk.7R

description: Targeted Bisulfite Sequencing


title: 4T1 cells, CTRL-ICB_2

description:
CTRL-ICB_2
TREX1_KO_invivoMouse1.xlsx


title: TDIMI137_seq_1


title: sample_Turk.9R

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix16-me


title: TDIMI136_seq_2


title: TDIMI138_seq_2


title: NC-PKU-mix18-me


title: sample_Turk.79

description: Targeted Bisulfite Sequencing


title: TDIMI136_seq_1


title: 4T1 cells, CTRL-ICB_1

description:
CTRL-ICB_1
TREX1_KO_invivoMouse1.xlsx


title: sample_Turk.77

description: Targeted Bisulfite Sequencing


title: NC-PKU-mix0-me


title: TDIMI135_seq_1


title: sample_Turk.7

description: Targeted Bisulfite Sequencing


title: 4T1 cells, CTRL-IgG_2

description:
CTRL-IgG_2
TREX1_KO_invivoMouse1.xlsx


title: NC-PKU-9-me


title: TDIMI134_seq_2


title: sample_Turk.69

description: Targeted Bisulfite Sequencing


title: 4T1 cells, CTRL-IgG_3

description:
CTRL-IgG_3
TREX1_KO_invivoMouse1.xlsx


title: TDIMI134_seq_1


title: sample_Turk.67

description: Targeted Bisulfite Sequencing


title: NC-PKU-14-me


title: NC-PKU-12-me


title: TDIMI133_seq_1


title: sample_Turk.68

description: Targeted Bisulfite Sequencing


title: sample_Turk.66

description: Targeted Bisulfite Sequencing


title: TDIMI132_seq_1


title: NC-PKU-11-me


title: TDIMI131_seq_1


title: KSP-Cre Tsc2+Tfeb DKO, Rapamycin treated, replicate 2

city: Boston

first: Damir

last: Khabibullin

state: MA

address: 20 Shattuck St

institute: Brigham and Women's Hospital

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP dko RAPA_2

data_processing:
Mapping to the reference sequence was performed using STAR (version 2.6.1d, mismatch=2) for Cagg cohort; Hisat2 (version 2.0.5, default parameters) was used for mapping in both KSP cohorts
FeatureCounts (version 1.5.0-p3) was used for read quantification
Differential gene expresison analysis was performed using DeSeq2 (version 1.20.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files of raw counts
Supplementary files format and content: tab-delimited text files of FPKM values

source_name: kidney

growth_protocol: Mice of all genotypes were maintained on PicoLab rodent diet 20 (5053). Cystic kidney disease was assesed at P30 in Cagg mice (whole-body tamoxifen inducible) and at P50 in KSP mice (kidney specific).

extract_protocol:
30-40mg of kidney tissues were homogenized using Bullet Blender and total RNA was extracted using a RNeasy mini kit (Qiagen, #74106).
poly-A capture followed by non-directional library preparation using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: KSP mouse cohort was treated with Rapamycin at 1mg/kg/3 times per week for a total of 11 injections intraperitoneally, control groups were treated with the delivery Vehicle for the same duration.

value: kidney

value: mixed

value: Tsc2+Tfeb DKO

value: Rapamycin 1mg/kg/3 times per week


title: sample_Turk.64

description: Targeted Bisulfite Sequencing


title: KSP-Cre Tsc2+Tfeb DKO, Rapamycin treated, replicate 1

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP dko RAPA_1


title: KSP-Cre Tsc2+Tfeb DKO, Vehicle treated, replicate 3

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP dko DMSO_3

value: vehicle control


title: NC-PKU-10-me


title: TDIMI130_seq_1


title: CRC-PKU-mix1-me

description: cfMeDIP-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital.


title: 4T1 cells, CTRL-IgG_1

description:
CTRL-IgG_1
TREX1_KO_invivoMouse1.xlsx


title: NC-PKU-mix15-me


title: TDIMI129_seq_2


title: KSP-Cre Tsc2+Tfeb DKO, Vehicle treated, replicate 2

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP dko DMSO_2


title: KSP-Cre Tsc2+Tfeb DKO, Vehicle treated, replicate 1

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP dko DMSO_1


title: CRC-PKU-mix0-me


title: sample_Turk.60

description: Targeted Bisulfite Sequencing

value: Buccal cells


title: CRC-PKU-9-me


title: NC-PKU-13-me


title: KSP-Cre Tsc2+Tfeb DKO, Rapamycin treated, replicate 3

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP dko RAPA_3


title: TDIMI129_seq_1


title: KSP-Cre Tsc2 KO kidney, Rapamycin treated, replicate 3

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Tsc2ko RAPA_3

value: Tsc2 KO


title: TDIMI128_seq_1


title: sample_Turk.5R

description: Targeted Bisulfite Sequencing


title: TDIMI126_seq_2


title: CRC-PKU-8-me

value: male


title: KSP-Cre Tsc2 KO kidney, Rapamycin treated, replicate 2

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Tsc2ko RAPA_2


title: sample_Turk.56

description: Targeted Bisulfite Sequencing

value: F


title: KSP-Cre Tsc2 KO kidney, Rapamycin treated, replicate 1

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Tsc2ko RAPA_1


title: TDIMI124_seq_1


title: sample_Turk.54

description: Targeted Bisulfite Sequencing

value: M


title: TDIMI126_seq_1

value: AML Patient Tissue Sample


title: KSP-Cre Tsc2 KO kidney, Vehicle treated, replicate 3

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Tsc2ko DMSO_3


title: sample_Turk.53

description: Targeted Bisulfite Sequencing


title: CRC-PKU-5-me

value: female


title: sample_Turk.63

description: Targeted Bisulfite Sequencing


title: CRC-PKU-4-me


title: KSP-Cre Tsc2 KO kidney, Vehicle treated, replicate 2

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Tsc2ko DMSO_2


title: CRC-PKU-3-me


title: TDIMI122_seq_2


title: sample_Turk.52

description: Targeted Bisulfite Sequencing


title: sample_Turk.51

description: Targeted Bisulfite Sequencing


title: TDIMI122_seq_1


title: KSP-Cre Tsc2 KO kidney, Vehicle treated, replicate 1

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Tsc2ko DMSO_1


title: sample_Turk.50

description: Targeted Bisulfite Sequencing


title: CRC-PKU-33-me


title: TDIMI123_seq_1


title: KSP-Cre control kidney, Rapamycin treated, replicate 2

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Ctrl RAPA_2

value: wild type


title: TDIMI121_seq_2


title: sample_Turk.58

description: Targeted Bisulfite Sequencing


title: CRC-PKU-6-me


title: sample_Turk.5

description: Targeted Bisulfite Sequencing


title: CRC-PKU-32-me


title: TDIMI121_seq_1


title: KSP-Cre control kidney, Rapamycin treated, replicate 1

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Ctrl RAPA_1


title: sample_Turk.48

description: Targeted Bisulfite Sequencing


title: CRC-PKU-30-me


title: KSP-Cre control kidney, Vehicle treated, replicate 3

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Ctrl DMSO_3


title: sample_Turk.47

description: Targeted Bisulfite Sequencing


title: TDIMI120_seq_2


title: CRC-PKU-2-me


title: sample_Turk.46

description: Targeted Bisulfite Sequencing


title: KSP-Cre control kidney, Vehicle treated, replicate 2

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Ctrl DMSO_2


title: TDIMI120_seq_1


title: CRC-PKU-29-me


title: KSP-Cre control kidney, Rapamycin treated, replicate 3

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Ctrl RAPA_3


title: TDIMI117_seq_1


title: KSP-Cre control kidney, Vehicle treated, replicate 1

description:
KSP DMSO RAPA gene_fpkm.txt
KSP DMSO RAPA gene_count.txt
KSP Ctrl DMSO_1


title: CRC-PKU-31-me


title: sample_Turk.44

description: Targeted Bisulfite Sequencing


title: CRC-PKU-27-me


title: TDIMI115_seq_3


title: sample_Turk.42

description: Targeted Bisulfite Sequencing


title: KSP-Cre Tsc2+Tfeb DKO, replicate 2

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP dko_2


title: TDIMI116_seq_1


title: KSP-Cre Tsc2+Tfeb DKO, replicate 3

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP dko_3


title: KSP-Cre Tfeb KO kidney, replicate 3

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Tfebko_3

value: Tfeb KO


title: KSP-Cre Tsc2+Tfeb DKO, replicate 1

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP dko_1


title: CRC-PKU-25-me

description: cfMeDIP-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital.


