title: Skin, MKR 2

city: Halle (Saale)

first: Yuan

state: Deutschland

address: Heinrich-Lammasch Platz, 4

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low-quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. Reads mapping to the reference sequence The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference. Known miRNA alignment Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively. Remove tags from these sources To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself. Novel miRNA prediction The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.
Small RNA annotation summary Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA tags may be mapped toto  more than one category. To make everevery unique small RNA mapped to only one one annotation, we follow the following  prioritpriority rule: known miRNA > rRNA > tRNA NA > snRNA > snoRNA > repeat > ggenene > NAT-siRNA > gene > novel miRNA > > ta-siRNA. The total rRNA proportion tion was used a marker as sample quality indicindicator. ator. Usually it should be less than 6060% in plant samples and 40% in animal samplessamples as high quality. miRNA editing anal analysisysis Position 2~8 of a maturemature miRNA were called seed region which which were highly conserved. The target get of a miRNA might be different with the the changing of nucleotides in this regregion. In our analysis pipeline, miRNA which which might have base edit could be detected detected by aligning all the sRNA tags to maturemature miRNA, allowing one mismatch. miRNA family analysisysis Exploring the occurrenceence of miRNA families identified from the samplessamples in other species. In our analanalysis pipeline, known miRNA used used miFam.dat (http://www.mirbase.or.org/ftp.shtml) to look for families; novel miRiRNA precursor was submitted to RfaRfam (http://rfam.sanger.ac.uk/search/) to look look for Rfam families.
Quantification of miRNA    miRNA expression levels were estimated by TPM (transcript per million) through the following criteria ia ((Zhou et al., 2010): Normalization formula:  Normalized expression = mapped readcount/Total reads*1000000
Differential expression of miRNA   For the samples with biological replicates: Differential expression  analysis of two conditions/groups was performed using the DESeq R package  (1.8.3). The P-values was adjusted using the  Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
GO and KEGG  enrichment analysis Gene Ontology (GO) ) enrichment analysis was used on the target gene candidates of differentially expressed miRNAs (“target gene candidates” in  the following). GOseq based Wallenniius non-central hyper-geometric distribution (Young et al, 2010），which could adjust for gene length bias, was  implemented for GO enrichment analysis.
Small RNA reads are mapped to the genome using Bowtie, to analyze their expression level and distribution on genome.Result Directory: Results/3.Mapping_Stat/reference.mapping.stat.
Assembly: miRBase20.0
Supplementary files format and content: Raw counts

source_name: Skin

extract_protocol:
the 3’UTR of tapasin (accession number: NM_001410875.1) was cloned upstream of two MS2 “stem-loop” structures in recombinant plasmid pcDNA™ 3.1(+) (Invitrogen). The plasmids were then in vitro transcribed overnight with T7 promoters (T7 RiboMAX™, Promega, Madison, Washington, USA) and cleaned with the MEGAclear™ Transcription Clean-Up Kit (Invitrogen). Amylose resin beads (NEB, Ipswich, MA, USA) were incubated with the fusion protein including MBP domains and MS2 loop and in vitro transcribed RNAs were immobilized on amylose resin, then blocked with yeast tRNA (Invitrogen) followed by incubation with the bait RNAs and the cell lysate equipping the specific binding of miRNAs to the 3’UTR of tapasin. MiRNAs were purified via chloroform RNA isolation and small RNA sequencing.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H– ). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

value: Skin

value: MZ-Mel 2

value: Input


title: Ctl-1-t1-rCD4

status: Public on Sep 15 2024

type: SRA

city: Baltimore

first: Annukka

last: Antar

state: MD

address: 733 North Broadway Room 869

department: Medicine - Infectious Diseases

country: USA

institute: Johns Hopkins School of Medicine

library_source: genomic

data_processing:
Proprietary to Adaptive Biotech. See these papers, PMID: 24157944 and PMID: 19706884
Supplementary files format and content: tab-deliminated text file includes productive and unproductive CDR3 TCRβ sequences (unproductive sequences not used in manuscript)

molecule: genomic DNA

organism: Homo sapiens

source_name: CD4 T Cell

extract_protocol:
Genomic DNA was isolated (QIAamp DNA Mini or Micro kit, Qiagen, or Quick-DNA Miniprep, Zymo Research) from sorted cells, quantified (Qubit 3.0 or 4 fluorometer, dsDNA quantitation, high sensitivity or broad range assays, ThermoFisher Scientific, or by NanoDrop 2000 spectrophotometer, ThermoFisher Scientific) and diluted in Tris-acetate-EDTA to a concentration of 10-50 ng/μL (for a total of up to 1-3 μg per sample).
Proprietary to Adaptive Biotech. See these papers, PMID: 24157944 and PMID: 19706884

tag: cell type

value: CD4 T Cell

tag: hiv serostatus

value: Negative

tag: cmv serostatus

value: Positive

tag: Sex

value: male


title: VM13, scRNAseq

city: St Leonards

first: Jose Antonio

last: Lopez-Escamez

state: NSW

address: 10 Westbourne St

department: Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute

country: Australia

institute: The University of Sydney

description: 10 X Genomics

library_source: transcriptomic single cell

data_processing:
The cellranger-arc mkfastq.gz function from Cell Ranger ARC V.2.0.0 was used to demultiplex Illumina’s base calling files (BCL) into a fastq.gz format for downstream analysis. FASTAQ files were analyzed using Cell Ranger ARC v.2.0.2 and aligned with GRCh38 for the human genome reference, as per 10x Genomics guidelines to generate a filtered matrix file for downstream analysis.
Assembly: GRch38
Supplementary files format and content: H5 files

molecule: total RNA

source_name: Blood

extract_protocol:
PBMCs were thawed and diluted in RPMI + 10% FBS, and cells were counted. To eliminate granulocytes with extracellular DNA, we sorted cells stained in CD66. We continued to isolate the nuclei from a million cells per sample. Briefly, we centrifuged cells (300rcf 5min 4C). The supernatant was removed, replaced with 1 mL refrigerated lysis buffer, and incubated for 3 min before resuspension. The nuclei were centrifuged again (500 rcf, 4°C, 5 min). The pellet was resuspended in 1 mL Diluted Nuclei Buffer and passed through a 40 μm cell strainer. All steps were performed on ice. Nuclei were stained and counted. Nuclei were collected into 10% BSA. 1 U/mL RNase inhibitor (Sigma–Aldrich, 03335402001) was added to all final solutions
RNA libraries were generated from amplified cDNA. Pair-end sequencing for the 24 samples was performed by using a Hiseq X Illumina sequencing platform.

tag: tissue

value: Blood

tag: disease

value: Vestibular Migraine

value: PBMC


title: Skin, MKR 1

last: Wang

country: Germany

library_source: transcriptomic

tag: cell line

tag: group


title: human_BMSC_3D_rep3

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

country: China

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg19 human genome using STAR.
For RNA-seq data, aligned reads with high quality were quantified by HTSeq.
For RNA-seq data, counts per million reads (CPM) were calculated.
For RNA-seq data, unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count.txt file.
Genome_build: hg19
Supplementary_files_format_and_content: We provided tab-delimited text files including raw count values for each sample.

molecule: polyA RNA

source_name: human bone marrow stromal cells

growth_protocol: human BMSCs were cultured in low-glucose Dulbecco’s modified Eagle medium (Corning, 10-014-CV) supplemented with 10% FBS (Gibco 10270-106, Lot #: 42F6480K) and 1% penicillin/streptomycin (Thermo).

extract_protocol:
Human bone marrow sample was obtained from the iliac crests of donors upon written consent, diluted 1:1 with Ca2+/Mg2+ HBSS, and digested with 3 mg/ml collagenase type I (Worthington Biochemical), 4 mg/ml Dispase II (Sigma) and 100 U/ml DNase I (Sigma) at 37°C for 15 min. Mononuclear bone marrow cells were isolated by Ficoll-Paque PREMIUM density gradient media (GE Healthcare, 1.073 g/ml) and cultured in low-glucose Dulbecco’s modified Eagle medium (Corning, 10-014-CV) supplemented with 10% FBS (Gibco 10270-106, Lot #: 42F6480K) and 1% penicillin/streptomycin (Thermo). BMSCs were cultured in a 37°C, 5% O2 and 5% CO2 incubator. 80,000 2D expaned and 3D cultured BMSC in GelMA for 7 days were dissociated, total RNA was extracted, digested with DNase I and purified using RNAclean Kit.
RNA-seq libraries were constructed by a modified Smart-seq2 method with UMI barcodes (Nature 533:487, 2016).

value: Bone marrow

value: stromal

tag: condition

value: 3D cluture

tag: age

value: 68 years old


title: human_BMSC_2D_rep3

value: 2D cluture


title: MD12, scRNAseq

description: 10 X Genomics

value: Meniere Disease


title: human_BMSC_2D_rep2

value: 54 years old


title: Skin, TPN1

value: Skin

value: miTRAP


title: human_BMSC_3D_rep2


title: human_BMSC_3D_rep1

value: 30 years old


title: MD11, scRNAseq

description: 10 X Genomics


title: MD10, scRNAseq

description: 10 X Genomics


title: human_BMSC_2D_rep1


title: Ctl-1-t0-rmCD4

value: CD4 T Cell


title: Skin, TPN2

value: MZ-Mel 2


title: G239.10w.Dox_scRNAseq

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Raw base call (BCL) files were demultiplexed and converted to FASTQ files, which were subsequently used to generate feature-barcode matrices using Cell Ranger RNA v3.0.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

organism: Mus musculus

source_name: pancreas

extract_protocol:
Pancreas tissues were enzymatically digested into a single-cell suspension
scRNAseq library was generated by 10X Chromium System

treatment_protocol: Mice were fed with 0.0060 % doxycycline or standard lab diet diet for 10 weeks from 8 weeks of age.

value: pancreas

value: 18 weeks

value: digested pancreas

tag: genotype

value: p48(Cre), Kras(LSL-G12D), Rosa26(LSL-rtTA)), Tg(TetO-GNAS(R201C)

tag: treatment

value: doxycycline feed


title: MD9, scRNAseq

description: 10 X Genomics

value: Blood

value: PBMC


title: G254.10w.Dox_scRNAseq


title: G314.NoDox_scRNAseq

value: normal feed


title: HuTu80 cells, SLC39A8 overexpression

city: Moscow

first: Alexander

last: Modestov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Assembly: hg38
Supplementary files format and content: comma-delimited file includes raw counts for each sample

extract_protocol:
Both knockout clones and wild-type cells from three different passages were detached using Versen solution, washed with PBS, and the resulting cell pellets were stored at −70 °C until further analysis. RNA extraction was performed immediately before the preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) following the manufacturer’s protocol.
RNA Integrity Number (RIN) was measured using Agilent 2100 bioanalyzer. Agilent RNA 6000 Nano or Qubit RNA Assay Kits were used to measure RNA concentration. KAPA RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for further depletion of ribosomal RNA and library preparation. Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay kit (Life Technologies) and Agilent Tapestation (Agilent).

value: Colorectal cancer cell line

value: SLC39A8 overexpression


title: HuTu80 cells, WT, biol rep 3

value: WT


title: MI8, scRNAseq

description: 10 X Genomics

value: Migraine


title: HuTu80 cells, WT, biol rep 2


title: WT_plus - replicate 2

city: Praha

first: Blanka

last: Holendova

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology, CAS

data_processing:
Low quality reads and adaptor sequence were filtered out using TrimmomaticSE (v. 0.36) with the parameters “HEADCROP:10 ILLUMINACLIP:~/TruSeq-PE3.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”. Ribosomal RNA reads were filtered out using Sortmerna (v. 2.1b)  (default parameters) and the cleaned reads were then aligned using STAR (v. 2.7.3a) to the Mus musculus genome version GRCm38 and annotation version vM8. A count table was then generated using the python script htseq-count (v. 0.6.1p1) with the parameter “–m union”.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files raw read count values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Libraries were prepared from 500 ng of tal RUNA using SureSelect XT HS2 mRNA Library prepration System (Agilent) according to manufacture protocol (Version A1, September 2020). It utilize using Poly-A Selection Module (Cat.No 5190-6411), cDNA Module (Cat.No 5500-0149) and XT HS2 Index Primer Pairs (Cat.No 5191-5688). Adaptor-ligated cDNA libraries were amplified using 9 PCR cycles.

