title: ZNHIT1_IgG_4

first: Neville

last: Sanjana

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Files were trimmed and with Trim Galore (version 0.6.10) with options –fastqc --paired, then aligned to hg38 (GRCh38.p14, downloaded from the UCSC Genome Browser at https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz) using bowtie270 (version 2.5.1) with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700. Paired reads were sorted and indexed with samtools (version 1.14). Reads were deduplicated with sambamba (version 0.7.0) view with the options -f bam -F "[XS] == null and not unmapped and not duplicate". Peaks were called with macs2 callpeak (version 2.2.7.1)  with options –f BAMPE -g hs –bdg with IgG as the control file (-c).
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: macs2 peaks .xls files
Library strategy: CUT&RUN

growth_protocol: Cells were maintained at 37 °C and 5% CO2 in D10 medium: DMEM with high glucose and stabilized L-glutamine (Caisson DML23) supplemented with 10% Serum Plus II (Sigma 14009C).

extract_protocol:
We used the CUTANA ChIC/CUT&RUN Kit (EpiCypher 14-1048) with antibodies against H2A.Z (Abcam ab4174), H3K4me3 (EpiCypher 14-1048), and IgG (EpiCypher 14-1048). Cells were dissociated using TrypLE, washed, and bound to 10 μl activated Concanavalin A-conjugated paramagnetic beads (EpiCypher), then resuspended with 0.5 μg of the antibody of interest and incubated overnight at 4°C on a rotator. The next day, the beads were washed twice with permeabilization buffer and incubated with 2.5 μl pAG-MNase (Epicypher) for 10 minutes at room temperature. Following binding, the beads were washed, and 2mM CaCl2 was added to begin digestion. Digestion was allowed to proceed for 2 hours at 4°C, then the reaction was terminated by adding 33 μl Stop Buffer (Epicypher) and incubating the reactions at 37°C for 10 minutes. We included a 0.5 ng E. coli DNA (Epicypher 18-1401) spike-in. DNA was purified with bead cleanup provided (EpiCypher).
Libraries were then prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645S), pooled, and sequenced on an Illumina NovaSeq S1 6000 v1.5 with 2 x 90 bp paired-end reads.

treatment_protocol: BT16 cells expressing a second-generation CRISPR repressor were transduced with a ZNHIT1-targeting or a non-targeting (negative control) guide RNA (n = 5 biological replicate transductions per guide RNA). Two days later, cells were dissociated using TrypLE and selected with 1 μg/ml puromycin for cells recieving a CRISPR perturbation. An in-line control was used to ensure complete selection. Five days following transduction, cells were collected for CUT&RUN. 500,000 cells were used per condition.


title: Hepatoblastoma, LCM-4, Embryonal, rep1

status: Public on Oct 13 2024

type: SRA

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Reads were aligned to the human reference genome with STAR and read counts were obtained using featureCounts (Subread).
Assembly: GRCh38 3.0.0
Supplementary files format and content: Comma-separated values file of non-normalized raw read counts from all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Liver

extract_protocol:
Fresh sections of formalin-fixed paraffin-embedded tumor blocks were cut on a microtome at 7 micron thickness and mounted on glass slides with polyethylene naphthalate membranes and stored in a nitrogen chamber. In preparation for laser capture microdissection, slides were immersed sequentially for 20 seconds each in xylenes (three times), 100% ethanol (three times), 95% ethanol (two times), 70% ethanol (two times), water, hematoxylin, water, bluing reagent, water, 70% ethanol (two times), 95% ethanol (two times), 100% ethanol (three times), and xylenes (three times). Immediately after staining, cells were dissected on an ArcturusXT LCM System using the ultraviolet (UV) laser to cut the sample and the infrared laser to adhere it to a CapSure HS LCM Cap. Roughly 500 cells were captured by area, based on density estimates by cell counting on small areas. After LCM, the cap was sealed in a 0.5 mL tube and stored at −80°C until library preparation.
The Smart-3SEQ protocol is available here: https://genome.cshlp.org/content/suppl/2019/10/24/gr.234807.118.DC1/Supplemental_File_2.pdf. Sequencing libraries were prepared using the Smart-3SEQ protocol for FFPE tissue on an Arcturus LCM HS cap, with the pre-SPRI pooling option and a single batch for all samples. Libraries were characterized immediately and stored at −20°C until sequencing.
Sequencing was performed on the pooled library using the NextSeq 500/550 High Output V2 kit with 75 cycles (read 1: 76 cycles, index 1: 2bp, index 2: 8bp)