title: TDIMI115_seq_1


title: TDIMI115_seq_2


title: sample_Turk.40R

description: Targeted Bisulfite Sequencing


title: CRC-PKU-24-me


title: KSP-Cre Tfeb KO kidney, replicate 2

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Tfebko_2


title: TDIMI112_seq_1


title: CRC-PKU-23-me


title: KSP-Cre Tfeb KO kidney, replicate 1

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Tfebko_1


title: sample_Turk.39

description: Targeted Bisulfite Sequencing


title: CRC-PKU-22-me


title: sample_Turk.41

description: Targeted Bisulfite Sequencing


title: CRC-PKU-28-me


title: KSP-Cre Tsc2 KO kidney, replicate 3

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Tsc2ko_3


title: sample_Turk.40

description: Targeted Bisulfite Sequencing


title: sample_Turk.43

description: Targeted Bisulfite Sequencing


title: CRC-PKU-26-me


title: TDIMI111_seq_2


title: sample_Turk.38R

description: Targeted Bisulfite Sequencing


title: CRC-PKU-21-me


title: KSP-Cre Tsc2 KO kidney, replicate 2

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Tsc2ko_2


title: TDIMI111_seq_1


title: TDIMI110_seq_1


title: KSP-Cre Tsc2 KO kidney, replicate 1

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Tsc2ko_1


title: sample_Turk.38

description: Targeted Bisulfite Sequencing


title: CRC-PKU-20-me


title: TDIMI109_seq_2


title: KSP-Cre control kidney, replicate 3

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Ctrl_3


title: sample_Turk.37

description: Targeted Bisulfite Sequencing


title: CRC-PKU-18-me


title: TDIMI112_seq_2


title: KSP-Cre control kidney, replicate 2

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Ctrl_2


title: TDIMI109_seq_1


title: sample_Turk.36R

description: Targeted Bisulfite Sequencing


title: CRC-PKU-17-me


title: TDIMI108_seq_2


title: sample_Turk.36

description: Targeted Bisulfite Sequencing


title: KSP-Cre control kidney, replicate 1

description:
KSP gene_fpkm.txt
KSP gene_count.txt
KSP Ctrl_1


title: Cagg-Cre Tsc2+Tfeb DKO kidney, replicate 3

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg dko_3


title: sample_Turk.35R

description: Targeted Bisulfite Sequencing


title: CRC-PKU-15-me


title: TDIMI108_seq_1


title: TDIMI107_seq_2


title: Cagg-Cre Tsc2+Tfeb DKO kidney, replicate 1

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg dko_1


title: Cagg-Cre Tsc2+Tfeb DKO kidney, replicate 2

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg dko_2


title: CRC-PKU-13-me


title: sample_Turk.37R

description: Targeted Bisulfite Sequencing


title: CRC-PKU-19-me


title: sample_Turk.34R

description: Targeted Bisulfite Sequencing


title: Cagg-Cre Tfeb KO kidney, replicate 3

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Tfebko_3


title: TDIMI106_seq_2


title: sample_Turk.34

description: Targeted Bisulfite Sequencing


title: CRC-PKU-12-me


title: TDIMI106_seq_1


title: Cagg-Cre Tfeb KO kidney, replicate 2

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Tfebko_2


title: Cagg-Cre Tfeb KO kidney, replicate 1

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Tfebko_1


title: CRC-PKU-10-me


title: sample_Turk.22R

description: Targeted Bisulfite Sequencing


title: TDIMI103_seq_2


title: CRC-PKU-16-me


title: TDIMI103_seq_1


title: sample_Turk.21R

description: Targeted Bisulfite Sequencing


title: Cagg-Cre Tsc2 KO kidney, replicate 2

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Tsc2ko _2


title: sample_Turk.22

description: Targeted Bisulfite Sequencing


title: TDIMI102_seq_2


title: sample_Turk.35

description: Targeted Bisulfite Sequencing


title: Cagg-Cre Tsc2 KO kidney, replicate 3

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Tsc2ko _3


title: CRC-PKU-14-me

description: cfMeDIP-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital.


title: STAD-PKU-7-wgs

description: DNA-seq of homo sapiens: stomach cancer's plasma; Provided by Peking University First Affiliated Hospital.

data_processing:
Library strategy: DNA-seq
Raw fastq files were firstly trimmed with trim_galore (version 0.6.6).
Clean reads were then aligned to hg38 human reference genome with default parameters using bwa-mem2.
Bam files were further filtered by requiring proper template length (20 bp to 1000 bp) using samtools (version 1.10).
Filtered bam files were de-duplicated using GATK MarkDuplicates (version 4.2.0) to collapse all reads with the same start and end site
Genome_build: hg38
Supplementary_files_format_and_content: CPM and log2RelativeDepth matrix table for every gene and every sample

extract_protocol:
cfDNA was extracted from 1-3 mL plasma using QIAamp MinElute ccfDNA Kit
End repair and A-tailing are done by Kapa Hyper Prep Kit. Adaptors are NEBNext Multiplex Oligos index. cfDNA library is amplificated by Kapa HiFi Hotstart ReadyMix (Roche) in 9-13 cycles


title: STAD-PKU-8-wgs


title: TDIMI107_seq_1


title: Cagg-Cre Tsc2 KO kidney, replicate 1

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Tsc2ko _1


title: TDIMI102_seq_1


title: sample_Turk.21

description: Targeted Bisulfite Sequencing


title: STAD-PKU-6-wgs


title: Cagg-Cre control kidney, replicate 3

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Ctrl_3


title: STAD-PKU-5-wgs


title: sample_Turk.20R

description: Targeted Bisulfite Sequencing


title: TDIMI101_seq_1


title: TDIMI101_seq_2


title: sample_Turk.20

description: Targeted Bisulfite Sequencing


title: STAD-PKU-4-wgs


title: Cagg-Cre control kidney, replicate 1

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Ctrl_1


title: TDIMI100_seq_2


title: sample_Turk.19

description: Targeted Bisulfite Sequencing


title: sample_Turk.19R

description: Targeted Bisulfite Sequencing


title: STAD-PKU-3-wgs


title: NS3

city: Shanghai

first: Yashu

last: Li

address: No,1665, Kongjiang Road, Yangpu District

department: Department of Plastic Surgery

institute: Xinhua hospital, Shanghai Jiaotong University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file included raw counts for each Sample
Supplementary files format and content: tab-delimited text file included normalized counts by edgeR for each Sample