value: Beta cells/pancreatic islets

value: Wild Type

value: High glucose


title: WT_plus - replicate 1


title: MI7, scRNAseq

description: 10 X Genomics


title: WT - replicate 3

value: Low glucose


title: HuTu80 cells, WT, biol rep 1


title: HuTu80 cells, GFP, biol rep 2

value: GFP


title: WT - replicate 1

value: pancreas


title: HC6, scRNAseq

description: 10 X Genomics

value: healthy


title: HuTu80 cells, SLC30A3 overexpression

value: SLC30A3 overexpression


title: HuTu80 cells, SLC30A10 overexpression

value: SLC30A10 overexpression


title: VM3, scRNAseq

description: 10 X Genomics

value: Vestibular Migraine


title: G323.NoDox_scRNAseq

value: 18 weeks

value: digested pancreas

value: p48(Cre), Kras(LSL-G12D), Rosa26(LSL-rtTA)), Tg(TetO-GNAS(R201C)


title: LC04_Pre_S3

city: Seoul

first: Songji

last: Oh

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Cancer Research Institute, Seoul National University

data_processing:
Several QC steps were performed in accordance with the manufacturer’s guidelines. To ensure high-quality data, technical QC was performed using the following settings: flag segments with less than 1,000 raw reads, flag segments when less than 80% of raw reads were aligned, flag segments when sequencing saturation was less than 50%, negative probe count geomean was less than 10, no template control count was greater than 1,000, minimum nuclei count was less than 200, and minimum surface area was less than 16,000 µm2. Biological probe QC was performed excluding probes from the target count calculation in all segments if (geomean probe in all segments)/ (geomean probes within target) ≤ 0.1, and if the failed grubs outlier test in ≥ 20% of the segments. A marginal threshold of the target frequency above 1% was set, and only 14,214 biological probes remained after this process.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: t-SCLC_DSP.xlsx
Supplementary files format and content: Q3 normalization
Library strategy: GeoMx Spatial Transcriptomics

source_name: SCC component in combined area

growth_protocol: We obtained formalin-fixed, paraffin-embedded (FFPE) tissue sections from 10 patients.

extract_protocol:
For spatial transcriptomic profiling, tissue sections from multiple patients were placed on the same slide (three slides in total), and 4 μm sections of the tissue microarray (TMA) were used for histological analysis following hematoxylin and eosin staining. Serial sections were stained simultaneously with fluorescently labeled antibodies to detect pan-cytokeratin (NanoString, AE1/AE3, cat. no. 121301310), and DNA-binding dye (ThermoFisher, Syto13, cat. no. S7575) was then applied to the slides. Using the instrument’s web interface, ROIs up to 780 × 660 μm were selected and outlined by two experienced pathologists (JK and YKJ).
Library preparation was performed according to manufacturer instruction (Nanostring DSP-Genomics Library Preparation Protocol, Nanostring Technologies, Seatle, WA) (Merritt et al., 2020). Photocleaved oligonucleotides from each ROI were PCR amplified using Illumina’s i5/i7 dual-indexing system to preserve ROI identity. PCR products were pooled and purified with two rounds of AMPure XP beads (Beckman Coulter, Brea, CA). Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA) was used to measure library concentration and purity. Paired-end (2 75 bp reads) sequencing was performed on an Illumina NextSeq instrument. Reads were then aligned to analyte barcodes with Bowtie

treatment_protocol: As shown in the table, our dataset includes lung adenocarcinoma (LADC), combined-SCLC/LADC (CSCLC), and transformed small cell lung cancer (t-SCLC) before and after EGFR-TKI treatment.

tag: age (years)

value: F

tag: patient id

tag: egfr status

value: mut

tag: egfr-tki state

value: Pre


title: LC07_Post_S3

source_name: SCC component

value: Post


title: LC04_Pre_A3

source_name: ADC component in combined area


title: LC05_Post_S2

value: M


title: WT_plus - replicate 3

value: Beta cells/pancreatic islets

value: Wild Type


title: VM4, scRNAseq

description: 10 X Genomics

value: Blood

value: PBMC


title: LC07_Post_S2


title: LC07_Post_S1


title: LC11_Pre_A2

source_name: ADC component

value: wt


title: LC11_Pre_A3


title: VM1, scRNAseq

description: 10 X Genomics


title: HuTu80 cells, SLC39A14 knockout

value: Colorectal cancer cell line

value: SLC39A14 knockout


title: HuTu80 cells, GFP, biol rep 1

value: GFP


title: WT - replicate 2

value: pancreas

value: Low glucose


title: LC11_Pre_A1


title: HuTu80 cells, SLC39A8 knockout

value: SLC39A8 knockout


title: HC5, scRNAseq

description: 10 X Genomics

value: healthy


title: MD24, scATACseq

description: 10 X Genomics

data_processing:
The cellranger-arc mkfastq function from Cell Ranger ARC V.2.0.0 was used to demultiplex Illumina’s base calling files (BCL) into a FASTQ format for downstream analysis. FASTAQ files were analyzed using Cell Ranger ARC v.2.0.2 and aligned with GRCh38 for the human genome reference, as per 10x Genomics guidelines to generate a peak coordinates, peak fragments cell metadata files for downstream analysis.
Assembly: GRch38
Supplementary files format and content: BED, CSV and TSV files

extract_protocol:
PBMCs were thawed and diluted in RPMI + 10% FBS, and cells were counted. To eliminate granulocytes with extracellular DNA, we sorted cells stained in CD66. We continued to isolate the nuclei from a million cells per sample. Briefly, we centrifuged cells (300rcf 5min 4C). The supernatant was removed, replaced with 1 mL refrigerated lysis buffer, and incubated for 3 min before resuspension. The nuclei were centrifuged again (500 rcf, 4°C, 5 min). The pellet was resuspended in 1 mL Diluted Nuclei Buffer and passed through a 40 μm cell strainer. All steps were performed on ice. Nuclei were stained and counted. Nuclei were collected into 10% BSA. 1 U/mL RNase inhibitor (Sigma–Aldrich, 03335402001) was added to all final solutions
ATAC libraries were generated from transposed DNA.  Pair-end sequencing for the 24 samples was performed by using a Hiseq X Illumina sequencing platform.

value: Meniere Disease


title: LC11_Pre_S2


title: LC11_Pre_S1


title: LC05_Post_S1

value: mut


title: LC10_Pre_A2

value: Pre


title: MI23, scATACseq

description: 10 X Genomics

value: Migraine


title: HuTu80 cells, GFP, biol rep 3


title: HCT-15 cells, SLC30A3 overexpression

value: SLC30A3 overexpression


title: LC10_Pre_A1

value: M


title: HC22, scATACseq

description: 10 X Genomics


title: VM2, scRNAseq

description: 10 X Genomics

value: Vestibular Migraine


title: LC10_Pre_C1

source_name: SCC + ADC component


title: HCT-15 cells, SLC30A10 overexpression

value: SLC30A10 overexpression


title: LC10_Pre_S2


title: HC21, scATACseq

description: 10 X Genomics

value: Blood

value: PBMC


title: LC10_Pre_S1

value: wt


title: LC04_Pre_A2

value: F


title: HCT-15 cells, GFP, biol rep 2

value: Colorectal cancer cell line

value: GFP


title: HCT-15 cells, GFP, biol rep 3


title: HCT-15 cells, GFP, biol rep 1


title: HC19, scATACseq

description: 10 X Genomics


title: LC04_Pre_C1


title: LC04_Pre_C2


title: MD18, scATACseq

description: 10 X Genomics


title: LC04_Pre_S1


title: LC03_Post_S3

value: Post


title: MD17, scATACseq

description: 10 X Genomics


title: LC03_Post_S2


title: LC10_Pre_C2


title: MI16, scATACseq

description: 10 X Genomics


title: LC03_Post_S1


title: LC03_Post_A3


title: DCs scRNAseq

city: Jerusalem

first: Ruth

last: Lubin

address: Ein-Kerem

department: The Institute of Biomedical and Oral Research

country: Israel

institute: Hebrew university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using cellranger, version 6.2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
In accordance with the Declaration of Helsinki, blood was drawn from healthy volunteer into a Sodium  Heparin Vacutainer. RosetteSep HLA Myeloid Cell Enrichment Kit and Ficoll-Paque Plus were used to enrich the myeloid HLA+ cell population using density centrifugation. Following the isolation of the layer containing the enriched HLA+ PBMCs, cells were diluted with FACS buffer (PBS containing 2% FCS and 2mM EDTA) and washed 400 xg. 5 minutes at 4∘C . Next, cells were stained with LIN (CD3, CD19, CD20, CD66b, CD314, CD88, CD89), HLA-DR, CD45RA, CD123, CD5, AXL, CD11c, CD141, and CD1c.  Subsequently, using a FACS ARIA III, cells that have a negative expression for LIN, positive one for HLA-DR and expressing either CD123/CD1c or CD141 were sorted. Immediately after sorting, cells were wash and re-suspended in sterile PBS.
Libraries were prepared and barcoded with UDIs using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics), according to the manufacturers protocol.

value: Dendritic cell


title: LC03_Post_A2


title: MD15, scATACseq

description: 10 X Genomics


title: HC20, scATACseq

description: 10 X Genomics

value: healthy


title: LC03_Post_A1


title: LC04_Pre_A1


title: LC09_Pre_S3


title: LC09_Pre_S2


title: LC09_Pre_S1


title: MI14, scATACseq

description: 10 X Genomics


title: IMA-treated K562 cells, rep2

city: Hangzhou

first: Peng

last: Xiao

address: No.3 East Qingchun Road

institute: Zhejiang University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38
Read count extraction and normalization were performed using featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Human chronic myelogenous leukemia K562 cell line

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

value: Imatinib


title: MLN+IMA-treated K562 cells, rep3

value: Human chronic myelogenous leukemia K562 cell line


title: MLN+IMA-treated K562 cells, rep2


title: LC04_Pre_S2

value: mut

value: Pre


title: IMA-treated K562 cells, rep3


title: VM13, scATACseq

description: 10 X Genomics


title: MLN+IMA-treated K562 cells, rep1


title: MD12, scATACseq

description: 10 X Genomics

value: Meniere Disease


title: LC09_Pre_A1

value: M


title: IMA-treated K562 cells, rep1


title: MLN-treated K562 cells, rep3


title: LC01_Pre_S4


title: MD11, scATACseq

description: 10 X Genomics


title: LC01_Pre_A4


title: MD10, scATACseq

description: 10 X Genomics


title: LC06_Post_S2


title: LC06_Post_S3


title: MD9, scATACseq

description: 10 X Genomics


title: LC06_Post_S1


title: LC09_Pre_A3


title: LC02_Post_S2


title: LC02_Post_S1


title: control K562 cells, rep3

value: control


title: MI8, scATACseq

description: 10 X Genomics

value: Migraine


title: LC09_Pre_A2


title: control K562 cells, rep2


title: LC01_Post_S3


title: control K562 cells, rep1


title: LC02_Pre_A4


title: HC6, scATACseq

description: 10 X Genomics

value: Blood


title: LC01_Post_S2


title: LC01_Post_S1


title: MI7, scATACseq

description: 10 X Genomics

value: PBMC


title: HC5, scATACseq

description: 10 X Genomics


title: LC02_Pre_A2


title: BEAS-2B cells, wild-type PDZ peptide and LPS treatment

city: Busan

first: Kyoung Seob

last: Song

address: Gamcheon-ro, Seo-gu, Busan 49267

department: College of Medicine

institute: Kosin University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Lung; Bronchus

growth_protocol: BEAS-2B cells were cultured in BEBM (Lonza, Basel, Switzerland) with a BEGM kit at 37℃ in a humidified incubation with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: BEAS-2B cells were treated with wild-type PDZ or mutant PDZ peptide for 24 h and then incubated with LPS for 2 h.

value: Lung; Bronchus

value: epithelial cell

value: wild type

value: wild-type PDZ peptide and LPS


title: LC02_Pre_A3

value: F


title: LC02_Pre_A1


title: MLN-treated K562 cells, rep2


title: VM4, scATACseq

description: 10 X Genomics

value: Vestibular Migraine


title: LC01_Pre_A2


title: LC01_Pre_A1


title: BEAS-2B cells, mutant PDZ peptide and LPS treatment

value: mutant PDZ peptide and LPS


title: MLN-treated K562 cells, rep1


title: VM3, scATACseq

description: 10 X Genomics


title: LC01_Pre_C3


title: LC01_Pre_A3


title: BEAS-2B cells, control, no treatment

value: no treatment


title: LC01_Pre_C1


title: LC01_Pre_C2


title: LC01_Pre_S3


title: LC01_Pre_S2


title: U6-driven Cas13bt1 EGFP crRNA#1 (5' RACE, Exp#2)