tag: tissue

value: Liver

tag: Sex

value: M

tag: treatment

value: Treated

tag: disease state

value: Hepatoblastoma


title: WT3 CD4T

city: Shinjuku

first: Daisuke

last: Aki

state: Tokyo

department: School of Medicine

country: Japan

institute: Keio University

data_processing:
RNA sequencing was performed using Illumina NovaSeq 6000 platform. After trimming adapters using Cutadapt and sequence reads were mapped to Grcm39/mm10 using  bowtie2.
Read counts were normalized to TPM.
Assembly: mm10
Supplementary files format and content: xls file includes raw counts and TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was isolated from the FACS sorted CD4 T cells using RNeasy Mini kit (QIAGEN) and used for library construction.
The libraries were generated using NEBNext UltraII FS DNA Library Prep Kit (NEB) according to manufacture's instruction.

value: liver

tag: cell type

value: mouse CD4+ T cell

tag: genotype

value: WT


title: ZNHIT1_IgG_5

city: New York

library_source: genomic

molecule: genomic DNA

tag: cell line


title: whole body, sinlge, male, 11 dph, biol rep 2

city: Kobe

first: Chika

last: Takahashi

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

institute: RIKEN

data_processing:
The quality check of raw sequencing data was performed using FastQC v0.11.8.
The raw data were processed using Trim-galore v0.6.4.
The processed reads were mapped to N. furzeri reference genome Nfu_20140520 using HISAT2 2.1.0.
The mapped reads were counted using featurecounts v.1.5.3.
Assembly: Nfu_20140520
Supplementary files format and content: tab-delimited text file including raw counts for each Sample
Supplementary files format and content: tab-delimited text file including TPM values for each Sample

organism: Nothobranchius furzeri

source_name: whole body of single-housed males at 11 dph

extract_protocol:
Total RNA was isolated with TRIzol reagent (Thermo Fisher Scientific), and subjected to DNase treatment with a TURBO DNA-free kit　(Invitrogen #AM1907) according to the manufacturer’s instructions.
For whole juvenile fish and livers, the libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490), NEBNext Ultra II Directional RNA Library Prep Kit (E7760), NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (E6440). For ovaries and testes, the libraries were prepared using TruSeq stranded mRNA Library (Illumina, CA, USA).


title: ZNHIT1_IgG_3


title: WT2 CD4T


title: whole body, sinlge, male, 11 dph, biol rep 1

value: whole body of single-housed males at 11 dph


title: Hepatoblastoma, LCM-3, Mesenchymal (Stromal), rep1

value: F


title: Hepatoblastoma, LCM-4, Fetal, rep1


title: Hepatoblastoma, LCM-3, Normal (Pericentral)

value: Non-tumor


title: ZNHIT1_IgG_1


title: dKO, scTCRseq

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger (10X GENOMICS)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Hepatic CD4 T cells were sorted from NASH induced mice by flow cytometry.
Library was generated using Chromium Next GEM Single Cell 5' Reagent kit v2 (10X GENOMICS). Sorted cells were resuspended in master mix and loaded to Chromium Next GEM Chip K, followed by microfluidic single cell partitioning and barcoding.  Transcribed cDNA was cleaned up and amplified.

value: Hepatic CD4 T cells

value: Nr4a1 and Nr4a2 knockout

value: fed a choline deficient, high-fat diet consisting of 60 kcal% fat and 0.1% methionine diet


title: whole body, sinlge, male, 10 dph, biol rep 3

source_name: whole body of single-housed males at 10 dph


title: Hepatoblastoma, LCM-3, Normal (Midlobular)


title: Mono_CAF_alone

city: Vienna

first: Matthias

last: Farlik

state: Vienna

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description: Single Cell 3'

data_processing:
Raw data files were demultiplexed using the 10X Genomics Cell ranger (v.6.1.2) pipeline for CAF+mono/macro co-culture experiment and 10X Genomics Cell Ranger (v.7.0.0) for Triple culture experiment,  with the command “mkfastq”, assembled, and aligned to the human reference genome using the “count” pipeline
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv file containing barcode information for each cell of the sample
Supplementary files format and content: tsv file containing feature information for the sample
Supplementary files format and content: mtx file containing matrix information for the sample

source_name: Monocytes, patient-derived colorectal cancer-associated fibroblasts

growth_protocol: Monocytes were isolated from the whole blood of healthy volunteers using the EasySep™ Direct Human Monocyte Isolation Kit. For macrophage generation monocytes were attached to cell culture plates for 2 h  in RPMI-1640. Adherent monocytes were further incubated in RPMI-1640 supplemented with 10% fetal calf serum (FCS) and 100 ng/ml M-CSF for 7 days. For triple cultures cells were embedded in Geltrex domes at a ratio of 20:10:1 (CAFs:monocytes:organoid-cells) and cultured in Advanced DMEM/F12 basal medium for 3 days before treatments.