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

value: skin

value: week 2 post operation

tag: group

value: normal scars formed in control group

value: WT

value: wound edges on the lower back sutured in situ with no tension


title: STAD-PKU-38-wgs


title: sample_Turk.18R

description: Targeted Bisulfite Sequencing


title: TDIMI100_seq_1


title: NS2


title: sample_Turk.18

description: Targeted Bisulfite Sequencing


title: TDIMI098_seq_2


title: STAD-PKU-36-wgs


title: STAD-PKU-37-wgs


title: TDIMI098_seq_1


title: HS3

value: hypertrophic scars generated in stretched group

value: wound edges on the upper back sutured to the rib cage with tension


title: NS1


title: HS2


title: STAD-PKU-35-wgs


title: TDIMI097_seq_2


title: STAD-PKU-34-wgs


title: sample_Turk.16R

description: Targeted Bisulfite Sequencing


title: sample_Turk.17

description: Targeted Bisulfite Sequencing


title: TDIMI097_seq_1


title: HS1


title: Cagg-Cre control kidney, replicate 2

description:
Cagg fpkm.txt
Cagg readcount.txt
Cagg Ctrl_2

value: kidney

value: mixed


title: STAD-PKU-33-wgs


title: TDIMI096_seq_2


title: STAD-PKU-31-wgs


title: sample_Turk.15R

description: Targeted Bisulfite Sequencing

value: Buccal cells


title: sample_Turk.16

description: Targeted Bisulfite Sequencing


title: TDIMI099_seq_1


title: X5

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: PEMs

growth_protocol: WT and Sun1/2DKO PEMs were cultured in RPMI1640 medium with 10% fetal bovine serum,  L-glutamine and penicillin/streptomycin at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: PEMs

value: Macrophages

tag: chip antibody


title: TDIMI096_seq_1


title: sample_Turk.17R

description: Targeted Bisulfite Sequencing

value: M


title: X6


title: STAD-PKU-9-wgs

value: male


title: STAD-PKU-30-wgs


title: TDIMI095_seq_2

value: AML Patient Tissue Sample


title: STAD-PKU-2-wgs


title: sample_Turk.14

description: Targeted Bisulfite Sequencing

value: F


title: TDIMI095_seq_1


title: sample_Turk.14R

description: Targeted Bisulfite Sequencing


title: STAD-PKU-29-wgs


title: TDIMI094_seq_2


title: STAD-PKU-28-wgs


title: Keto-WT-Mock-L-2

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

data_processing:
The libraries were sequenced with 100bp paired end reads on an Ilumina Novaseq 6000.
The reads were mapped with STAR 2.5.3a to the mouse genome (mm10) for the mouse cell libraries. The counts for each gene were obtained using quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default.
Assembly: mm10
Supplementary files format and content: raw expression counts

source_name: Liver

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (74134, Qiagen).
Libraries were prepared by the Technology Center for Genomics & Bioinformatics at UCLA using Illumina TruSeq Stranded Total RNA Sample Prep kit.

value: Liver

tag: diet

value: Keto

value: Mock


title: Keto-WT-Mock-L-3


title: Keto-WT-Mock-K-3

source_name: Kidney

value: Kidney


title: sample_Turk.12

description: Targeted Bisulfite Sequencing


title: sample_Turk.12R

description: Targeted Bisulfite Sequencing


title: Keto-WT-Mock-L-1

value: WT


title: STAD-PKU-27-wgs


title: TDIMI094_seq_1


title: STAD-PKU-26-wgs


title: TDIMI093_seq_1


title: Keto-WT-Mock-K-2


title: X3

value: IgG


title: TDIMI093_seq_2


title: sample_Turk.11R

description: Targeted Bisulfite Sequencing


title: sample_Turk.15

description: Targeted Bisulfite Sequencing


title: sample_Turk.110

description: Targeted Bisulfite Sequencing


title: STAD-PKU-25-wgs


title: Keto-WT-Mock-K-1


title: TDIMI092_seq_1


title: STAD-PKU-24-wgs


title: TDIMI091_seq_2


title: Keto-WT-Mock-H-3

source_name: Heart

value: Heart


title: sample_Turk.11

description: Targeted Bisulfite Sequencing


title: STAD-PKU-23-wgs

value: female


title: TDIMI091_seq_1


title: Keto-WT-Mock-H-2


title: sample_Turk.10R

description: Targeted Bisulfite Sequencing


title: sample_Turk.109

description: Targeted Bisulfite Sequencing


title: STAD-PKU-22-wgs


title: TDIMI090_seq_2


title: sample_Turk.108

description: Targeted Bisulfite Sequencing


title: STAD-PKU-21-wgs


title: TDIMI090_seq_1


title: sample_Turk.107

description: Targeted Bisulfite Sequencing


title: Keto-hACE2-Mock-L-2


title: STAD-PKU-1-wgs


title: TDIMI089_seq_2


title: sample_Turk.105

description: Targeted Bisulfite Sequencing


title: Keto-hACE2-Mock-L-1


title: Keto-hACE2-Mock-K-3


title: sample_Turk.10

description: Targeted Bisulfite Sequencing


title: TDIMI088_seq_2


title: STAD-PKU-18-wgs


title: STAD-PKU-17-wgs


title: STAD-PKU-16-wgs


title: Keto-hACE2-Mock-K-2


title: sample_Turk.104

description: Targeted Bisulfite Sequencing


title: TDIMI087_seq_2


title: Keto-hACE2-Mock-K-1


title: Keto-WT-Mock-H-1


title: Keto-hACE2-Mock-H-3


title: STAD-PKU-15-wgs


title: TDIMI087_seq_1


title: Keto-hACE2-Mock-L-3


title: neg. control, patient id:13778, day: 0, SARS-CoV-2 Ct:46

city: Houston

first: Sarah

middle: Yvette

last: Ponce

state: TX

address: 1 Baylor Plaza

department: HGSC

institute: Baylor College of Medicine

data_processing:
bcls are converted to FASTQ files using casava
RSEM (v.1.3.3) for measuring gene expression and RNA-SeQC (v.1.1.9), Qualimap2 (v2.2.1) and ERCCQC (v.1.0) to generate quality control metrics on the RNA-Seq data
raw gene features counts by using featureCounts (v2.0.1). These expressions are further used to calculate differential gene and isoform expression using DESeq2 or edgeR R packages
Where RNA-seq data were generated in different batches involving time and differences in extraction and processing methods, Combat algorithm (PMID: 16632515) was used to correct for any observed batch effects. Batch-corrected Fragments Per Kilobase Million (FPKM) values were then quantile normalized (PMID: 12538238).
Assembly: reads mapped to GRCh38,(STAR v2.7.3a)
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: mid-turbinate (MT) swab

extract_protocol:
mid-turbinate (MT) swab samples originally collected from SARS-CoV-2 cases or SARS-CoV-2 negative adults
TruSeq Total RNA-) Ribosomal RNA(rRNA) is removed using biotinylated, target-specific oligos : Ribo-Zero Globin depletes globin-encoding mRNA inaddition to the rRNA species. The elution is used for cDNA synthesis using random primers
To prepare paired-end libraries, double stranded cDNA is A-tailed followed by ligation of the Illumina TruSeq UD Indexes (Cat # 20022370) and amplified for 15 PCR cycles following manufacturer’s recommendation

tag: patient id

tag: ct value

value: mid-turbinate (MT) swab

tag: disease


title: neg. control, patient id:14904, day: 0, SARS-CoV-2 Ct:46


title: TDIMI088_seq_1


title: Keto-hACE2-Mock-H-2

tag: genotype

tag: treatment


title: neg. control, patient id:7372, day: 0, SARS-CoV-2 Ct:46

tag: time


title: neg. control, patient id:7161, day: 0, SARS-CoV-2 Ct:46


title: STAD-PKU-13-wgs

tag: age


title: TDIMI086_seq_2


title: STAD-PKU-12-wgs


title: Keto-hACE2-Mock-H-1


title: STAD-PKU-19-wgs


title: low initial viral load, patient id:10589, day: 4, SARS-CoV-2 Ct:34

tag: cell type


title: TDIMI089_seq_1


title: STAD-PKU-11-wgs

tag: gender


title: Keto-hACE2-CoV2-L-3


title: low initial viral load, patient id:7289, day: 9, SARS-CoV-2 Ct:31


title: TDIMI036_seq_2


title: STAD-PKU-10-wgs

tag: Stage


title: TDIMI036_seq_1

tag: tissue


title: low initial viral load, patient id:493, day: 0, SARS-CoV-2 Ct:34


title: Keto-hACE2-CoV2-L-2


title: low initial viral load, patient id:14698, day: 32, SARS-CoV-2 Ct:34


title: TDIMI035_seq_1

tag: groupid


title: low initial viral load, patient id:14698, day: 12, SARS-CoV-2 Ct:36


title: NC-PKU-mix8-wgs

description: DNA-seq of homo sapiens: healthy donor's plasma; Provided by Peking University First Affiliated Hospital.