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
5RACE-B09-pEZ115
Cheng_Suppl_Table3_5RACE_v1.xlsx

library_source: other

data_processing:
After removing 3' adaptor sequence from FASTQ files using cutadapt (ver 3.4; -a <adaptor> --trimmed-only -m 20), high-quality reads were selected using fastq_quality_filter (ver 0.0.14; -q 30 -p 95). Four random nucleotides at the 5' end of 3' RACE adaptor were trimmed using fastx_trimmer, and 5' adaptor sequence was removed using cutadapt (-g <adaptor> --trimmed-only). Top 20 abundant sequences per sample were used to find end positions and modifications.
Assembly: hg38
Supplementary files format and content: Excel spreadsheets containing read counts and end positions of crRNAs

molecule: other

growth_protocol: HEK293E was cultured in DMEM (Thermo) supplemented with 10% fetal bovine serum (Thermo).

extract_protocol:
HEK293E cells were seeded on 60 mm cell culture dishes, and plasmids expressing crRNAs were transfected with calcium phosphate. 48 hours after transfection, total RNA was purified using Trizol (Thermo).
For 5' RACE, the 5′ adaptor was added during the reverse-transcription reaction. 2 μL of RNA (2 μg/μL) was mixed with 0.5 μL of 4 μM reverse-transcription primer, topped up to 10.5 μL with UltraPure water, and incubated at 70˚C for 2 minutes in a thermocycler. The mixture was then added to 12 μL of reverse-transcription master mix (3 µL of 10 µM 5′-adaptor template-switching oligo , 4 µL of Invitrogen 5× SuperScript IV buffer, 1 µL of Takara Bio 10 mM dNTP, 1 μL of Invitrogen 0.1 M dithiothreitol, and 0.5 μL of Invitrogen SuperScript IV reverse transcriptase) and incubated at 37˚C in a thermocycler. After 1 hour, the temperature of the thermocycler was changed to 80˚C for 10 minutes. After reverse transcription, 1.25 µL of adaptor-ligated cDNA was added to 23.75 µL of PCR master mix (12.5 µL of 2× Vazyme Phanta buffer, 0.5 µL of Vazyme 10 mM dNTP, 1 µL of 10 µM forward primer with NEB index binding site, 1 µL of 10 µM reverse primer, 0.3 µL of Vazyme Phanta Max Super-Fidelity DNA Polymerase, and 8.45 µL of UltraPure water). The PCR reaction was performed for 17 cycles. The PCR product was then purified using PCRClean DX (Aline Biosciences). 25 µL of PCR product was mixed with 32.5 µL of PCRClean DX solution (1:1.3 ratio) and incubated at room temperature. After 5 minutes, the mixture was put on a magnetic rack. After 5 minutes, 50 µL of  the unbound fraction was collected and mixed with 185 µL of PCRClean DX solution (1:3.7 ratio). After 5 minutes, the mixture was put on a magnetic rack. After 10 minutes, supernatant was removed, and the pellet was washed with 1 mL of 75% ethanol twice. After washing, the pellet was air-dried for 90 seconds, and then resuspended in 20 µL of UltraPure water. The resuspension was incubated at room temperature for 5 minutes, and then put on a magnetic rack for 10 minutes. 18 µL of supernatant was collected as purified PCR product. To attach the Illumina adaptor sequences, 8 µL of purified PCR product was added to 17 µL of PCR master mix (12.5 µL of 2× Vazyme Phanta buffer, 0.5 µL of Vazyme 10 mM dNTP, 1 µL of 10 µM NEB index-containing forward primer, 1 µL of 10 µM NEBNext reverse primer, 0.3 µL of Vazyme Phanta Max Super-Fidelity DNA Polymerase, and 1.7 µL of UltraPure water). The PCR reaction was performed for 12 cycles. The PCR product was then purified using PCRClean DX. 25 µL of PCR product was mixed with 50 µL of PCRClean DX solution (1:2 ratio) and incubated at room temperature. After 5 minutes, the mixture was put on a magnetic rack. After 10 minutes, supernatant was removed, and the pellet was washed with 1 mL of 75% ethanol twice. After washing, the pellet was air-dried for 90 seconds, and then resuspended in 20 µL of UltraPure water. The resuspension was incubated at room temperature for 5 minutes, and then put on a magnetic rack for 10 minutes. 18 µL of supernatant was collected as purified final PCR product.  For 3′ RACE, 2 μL of RNA (2 μg/μL) was mixed with 0.5 μL of 5 μM NEB 3′ adaptor oligo, and incubated at 70˚C for 2 minutes in a thermocycler. The mixture was then added to 7.5 μL of adaptor ligation master mix (1 µL of NEB 10× T4 RNA ligase buffer, 1 µL of NEB T4 RNA ligase 2 truncated KQ, 0.5 µL of Invitrogen SUPERase-IN, 4 μL of NEB 50% PEG8000, and 1 μL of UltraPure water) and incubated at 25˚C for 4 hours in a thermocycler. 1 μL of 4 μM 5OHseq reverse-transcription primer was mixed with the 10 μL of adaptor ligation product, and incubated at 70˚C for 2 minutes in a thermocycler. The mixture was then added to 9 μL of reverse-transcription master mix (4 µL of Invitrogen 5× SuperScript III buffer, 1 µL of Takara Bio 10 mM dNTP, 1 μL of Invitrogen 0.1 M dithiothreitol, 0.5 μL of Invitrogen SuperScript III reverse transcriptase, and 2.5 μL of UltraPure water) and incubated at 50˚C in a thermocycler. After 1 hour, the temperature of the thermocycler was changed to 70˚C for 15 minutes. After reverse transcription, 1.25 µL of adaptor-ligated cDNA was added to 23.75 µL of PCR master mix (12.5 µL of 2× Vazyme Phanta buffer, 0.5 µL of Vazyme 10 mM dNTP, 1 µL of 10 µM forward primer with NEB index binding site, 1 µL of 10 µM 5OHseq reverse-transcription primer, 0.3 µL of Vazyme Phanta Max Super-Fidelity DNA Polymerase, and 8.45 µL of UltraPure water). The PCR reaction was performed for 17 cycles. The PCR product was then purified using PCRClean DX. 25 µL of PCR product was mixed with 50 µL of PCRClean DX solution (1:2 ratio) and incubated at room temperature. After 5 minutes, the mixture was put on a magnetic rack. After 10 minutes, supernatant was removed, and the pellet was washed with 1 mL of 75% ethanol twice. After washing, the pellet was air-dried for 90 seconds, and then resuspended in 20 µL of UltraPure water. The resuspension was incubated at room temperature for 5 minutes, and then put on a magnetic rack for 10 minutes. 18 µL of supernatant was collected as purified PCR product. To attach the Illumina adaptor sequences, 5 µL of purified PCR product was added to 20 µL of PCR master mix (12.5 µL of 2× Vazyme Phanta buffer, 0.5 µL of Vazyme 10 mM dNTP, 1 µL of 10 µM NEB index-containing forward primer, 1 µL of 10 µM NEBNext reverse primer, 0.3 µL of Vazyme Phanta Max Super-Fidelity DNA Polymerase, and 4.7 µL of UltraPure water). The PCR reaction was performed for 12 cycles. The PCR product was then purified using PCRClean DX. 25 µL of PCR product was mixed with 50 µL of PCRClean DX solution (1:2 ratio) and incubated at room temperature. After 5 minutes, the mixture was put on a magnetic rack. After 10 minutes, supernatant was removed, and the pellet was washed with 1 mL of 75% ethanol twice. After washing, the pellet was air-dried for 90 seconds, and then resuspended in 20 µL of UltraPure water. The resuspension was incubated at room temperature for 5 minutes, and then put on a magnetic rack for 10 minutes. 18 µL of supernatant was collected as purified final PCR product.
5' RACE (Template-switching reverse transcription) and 3' RACE (3' adaptor ligation)

value: Transfection of crRNA-expressing plasmids


title: Res21_pSRS21_RNA

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

description: 10x Genomics

data_processing:
For hashed samples, pSRS (irradiated) patients were hashed with hashtag #5 (sequence: AAGTATCGTTTCGCA) and Res (unirradiated) patients were hashed with hashtag #4 (sequence:AGTAAGTTCAGCGTA)
Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1
VDJ TCR alignment were performed using MiXCR
Assembly: Hg38
Supplementary files format and content: Cellranger output

source_name: Brain Metastases

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

value: Brain Metastases

tag: primary tumor

value: Germ cell

value: CD45+ TILS and CD8+ TILS

tag: steroid dose

value: No treatment

value: Untreated


title: Res19_VDJ

description: VDJ TCR

data_processing:
For hashed samples, pSRS (irradiated) patients were hashed with hashtag #5 (sequence: AAGTATCGTTTCGCA) and Res (unirradiated) patients were hashed with hashtag #4 (sequence:AGTAAGTTCAGCGTA)
Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1
VDJ TCR alignment were performed using MiXCR
Assembly: Hg38
Supplementary files format and content: Cellranger output
Library strategy: VDJ

value: NSCLC

tag: cell type


title: LC01_Pre_S1

value: mut

value: Pre


title: VM1, scATACseq

description: 10 X Genomics

value: Blood

value: PBMC


title: VM2, scATACseq

description: 10 X Genomics


title: U1-driven Cas13bt1 EGFP crRNA#1 extended (5' RACE, Exp#2)

description:
5RACE-B05-pEZ109
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res21_pSRS21_VDJ

description: VDJ TCR


title: BCR of mice_2 immunized with LNP

city: Shenzhen

first: Yansheng

last: Li

address: 3002 Sungang West Road, Futian District

institute: Shenzhen Second People's Hospital

description: Single-Cell V(D)J sequencing of mice11

data_processing:
CellRanger v7.2.0,Seurat v4.1.1
Assembly: The scRNA-seq sequencing data were aligned to Ensembl genome GRCm38 reference genome
Supplementary files format and content: Processed data of each single-cell  sample includes Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: tab-delimited text files include contig annotations and cell barcode information values for each single-cell TCR and BCR Sample.

source_name: spleen

extract_protocol:
The spleens were isolated from groups of BALB/c mice (n=3 each) treated with either AALI or LNP, then were dissociated into single cells using a dissociation solution，
The libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' Kit， 10X Genomics Chromium Single Cell V(D)J Kit.
RNA-seq,AMPLICON

value: spleen

value: splenic cells

value: tissue

value: immunized with LNP


title: BCR of mice_3 immunized with LNP

description: Single-Cell V(D)J sequencing of mice12


title: BCR of mice_1 immunized with LNP

description: Single-Cell V(D)J sequencing of mice10


title: Res19_RNA

description: 10x Genomics


title: BCR of mice_3 immunized with AALI

description: Single-Cell V(D)J sequencing of mice9

value: immunized with AALI


title: U1-driven PspCas13b EGFP crRNA#1 extended (5' RACE, Exp#2)

description:
5RACE-B07-pEZ114
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: BEAS-2B cells, LPS treatment

value: Lung; Bronchus

value: epithelial cell

value: wild type

value: LPS


title: U1-driven Cas13bt1 EGFP crRNA#1 +1T (5' RACE, Exp#2)

description:
5RACE-B04-pEZ112
Cheng_Suppl_Table3_5RACE_v1.xlsx

value: Transfection of crRNA-expressing plasmids


title: Res17_VDJ

description: VDJ TCR

value: Brain Metastases

value: CD45+ TILS and CD8+ TILS

value: No treatment


title: BCR of mice_2 immunized with AALI

description: Single-Cell V(D)J sequencing of mice8


title: U1-driven Cas13bt1 EGFP crRNA#1 +1C (5' RACE, Exp#2)

description:
5RACE-B03-pEZ111
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res17_RNA

description: 10x Genomics

value: NSCLC

value: Untreated


title: Res16_VDJ

description: VDJ TCR

value: Breast


title: Res18_RNA

description: 10x Genomics

value: Neuroendocrine


title: BCR of mice_1 immunized with AALI

description: Single-Cell V(D)J sequencing of mice7

value: spleen


title: U1-driven Cas13bt1 EGFP crRNA#1 +1G (5' RACE, Exp#2)

description:
5RACE-B02-pEZ110
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res16_RNA

description: 10x Genomics


title: TCR of mice_3 immunized with LNP

description: Single-Cell V(D)J sequencing of mice6

value: splenic cells


title: Res15_VDJ

description: VDJ TCR

value: Melanoma


title: U1-driven PspCas13b EGFP crRNA#1 (5' RACE, Exp#2)

description:
5RACE-B06-pEZ113
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res15_RNA

description: 10x Genomics


title: U1-driven Cas13bt1 EGFP crRNA#1 (5' RACE, Exp#2)

description:
5RACE-B01-pEZ108
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res18_VDJ

description: VDJ TCR


title: Res13_VDJ

description: VDJ TCR

value: Pancreatic


title: TCR of mice_2 immunized with LNP

description: Single-Cell V(D)J sequencing of mice5

value: tissue

value: immunized with LNP


title: Res13_RNA

description: 10x Genomics


title: U1-driven Cas13bt1 EGFP crRNA#1 extended (5' RACE, Exp#1)