extract_protocol:
Co-cultures of CAFs and monocytes/macrophages were treated with TrypLE to realease the single cells. Triple cultures were subjected to dispase and TrypLE incubation resulting in single-cell suspension.
Libraries were performed using 10x Genomics Chromium Next GEM 3’ v3.1 (CAF+mono/macro experiment) or 5’ v2 (Triple culture experiment) kit and run on a Chromium Single Cell Controller. cDNA recovery, amplification and gene expression libraries were prepared according to the manufacturer’s protocol. Quality control was performed using TapeStation (Agilent) and Qubit Fluorometer (ThermoFisher). Libraries were sequenced on a NovaSeqSP flow cell (Illumina) with 50bp read length in paired-end mode.

treatment_protocol: Triple cultures were infected (using 5*100 TCID50/initially seeded cells) with oncolytic virus  (H1N1-NS1116) for 1 h and cultured in basal medium for further 24 h. For chemotherapy, domes with triple cultures were incubated in ENAS medium containing 20 μM oxaliplatin and 0.5 mM 5-FU for 24 hours.

tag: diagnosis

value: colorectal cancer


title: Hepatoblastoma, LCM-5, Fetal, rep1


title: WT, scTCRseq

description: 10X Genomics


title: whole body, sinlge, male, 11 dph, biol rep 3


title: Hepatoblastoma, LCM-3, Embryonal, rep1


title: dKO, scRNAseq

description: 10X Genomics


title: ZNHIT1_H3K4me3_5


title: ZNHIT1_IgG_2


title: ZNHIT1_H3K4me3_3


title: WT, scRNAseq

description: 10X Genomics


title: whole body, sinlge, male, 10 dph, biol rep 1

value: whole body of single-housed males at 10 dph


title: Hepatoblastoma, LCM-3. Fetal, rep1


title: WT1 CD4T


title: ZNHIT1_H3K4me3_2


title: whole body, sinlge, male, 9 dph, biol rep 4

source_name: whole body of single-housed males at 9 dph


title: Hepatoblastoma, LCM-2, Normal (Midlobular)

value: Untreated


title: whole body, sinlge, male, 10 dph, biol rep 2


title: whole body, sinlge, male, 10 dph, biol rep 4


title: whole body, sinlge, male, 9 dph, biol rep 3

value: whole body of single-housed males at 9 dph


title: Septum

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

country: France

institute: Inserm

description: 10x Genomics

data_processing:
Raw sequencing reads were processed to counts matrix with Cell Ranger version 2.1.1 using default parameters and the mm10 mouse genome reference to which the sequenced of YFP and tdTomato were added.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryonic brain

extract_protocol:
Tissue was dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) and a gentleMACS Octo Dissociator following the manufacturer’s instructions. Cell clumps and debris were removed via filtration through 30 µm cell strainers (Miltenyi Biotec) followed by two consecutive rounds of centrifugation for 3 min at 200 g. Pipetting through Gel Saver tips (QSP) and a final filtration using a 10 µm cell strainer (pluriSelect) allowed to obtain a single-cell suspension.  Cell viability and concentration were assessed using a MACSQuant flow cytometer (Miltenyi Biotec). Approximatively 10000 cells were used as input on the 10X Genomics Chromium controller.
Chromium Single Cell 3' Library & Gel Bead Kit v2

value: embryonic brain

tag: strain

tag: developmental stage

value: wild-type


title: Anti-stab1 antibody+Foxp3-ASO_3

city: London

first: Samar

last: Elorbany

address: Barbican

department: Tumour Microenvironment

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Raw sequencing data from the Illumina platform were converted into Fastq files and aligned to the reference genome mm10 using Salmon . Counts were then imported into R using tximport to create raw matrix counts. DESEq2 was used for data processing, normalization, and differential expression analysis according to standard procedures. Genes with counts of at least 5 in at least 25% of the samples were kept.
Assembly: mm10
Supplementary files format and content: lognormalized counts from DEseq2 for all samples in xlsx file

source_name: Omentum

growth_protocol: Tumors were harvested 1 week after the 4th cycle of treatment

extract_protocol:
Tissue was homogenized with Miltenyi GentleMACS in RLT buffer and further processed using Qiagen RNeasy Mini kit with on-column DNAse digestion.
Library preparation and RNASeq were performed by the Novogene (Cambridge, UK) using Ribodepletion to deplete ribosomal RNA.