value: No stage (healthy donor)


title: NC-PKU-mix9-wgs


title: low initial viral load, patient id:14698, day: 0, SARS-CoV-2 Ct:36


title: TDIMI035_seq_2


title: Keto-hACE2-CoV2-L-1


title: TDIMI034_seq_2


title: NC-PKU-mix7-wgs


title: TDIMI034_seq_1


title: Keto-hACE2-CoV2-K-1


title: Keto-hACE2-CoV2-K-3


title: NC-PKU-mix4-wgs


title: TDIMI086_seq_1


title: Keto-hACE2-CoV2-H-3


title: low initial viral load, patient id:10463, day: 18, SARS-CoV-2 Ct:36


title: NC-PKU-mix6-wgs


title: TDIMI032_seq_1


title: NC-PKU-mix3-wgs


title: low initial viral load, patient id:10463, day: 7, SARS-CoV-2 Ct:38


title: TDIMI031_seq_1


title: low initial viral load, patient id:10463, day: 0, SARS-CoV-2 Ct:36


title: Keto-hACE2-CoV2-H-2


title: NC-PKU-mix30-wgs


title: TDIMI030_seq_2


title: low initial viral load, patient id:8408, day: 13, SARS-CoV-2 Ct:37


title: Keto-hACE2-CoV2-H-1


title: NC-PKU-mix29-wgs


title: Keto-hACE2-CoV2-K-2


title: Chow-WT-Mock-L-3

value: Chow


title: TDIMI030_seq_1


title: low initial viral load, patient id:8408, day: 0, SARS-CoV-2 Ct:35


title: Chow-WT-Mock-L-2


title: low initial viral load, patient id:16533, day: 21, SARS-CoV-2 Ct:34


title: NC-PKU-mix27-wgs


title: TDIMI029_seq_1


title: Chow-WT-Mock-L-1


title: low initial viral load, patient id:16533, day: 0, SARS-CoV-2 Ct:33


title: low initial viral load, patient id:16533, day: 14, SARS-CoV-2 Ct:37


title: Chow-WT-Mock-K-3


title: TDIMI027_seq_2


title: TDIMI028_seq_1


title: low initial viral load, patient id:13264, day: 15, SARS-CoV-2 Ct:34


title: NC-PKU-mix24-wgs


title: Chow-WT-Mock-K-1


title: TDIMI027_seq_1


title: low initial viral load, patient id:13264, day: 11, SARS-CoV-2 Ct:33


title: TDIMI026_seq_1


title: NC-PKU-mix23-wgs


title: Chow-WT-Mock-H-3


title: NC-PKU-mix22-wgs


title: TDIMI025_seq_1


title: Chow-WT-Mock-H-2


title: TDIMI024_seq_1


title: NC-PKU-mix28-wgs


title: high initial viral load, patient id:15781, day: 13, SARS-CoV-2 Ct:33


title: NC-PKU-mix21-wgs


title: NC-PKU-mix26-wgs


title: NC-PKU-mix25-wgs


title: high initial viral load, patient id:15781, day: 7, SARS-CoV-2 Ct:25


title: Chow-WT-Mock-H-1


title: TDIMI023_seq_1


title: Chow-WT-Mock-K-2


title: TDIMI023_seq_2


title: high initial viral load, patient id:15781, day: 0, SARS-CoV-2 Ct:16


title: Chow-hACE2-Mock-L-3


title: high initial viral load, patient id:15527, day: 27, SARS-CoV-2 Ct:36


title: NC-PKU-mix20-wgs


title: TDIMI022_seq_2


title: Chow-hACE2-Mock-L-1


title: NC-PKU-mix15-wgs


title: Chow-hACE2-Mock-L-2


title: high initial viral load, patient id:15527, day: 7, SARS-CoV-2 Ct:25


title: Chow-hACE2-Mock-K-3


title: NC-PKU-9-wgs


title: TDIMI021_seq_2


title: low initial viral load, patient id:13264, day: 0, SARS-CoV-2 Ct:32


title: NC-PKU-14-wgs


title: Chow-hACE2-Mock-K-2


title: high initial viral load, patient id:14593, day: 13, SARS-CoV-2 Ct:33


title: TDIMI021_seq_1


title: Chow-hACE2-Mock-K-1


title: NC-PKU-13-wgs


title: high initial viral load, patient id:14593, day: 0, SARS-CoV-2 Ct:16


title: TDIMI020_seq_1


title: high initial viral load, patient id:10112, day: 15, SARS-CoV-2 Ct:38


title: NC-PKU-11-wgs


title: TDIMI019_seq_1


title: TDIMI022_seq_1


title: NC-PKU-12-wgs


title: high initial viral load, patient id:10112, day: 5, SARS-CoV-2 Ct:26


title: CRC-PKU-9-wgs

description: DNA-seq of homo sapiens: colorectal cancer patient's plasma; Provided by Peking University First Affiliated Hospital.


title: NC-PKU-10-wgs


title: Chow-hACE2-Mock-H-1


title: high initial viral load, patient id:10112, day: 0, SARS-CoV-2 Ct:15


title: NC-PKU-mix16-wgs


title: TDIMI016_seq_1


title: Chow-hACE2-CoV2-L-3


title: high initial viral load, patient id:6241, day: 21, SARS-CoV-2 Ct:34


title: Chow-hACE2-CoV2-L-2


title: CRC-PKU-8-wgs


title: TDIMI015_seq_1


title: TDIMI018_seq_1


title: TDIMI017_seq_1


title: high initial viral load, patient id:6241, day: 14, SARS-CoV-2 Ct:32


title: CRC-PKU-6-wgs


title: Chow-hACE2-CoV2-L-1


title: high initial viral load, patient id:6241, day: 7, SARS-CoV-2 Ct:24


title: CRC-PKU-5-wgs


title: Chow-hACE2-Mock-H-3


title: Chow-hACE2-Mock-H-2


title: TDIMI014_seq_1


title: Chow-hACE2-CoV2-K-3


title: high initial viral load, patient id:15527, day: 0, SARS-CoV-2 Ct:16


title: CRC-PKU-3-wgs


title: Chow-hACE2-CoV2-K-2


title: high initial viral load, patient id:6241, day: 0, SARS-CoV-2 Ct:14


title: high initial viral load, patient id:6038, day: 13, SARS-CoV-2 Ct:38


title: TDIMI013_seq_1


title: CRC-PKU-33-wgs


title: TDIMI013_seq_2


title: Chow-hACE2-CoV2-K-1


title: high initial viral load, patient id:17089, day: 17, SARS-CoV-2 Ct:37


title: Chow-hACE2-CoV2-H-3


title: high initial viral load, patient id:17089, day: 9, SARS-CoV-2 Ct:34


title: CRC-PKU-31-wgs


title: TDIMI011_seq_1


title: CRC-PKU-32-wgs


title: Chow-hACE2-CoV2-H-2


title: CRC-PKU-30-wgs


title: high initial viral load, patient id:17089, day: 0, SARS-CoV-2 Ct:12


title: CRC-PKU-29-wgs


title: TDIMI009_seq_1


title: high initial viral load, patient id:8002, day: 15, SARS-CoV-2 Ct:34


title: 3v31_LDHA_KO_TEa

first: Dawei

last: Zou

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw Illumina sequencing reads were aligned to reference mouse genome mm10 (Ensembl 93) using Cell Ranger v7.0.0 with default parameters, generating one Fastq dataset for cells from heart and one for cells from spleen. Genes were quantified as UMI counts using Cell Ranger count and initially visualized using Loupe Browser v5.0.0.
Downstream analysis was performed using Seurat V4.0.0 on filtered feature counts generated by Cell Ranger count. Low-quality single cells containing >2.5% mitochondrial transcripts or >50% ribosomal transcripts were removed. Additionally, genes expressed in fewer than three single cells were removed. We identified potential single-cell doublets using DoubletFinder V2.0.3, with an expectation of a 7.5% doublet rate assuming Poisson statistics.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: from spleen

extract_protocol:
The adoptively transferred WT or Ldha‒/‒ TEa cells were labeled with fluorochrome-conjugated antibodies and subsequently sorted from the spleens or heart allografts of the recipient mice using a cell sorter.
Single cell Gene Expression Library was prepared according toChromium Next GEM Single Cell 3' Reagent Kits v3(10x Genomics). In Brief, single nuclei suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: from spleen

value: CD4+ T cells

value: Ldha-/-


title: TDIMI008_seq_1


title: CRC-PKU-28-wgs

value: male


title: high initial viral load, patient id:8002, day: 6, SARS-CoV-2 Ct:25


title: WT-R4

data_processing:
Samples were sequenced using Novaseq 6000(Illumina) using 100 cycles. 200M reads were targeted for each sample, targeting20,000 reads per nuclei. Samples were analyzed using Cell Ranger and Loupe (10x Genomics).
Raw reads were aligned to the mouse genome (mm10), and the digital expression matrix was generated using cellranger count.
Assembly: mm10
Supplementary files format and content: Raw count expression matrix for snRNA-seq.