description:
5RACE-A04-pEZ109
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res12_VDJ

description: VDJ TCR


title: Res12_RNA

description: 10x Genomics


title: U1-driven Cas13bt1 EGFP crRNA#1 (5' RACE, Exp#1)

description:
5RACE-A03-pEZ108
Cheng_Suppl_Table3_5RACE_v1.xlsx


title: Res11_VDJ

description: VDJ TCR

value: Prostate


title: TCR of mice_3 immunized with AALI

description: Single-Cell V(D)J sequencing of mice3

value: immunized with AALI


title: U6-driven CasRx EGFP crRNA#2 (3' RACE, Exp#2)

description:
3RACE-B10-pEZ20
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: TCR of mice_1 immunized with LNP

description: Single-Cell V(D)J sequencing of mice4


title: Res11_RNA

description: 10x Genomics


title: TCR of mice_2 immunized with AALI

description: Single-Cell V(D)J sequencing of mice2


title: Res10_RNA

description: 10x Genomics

value: Germ cell


title: Res9_Res22_VDJ

description: VDJ TCR

value: Germ cell/RR

value: Untreated/Untreated


title: U1-driven Cas13bt1 EGFP crRNA#1 extended (3' RACE, Exp#2)

description:
3RACE-B09-pEZ109
Cheng_Suppl_Table2_3RACE_v1.xlsx

value: Transfection of crRNA-expressing plasmids


title: TCR of mice_1 immunized with AALI

description: Single-Cell V(D)J sequencing of mice1


title: Res10_VDJ

description: VDJ TCR

value: Brain Metastases

value: CD45+ TILS and CD8+ TILS

value: No treatment


title: Res9_Res22_RNA

description: 10x Genomics


title: scRNA-seq of mice_3 immunized with LNP

description: scRNA-seq of mice6


title: Res8_VDJ

description: VDJ TCR

value: NSCLC

value: Untreated


title: U1-driven PspCas13b EGFP crRNA#1 extended (3' RACE, Exp#2)

description:
3RACE-B07-pEZ114
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: Res7_VDJ

description: VDJ TCR


title: scRNA-seq of mice_2 immunized with LNP

description: scRNA-seq of mice5

value: spleen


title: Res8_RNA

description: 10x Genomics


title: Res7_RNA

description: 10x Genomics


title: scRNA-seq of mice_1 immunized with LNP

description: scRNA-seq of mice4

value: splenic cells


title: U1-driven CasRx KRAS crRNA#2 (3' RACE, Exp#2)

description:
3RACE-B05-pEZ107
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: Res5_RNA

description: 10x Genomics

value: Breast


title: Res4_RNA

description: 10x Genomics

value: Melanoma


title: U1-driven CasRx KRAS crRNA#1 (3' RACE, Exp#2)

description:
3RACE-B04-pEZ106
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: Res2_VDJ

description: VDJ TCR


title: pSRS20_VDJ

description: VDJ TCR

value: Adrenal

value: Steroid B

value: Irradiation


title: scRNA-seq of mice_3 immunized with AALI

description: scRNA-seq of mice3

value: tissue

value: immunized with AALI


title: pSRS20_RNA

description: 10x Genomics


title: scRNA-seq of mice_2 immunized with AALI

description: scRNA-seq of mice2


title: U1-driven CasRx EGFP crRNA#2 extended (3' RACE, Exp#2)

description:
3RACE-B03-pEZ105
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: pSRS19_RNA

description: 10x Genomics


title: U1-driven CasRx EGFP crRNA#2 (3' RACE, Exp#2)

description:
3RACE-B02-pKW151
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: scRNA-seq of mice_1 immunized with AALI

description: scRNA-seq of mice1


title: Res2_RNA

description: 10x Genomics


title: pSRS17_RNA

description: 10x Genomics

value: Steroid A


title: U1-driven CasRx EGFP crRNA#2 w/ SL4 (3' RACE, Exp#2)

description:
3RACE-B01-pEZ17
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: pSRS17_VDJ

description: VDJ TCR


title: U1-driven Cas13bt1 EGFP crRNA#1 (3' RACE, Exp#2)

description:
3RACE-B08-pEZ108
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: U1-driven PspCas13b EGFP crRNA#1 (3' RACE, Exp#2)

description:
3RACE-B06-pEZ113
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: pSRS15_RNA

description: 10x Genomics


title: U1-driven CasRx EGFP crRNA#2 (3' RACE, Exp#1)

description:
3RACE-A01-pKW151
Cheng_Suppl_Table2_3RACE_v1.xlsx


title: Lung CD31+ cells, HO, rep3

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

data_processing:
FASTQ files were aligned to the genome (GRCm39) with HISAT2 (v2.2.1). Gene counts were obtained with FeatureCounts in Subread tool(v2.0.6). DESeq2 was used for differential expression testing.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file for raw count table

source_name: whole lung from postnatal day 7

extract_protocol:
Lung tissues were harvested and placed into 1.5 ml microcentrifuge tubes. Subsequently, 1 ml of digestion solution was added (50 μg/ml Liberase TM(Sigma) in RPMI1640 culture medium (Gibco)). The lung tissue was finely minced with scissors and incubated at 37°C on a rotary shaker at 300 rpm for 30 minutes, tissues were then transferred to C-tubes, and single-cell suspension was obtained using the GentleMACS Dissociator (Miltenyi). Cell pellet was collected by centrifugation at 300g for 5 minutes in FACS Buffer (1 mM EDTA, 25 mM HEPES, 0.5% BSA in DPBS). 100 μL of FcR (BioLegend, 101302, 1:200) blocking solution was then added, and incubated at 4°C for 45 minutes. Cells were incubated with anti-mouse CD31-micro beads (MiltenylBiotec, 130-097-418), at 4°C for 45 minutes. Magnetic columns were balanced with FACS Buffer, and the cell-bead suspension was applied to the column on a magnetic field to obtain CD31+ endothelial cells.
RNA-seq library was prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina from Vazyme according to the manufacture's instruction.

value: whole lung from postnatal day 7

value: CD31+ lung endothelial cells

value: HO


title: Lung CD31+ cells, HO, rep2


title: Res5_VDJ

description: VDJ TCR

value: Brain Metastases

value: CD45+ TILS and CD8+ TILS


title: U1-driven CasRx EGFP crRNA#2 extended (3' RACE, Exp#1)

description:
3RACE-A02-pEZ105
Cheng_Suppl_Table2_3RACE_v1.xlsx

value: Transfection of crRNA-expressing plasmids


title: pSRS19_VDJ

description: VDJ TCR


title: Res4_VDJ

description: VDJ TCR

value: No treatment

value: Untreated


title: Lung CD31+ cells, RA, rep3

value: RA


title: pSRS12_VDJ

description: VDJ TCR

value: NSCLC


title: pSRS12_RNA

description: 10x Genomics


title: pSRS11_VDJ

description: VDJ TCR

value: Melanoma


title: Lung CD31+ cells, RA, rep2


title: pSRS11_RNA

description: 10x Genomics


title: pSRS10_VDJ

description: VDJ TCR

value: SCLC


title: Lung CD31+ cells, RA, rep1


title: pSRS10_RNA

description: 10x Genomics


title: HCC1806 cells, shASCT2, dox+,1

city: Kensington

first: Jeff

last: Holst

address: Cnr of High and Botany

institute: University of New South Wales

data_processing:
Adaptor reads and low quality base reads were removed by NovogeneAIT. Mapping and counting of reads were carried out by running modified STAR scripts (Dobin et al., 2013) in the computational cluster Katana (UNSW Sydney, Sydney).
Assembly: Human genome, GRCh38.p13 from Ensembl 101
Supplementary files format and content: Comma-separated values files includes raw reads for each file

growth_protocol: HCC1806 cells were maintained at 37°C at 5% CO2 in RPMI supplemented with 10 % (v/v) Sterile Foetal Bovine Serum (FBS) (Bovogen Biologicals, Melbourne, Australia) 1 % penicillin/streptomycin solution

extract_protocol:
RNA was extracted from 1 × 106 cells using TRIzolTM Reagent (InvitrogenTM). Two biological replicates of each sample. Quality control involved nanodrop quantitation, gel electrophoresis and Agilent 2100 for RNA integrity.
mRNA is enriched using Oligo dT beads followed by manufacturer's protocol for cDNA synthesis.

value: Triple negative breast cancer cells

value: ASCT2 KD


title: pSRS9_VDJ

description: VDJ TCR

value: Steroid B

value: Irradiation


title: pSRS15_VDJ

description: VDJ TCR


title: HCC1806 cells, shCtrl, dox+, 2

value: WT


title: pSRS7_Res6_VDJ

description: VDJ TCR

value: NSCLC/Sarcoma

value: Steroid B/Untreated

value: Irradiation/Untreated


title: HCC1806 cells, ASCT2 K6, 2

value: ASCT2 KO


title: c-MYC/FOXO1AAA1

city: Honolulu

first: Xue

state: Hawaii

address: 701 Ilalo Street

institute: University of Hawaii Cancer Center

data_processing:
Poor quality reads were trimmed using the fastq-mcf (1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Mm.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
Only the genes having CPM values above 0.5 in at least two libraries were kept. Normalization by TMM (Trimmed mean of M values) was performed by using calcNormFactors function to eliminate composition biases between libraries.
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample

source_name: liver tumor tissue

growth_protocol: Hydrodynamic tail vein injections was used to deliver DNA specifically into the hepatocytes to create mouse HCC.Mice were housed and monitored according to protocols approved by the committee for animal research at the University of California, San Francisco (Protocol number AN185770) and the University of Hawaii Cancer Center.

extract_protocol:
Total RNA was extracted from mouse c-MYC/pT3 HCCs  (n=3) HCCs, c-MYC/pT3-FOXO1AAA (n=3) HCCs, and FVB wild-type normal livers (n=4) using the Quick-RNA Miniprep Kit (Zymo Research, CA, USA)
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA.

value: liver tumor tissue

tag: strain


title: c-MYC/FOXO1AAA2


title: c-MYC/FOXO1AAA3


title: HCC1806 cells, ASCT2 K6, 1


title: MYC tumor3


title: HCC1806 cells, shASCT2, dox+,2


title: HCC1806 cells, ASCT2 K5, 2


title: MYC tumor2


title: HCC1806 cells, ASCT2 K5, 1


title: pSRS9_RNA

description: 10x Genomics

value: Brain Metastases

value: CD45+ TILS and CD8+ TILS


title: pSRS6_VDJ

description: VDJ TCR

value: Steroid A


title: pSRS1_VDJ

description: VDJ TCR


title: pSRS2_VDJ

description: VDJ TCR


title: pSRS5_VDJ

description: VDJ TCR

value: Breast


title: pSRS1_RNA

description: 10x Genomics

value: NSCLC


title: pSRS6_RNA

description: 10x Genomics


title: pSRS5_RNA

description: 10x Genomics


title: pSRS7_Res6_RNA

description: 10x Genomics


title: HCC1806 cells, ASCT2 K4, 2


title: NL4

source_name: normal liver

value: normal liver


title: HCC1806 cells, shCtrl, dox+,1


title: HCC1806 cells, ASCT2 K4, 1


title: NL3


title: Lung CD31+ cells, HO, rep1

value: whole lung from postnatal day 7

value: CD31+ lung endothelial cells

value: HO


title: BEAS-2B_pl2_FOSL1_2_A, BEAS-2B, FOSL1

city: Ghent

first: Jasper

last: Anckaert

address: Corneel Heymanslaan 10

country: Belgium

institute: OncoRNAlab

data_processing:
high performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

growth_protocol: BEAS-2B cells were cultured in RPMI medium (Gibco) supplemented with 10% fetal calf serum, 100U/ml penicillin, 100 µg/ml streptomycin and 2mM glutamine (Gibco). HEK-293T cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin (Gibco) and 2mM L-glutamine (Gibco). Cell lines were grown in a 37°C humidified incubator under 5% CO2.

extract_protocol:
miRNEasy kit (Qiagen) with on-column Dnase treatment (Qiagen)
Library preparation for 3’-end shallow sequencing was performed using the Quantseq 3’ mRNA-seq library prep kit from Lexogen and following the manufacturer’s instructions
Library preparation for total RNA sequencing was done using the SMARTer® Stranded Total RNA-Seq Kit v3 kit from Takara following the manufacturer’s instructions

treatment_protocol:
DEP was dissolved in saline at a concentration of 1000 µg/ml. LPS(Sigma Aldrich) and TNF-α (Thermo Fisher) were dissolved in PBS at respectively 1000 µg/ml and 0.05 µg/µl. Total volume per well was always 200 µl. Exposures were done 24 hours after seeding or 48 hours after selection. Supernatans was collected and cells were lysed 24 hours after exposure.
dCas9-KARB-MeCP2 was introduced into the BEAS-2B cells by transfecting PiggyBac transposase (from System Biosciences) and dCas9-KRAB-MeCP2 plasmid (#110821 from addgene) simultaneously using CRISPRmax (from ThermoFisher). 24 hours after transfection cells were selected with 6 µg/ml blasticidin. dCas9-KRAB-MeCP2 presence was confirmed using immunoblotting and qPCR.