treatment_protocol: Omental samples were harvested and immediately placed in RNAlater solution then at 4C. RNA was extracted within 48-72h after and snap frozen in dry ice then at -80 C

value: Omentum

value: Ovarian cancer cell line

value: Anti-stab1 antibody+Foxp3-ASO


title: Hepatoblastoma, LCM-2, Embryonal

value: Liver

value: M

value: Hepatoblastoma


title: ZNHIT1_H2AZ_5


title: Hepatoblastoma, LCM-2, Fetal


title: whole body, sinlge, male, 9 dph, biol rep 2


title: Anti-stab1 antibody+Foxp3-ASO_2

value: WT


title: whole body, sinlge, male, 9 dph, biol rep 1


title: ZNHIT1_H2AZ_4


title: ZNHIT1_H3K4me3_4


title: Foxp3-ASO_3

value: Foxp3-ASO+ isotype antibody


title: whole body, group, male, 35 dph, biol rep 4

source_name: whole body of group-housed males at 35 dph


title: Anti-stab1 antibody+Foxp3-ASO_1


title: Hepatoblastoma, LCM-1, Embryonal

value: F


title: whole body, group, male, 35 dph, biol rep 3

value: whole body of group-housed males at 35 dph


title: Foxp3-ASO_2


title: Hepatoblastoma, LCM-1, Fetal


title: ZNHIT1_H2AZ_3


title: ZNHIT1_H3K4me3_1


title: Pachon_embryonic_fibroblast_3

city: Tallahassee

first: Evan

last: Lloyd

state: FL

address: 107 Chieftain Way

institute: Florida State University

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert 3.10.5 Reads were aligned to Ensembl genome astMex_2.0 with STAR aligner (version 2.7.3a ), using Ensembl 106 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Assembly: Astyanax_mexicanus-2.0
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file includes TPM values for each sample

organism: Astyanax mexicanus

growth_protocol: Cells were maintained and incubated with growth media in the incubator at 28°C without CO2 and were observed every day with media changes 3 times per week.

extract_protocol:
RNA was extracted through phenol chloroform extraction and purified through RNeasy Kits (QIAGEN, #74104).
Libraries were constructed using TruSeq Stranded mRNA LT Kit with 500ng of starting material.

value: PEF

value: Embryonic fibroblast


title: whole body, group, male, 35 dph, biol rep 1


title: whole body, group, male, 35 dph, biol rep 2


title: NT_IgG_5

value: Non-targeting gRNA (control perturbation)


title: Foxp3-ASO_1


title: ZNHIT1_H2AZ_1


title: Pachon_embryonic_fibroblast_2


title: NT_IgG_4


title: Pachon_embryonic_fibroblast_1


title: Granulosa cells from wild type mice-Week7-Sample3

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-wt7-3

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA), And R
Sequenced raw FASTQ files were trimmed for Nextera transposase adapters.
Trimmed reads were mapped to the reference genome mus musculus mm10 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using mm10 assembly and GENCODE Genes- release M25.
Assembly: mm10
Supplementary files format and content: txt file with deseq2 normalised values for each sample

source_name: Ovary

extract_protocol:
RNA is extracted by RLT and ethanol precipitation
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014) and  miRNA sequencing was performed as per the Hagemann et al 2018 protocol

value: Ovary

value: Granulosa cells


title: whole body, group, male, 28 dph, biol rep 4

source_name: whole body of group-housed males at 28 dph


title: CT+Foxp3-ASO_3


title: Surface_fish_embryonic_fibroblast_3

value: SEF


title: NT_IgG_3


title: whole body, group, male, 28 dph, biol rep 3

value: whole body of group-housed males at 28 dph


title: ZNHIT1_H2AZ_2


title: Hepatoblastoma, LCM-1, Normal (Midlobular)