source_name: heart

extract_protocol:
Hearts were harvested on day 7 post injury and used for single nuclei preparation for 10X genomics sequencing. Briefly, the heart tissue was minced with razor blade and gently homogenized by Dounce homogenizer containing 1.5 ml of chilled lysis buffer (in mM) (10 Tris-HCl (pH 7.4), 10 NaCl, 3 MgCl2, 0.1% NP-40). Then the homogenate was filtered through a 40 µm cell strainer and centrifuged at 500 g for 5 min at 4 °C. The pellet was resuspended in 1 ml nuclei wash buffer (1x PBS with 2% BSA and 0.2 U/mL RNase inhibitor). The suspension was filtered through a 20 µm cell strainer and centrifuged at 500 g for 5 min at 4 °C. The nuclei pellet was resuspended in 300 mL nuclei wash buffer followed by library preparation. Equal number of cells from 3 mouse hearts were mixed for each group.
Single nuclei gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions. Briefly, samples were loaded to target10,000nuclei to form GEMs and barcode individual cells. GEMs were then cleaned cDNA and libraries were also created according to manufacturer’s instructions. Library quality was assessed using 4200 TapeStation System and D1000 ScreenTape (both from Agilent) and Qubit 2.0 (Invitrogen) for concentration and size distribution.

value: heart

value: heart cell

value: Myocardial infarction


title: TDIMI007_seq_1

value: AML Patient Tissue Sample


title: high initial viral load, patient id:6038, day: 0, SARS-CoV-2 Ct:14


title: WT-R3


title: CRC-PKU-27-wgs


title: high initial viral load, patient id:8002, day: 0, SARS-CoV-2 Ct:10


title: TDIMI006_seq_2


title: CRC-PKU-26-wgs


title: 6DAYSARS

data_processing:
bcls are converted to FASTQ files using casava
RSEM (v.1.3.3) for measuring gene expression and RNA-SeQC (v.1.1.9), Qualimap2 (v2.2.1) and ERCCQC (v.1.0) to generate quality control metrics on the RNA-Seq data
raw gene features counts by using featureCounts (v2.0.1). These expressions are further used to calculate differential gene and isoform expression using DESeq2 or edgeR R packages
Fragments Per Kilobase Million (FPKM) values were quantile normalized (PMID: 12538238) prior to analysis.
Assembly: reads mapped to GRCh38,(STAR v2.7.3a)
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: human nose organoid model HNO204

extract_protocol:
We sampled HNO204 cells infected with SARS-CoV-2 and Mock control cells at 6hrs, 72hrs, and 6 days post-infection. At the respective time points, the apical side of the transwells was washed twice and the cells were lysed using lysis buffer of RNeasy mini kit and RNA extracted.
TruSeq Total RNA-) Ribosomal RNA(rRNA) is removed using biotinylated, target-specific oligos : Ribo-Zero Globin depletes globin-encoding mRNA inaddition to the rRNA species. The elution is used for cDNA synthesis using random primers
To prepare paired-end libraries, double stranded cDNA is A-tailed followed by ligation of the Illumina TruSeq UD Indexes (Cat # 20022370) and amplified for 15 PCR cycles following manufacturer’s recommendation

treatment_protocol: The differentiated human nose organoid derived air liquid interface (HNO-ALI) cells were apically infected with SARS-CoV-2 [Isolate USA-WA1/2020, obtained from Biodefense and Emerging Infectious resources (BEI)] at a multiplicity of infection 0.01 or mock infected with airway organoid differentiation media.

value: 6 days

value: human nose organoid model HNO204


title: TDIMI012_seq_1


title: WT-R2

value: WT


title: CRC-PKU-25-wgs


title: TDIMI010_seq_1


title: TDIMI004_seq_2


title: 72hrSARS


title: Chow-hACE2-CoV2-H-1


title: OMPtTAtetOP2, control HiC, r2

city: New York

first: Ariel

last: Pourmorady

state: NY

address: 3227 Broadway

department: Neurobiology and Behavior

institute: Columbia University

description: Control Hi-C libraries performed on an individual biological replicate of GFP+ OSNs sorted from adult mice

data_processing:
Reads were aligned to the mm10 genome using the distiller pipeline (https://github.com/mirnylab/distiller-nf), uniquely mapped reads (mapq > 30) were retained and duplicate reads discarded. Contacts were then binned into matrices using cooler 45. Analysis was performed on data pooled from two (HiChIP, Hi-C) or three biological replicates (Liquid Hi-C), after confirming that the results of analysis of individual replicates were similar.
mm10

source_name: Olfactory Sensory Neurons

extract_protocol: MOE were dissociated using the Worthington Papain Dissociation kit, and cells were fixed in 1% formaldehyde in 1x PBS, and quenched with 1/10th vol. 1.25M Glycine, and washed with 1x PBS either immediately before or after cell sorting. Nuclei were processed for HiC exactly as described in "LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice" (Horta et al. 2019). Briefly nuclei were lysed, permeabilized, quenched, and then digested over night in DpnII . The next day we performed biotin-fill in with biotinylated dUTP, ligation with T4, and shearing. Cross-links were reversed overnight and DNA was purified with a 2x AMPure bead purification. Library prep was performed on MyOne Streptavidin beads to purify biotinylated contacts. Libraries were prepared using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit.

value: OMPtTA > tetO-P2

tag: sample type

value: HiC

value: Olfactory Sensory Neurons


title: TDIMI004_seq_1


title: 6hrSARS

tag: cell line


title: OMPtTAtetOP2, control HiC, r1


title: TDIMI003_seq_1


title: 6DAYMock

value: Mock


title: CRC-PKU-22-wgs

source_name: plasma


title: WT-R1


title: TDIMI002_seq_1

source_name: AML Patient Tissue Sample_trizol_testset


title: P2-ImmFix-dipc-9

description: DipC on GFP+ cells from gg8tTAtetOP2/CAST hybrid mice

data_processing:
We excluded cells that had contacts < ~400,000 contacts, cells that had a low contact-to-read ratio, and cells that had high variability in 3D structure across computational replicates. Overall, the median number of contacts across nuclei was 715,690 contacts per cell for 74 cells for mor28-IRES-GFP Dip-C and 694,462 contacts per cell for 84 cells for gg8-tTA>tetO-P2-IRES-GFP Dip-C, for a total of 161 cells. 3D reconstruction of Dip-C models was performed exactly as described in (https://github.com/tanlongzhi/dip-c).
To characterize Greek Island and OR gene 3D relationships, we used the dip-c function 'dip-c pd' to generate symmetric matrices, measured in particle radii, of the pairwise distance relationships between these DNA elements. These processed data files end in "pd.txt".
To characterize Greek Island and OR gene genomic contacts, we used the haplotype imputed contacts file generated in the Dip-C pipelie "contacts.con.gz", to extract all contacts per cell at 50-kb resolution, normalized to contacts per million. Contacts for all male and female cells are compiled in separate text files ending in "50kb.contacts.haplotyped.txt".
Assembly: mm10
Supplementary files format and content: pd.txt: tab-delimited text files containing symmetric distance matrices.
Supplementary files format and content: "50kb.contacts.haplotyped.txt".: tab-delimited text files describing pairwise genomic contacts binned at 50-kb resolution.
Library strategy: Dip-C

source_name: olfactory sensory neurons

growth_protocol: Castaneous (Cas) mice were crossed to gg8-tTA>tetO-P2-IRES-GFP or mor28-IRES-GFP mice heterozygous F1 hybrids with SNPs to allow for downstream haplotype imputation.