title: BEAS-2B_pl2_HSPA9_2_B, BEAS-2B, HSPA9


title: BEAS-2B_pl2_FOSL1_2_B, BEAS-2B, FOSL1


title: NL2


title: BEAS-2B_pl2_FOSL1_2_C, BEAS-2B, FOSL1


title: HCC1806 cells, ASCT2 K3, 2

value: Triple negative breast cancer cells


title: BEAS-2B_pl2_HSPA9_2_C, BEAS-2B, HSPA9


title: BEAS-2B_pl2_HSPA9_2_A, BEAS-2B, HSPA9


title: pSRS2_RNA

description: 10x Genomics

value: Irradiation


title: NL1

value: WT


title: HCC1806 cells, ASCT2 K3, 1


title: BEAS-2B_pl2_ATF4_2_C, BEAS-2B, ATF4


title: BEAS-2B_pl2_ATF4_2_B, BEAS-2B, ATF4


title: MYC tumor1


title: HCC1806 cells, ASCT2 K2, 2


title: HCC1806 cells, ASCT2 K2, 1


title: BEAS-2B_pl2_NC34_B, BEAS-2B, NC

value: NC


title: EVE treatment2

city: Xi'an

first: Yi

last: Zhou

state: Shaanxi

address: 277# Yanta West Road

institute: The First Affiliated Hospital of Xi'an Jiaotong university

description:
EVE_2
Processed data_Tissue fpkm.csv

extract_protocol:
Total RNA was extracted from mouse c-MYC/MCL1/RictorKOTsc2KO HCCs treated with MLN0128 (n=3), everolimus (n=3), vehicle (n=3) as well as C57BL/6 wild-type normal livers (n=3) using the Quick-RNA Miniprep Kit (Zymo Research, CA, USA)
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA.

treatment_protocol: MLN0128 (1mg/kg/day), everolimus (1mg/kg/day) or vehicle was orally administered via gavage for 3 weeks (6 days a week) starting 6 days after plasmid injection, respectively. Mice were sacrificed 3.7 weeks after hydrodynamic injection (3 weeks after treatment)

value: everolimus


title: EVE treatment3

description:
EVE_3
Processed data_Tissue fpkm.csv


title: BEAS-2B_pl2_NEAT1_seq_C, BEAS-2B, NEAT1_seq


title: HCC1806 cells, ASCT2 K1, 2


title: BEAS-2B_pl2_NC34_A, BEAS-2B, NC


title: BEAS-2B_pl2_NEAT1_seq_B, BEAS-2B, NEAT1_seq


title: BEAS-2B_pl2_ATF4_2_A, BEAS-2B, ATF4


title: EVE treatment1

description:
EVE_1
Processed data_Tissue fpkm.csv


title: BEAS-2B_pl2_NC34_C, BEAS-2B, NC


title: HCC1806 cells, ASCT2 K1, 1

value: KO


title: BEAS-2B_pl2_NEAT1_seq_A, BEAS-2B, NEAT1_seq


title: BEAS-2B_pl2_FOSL1_1_C, BEAS-2B, FOSL1


title: BEAS-2B_pl2_LYAR_1_B, BEAS-2B, LYAR

value: LYAR


title: HCC1806 cells, ASCT2 KO, 1


title: BEAS-2B_pl2_FOSL1_1_B, BEAS-2B, FOSL1


title: MLN treatment3

description:
INK_3
Processed data_Tissue fpkm.csv

value: liver tumor tissue


title: MLN treatment1

description:
INK_1
Processed data_Tissue fpkm.csv


title: BEAS-2B_pl2_FOSL1_1_A, BEAS-2B, FOSL1


title: BEAS-2B_pl2_LYAR_1_C, BEAS-2B, LYAR


title: HCC1806 cells, wildtype,1


title: HCC1806 cells, wildtype,2


title: BEAS-2B_pl2_JUN_2_C, BEAS-2B, JUN

value: JUN


title: MYC tumor2

description:
T_2
Processed data_Tissue fpkm.csv

value: vehicle


title: MYC tumor3

description:
T_3
Processed data_Tissue fpkm.csv


title: HCC1806 cells, ASCT2 KO, 2


title: BEAS-2B_pl2_LYAR_1_A, BEAS-2B, LYAR


title: BEAS-2B_pl2_JUN_2_B, BEAS-2B, JUN


title: BEAS-2B_pl2_JUN_2_A, BEAS-2B, JUN


title: MYC tumor1

description:
T_1
Processed data_Tissue fpkm.csv


title: Inflammatory Knockout Astrocytes rep 2

city: Houston

first: Robert

last: Krencik

state: Texas

address: 6670 Bertner Ave

department: Department of Neurosurgery, Center of Neuroregeneration

institute: Houston Methodist

data_processing:
DESeq2 R package
Assembly: Ensembl GRCh38.p14
Supplementary files format and content: FPKMs for all samples

source_name: Induced astrocytes

extract_protocol:
Direct-zol RNA kit (Zymo) with on-column Dnase treatment
Novogene Eukaryotic RNA-seq (cDNA library), NEB poly-A selected

treatment_protocol: With or without ITC treatment

value: Induced astrocytes

value: GBA Knockout

value: ITC (inflammatory)


title: BEAS-2B_pl2_NAT10_2_B, BEAS-2B, NAT10


title: BEAS-2B_pl2_NAT10_2_C, BEAS-2B, NAT10


title: Inflammatory Knockout Astrocytes rep 3


title: Inflammatory Knockout Astrocytes rep 1


title: MLN treatment2

description:
INK_2
Processed data_Tissue fpkm.csv


title: NL2

description:
NL_2
Processed data_Tissue fpkm.csv

value: normal liver


title: Knockout Astrocytes rep 3

value: DMSO (sham)


title: BEAS-2B_pl2_SNAI2_1_B, BEAS-2B, SNAI2


title: BEAS-2B_pl2_SNAI2_1_A, BEAS-2B, SNAI2


title: Knockout Astrocytes rep 2


title: BEAS-2B_pl2_HSPA9_1_A, BEAS-2B, HSPA9


title: BEAS-2B_pl2_HSPA9_1_B, BEAS-2B, HSPA9


title: NL1

description:
NL_1
Processed data_Tissue fpkm.csv


title: BEAS-2B_pl2_HSPA9_1_C, BEAS-2B, HSPA9


title: BEAS-2B_pl2_SNAI2_1_C, BEAS-2B, SNAI2


title: Knockout Astrocytes rep 1


title: Ovary, Chek2KO, IR

city: Bar Harbor

first: Ewelina

last: Bolcun-Filas

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina) and FASTQ files associated with the gene expression libraries were aligned to the GRCm38 release 93 reference assembly and annotations (10x Genomics mm10-3.0.0 reference) using the version 3.0.2 Cell Ranger multi pipeline (10x Genomics).
The potential doublets were removed by applying the DoubletFinder (RRID:SCR_018771) and DoubletDecon packages with default parameters. Only the cells marked as doublets by both the algorithms were removed.
The remaining QC-pass cells were analyzed using the Seurat package (RRID:SCR_016341) and batch-corrected using the Harmony package.
Assembly: 10x Genomics mm10-3.0.0 reference
Supplementary files format and content: mtx

source_name: ovary

extract_protocol:
Cells were washed and suspended in PBS containing [0.04% BSA] and immediately processed as follows. Cell viability was assessed on a Countess II automated cell counter (ThermoFisher), and up to 12,000 cells were loaded onto one lane of a 10X Chromium X. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform version 3.1 single-indexed chemistry and according to the manufacturer’s protocol (#CG000204).
Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform version 3.1 single-indexed chemistry and according to the manufacturer’s protocol (#CG000204).

treatment_protocol: Female mice were irradiated with 0.5Gy (IR) or 0Gy (nonIR). Wildtype (WT) and Chek2-/- (CHEK2KO) mice were used in this study . Ovaries were collected at 6hrs after treatment for scRNA-sequencing. Ovaries were first incubated in collagenase IV (1mg/ml, Worthington) and DNAse (0.02%, Worthington) solution in HBSS. After 15 min incubation at 37ºC, trypsin was added to a final concentration of 0.125% and solution with ovaries was mixed by gentle pipetting. Following additional 10 min incubation at 37ºC trypsin was inactivated by adding FBS and solution with ovaries was mixed by gentle pipetting with a wide-bore tip to mechanically facilitate the dissociation of the tissue into a single-cell suspension. Cell suspensions were filtered with a 40μm mesh filter to remove debris and cell aggregates and spun down at 2000 rpm for 5 min in a swing-bucket centrifuge. Cell pellets were resuspended in 2% BSA PBS.

value: ovary

value: irradiated 0.5Gy


title: BEAS-2B_pl2_AATF_2_B, BEAS-2B, AATF

value: AATF


title: BEAS-2B_pl2_AATF_2_C, BEAS-2B, AATF


title: BEAS-2B_pl2_DKC1_2_C, BEAS-2B, DKC1


title: Ovary, WT, IR

value: wildtype


title: Wildtype Astrocytes rep 3

value: GBA Wildtype


title: Ovary, Chek2KO, nonIR

value: non-irradiated


title: BEAS-2B_pl2_NAT10_2_A, BEAS-2B, NAT10


title: BEAS-2B_pl2_DKC1_2_B, BEAS-2B, DKC1


title: NL3

description:
NL_3
Processed data_Tissue fpkm.csv

value: WT


title: BEAS-2B_pl2_AATF_2_A, BEAS-2B, AATF


title: Wildtype Astrocytes rep 1


title: Ovary, WT, nonIR


title: BEAS-2B_pl2_DKC1_2_A, BEAS-2B, DKC1


title: BEAS-2B_pl2_SBDS_1_C, BEAS-2B, SBDS

value: SBDS


title: BEAS-2B_pl2_SBDS_1_B, BEAS-2B, SBDS


title: BEAS-2B_pl2_SBDS_1_A, BEAS-2B, SBDS


title: Wildtype Astrocytes rep 2


title: g-78

city: Shanghai

first: Xiaoshen

last: Zhang

state: Shanghai

address: 1239 siping road

institute: Tongji University

data_processing:
The data volume is about 5G/sample, and the proportion of base mass greater than 20 (Q20) in each direction is not less than 85%
HISAT2 was used for sequence alignment and HT-seq count was used fot generating read count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: bone metastasis

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Strand-specific libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina

value: bone metastasis

tag: disease state

tag: Stage

value: IV

tag: Sex

value: f

tag: driver gene_mutations

value: EGFR L859R


title: BEAS-2B_pl2_DKC1_1_C, BEAS-2B, DKC1

tag: cell line


title: BEAS-2B_pl2_DKC1_1_B, BEAS-2B, DKC1


title: BEAS-2B_pl2_Not_treated_C, BEAS-2B, NT

value: NT


title: BEAS-2B_pl2_DKC1_1_A, BEAS-2B, DKC1


title: g-1516

tag: tissue

value: m

value: EGFR L858R


title: BEAS-2B_pl2_Not_treated_B, BEAS-2B, NT


title: g-56

value: Kras+


title: 39˚C iTreg Replicate 3

city: Nashville

first: Jeffrey

last: Rathmell

state: Tennessee

address: 110 21st Avenue South

institute: Vanderbilt University

data_processing:
Prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, following the manufacturer's protocols.
150 bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50M reads per sample.  Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 was subjected to quality control analysis, including read quality assessment.
Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments.
Assembly: MM10
Supplementary files format and content: a tab-separated file containing the read counts for genes

source_name: Purified T-cell

growth_protocol: Cells were cultured in complete RPMI supplemented with 10% FBS, glutamine, and pen/strep.

extract_protocol:
CD4+T cells from WT mice were isolated and stimulated for 4 days with αCD3/αCD28 as described above. Cells were washed with cold PBS and RNA extraction was conducted with DNAse treatment according to the RNeasy Plus Mini kit (Qiagen).
Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit (NEB) (P/N: E7765L) following the manufacturer’s instructions.  End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument.