value: Untreated

value: Non-tumor


title: whole body, group, female, 17 dph, biol rep 4

source_name: whole body of group-housed females at 17 dph


title: CT+Foxp3-ASO_2

value: Omentum

value: Ovarian cancer cell line


title: NT_IgG_2


title: whole body, group, male, 28 dph, biol rep 2


title: CT+Foxp3-ASO_1


title: NT_IgG_1


title: whole body, group, male, 28 dph, biol rep 1


title: Surface_fish_embryonic_fibroblast_1


title: CT+anti-stab1 antibody+Foxp3-ASO_4


title: whole body, group, male, 21 dph, biol rep 4

source_name: whole body of group-housed males at 21 dph


title: CT+Foxp3-ASO_4


title: NT_H3K4me3_5


title: CT+anti-stab1 antibody+Foxp3-ASO_3


title: NT_H3K4me3_4


title: whole body, group, male, 21 dph, biol rep 3

value: whole body of group-housed males at 21 dph


title: whole body, group, female, 21 dph, biol rep 3

source_name: whole body of group-housed females at 21 dph


title: CT+anti-stab1 antibody+Foxp3-ASO_2


title: Gr64f_w1118

description: 10x genomics

data_processing:
The snRNA-seq raw sequencing files were processed with CellRanger 6.0 (10x Genomics; Pleasanton, CA).
Assembly: dmel_r6.54
Supplementary files format and content: tab-separated files and matrix files

organism: Drosophila melanogaster

source_name: Labellum

extract_protocol:
Fly labellums were dissected at 10 and 40 days (for aging samples) or at 20 days (for control and AD model samples) and then placed into 1.5 mL RNase-free Eppendorf tubes, flash-frozen in liquid nitrogen, and then stored at -80°C. Approximately ~400 labellum were collected for each treatment and stored on dry ice. Nuclei isolation and snRNAseq were performed by Singulomics Corporation (Singulomics.com; New York). To isolate nuclei, tissue was homogenized and lysed with Triton X-100 in RNase-free water. The nuclei were then purified, centrifuged, resuspended in PBS with RNase Inhibitor, and diluted to 700 nuclei/µL.
Standardized 10x capture and library preparation were performed using the 10x Genomics Chromium Next GEM 3’ Single Cell Reagent kit v3.1 (10x Genomics; Pleasanton, CA). The libraries were then sequenced with Illumina NovaSeq 6000 (Illumina; San Diego, CA).

value: Labellum

value: Female

value: 20d - Control


title: whole body, group, male, 21 dph, biol rep 2


title: Granulosa cells from knock-out mice-Week4-Sample7

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-7


title: NT_H3K4me3_3


title: CT+anti-stab1 antibody+Foxp3-ASO_1

value: WT


title: whole body, group, male, 21 dph, biol rep 1


title: NT_H3K4me3_2


title: w1118_10d

description: 10x genomics


title: w1118_40d

description: 10x genomics


title: Surface_fish_embryonic_fibroblast_2


title: Anti-stab1 antibody_3


title: whole body, group, male, 17 dph, biol rep 4

source_name: whole body of group-housed males at 17 dph


title: NT_H3K4me3_1


title: NT_H2AZ_5


title: Anti-stab1 antibody_2


title: whole body, group, male, 17 dph, biol rep 3

value: whole body of group-housed males at 17 dph


title: Old_40d

description: 10x genomics


title: Gr64f_Arctic

description: 10x genomics

value: 20d - AD model


title: Young_10d

description: 10x genomics


title: Anti-stab1 antibody_1


title: whole body, group, male, 17 dph, biol rep 2


title: whole body, group, male, 17 dph, biol rep 1


title: CT+anti-stab1 antibody_3


title: NT_H2AZ_3


title: CT+anti-stab1 antibody_2


title: CD8, WT, ID3

city: Montreal

first: John

last: Stagg

state: QC

address: 900 St-Denis

country: Canada

institute: CRCHUM

data_processing:
Adapter sequences and low-quality bases in the resulting FASTQ files were removed using Trimmomatic version 0.35 and genome alignments were conducted using STAR version 2.7.1a.
The sequences were aligned to the mouse genome version GRCm39, with gene annotations from Gencode version M29 based on Ensembl 106.
As part of quality control, the sequences were aligned to several different genomes to verify that there was no sample contamination.
Expression levels were obtained as gene readcounts from STAR as well as estimated using RSEM in order to obtain gene and transcript level expression in reads per transcripts per million (TPM) for these stranded RNA libraries.
DESeq2 version 1.30.1 was then used to normalize gene readcounts and compute differential expression between the two experimental conditions.
Significant gene sets were chosen according to a false discovery rate (FDR) cutoff of 5% (padj < 0.05).
Assembly: Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.38[1] and aligned to the reference human genome version GRCm39 (gene annotation from Gencode version 29, based on Ensembl 106) using STAR version 2.7.1a
Supplementary files format and content: tab-separated values file including normalized read counts and log2 fold change of all significantly and non significanlty DEGs (DESEQ).
Supplementary files format and content: tab-separated values file