extract_protocol:
Nuclei were extracted exactly as described in "Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice" (Bashkirova et al. 2023). Briefly, MOE was collected from at least 3 adult heterozygous mice resulting from this cross, and dissociated using the Worthing Dissociation Kit. GFP+ cells were sorted using FACs, and the sorted cells were fixed for 10 minutes in 2% formaldehyde and FAC-sorted to isolate GFP+ mOSNs. Dip-C was performed on 96 cells for each experiment.. Briefly, cells were lysed in Hi-C Lysis Buffer (10mM Tris pH8, 10mM NaCl, 0.2% NP40, 1x protease inhibitors) on ice for 15 minutes, nuclei were pelleted at 2500 rcf for 5 min at 4°C, then resuspended in 0.5% SDS and permeabilized 10 minutes at 62 °C then quenched in 1.1% Triton X-100 15min at 37 °C. Nuclei were digested in 1x DpnII buffer and 6U/ul DpnII enzyme and digested overnight at 37°C. Nuclei were then washed once in Ligation Buffer, and resuspended in Ligation buffer with 10U T4 DNA Ligase (Life Tech), and incubated for 4 hours at 16oC shaking at 600rpm. After ligation nuclei were pelleted and resuspended in cold PBS with DAPI to a final concentration of 300nM and GFP+ cells were FAC-sorted into a 96 well plate with 2ul lysis buffer (20mM Tris pH 8, 20mM NaCl, 0.15% Triton X-100, 25mM DTT, 1mM EDTA, 500nM Carrier ssDNA, and 15ug/mL Qiagen Protease) and lysed for 1 hour at 50°C and inactivated 15 minutes at 70°C.
DNA was transposed by adding 8ul transposition buffer (12.5 mM TAPS pH 8.5, 6.25mM MgCl2, 10% PEG 8000) with ~0.0125 uLTn5 (Vanzyme) and incubated at 55°C for 10 min, then stopped with transposome removal buffer (300nM NaCl, 45 mM EDTA, 0.01% Triton X-100 with 100ug/mL Qiagen Protease) and incubated at 50°C for 40 minutes and 70°C for 20 minutes. Libraries were amplified 14 cycles with i5 and i7 Nextera primers, with unique barcodes for each cell. Libraries from all cells were pooled and cleaned up with Zymo DNA Clean and Concentrate Kit.Libraries were sequenced 150PE on a full-lane of a Illumina NovaSeq2000.

value: olfactory sensory neurons

value: DipC

value: adult


title: TDIMI006_seq_1

data_processing:
Picard tools and samtools preprocessing of FASTQ.
RNA-SeQC and RSeQC quality control processing.
Bowtie2 alignment to contaminating sequences.
STAR alignment to the genome.
Quantification with featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: TSV-formatted count matrix files


title: P2-ImmFix-dipc-96


title: 72hrMock


title: 6hrMock


title: TDIMI001_seq_1


title: P2-ImmFix-dipc-95


title: P2-ImmFix-dipc-94


title: CRC-PKU-17-wgs


title: CRC-PKU-24-wgs


title: CRC-PKU-21-wgs


title: CRC-PKU-18-wgs


title: OMP-GFP, ATAC, rep2

description: ATAC-seq generated from individual biological replicate of OSNs FACsorted from adult mice

data_processing:
Adapter sequences were removed from raw sequencing data with CutAdapt. ATAC-seq reads were aligned to the mouse genome (mm10) using Bowtie2 (Langmead and Salzberg, 2012). Default settings were used, except a maximum insert size of 1000 (-X 1000) was allowed for ATAC-seq data since these data sets contained some large fragments. PCR duplicate reads were identified with Picard and removed with Samtools (Li et al., 2009). Samtools was used to select uniquely aligning reads by removing reads with alignment quality alignments below 30 (-q 30). Regions of open chromatin were identified by running HOMER peak calling in ‘region’ mode, with a fragment size of 150 bp and a peak size of 300 bp. For ATAC-seq signal tracks, replicate experiments were merged, and HOMER was used to generate 1 bp resolution signal tracks normalized to a library size of 10,000,000 reads. Reads were shifted 4 bp upstream in order to more accurately map the Tn5 insertion site. Reads were extended to the full fragment length, as determined by paired-end sequencing.
mm10

source_name: main olfactory epithelium

extract_protocol: ATAC-seq libraries were prepared from live sorted cells using the protocol developed by Buenrostro et al., 2015. Cells were pelleted (500 rcf, 5 min, 4°C) and then resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were immediately pelleted (1000 rcf, 10 min, 4°C). Pelleted nuclei were resuspended in transposition reaction mix prepared from Illumina Nextera reagents (for 50 uL: 22.5 uL water, 25 uL 2xTD buffer, 2.5 uL Tn5 Transposase). The volume of the Tn5 transposition reaction was scaled to the number of cells collected: 1 uL mix per 1000 cells. If fewer than 10,000 cells were collected by FACS, 10 uL scale reactions were performed. Transposed DNA was column purified using a Zymo DNA Clean & Concentrator-5 (Zymo). The transposed DNA was then amplified using barcoded primers and NEBNext High Fidelity 2x PCR Master Mix (NEB). Amplified libraries were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1.6 ul of beads per 1 uL of library and eluted in 30 uL of elution buffer (10 mM Tris-HCl pH 8, 0.1 mM EDTA).

value: main olfactory epithelium

value: OMP-GFP

value: 8 weeks old


title: CRC-PKU-16-wgs

value: female


title: OMP-GFP, ATAC, rep1


title: CRC-PKU-23-wgs

value: male


title: CRC-PKU-15-wgs


title: P2-ImmFix-dipc-92


title: input_2

city: Zhengzhou

first: Yan-li

last: Zeng

state: Henan

address: No.7 of Weiwu Road

department: Department of Infectious Diseases

institute: Henan Provincial People’s Hospital

data_processing:
Reads were aligned to the human GRCh38 genome using bowtie2 (Langmead and Salzberg 2012). only uniquely mapped reads were used for the following analysis.
The input samples without immunoprecipitation were treated as background.  DeepTools (Ramírez, Ryan et al. 2016) was used for the assignment of genomic features, such as relative location to TSS to the peaks and visualization of binding profiles.
HOMER (Hypergeometric Optimization of Motif EnRichment) software (Heinz, Benner et al. 2010) was used to search the enriched binding motifs in peaks.
For reverse transcription (RT), cDNA synthesis was done by reverse transcription kit (R323-01, Vazyme, China) at 42˚C for 5min，37 ˚C for 15min，85 ˚C for 5 seconds performed on the thermocycler (T100, Bio-Rad, USA). The chromatin immunoprecipitation assay had been performed according to the above description. The quantitative PCR (qPCR) was performed on the ABI QuantStudio 5 (Thermo, USA), followed by denaturing at 95˚C for 10 min, 40 cycles of denaturing at 95˚C for 15 sec and annealing and extension at 60˚C for 1 min. Each sample had three technical replicates. The concentration of each transcript was then normalized to GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and mRNA level using 2- ΔΔCT method (Livak and Schmittgen 2001) for analysis. Comparisons were performed with the paired Student’s t-test by using GraphPad Prism software (Version number8.0, San Diego, CA).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

source_name: Huh7 cells

extract_protocol:
Approximately 1 × 10^7 cells were crosslinked in 1% Formaldehyde for 10 min and stop the reaction by 0.125 M glycine for 5 min. The crosslinked cells were lyses in Lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) and sonicated to generate DNA fragments for 200-1000 bp. For immunoprecipitation, Protein-DNA complex was immunoprecipitated by incubating with ChIP-grade Protein A/G Magnetic Beads (26162, Invitrogen, USA) conjugated with anti-FLAG antibody (F7425, sigma, USA), or IgG (B900610, Proteintech, China) at 4℃ for 2h. The beads were washed with LiCl Immune Complex wash buffer (0.5 M LiCl) for five times, TE buffer (10Mm Ttis (PH 8.0), 1mM EDTA (PH 8.0)) for one time, respectively. Resuspend the beads with 100ul Elution Buffer (100 mM NaHCO3 ,1% SDS) and reverse cross-linked by overnight incubation at 65 ℃. After sequential RNase A and proteinase K treatment, DNA fragments were purified by phenol extraction and ethanol precipitation.
The libraries were performed by using VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607, Vazyme, China) according to manufacturer’s instructions and PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina, USA) with PE150 model.