value: Purified T-cell

value: male


title: 39˚C iTreg Replicate 4


title: BEAS-2B_pl2_NC12_C, BEAS-2B, NC

value: NC


title: BEAS-2B_pl2_NC12_B, BEAS-2B, NC


title: 39˚C iTreg Replicate 2


title: g-910


title: 39˚C iTreg Replicate 6


title: BEAS-2B_pl2_WDR43_1_C, BEAS-2B, WDR43


title: 37˚C iTreg Replicate 6


title: g-34

value: EGFR 19del


title: 39˚C iTreg Replicate 1


title: BEAS-2B_pl2_NC12_A, BEAS-2B, NC


title: g-1718


title: BEAS-2B_pl2_PNO1_1_C, BEAS-2B, PNO1


title: 37˚C iTreg Replicate 5


title: BEAS-2B_pl2_PNO1_1_B, BEAS-2B, PNO1


title: 39˚C iTreg Replicate 5


title: BEAS-2B_pl2_PNO1_1_A, BEAS-2B, PNO1


title: g-1314


title: 37˚C iTreg Replicate 4


title: BEAS-2B_pl2_PNO1_2_C, BEAS-2B, PNO1


title: BEAS-2B_pl2_Not_treated_A, BEAS-2B, NT


title: lu-b-10

source_name: lung

value: lung


title: 37˚C iTreg Replicate 3


title: BEAS-2B_pl2_PNO1_2_A, BEAS-2B, PNO1


title: BEAS-2B_pl2_PNO1_2_B, BEAS-2B, PNO1


title: lu-f-9

value: lung Intrathoracic


title: BEAS-2B_pl2_ATF4_1_C, BEAS-2B, ATF4


title: 37˚C iTreg Replicate 2


title: BEAS-2B_pl2_WDR43_1_B, BEAS-2B, WDR43


title: lu-b-9


title: BEAS-2B_pl2_WDR43_1_A, BEAS-2B, WDR43


title: 39˚C Th17 Replicate 6


title: BEAS-2B_pl2_AATF_1_B, BEAS-2B, AATF

value: AATF


title: BEAS-2B_pl2_ATF4_1_B, BEAS-2B, ATF4


title: BEAS-2B_pl2_AATF_1_C, BEAS-2B, AATF


title: BEAS-2B_pl2_AATF_1_A, BEAS-2B, AATF


title: g-1112


title: lu-b-8

value: ALK+


title: 39˚C Th17 Replicate 5

value: WT


title: lu-f-8


title: lu-f-7


title: BEAS-2B_pl2_NFkB_17_A, BEAS-2B, NFkB

value: NFkB


title: BEAS-2B_pl2_NFkB_17_B, BEAS-2B, NFkB


title: 39˚C Th17 Replicate 4


title: lu-f-6 (f15)

value: IV


title: BEAS-2B_pl2_NEAT1_C, BEAS-2B, NEAT1


title: BEAS-2B_pl2_NEAT1_B, BEAS-2B, NEAT1


title: lu-b-6

value: bone metastasis


title: 39˚C Th17 Replicate 2


title: BEAS-2B_pl2_NAT10_1_B, BEAS-2B, NAT10


title: BEAS-2B_pl2_ATF4_1_A, BEAS-2B, ATF4


title: 37˚C iTreg Replicate 1


title: 39˚C Th17 Replicate 3


title: BEAS-2B_pl2_NAT10_1_A, BEAS-2B, NAT10


title: BEAS-2B_pl2_NEAT1_A, BEAS-2B, NEAT1


title: BEAS-2B_pl2_NAT10_1_C, BEAS-2B, NAT10


title: BEAS-2B_pl2_NFkB_17_C, BEAS-2B, NFkB


title: lu-f-6 (f12)

value: f


title: BEAS-2B_pl2_NC12_+_not_treated_C, BEAS-2B, NC_NT


title: 39˚C Th17 Replicate 1


title: 37˚C Th17 Replicate 5


title: BEAS-2B_pl2_NC12_+_not_treated_A, BEAS-2B, NC_NT


title: BEAS-2B_pl2_NC12_+_not_treated_B, BEAS-2B, NC_NT


title: 37˚C Th17 Replicate 6


title: BEAS-2B_pl2_JUN_1_C, BEAS-2B, JUN

value: JUN


title: BEAS-2B_pl2_JUN_1_B, BEAS-2B, JUN


title: lu-f-5

value: m


title: lu-b-5


title: BEAS-2B_pl2_WDR43_2_C, BEAS-2B, WDR43


title: lu-f-4

value: EGFR L858R


title: BEAS-2B_pl2_JUN_1_A, BEAS-2B, JUN


title: 37˚C Th17 Replicate 4


title: BEAS-2B_pl2_WDR43_2_B, BEAS-2B, WDR43


title: lu-b-7


title: 37˚C Th17 Replicate 3


title: BEAS-2B_pl2_WDR43_2_A, BEAS-2B, WDR43


title: lu-b-4


title: BEAS-2B_pl2_SBDS_2_C, BEAS-2B, SBDS

value: SBDS


title: 37˚C Th17 Replicate 2

value: Purified T-cell


title: BEAS-2B_pl2_SBDS_2_A, BEAS-2B, SBDS


title: lu-f-3


title: BEAS-2B_pl2_SBDS_2_B, BEAS-2B, SBDS


title: 37˚C Th17 Replicate 1

value: male


title: BEAS-2B_pl2_SNAI2_2_B, BEAS-2B, SNAI2


title: BEAS-2B_pl2_SNAI2_2_A, BEAS-2B, SNAI2


title: 39˚C Th0 Replicate 6


title: lu-f-1

value: EGFR exon 20 ins


title: BEAS-2B_pl2_LYAR_2_C, BEAS-2B, LYAR

value: LYAR


title: 39˚C Th0 Replicate 5


title: BEAS-2B_pl2_LYAR_2_B, BEAS-2B, LYAR


title: lu-b-3

value: lung


title: 39˚C Th0 Replicate 4


title: BEAS-2B_pl1_MSTRG.36534_2_C, BEAS-2B, MSTRG.36534


title: BEAS-2B_pl1_MSTRG.36534_2_B, BEAS-2B, MSTRG.36534


title: lu-b-2


title: 39˚C Th0 Replicate 3


title: 39˚C Th0 Replicate 2


title: lu-b-1

value: EGFR 19del


title: BEAS-2B_pl1_LINC00973_2_B, BEAS-2B, LINC00973


title: BEAS-2B_pl1_LINC00973_2_C, BEAS-2B, LINC00973


title: 39˚C Th0 Replicate 1


title: BEAS-2B_pl2_SNAI2_2_C, BEAS-2B, SNAI2


title: lu-f-2

value: lung Intrathoracic


title: BEAS-2B_pl1_MSTRG.3621_2_B, BEAS-2B, MSTRG.3621


title: BEAS-2B_pl1_LINC00973_2_A, BEAS-2B, LINC00973


title: HUVECs Bsi1

first: Jieyu

last: Guo

address: 138 Yixueyuan Rd,

institute: fudan university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hista2
fragments per kilobase of transcript per million fragments mapped (FPKM)were calculated used by cuffinks
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: HUVECs Bsi

growth_protocol: HUVEC cells were maintained with ECM at 37 °C in a humidiﬁed incubator with 5% CO2, and were passaged when about 70-90% intensity.

extract_protocol:
Total RNA was extracted using Trizol reagent
non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module, and sequencing libraries were prepared by using the TrueLib mRNA Library Prep Kit for Illumina

treatment_protocol: HUVEC cells were treated with consiRNA or Bach1 siRNA

value: HUVECs

value: Human umbilical vein endothelial cells

value: Bach1 siRNA


title: 37˚C Th0 Replicate 6

value: WT


title: BEAS-2B_pl1_MSTRG.3621_2_A, BEAS-2B, MSTRG.3621


title: BEAS-2B_pl1_NFkB_17_B, BEAS-2B, NFkB

value: NFkB


title: BEAS-2B_pl1_NFkB_17_C, BEAS-2B, NFkB


title: HUVECs Con2

source_name: HUVECs Con

value: Con siRNA


title: 37˚C Th0 Replicate 5


title: HUVECs Con1


title: BEAS-2B_pl1_NFkB_17_A, BEAS-2B, NFkB


title: BEAS-2B_pl1_NEAT1_seq_B, BEAS-2B, NEAT1_seq


title: 37˚C Th0 Replicate 4


title: 293T-shCFIm25-2-8h

city: wuhan

first: linjian

last: xia

address: wuhan

institute: wuhan University

data_processing:
Quality control of Ψ-RIP Seq data was performed using FastQC. Low quality bases and adaptor contamination were deleted by Trimmomatic (v. 0.33.0) . Raw Sequencing reads were aligned using Hisat2 (v. 2.1.0) to the hg38, mm10, dm6 or spike-in reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools (v. 1.7)  to remove the reads with mapping quality below 30. METPEAK was used to identify peaks .
For RIP-seq, reads mapping and processing were performed as described for Ψ-RIP Seq data above. MACS2  was used to identify peaks.
For RNA-seq,  reads mapping and processing were performed as described for Ψ-RIP Seq data above. FeatureCounts (v. 1.6.3) was used to calculate the number of reads mapped to each gene. Dapars were used to calculate APA events.
Genome_build: hg38/mm10/dm6

growth_protocol: HEK293T and HeLa cells were grown in DMEM medium (C11995500BT, Gibco) containing 10% FBS (Biological Industries) and 1% Penicillin-Streptomycin (15140-122, Gibco) at 37°C with 5% CO2. Mouse embryonic stem cells (mESCs) E14TG2a were cultured with N2 (17502048, Gibco), B27 (17504044, Gibco) base medium supplemented with 1× GlutaMAX (35050061, Gibco), 1× MEM Non-Essential Amino Acids (11140050, Gibco), 0.15 mM L-thioglycerol (M6145, Sigma), 1% Penicillin-Streptomycin (15140-122, Gibco), 25 μg/ml BSA (A1933, Sigma), 1μM MEK inhibitor PD0325901 (S1036, Selleck Chemicals), 3μM GSK3β inhibitor CHIR99021 (S1263, Selleck Chemicals), 2% KOSR (A3181502, Gibco) and 1000 U/ml ESGRO leukemia inhibitory factor LIF (ESG1107, Millipore) on plates coated with 0.2% gelatin (V900863, Sigma) at 37°C with 5% CO2.

extract_protocol:
For RNA-seq, total RNA was extracted with TRNzol reagent (DP424, Tiangen). For Ψ-RIP seq, total RNA was extracted with TRNzol reagent (DP424, Tiangen). mRNA was isolated from the total RNA using the Dynabeads mRNA Purification Kit (61006, Invitrogen) for two round of poly(A)+ RNA selection and then using the RiboMinus Transcriptome Isolation Kit (K155002, Invitrogen) for rRNA depletion. RNA was fragmented into 150-300 nt fragments and incubated with anti-Pseudouridine mAb (D347-3, MBL). Then the mixture was subjected to Dynabeads protein G binding. After washing, the bound RNA was eluted by competition with Pseudouridine (HY-113061, MCE). RNA was recovered with Hieff NGS RNA Cleaner (12602ES03, Yeasen). For CFIm25-RIP seq, flag-3C-HA-CFIm25 stable overexpression HEK293T cells were crosslinked in 0.5% formaldehyde containing PBS. After DNase I treated, sonicated, incubated with MonoRab Anti-DYKDDDDK Affinity Resin (L00766, GenScript) and extensive washed, RNA was eluted by Recombinant HRV 3C Protease (S3CP01, SinoBiological ) cleavage.
RNA-seq libraries were generated using  NEBNext Ultra II RNA Library Prep Kit (E7770, NEB ). RIP-seq libraries were generated using SMARTer Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian (Takara) following the manual.

treatment_protocol: NC/CFIm25 shRNA knockdown cells were generated by lentiviral infection and puromycin selection.