source_name: MCA205 tumor

growth_protocol: MCA205 tumor cells were implanted in WT (C57Bl/6) or ENT1KO (Slc29a1-/-) mice subcutaneously in PBS1X. Tumors were harvested after 14 days, processed into single cell suspension and sorted for Live CD45+ CD8+ T cells by FACS in trizol and stored at -80°C until sent for RNA extraction at IRIC Genomic platform.

extract_protocol:
Trizol followed by a Qiagen RNeasy mini column purification. 75ng RNA was used for library construction.
PolyA selection followed by KAPA RNA Hyperprep.

value: MCA205 tumor

value: sorted CD45+ CD8+

value: C57Bl/6 WT


title: NT_H2AZ_4

value: Non-targeting gRNA (control perturbation)


title: CD8, WT, ID2


title: whole body, group, male, 13 dph, biol rep 4

source_name: whole body of group-housed males at 13 dph


title: NT_H2AZ_2


title: NT_H2AZ_1


title: CT+anti-stab1 antibody_1


title: CD8, WT, ID1


title: CD8, ENT1KO, ID15


title: CT-treated_3


title: whole body, group, male, 13 dph, biol rep 2

value: whole body of group-housed males at 13 dph


title: PXGL treated iPSCs

city: Thuwal

first: Ali

last: Balubaid

address: Technology drive

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: 10x Genomics

data_processing:
The data mapped using the cell ranger pipeline (v6.1.2)
Assembly: GRCh38 (v105)
Supplementary files format and content: Tab seperated values and matrix file.

source_name: embryonic

extract_protocol: For 10x genomics scRNAseq library preparation, 10X Chromium Single Cell 3’ Solution V2 was used; 5000 cells per cell type were targeted, single-indexed, and sequenced.

treatment_protocol:
For PXGL treated iPSCs, primed iPSCs were chemically reset on iMEF using N2B27 as basal media supplemented with 1 µM PD0325901 (Selleck, S1036), 10 ng/ml LIF (R&D Systems, 7734), and 1 mM VPA (Sigma, PHR1061) for three days. This was followed by propagating these cells in PXGL media, which consists of 1 µM PD0325901 (Selleck, S1036), 2 µM XAV-939 (Selleck, S1180), 2 µM Gö6983 (Axon, 2466), and 10 ng/ml LIF (R&D Systems, 7734).
see SAMPLE section for sample specific protocols under "treatment protocol" column

value: embryonic

value: iPSCs

value: Pluripotent stem cells

value: wild type


title: CD8, ENT1KO, ID14


title: whole body, group, male, 13 dph, biol rep 1


title: CT-treated_2

value: Omentum

value: Ovarian cancer cell line


title: EPS treated iPSCs

description: 10x Genomics

treatment_protocol:
Primed PSCs were treated with an EPS medium termed LCDM, using N2B27 as a basal medium to generate EPS. LCDM medium was comprised of N2B27 basal medium supplemented with 10 ng/ml human LIF (R&D Systems, 7734), 3 µM CHIR99021 (Tocris, 4423), 2 µM (S)-(+)-Dimethindene maleate (Tocris, 1425), and 2 µM minocycline hydrochloride (Selleckchem, S4226), 1 µM IWR endo-1 (Selleckchem, S7086), and 2 µM Y-27632 (Selleckchem, S1049). Both nPSCs and EPS were passaged until domed-shaped colonies appeared in culture before using them for scRNAseq.
see SAMPLE section for sample specific protocols under "treatment protocol" column


title: CD8, ENT1KO, ID12


title: whole body, group, male, 9 dph, biol rep 4

source_name: whole body of group-housed males at 9 dph


title: CD8, ENT1KO, ID11


title: control_3

value: Isotype ab+Control-ASO+vehicle


title: HCT116, siKAT7

city: Beijing

first: 萌

last: 王

state: beijing

address: peking university

country: China

institute: Peking university

data_processing:
DEGseq v 1.30.0
Based on the quantitative expression results, differential gene analysis between groups was performed to obtain the genes that were differentially expressed between the two groups. The software for differential analysis was: DEGseq , and the screening thresholds were: |log2FC| >=1 & padjust <0.05
RSEM v 1.3.3
Using RSEM, Read Counts for each sample gene/transcript were obtained using the results of the paired-to-genome and the genome annotation file.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes gene counts for each sample.
Supplementary files format and content: Tab-delimited text file includes information of differential genes.