value: Huh7 cells

value: input


title: P2-ImmFix-dipc-93


title: IP_2

value: USF1 IP


title: gg8tTAtetOGFP, RNA-seq, r2

description: RNA-seq performed on FAC sorted cells from the main olfactory epithelium of adult mice using the following kit: Truseq RNA Library Prep Kit v2.

data_processing:
Data processing and analysis was performed as described in "Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons" (Monahan et al. 2017). Briefly Adapter sequences were removed from raw sequencing data with CutAdapt. RNA-seq reads were aligned to the mouse genome (mm10) using STAR. Samtools was used to select uniquely aligning reads by remove reads with alignment quality alignments below 30 (-q 30). RNA-seq data analysis was performed in R with the DESeq2 package.
mm10

extract_protocol: All RNA-seq experiments were performed under RNA clean conditions. For RNA-seq, live cells were sorted into RNase free 1x PBS, pelleted at 600-g, for 5-min, at 4 ̊C, then resuspended in 500-uL Trizol, flash frozen in liquid nitrogen and stored O/N at -80 ̊C. RNA extraction was performed the next day. Trizol suspensions were thawed on ice, 1/5V of 1-bromo-3-chloropropane was added, and tubes were shook vigorously to combine phases. Phases were allowed to separate for 2-min at room temperature and then tubes were centrifuged at 10,500 rpm, for 15-min at 4  ̊C in an Eppendorf centrifuge C5424R. We collected the upper aqueous phase which was transferred to a new tube. 1/2V of Isopropanol and 1-uL of linear polyacrylamide (Sigma Aldrich 56575) were added, tube was inverted to mix, and RNA was allowed to precipitate for 10-min at RT. Tubes were centrifuged for 10-min at 10,500 rpm and 4- ̊C. The supernatant was removed and 1V of 75% EtOH was added to the pellet, which was dislodged by flicking the tube. Tubes were centrifuged for another 5-min, at 10,500-rpm, and 4  ̊C. EtOH was removed and tubes were allowed to air dry for 5-min until the pellet turned clear. Next we added 26- uL of RNase free water, 3-uL of Ambion DNase I 10x buffer and 1-uL of DNase I (AM2222) to remove all DNA, and incubated tubes at 37  ̊C for 30-min. RNA was purified doing a 1.5x AMPure bead cleanup, measured on a nanodrop, and used as the input for library preparation with SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2 (Takara Bio USA). OMP-tTA>tetO-GFP and gg8-tTA>tetO-GFP libraries were prepared with the TruSeq kit. However, mature OSN samples were compared to both OMP-tTA>tetO-GFP (TruSeq prep) and OMP-IRES-GFP (Takara Bio USA), which label the same neurons, and produced the same results. Libraries were sequenced on either a NextSeq550 or a NextSeq2000 and were sequenced to a targeted coverage of ~25M reads. All RNA-seq experiments were performed with 2-3 biological replicates.

value: gg8tTA > tetO-GFP

value: RNA-seq


title: CRC-PKU-14-wgs


title: IP_1


title: P2-ImmFix-dipc-91


title: OMP-GFP, ATAC, rep3


title: CRC-PKU-13-wgs


title: gg8tTAtetOGFP, RNA-seq, r1


title: USF1_3rd

data_processing:
For data analysis, raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After that, clean reads were aligned to the human GRCh38 genome by HISAT2 (Kim, Langmead et al. 2015) allowing no more than 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) (Trapnell, Williams et al. 2010).
The R Bioconductor package edgeR (Robinson, McCarthy et al. 2010) was utilized to screen out the differentially expressed genes (DEGs). The P value <0.01 and fold change>2 or < 0.5 were set as the cut-off criteria for identifying DEGs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
The collected Huh7 cells were subjected to total RNA extraction using TRIZOL (15596-018, Ambion, USA).  The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (M6101, Promega, Madison, WI, USA) to remove DNA.  The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Ultrafine spectrophotometer (N50 touch, IMPLEN, Germany).  The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (NR605-02, Vazyme, China). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters. Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Nova6000 system for 150 nt paired-end sequencing.

value: hepatocellular carcinoma (HCC)

value: USF1 overexpression


title: CRC-PKU-12-wgs


title: OMPtTAtetOGFP, RNA-seq, r1

value: OMPtTA > tetO-GFP

value: Olfactory Sensory Neurons


title: input_1


title: USF1_1st


title: OMPtTAtetOGFP, RNA-seq, r2


title: CRC-PKU-10-wgs


title: Ctrl_3rd

value: control  plasmid


title: P2-ImmFix-dipc-8

value: olfactory sensory neurons

value: DipC


title: USF1_2nd


title: P2-ImmFix-dipc-89

value: adult


title: U251_NOP58

first: Lihui

last: Liu

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
3-U251-NOP58-rRNA
NOP58-RIP-U251-featurecounts.txt

data_processing:
Library strategy: uvRIP-seq
For ribometh-seq, sdapters were removed by cutadapt v2.7 with parameters (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAAC). Trimmed reads were mapped to ribosome DNA sequence by bowtie v2.2.9 and then sorted by samtools v1.10. BAM files were converted to BED format by bamToBed (bedtools v2.26). Positions of 5' (beginnings) and 3' (ends) were extracted and converted to bedGraph using custom python script. The methylation level was further quantified by MethScore A2 calculation.
For RNA-seq, reads were aligned and counted by STAR with --quantMode GeneCounts option and differential expressed genes were identified by edgeR.
For uvRIP-seq, read were aligned by STAR and counted by featureCounts, then enriched transcripts by NOP58 antibody relative to input or IgG control were identified by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, the count table is the read counts for each sample calcualted from STAR with --quantMode GeneCounts mode. For ribometh-seq, methScore are provided for each nucleotide at each sample. For uvRIP-seq, the count tables are the read counts for each sample  calcualted from featureCounts.

source_name: glioma cells

extract_protocol:
Cell culture medium were removed and RNA was harvested using Trizol reagent. For RiboMeth-seq, total RNA was fragmented in 50 mM sodium carbonate/bicarbonate buffer (pH 9.2) at 95°C. Next, Fragmented RNA was 3′-end dephosphorylated and purified with the RNA Clean & Concentrator-5 kit (Zymo Research). RNA was then 5′-end phosphorylated with T4 polynucleotide kinase (NEB) and purified again. For uvRIP-seq, RNA were harvested with Trizol reagent after NOP58 UV-crosslinked immunoprecipitaion.
For RiboMeth-seq, sequencing libraries were prepared with the VAHTSTM Small RNA Library Prep Kit for Illumina® (Vazyme) following the manufacturer's instruction. For RNA-seq and uvRIP-seq, RNA libraries were prepared for sequencing using VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme) with total RNA.


title: OMPtTAtetOP2(nc), RNA-seq, r3

description: RNA-seq performed on FAC sorted cells from the main olfactory epithelium of adult mice using the following kit: SMARTER Stranded Total RNA-Seq Kit- Pico Input Mammalian v2.