tag: protocol

value: RNA-seq

tag: replicate

value: Treated with Actinomycin D for 8 h


title: 37˚C Th0 Replicate 3

tag: genotype

tag: treatment


title: HUVECs Bsi2


title: BEAS-2B_pl1_NEAT1_seq_A, BEAS-2B, NEAT1_seq


title: BEAS-2B_pl1_MSTRG.36534_2_A, BEAS-2B, MSTRG.36534


title: 293T-shCFIm25-2-4h

value: Treated with Actinomycin D for 4 h


title: BEAS-2B_pl1_RRS1_1_C, BEAS-2B, RRS1


title: 37˚C Th0 Replicate 2


title: BEAS-2B_pl1_RRS1_1_B, BEAS-2B, RRS1


title: BEAS-2B_pl1_MSTRG.3621_2_C, BEAS-2B, MSTRG.3621


title: 293T-shCFIm25-2-0h

value: Treated with Actinomycin D for 0 h


title: BEAS-2B_pl1_RRS1_1_A, BEAS-2B, RRS1


title: BEAS-2B_pl1_DUSP6_1_C, BEAS-2B, DUSP6


title: BEAS-2B_pl1_DUSP6_1_B, BEAS-2B, DUSP6


title: 39˚C Naïve Replicate 6

value: Purified T-cell


title: 293T-shCFIm25-1-8h


title: BEAS-2B_pl1_DUSP6_1_A, BEAS-2B, DUSP6


title: 37˚C Th0 Replicate 1

value: male


title: 293T-shCFIm25-1-4h


title: BEAS-2B_pl1_NEAT1_seq_C, BEAS-2B, NEAT1_seq


title: BEAS-2B_pl1_TRIB3_2_C, BEAS-2B, TRIB3


title: 39˚C Naïve Replicate 4


title: 293T-shCFIm25-1-0h


title: BEAS-2B_pl1_TRIB3_2_A, BEAS-2B, TRIB3


title: BEAS-2B_pl1_TRIB3_2_B, BEAS-2B, TRIB3


title: 39˚C Naïve Replicate 5


title: BEAS-2B_pl1_Not_treated_B, BEAS-2B, NT

value: NT


title: BEAS-2B_pl1_Not_treated_C, BEAS-2B, NT


title: 39˚C Naïve Replicate 3


title: 293T-shNC2-4h

value: shNC


title: 293T-shNC2-8h


title: 293T-shNC2-0h


title: BEAS-2B_pl1_Not_treated_A, BEAS-2B, NT


title: BEAS-2B_pl1_MSTRG.66333_1_A, BEAS-2B, MSTRG.66333


title: BEAS-2B_pl1_MSTRG.66333_1_C, BEAS-2B, MSTRG.66333


title: 39˚C Naïve Replicate 2


title: 39˚C Naïve Replicate 1


title: BEAS-2B_pl1_RP11-221_1_C, BEAS-2B, RP11221


title: BEAS-2B_pl1_RP11-221_1_B, BEAS-2B, RP11221


title: BEAS-2B_pl1_MSTRG.66333_1_B, BEAS-2B, MSTRG.66333


title: 37˚C Naïve Replicate 6


title: 293T-shNC1-8h


title: 293T-shNC1-4h


title: BEAS-2B_pl1_NC34_B, BEAS-2B, NC

value: NC


title: BEAS-2B_pl1_NC34_C, BEAS-2B, NC


title: BEAS-2B_pl1_RP11-221_1_A, BEAS-2B, RP11221


title: 293T-shNC1-0h


title: 37˚C Naïve Replicate 4


title: CFIm25-Input2

description:
CFIm25-Input2.bw
fag-3C-HA-CFIm25 stable overexpression HEK293T cells

value: untreated

value: RIP

tag: rip reagent


title: 37˚C Naïve Replicate 3


title: BEAS-2B_pl1_NC34_A, BEAS-2B, NC


title: BEAS-2B_pl1_RRS1_2_C, BEAS-2B, RRS1


title: BEAS-2B_pl1_RRS1_2_B, BEAS-2B, RRS1


title: CFIm25-Input1

description:
CFIm25-Input1.bw
fag-3C-HA-CFIm25 stable overexpression HEK293T cells


title: 37˚C Naïve Replicate 2


title: BEAS-2B_pl1_MSTRG.3621_1_A, BEAS-2B, MSTRG.3621


title: BEAS-2B_pl1_MSTRG.3621_1_B, BEAS-2B, MSTRG.3621


title: BEAS-2B_pl1_MSTRG.3621_1_C, BEAS-2B, MSTRG.3621


title: 37˚C Naïve Replicate 1


title: CFIm25-IP2

description:
CFIm25-IP2.bw
fag-3C-HA-CFIm25 stable overexpression HEK293T cells

value: MonoRab Anti-DYKDDDDK Affinity Resin (L00767, GenScript).


title: BEAS-2B_pl1_CCND1_1_B, BEAS-2B, CCND1


title: Infected_TNFR2_HTO

city: Woolloongabba

first: Timothy

middle: Ryan

last: McCulloch

state: QLD

address: 37 Kent St

department: Frazer Institute

institute: University of Queensland

data_processing:
Pre-processing of raw sequencing data was performed using 10x Genomics Cell Ranger Multi pipeline (v7.1.0) to generate count matrices and demultiplex biological replicates.
The count output was loaded into R for further analysis usign the Seurat R function "Read10X".
Assembly: mm10
Supplementary files format and content: Output of Cell Ranger containing barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: Spleen

extract_protocol:
RNA was extracted using a Chromium Next GEM Single Cell 3' Reagent Kit v3.1 according to manufacturer instructions
Libraries were prepped using a Chromium Next GEM Single Cell 3' Reagent Kit v3.1 according to manufacturer instructions

treatment_protocol: Mice were infected with 5 x 10^6 CFU of Salmonella Typhimurium SL3261 by i.p. injection, and splenic NK cells isolated at day 4 post infection. NK cells were stained with TotalSeq HTO antibodies, pooled, and processed for scRNA-seq.

value: Spleen

value: NK cells

value: Ncr1Cre (KI/WT) Tnfrsf1b (flox/flox)

value: S. Typhimurium infected


title: BEAS-2B_pl1_CCND1_1_C, BEAS-2B, CCND1


title: 37˚C Naïve Replicate 5

value: WT


title: 293T-shCFIm25-Input2


title: BEAS-2B_pl1_CCND1_2_C, BEAS-2B, CCND1


title: BEAS-2B_pl1_CCND1_1_A, BEAS-2B, CCND1


title: BEAS-2B_pl1_CCND1_2_B, BEAS-2B, CCND1


title: Infected_TNFR2_GEX


title: 293T-shCFIm25-Input1


title: Infected_TNFR1_HTO

value: Ncr1Cre (KI/WT) Tnfrsf1a (flox/flox)


title: 293T-shCFIm25-IP2

value: anti-Pseudouridine mAb (D347-24, MBL)


title: BEAS-2B_pl1_SNHG15_1_C, BEAS-2B, SNHG15


title: BEAS-2B_pl1_SNHG15_1_B, BEAS-2B, SNHG15


title: BEAS-2B_pl1_RRS1_2_A, BEAS-2B, RRS1


title: Infected_TNFR1_GEX


title: 293T-shCFIm25-IP1

value: anti-Pseudouridine mAb (D347-23, MBL)


title: BEAS-2B_pl1_LINC00973_1_C, BEAS-2B, LINC00973


title: Infected_WT_HTO

value: Ncr1Cre (KI/WT)


title: BEAS-2B_pl1_LINC00973_1_B, BEAS-2B, LINC00973


title: BEAS-2B_pl1_SNHG15_1_A, BEAS-2B, SNHG15


title: CFIm25-IP1

description:
CFIm25-IP1.bw
fag-3C-HA-CFIm25 stable overexpression HEK293T cells

value: MonoRab Anti-DYKDDDDK Affinity Resin (L00766, GenScript).


title: 293T-shNC-Input2


title: Infected_WT_GEX


title: BEAS-2B_pl1_HMGA2_1_C, BEAS-2B, HMGA2


title: 293T-shNC-Input1


title: BEAS-2B_pl1_LINC00973_1_A, BEAS-2B, LINC00973


title: Naïve_WT_HTO


title: RNC S1WT-3

city: 上海

first: 利

last: 赵

state: State/Province

address: 梅陇路130号

institute: 华东理工大学

data_processing:
The obtained RNA-Seq library  was  sequenced on Illumina NovaSeq 6000.
Low-quality reads were trimmed by using Cutadapt (v4.3).
Assembly: Escherichia coli K-12 MG1655 (NCBI,ASM584v2)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria

growth_protocol: LB（Luria-Bertani） medium

extract_protocol:
Bacterial samples were treated with pre-chilled cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer): 20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200 mM KCl, 100 𝜇g/ml cycloheximide, and 2 mM dithiothreitol]. After a 30 min ice bath, cell lysates were collected and transferred to pre-chilled 1.5 mL tubes. After that, cell debris was removed by centrifuging at 4 °C for 10 min. Supernatants were transferred to the surface of sucrose buffer (30% sucrose in ribosome buffer), then ultracentrifuged at 4°C by T-865 fixed angle rotor (ThermoFisher, Germany) to pellet RNCs. Pellets were then resuspended with RB buffer.
Isolation of total RNA was carried out by the Trizol Reagent (Invitrogen, USA) according to the manufacturer's instructions. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer’s instructions.

treatment_protocol: When strains  cultrued to OD600 0.6，1mM IPTG was added to the strains. After induction for 3h, strains were collected respectively.

value: bacteria

value: S1 overexpression


title: RNC S1WT-2


title: Naïve_WT_GEX


title: BEAS-2B_pl1_CCND1_2_A, BEAS-2B, CCND1


title: BEAS-2B_pl1_HMGA2_1_A, BEAS-2B, HMGA2


title: 293T-shNC-IP1

value: shNC

value: anti-Pseudouridine mAb (D347-19, MBL)


title: RNC S1WT-1


title: C57BL/6, Pink1 KO, 5

city: Seoul

first: HAN SAI

last: LEE

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

institute: Seoul National University Seoul Metropolitan Government Boramae Medical Center

data_processing:
RNA sequencing was conducted on an Illumina NovaSeq 6000 platform.
Sequenced reads were trimmed using Trimmomatic v0.39 before mapping
Trimmed sequence reads were mapped on mm10 mouse reference genome using STAR alinger v2.7.4
Mapped sequence reads were quantified using RSEM v1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RSEM generated FPKM results values for each Sample

source_name: Thyroid glands

extract_protocol:
Total RNA was extracted from dissected mouse thyroids using NucleoZOL (Macherey Nagel, Düren, Germany) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following the manufacturer’s instructions.

value: Thyroid glands

value: Pink1 Knock-out

tag: age


title: BEAS-2B_pl1_HMGA2_2_C, BEAS-2B, HMGA2


title: RNC S1K247Q-3


title: T24_COMB_4

city: BRONX

first: Fabien

last: Delahaye

address: 1300 Morris Park Avenue

department: Genetics

institute: AECOM

data_processing:
RNAseq reads were aligned to human genome Hg38 using STAR
Normalization and Comparative analysis were performed with DESeq2 (v 1.10.1)
Genome_build: Hg38
Supplementary_files_format_and_content: count files

source_name: HeLa cells

growth_protocol: HeLa cells were grown in monolayer culture at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s (DMEM) GlutaMAX™, high glucose, pyruvate medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
Total RNA of HeLa cells was extracted using the NucleoSpin® RNA extraction (Macherey-Nagel, Hoerdt, France)
TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: HeLa cells were treated with DMSO, 20nM carfilzomib (CFZ), 15µM of compound 1a (CPD 1a) or the combination of these two compounds for 0h, 8h or 24h

value: Cervix

value: HeLa

tag: passage

tag: time (hours)

value: combination


title: C57BL/6, Pink1 KO, 4


title: T24_COMB_3


title: RNC S1K247Q-2


title: BEAS-2B_pl1_HMGA2_2_A, BEAS-2B, HMGA2


title: C57BL/6, Pink1 KO, 3


title: RNC S1K247Q-1


title: T24_COMB_2


title: 293T-shNC-IP2

value: RIP

value: anti-Pseudouridine mAb (D347-20, MBL)

value: untreated


title: BEAS-2B_pl1_HMGA2_1_B, BEAS-2B, HMGA2


title: BEAS-2B_pl1_NFATC2_1_C, BEAS-2B, NFATC2


title: RNA S1WT-3


title: C57BL/6, Pink1 KO, 1


title: T24_CF7_4


title: T24_COMB_1


title: RNA S1WT-1


title: C57BL/6, Pink1 WT, 4

value: Pink1 Wild type


title: T24_CF7_3


title: RNA S1WT-2


title: BEAS-2B_pl1_NFATC2_1_A, BEAS-2B, NFATC2


title: C57BL/6, Pink1 WT, 5


title: BEAS-2B_pl1_NC12_+_not_treated_C, BEAS-2B, NC_NT


title: C57BL/6, Pink1 WT, 3


title: T24_CF7_2


title: BEAS-2B_pl1_NC12_+_not_treated_B, BEAS-2B, NC_NT


title: BEAS-2B_pl1_HMGA2_2_B, BEAS-2B, HMGA2


title: RNA S1K247Q-3


title: RNA S1K247Q-2


title: T24_CF7_1


title: C57BL/6, Pink1 KO, 2


title: C57BL/6, Pink1 WT, 2


title: RNA S1K247Q-1


title: T24_CPD1A_4


title: C57BL/6, Pink1 WT, 1


title: BEAS-2B_pl1_NC12_+_not_treated_A, BEAS-2B, NC_NT


title: BEAS-2B_pl1_NFATC2_1_B, BEAS-2B, NFATC2


title: BEAS-2B_pl1_NFATC2_2_C, BEAS-2B, NFATC2


title: T24_CPD1A_3


title: LGKC4861-1_p4_Dox24h

city: New York

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

institute: New York University Grossman School of Medicine

data_processing:
76 bp paired-end stranded RNA sequencing
Sequencing reads were mapped using STAR against the Mus musculus genome (UCSC mm10), and gene level quantification was performed with featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file with featureCounts for all the samples combined

growth_protocol: Cell cultures were maintained at 37°C with 5% CO2 in RPMI supplemented with 10 % FBS and 1% penicillin and streptomycin

extract_protocol:
RNeasy Mini Kit (Qiagen) according to manufacturer's instructions
Stranded Total RNA-seq

treatment_protocol: Cell cultures were treated with 1000 ng/ml doxycycline in complete media for 24 hours prior to harvest

value: pancreatic tumor

value: p48(Cre), Kras(LSL-G12D), Rosa26(LSL-rtTA)), Tg(TetO-GNAS(R201C)

value: doxycycline


title: BEAS-2B_pl1_NFATC2_2_B, BEAS-2B, NFATC2


title: T24_CPD1A_2


title: HCT-15 cells, SLC39A14 knockout

city: Moscow

first: Alexander

last: Modestov

address: 8-2 Trubetskaya str.