growth_protocol: Human colon cancer HCT116 cells were cultured by McCoy's 5A supplemented with 10% heat-inactivated fetal bovine serum in a humidified chamber containing 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol (Applygen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA library construction were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: Cells were transfected with non-specific siRNA and KAT siRNA duplexes respectively using Lipofectamine 2000 following the manufacturer's instructions.

value: Colon cancer cell lines

value: transfect KAT7 siRNA


title: whole body, group, male, 9 dph, biol rep 3

value: whole body of group-housed males at 9 dph


title: HCT116, siControl

value: WT

value: transfect non-specific siRNA


title: whole body, group, male, 9 dph, biol rep 2


title: whole body, group, male, 13 dph, biol rep 3


title: M1 mouse heart_cKO_ReD

city: Guangzhou

first: Tailai

last: Du

state: Guangdong

address: No.58, Zhongshan 2nd road

department: The First Affiliated Hospital

institute: Sun Yat-sen University

library_source: other

data_processing:
For RNA-seq data analysis, the sequencing data was filtered with cutadapt. The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) or rat genome (Rattus_norvegicus.Rnor_6.0) using STAR or HISAT2, respectively. Expression level of gene was calculated by featureCounts and StringTie, respectively. The raw counts were then analyzed using DESeq2.
For Ribo-seq data analysis, the Ribo-seq raw data underwent adapter trimming and low-quality sequence filtering using cutadapt, followed by rRNA sequence removal using bowtie. Subsequently, the clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) using STAR. Then ORF analysis and ORF counts analysis were conducted using RiboCode.
For TRAC-seq data analysis, following adapter trimming and quality filtering, the clean sequencing data were initially aligned to the tRNA sequences using Bowtie2. Subsequently, read counts for each tRNA were calculated using the method described in (Cozen et al., 2015).
Assembly: Mus_musculus.GRCm38; Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: txt;raw counts
Library strategy: TRAC-seq

molecule: other

source_name: Heart

growth_protocol: H9C2 cardiomyocytes were cultured in DMEM high-glucose medium (Gibco) containing 10% fetal bovine serum and antibiotics.

extract_protocol:
Total RNAs were isolated using Trizol Reagent from H9C2 cardiomyocytes and tissue samples. Small RNAs (<200 nt) were initially purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
RNA libraries were constructed following the protocols provided by Illumina and MGISEQ. For Ribo-seq, libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina NovaSeq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: A line of genome-edited H9C2 cardiomyocytes was generated by CRISPR-Cas9, introducing a frameshift mutation to abolish the translation of Mettl1 protein. H9C2 cardiomyocytes with normal expression of Mettl1 were used as control.

value: Heart

tag: age


title: control_1


title: N87_NC2

city: tianjin

first: ren

middle: bao

last: qing

state: hexi

address: huanhu west road

institute: Cancer Hospital affiliated to Tianjin Medical University

data_processing:
Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to and size selection was performed with AMPureXP beads.
cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used hisat2-2.0.4 (ccb.jhu.edu/software/hisat2/)to map reads to the genome, Ensembl v96 (command line: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) x exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR (v3.2.5)(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Ensembl_v101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: stomach

growth_protocol: NCI-N87 cells cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) (HyClone, South Logan, UT, USA), penicillin (100 U/ml), and  streptomycin (100 U/ml) at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
cells were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NCI-N87 cells were transfected with PLVX-IRES-Puro-ZSCAN18 or empty vector (PLVX-IRES-Puro) respectively for 24 hours,then added puro screening for 4days

value: treated with PLVX-IRES-Puro-empty vector for 5 days,puro screening for 4days


title: whole body, group, male, 9 dph, biol rep 1


title: M1 mouse heart_cKO_DeM


title: control_2


title: Turmeric-2_S15_L001

city: Mysore

first: Gopinath

last: Meenakshisundaram

state: Karnataka

address: Cheluvamba Mansion

department: Molecular Nutrition

country: India

institute: Central Food Technological Research Institute

data_processing:
Processing small RNA seq data involves quality control, adapter removal, alignment to a reference, annotation, and quantification. Differential expression analysis identifies changes, and miRNA tools uncover known and novel miRNAs. Normalization corrects biases, and visualization aids exploration. Functional analysis offers biological insights, validated by methods like qRT-PCR. Integration with other omics data and a comprehensive report conclude the process.
Assembly: not applicable
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel files include normalised values for each Sample