value: OMPtTA > tetO-P2(nc)


title: P2-ImmFix-dipc-87


title: U251_IgG

description:
2-U251-IgG-rRNA
NOP58-RIP-U251-featurecounts.txt


title: OMPtTAtetOP2, RNA-seq, r2

value: OMPtTA > tetO-P2


title: U251_input

description:
4-U251-input-rRNA
NOP58-RIP-U251-featurecounts.txt


title: gg8tTAtetOP2(nc), RNA-seq, r3

value: gg8tTA > tetO-P2(nc)


title: Ctrl_1st


title: P2-ImmFix-dipc-90


title: P2-ImmFix-dipc-86


title: U87_NOP58

description:
9-U87-NOP58-rRNA
NOP58-RIP-U87-featurecounts.txt


title: GIMEN cells treated with Veh72 rep2

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

library_source: other

data_processing:
CRISPR KO screens were analyzed using Mageck-Vispr/0.5.7
Supplementary files format and content: Mageck default output describing resulting RRA scores

molecule: other

source_name: Peripheral Nervous System

extract_protocol: sgRNAs for the human CRISPR KO library were first designed using CRISPick . The top 30 sgRNAs for each gene then underwent an additional round of filtering using in-house off-target analysis to identify highly unique sgRNAs.  Up to 6 sgRNAs per gene were selected for the library along with non-targeting controls making up ~10% of the final library.

treatment_protocol: 72H treatments

value: Peripheral Nervous System

value: Neuroblastoma

tag: molecule type

value: gRNA


title: GIMEN cells treated with Phosphoramide mustard

value: Phosphoramide mustard


title: P2-ImmFix-dipc-85


title: gg8tTAtetOP2(nc), RNA-seq, r2


title: gg8tTAtetOP2, RNA-seq, r1

value: gg8tTA > tetO-P2


title: P2-ImmFix-dipc-84


title: Ctrl_2nd

value: Huh7 cells


title: OMPtTAtetOP2(nc), RNA-seq, r1

value: RNA-seq


title: BJ-hTERT cells treated with JQAD1

source_name: Foreskin

value: Foreskin

value: Fibroblast


title: BJ-hTERT cells treated with Retinoic acid

value: Retinoic acid


title: P2-ImmFix-dipc-83


title: OMPtTAtetOP2, RNA-seq, r1

value: Olfactory Sensory Neurons


title: P2-ImmFix-dipc-82

value: olfactory sensory neurons


title: U87_input

description:
7-U87-input-rRNA
NOP58-RIP-U87-featurecounts.txt


title: BJ-hTERT cells treated with Veh144


title: P2-ImmFix-dipc-81

value: DipC


title: P2-ImmFix-dipc-88

value: adult


title: 18tg-DN-1

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

data_processing:
sequenced on the Illumina NextSeq 500
mapped to Mus_musculus_ensembl_v80 reference sequence, and quantified using CLC Genomics Workbench software (V22.0, Qiagen)
Fold changes were not calculated directly from RPKM values but from the generalized linear model, which corrects for differences in library size between the samples and the effects of confounding factors.
Assembly: Mus_musculus_ensembl_v80 reference sequence
Supplementary files format and content: .xlsx is count (RPKM and TPM) tables of mapped genes

source_name: CD44lowCD62L- CD8 T cells- spleen

growth_protocol: Adult Mice (>6wks) were held in SPF conditions and spleens were harvested.

extract_protocol:
fluorescence-activated cell sorting directly into lysis/stabilization media
Messenger RNA purification and fragmentation, complementary DNA synthesis and target amplification were performed with Smart-Seq v4 ultra Low input RNA sequencing preparation kit. Pooled complementary DNA libraries were sequenced on the Illumina NextSeq 500.

treatment_protocol: Magnetic Cd8 T cell enrichment then FACS sorted live CD44+ CD8 T lymphocytes

value: Spleen

value: CD44lowCD62L- CD8 T cells


title: OMPiGFP, RNA-seq, r2

value: OMPiresGFP


title: OMPiGFP, RNA-seq, r1


title: BJ-hTERT cells treated with Vincristine

value: Vincristine


title: BJ-hTERT cells treated with Topotecan

value: Topotecan


title: P2-ImmFix-dipc-80


title: P2-ImmFix-dipc-7


title: DS-DN-2

value: DS


title: Ngn1iGFP, RNA-seq, r2


title: DSHET-DN-1

value: DSHET


title: P2-ImmFix-dipc-79


title: Ngn1iGFP, RNA-seq, r1


title: 18tg-DN-2


title: BJ-hTERT cells treated with Doxorubicin

value: Doxorubicin

value: gRNA


title: BJ-hTERT cells treated with Phosphoramide mustard

value: PM


title: P2-ImmFix-dipc-78


title: Mash1iCrerosa26tdT/Ngn1GFP, RNA-seq, r2

value: Mash1iCre, Rosa26tdTom, Ngn1iresGFP

value: RNA-seq


title: DS-DN-1


title: PRFKO-CD44-3

source_name: CD44+ CD8 T cells- spleen

value: CD44+ CD8 T cells

value: PRFKO


title: DSHET-DN-2


title: U87_IgG

description:
8-U87-IgG-rRNA
NOP58-RIP-U87-featurecounts.txt


title: OMPtTAtetOP2(nc), RNA-seq, r2

value: OMPtTA > tetO-P2(nc)

value: Olfactory Sensory Neurons


title: Mash1iCrerosa26tdT/Ngn1GFP, RNA-seq, r1


title: BJ-hTERT cells treated with Cisplatin

value: Foreskin

value: Fibroblast

value: Cisplatin


title: P2-ImmFix-dipc-77

value: olfactory sensory neurons

value: DipC

value: adult


title: PRFKO-CD44-2

value: Spleen


title: Mash1iCrerosa26tdT, RNA-seq, r2

value: Mash1iCre, Rosa26tdTom


title: P2-ImmFix-dipc-76


title: BJ-hTERT cells treated with Veh72


title: BJ-hTERT cells treated with Etoposide

value: Etoposide


title: Mash1iCrerosa26tdT, RNA-seq, r1


title: RH30 cells treated with JQAD1

source_name: Soft bone

value: Soft bone

value: Rhabdomyosarcoma

value: gRNA


title: P2-ImmFix-dipc-75


title: RH30 cells treated with Retinoic acid

value: Retinoic acid


title: PRFKO-CD44-1

value: CD44+ CD8 T cells


title: Krt5CreERrosa26tdT, RNA-seq, r2

value: Krt5CreER, Rosa26tdTom

value: RNA-seq


title: P2-ImmFix-dipc-74


title: 18tg-CD44-3


title: 18tg-CD44-2


title: P2-ImmFix-dipc-73


title: Krt5CreERrosa26tdT, RNA-seq, r1

value: Olfactory Sensory Neurons


title: RH30 cells treated with Veh144


title: P2-ImmFix-dipc-72


title: DSHET-CD44-3

value: DSHET


title: RH30 cells treated with Vincristine

value: Vincristine


title: OMPiGFP/Atf5iRFP, RNA-seq, r2

value: OMPiresGFP, Atf5iresRFP


title: P2-ImmFix-dipc-71

value: olfactory sensory neurons


title: OMPiGFP/Atf5iRFP, RNA-seq, r1


title: 18tg-CD44-1


title: P2-ImmFix-dipc-6

value: DipC


title: DSHET-CD44-1


title: DSHET-CD44-2


title: P2-ImmFix-dipc-70

value: adult


title: DS-CD44-3

value: Spleen

value: DS


title: RH30 cells treated with Topotecan

value: Topotecan


title: P2-ImmFix-dipc-69


title: OMPiGFP/Atf5iRFP, control HiC, r2

description: Control Hi-C libraries performed on an individual biological replicate of GFP-/RFP+ OSNs sorted from adult mice

value: HiC


title: OMPiGFP/Atf5iRFP, control HiC, r1


title: P2-ImmFix-dipc-68


title: P2-ImmFix-dipc-67