institute: I.M. Sechenov First Moscow State Medical University

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Assembly: hg38
Supplementary files format and content: comma-delimited file includes raw counts for each sample

extract_protocol:
Both knockout clones and wild-type cells from three different passages were detached using Versen solution, washed with PBS, and the resulting cell pellets were stored at −70 °C until further analysis. RNA extraction was performed immediately before the preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) following the manufacturer’s protocol.
RNA Integrity Number (RIN) was measured using Agilent 2100 bioanalyzer. Agilent RNA 6000 Nano or Qubit RNA Assay Kits were used to measure RNA concentration. KAPA RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for further depletion of ribosomal RNA and library preparation. Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay kit (Life Technologies) and Agilent Tapestation (Agilent).

value: Colorectal cancer cell line

value: SLC39A14 knockout


title: LGKC4861-1_p2_Dox24h


title: HCT-15 cells, WT, biol rep 3

value: WT


title: T24_CPD1A_1


title: BEAS-2B_pl1_NFATC2_2_A, BEAS-2B, NFATC2


title: HCT-15 cells, WT, biol rep 2


title: LGKC4861-1_p2_NoDox

value: untreated control


title: T24_DMS0_4

value: DMSO


title: BEAS-2B_pl1_NEAT1_C, BEAS-2B, NEAT1


title: LGKC4838-2_p6_Dox24h


title: T24_DMS0_3


title: HCT-15 cells, WT, biol rep 1


title: T24_DMS0_2


title: BEAS-2B_pl1_NEAT1_A, BEAS-2B, NEAT1


title: BEAS-2B_pl1_NEAT1_B, BEAS-2B, NEAT1


title: LGKC4838-2_p4_Dox24h


title: BEAS-2B_pl1_MSTRG.36534_1_C, BEAS-2B, MSTRG.36534


title: T24_DMS0_1


title: Stationary phase cell total replicate2

city: Guangzhou

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

data_processing:
the raw reads were trimmed and low quality sequences were filtered.
The clean reads were mapped to the S. cerevisiae Apr. 2011 SacCer_Apr2011/sacCer3 reference genomes using Bowtie (version 0.12.5, parameter: -q -p 5 -k2 --best -v 2)
the uniquely mapped reads were clustered to into poly(A) sites as described previously (Fu et al., 2015; Fu et al., 2011)
Total reads from each samples were normalized to eliminate bias introduced by unequal read counts from different samples, and normalized poly(A) reads less than six was discarded and left reads were used for further analysis
Assembly: SacCer_Apr2011/sacCer3
Supplementary files format and content: txt file descript position and supports reads of poly(A) sites
Library strategy: polysome profiling

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: 30°C in rich YPD

extract_protocol:
exponential and stationary phase total RNA was extracted according to previous report (Liu et al., 2017). Polysome RNA were extracted with Trizol (Invitrogen, 10296010) and digested with DNase I (Ambion, AM2222) according to the manufacturer’s recommendations.
2 ug total RNA was fragmented by heating at 95 °C for 40 mins. The first strand cDNA was transcribed by SuperScript III Reverse Transcriptase (Invitrogen, 18080044) with an T7 primer (AAGCTTAGATATCTAATACGACTCACTATAGGGACCTACACGACGCTCTTCCGATC (T) 20VN) tagged with Illumina A adaptor and T7 promoter, and then the second strand was synthesized with PrimeScript™ Double Strand cDNA Synthesis Kit (Takara, 6111A). The libraries were amplified by in vitro transcription with RiboMAX Large Scale RNA production Systems- T7 (Promega, P1320). Next, first strand cDNA was reversed with random primers (AGTTCAGACGTGCTCTTCCGATCTNNNNNN), and then cDNAs used as template to amplify the library. The P5 and P7 adapters were linked by PCR with Platinum Taq DNA polymerase (Invitrogen, 15966025) for 12-15 cycles. Finally, 200-500 bp library products were enriched by size selection with AMPure XP Beads (Beckman Coulter, A63881).

value: yeast cells

value: 30 degrees C in rich YPD to stationary phase


title: LGKC4838-2_p6_NoDox


title: Stationary phase cell total replicate3


title: Stationary phase cell total replicate1


title: BEAS-2B_pl1_MSTRG.36534_1_B, BEAS-2B, MSTRG.36534


title: LGKC4861-1_p4_NoDox


title: LGKC4838-2_p4_NoDox


title: Exponential phase cell total replicate3

value: 30 degrees C in rich YPD to exponential phase


title: T8_COMB_4

value: Cervix

value: HeLa


title: T8_COMB_3

value: combination


title: LGKC4373-3-p7-Dox24h


title: Exponential phase cell total replicate2


title: BEAS-2B_pl1_MSTRG.36534_1_A, BEAS-2B, MSTRG.36534


title: LGKC4373-3-p6-Dox24h


title: T8_COMB_2


title: Exponential phase cell total replicate1


title: BEAS-2B_pl1_NC12_B, BEAS-2B, NC

value: NC


title: LGKC4373-3-p7-NoDox


title: BEAS-2B_pl1_NC12_A, BEAS-2B, NC


title: Stationary phase cell polysome unbound replicate3


title: LGKC4373-3-p6-NoDox


title: T8_CF7_4


title: Stationary phase cell polysome unbound replicate2


title: BEAS-2B_pl1_TRIB3_1_C, BEAS-2B, TRIB3


title: LGKC4301-1-p8-Dox24h


title: Stationary phase cell polysome unbound replicate1


title: BEAS-2B_pl1_TRIB3_1_B, BEAS-2B, TRIB3


title: LGKC4301-1-p6-Dox24h


title: Stationary phse cell polysome bound replicate3


title: T8_CF7_3


title: T8_CF7_2


title: BEAS-2B_pl1_NC12_C, BEAS-2B, NC


title: Stationary phase cell polysome bound replicate2


title: BEAS-2B_pl1_MSTRG.66333_2_C, BEAS-2B, MSTRG.66333


title: T8_CPD1A_4


title: BEAS-2B_pl1_TRIB3_1_A, BEAS-2B, TRIB3


title: LGKC4301-1-p6-NoDox


title: LGKC4301-1-p8-NoDox


title: T8_CF7_1


title: T8_COMB_1


title: T8_CPD1A_3


title: exponential phase cell polysome unbound replicate3


title: BEAS-2B_pl1_MSTRG.66333_2_A, BEAS-2B, MSTRG.66333


title: BEAS-2B_pl1_MSTRG.66333_2_B, BEAS-2B, MSTRG.66333


title: Fly-WT-IP3

description: Fly.bed

organism: Drosophila melanogaster

value: embryo

value: untreated

value: RIP

value: anti-Pseudouridine mAb (D347-16, MBL)


title: T8_CPD1A_2


title: exponential phase cell polysome unbound replicate2


title: BEAS-2B_pl1_SNHG15_2_C, BEAS-2B, SNHG15


title: Fly-WT-IP2

description: Fly.bed


title: exponential phase cell polysome unbound replicate1


title: BEAS-2B_pl1_SNHG15_2_B, BEAS-2B, SNHG15


title: Fly-WT-IP1

description: Fly.bed

value: anti-Pseudouridine mAb (D347-15, MBL)


title: T8_DMS0_4


title: exponential phase cell polysome bound replicate3


title: T8_DMS0_3


title: exponential phase cell polysome bound replicate2


title: Fly-WT-Input

description: Fly.bed


title: BEAS-2B_pl1_DUSP6_2_B, BEAS-2B, DUSP6


title: Stationary phase cell polysome bound replicate1


title: BEAS-2B_pl1_DUSP6_2_C, BEAS-2B, DUSP6


title: exponential phase cell polysome bound replicate1


title: T8_DMS0_1


title: Nmus_rough_1

city: Athens

first: Nathan

middle: John

last: Weyand

state: OH

address: 7 Depot Street

department: Biological Sciences

institute: Ohio University

description: total RNA,rRNA depleted

data_processing:
Illumina reads were mapped using Bowtie to Neisseria musculi strain NW831, GenBank CP060414.1. Gene expression counts for all samples were estimated using HTseq. Counts were then tabularized and imported into R studio for analyses. Differentially expressed genes were analyzed using the DESeq2 R package. Expression values for each gene were calculated as TPM values. The TPM values are presented in the excel files.

Important note: Two separate analyses were performed. One analysis was done using two replicates for each condition (GSM5582130 and GSM5582131 [smooth] and GSM5582134 and GSM5582135 [rough]) and one analysis was done using all three replicates per condition.
Samples include the normalized data for the two replicate analysis and the three replicate analysis.

Genome_build: The reference genome used for the analysis was based on GenBank CP060414.1
Supplementary_files_format_and_content: TPM values.  The DESeq output files for each analysis are available on the series record.

organism: Neisseria musculi

source_name: bacterial biofilm,pelleted

growth_protocol: Strains were grown as static biofilms in 90 mm petri dishes for 16 hours.

extract_protocol:
Each pellet was suspended inTris EDTA buffer pH 8.0 containing of lysozyme, incubated for 5 min at room temperature with vortexing every 1 min. RNA extraction was done using RNeasy Mini kit (Qiagen) and contaminating DNA was removed by DNase digestion using the Turbo DNA-free kit (Invitrogen).
Libraries were constructed using Illumina Truseq Stranded mRNA Library Prep kit.

treatment_protocol: One ml of RNA laterTM solution was added to each plate and biofilms were scraped and collected in  sterile microfuge tubes. The tubes were centrifuged for 3 min at 14, 000 x g at 4 °C to pellet the cells.

tag: morphotype

value: rough

value: wild-type


title: T0_4


title: mES-WT-Input2


title: T8_CPD1A_1


title: mES-WT-Input1


title: BEAS-2B_pl2_LYAR_2_A, BEAS-2B, LYAR

value: LYAR


title: Nmus_smooth_3

description: total RNA,rRNA depleted

value: smooth


title: BEAS-2B_pl1_DUSP6_2_A, BEAS-2B, DUSP6


title: Nmus_smooth_2

description: total RNA,rRNA depleted


title: T0_3


title: BEAS-2B_pl1_SNHG15_2_A, BEAS-2B, SNHG15


title: mES-WT-IP2

value: anti-Pseudouridine mAb (D347-12, MBL)


title: Nmus_rough_3

description: total RNA,rRNA depleted


title: T0_2


title: Nmus_smooth_1

description: total RNA,rRNA depleted


title: mES-WT-IP1

value: anti-Pseudouridine mAb (D347-11, MBL)


title: Nmus_rough_2

description: total RNA,rRNA depleted


title: T8_DMS0_2

value: DMSO


title: CD8+T cells, Aged, TRM condition

status: Public on Sep 14 2024

first: Siyu

last: Pei

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (GRCm38/mm10) using Bowtie.
Assembly: mm10
Supplementary files format and content: Processed data were csv format and all gene FPKM/TPM of each sample were contained in the file called gene_expression.

source_name: spleen and lymph node

growth_protocol: The 6-weeks-old young and 18-months-old aged mice were sacrificed, and primary CD8+T cells isolated from the spleen and lymph nodes were cultured under TCR condition (α-CD3/28: 1μg/ml) or TRM condition (α-CD3/28: 1μg/ml, IL-15: 20ng/ml, TGFβ: 5ng/ml) for 3 days.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: spleen and lymph node

tag: cell type

value: CD8+T cells

value: Aged WT

value: TRM