organism: Curcuma longa

source_name: exosome-like nanovesicle (ENV)

extract_protocol:
ENVs were isolated from soy bean, ginger, amla and turmeric using a cost effective Polyethylene glycol- based (PEG) precipitation method developed in our lab (Kalarikkal et al., Scientific Reports, 2020). In brief, edible portion of plants were ground in phosphate buffered saline (PBS) using a kitchen mixer. In the case of Soybeans, they were soaked in PBS for overnight prior to grinding. Aqueous extracts were subjected to three rounds of centrifugation at 1200g for 20 min (remove cells/nuclei), 3000g for 20 min and 10,000g for 45 min (remove fibers and insoluble contents). This is known as S10 extract (crude extracellular extract). To purify ENVs, S10 extract was subjected precipitation with 10% PEG-6000, overnight followed by centrifugation at 10000g for 30 min. ENV pellets are suspended in sterile water and stored at -80 in aliqouts. ENVs were quantified by measuring the lipids by vanillin assay. Total RNA was isolated from two independent batches of ENVs (5mg lipid equivalent) for each plant by TRI RNA extraction reagent (Sigma Aldrich) as per manufacturers protocol.
1 μg of total RNA was subjected to library preparation

value: exosome-like nanovesicle (ENV)


title: N87_ZSCAN18_2

value: treated with PLVX-IRES-Puro-ZSCAN18 for 5 days,puro screening for 4days


title: M1 mouse heart_Ctrl_ReD

value: Ctrl


title: Garlic-2_S13_L001

organism: Allium sativum


title: Garlic-1_S12_L001


title: M1 mouse heart_Ctrl_DeM


title: N87_ZSCAN18_1


title: Liver, C57BL/6J Wild-Type, 13

status: Public on Oct 12 2024

city: Chicago

first: Rogan

middle: A

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

data_processing:
FASTQ files were generated using bcl-convert 4.0.3 using default parameters.  To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.12.0 implemented in Nextflow 24.04.2.5914 using Singularity 3.8.1 with the minimal command nextflow run nf-core/rnaseq \ -r ‘3.12.0’ \ -profile nu_genomics \--additional_fasta ‘transgenes.fa’ \ --star_index false \ --genome ‘GRCm38’.  Briefly, lane-level reads were trimmed using trimGalore! 0.6.7 and aligned to the hybrid genome described above using STAR 2.6.1d.  Gene-level assignment was then performed using salmon 1.5.2.
Assembly: GRCm38
Supplementary files format and content: Raw counts matrix from STAR-salmon output (CSV)
Supplementary files format and content: Sample metadata (CSV)

source_name: Liver

extract_protocol:
On the day of harvest, mice were euthanized with isoflurane and whole liver tissue was placed in a cryovial and snap frozen in liquid nitrogen.  The liver tissues were stored at -80°C until all samples were collected.  RNA was extracted from liver tissues using a TissueRuptor II (Qiagen) to homogenize the livers and the AllPrep DNA/RNA Micro Kit (Qiagen, #80284) according to the manufacturer’s protocol.
RNA quality and quantity were assessed by Agilent 4200 TapeStation, using the RNA ScreenTape System (Agilent Technologies).  RNA-seq libraries were prepared from 500 ng of total RNA using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB E7370L).  Library QC was then performed using TapeStation 4200 High Sensitivity DNA tapes (Agilent Technologies).  Dual-indexed libraries were pooled and sequenced on a NextSeq2000 instrument (Illumina) for 100 cycles, single-end, to an average sequencing depth of 20.2 million reads per sample.

treatment_protocol: Standard chow diet-fed control and NDI1 mice, 12-16 weeks of age, were used for all sequencing experiments

value: Liver

value: Wild-Type


title: Liver, C57BL/6J Wild-Type, 11


title: Liver, C57BL/6J Wild-Type, 10


title: CT-treated_1

source_name: Omentum


title: Turmeric-1_S14_L001


title: Liver, C57BL/6J Wild-Type, 12


title: Liver, C57BL/6J Wild-Type, 8


title: Liver, C57BL/6J Wild-Type, 7


title: Liver, NDI1, 7


title: Liver, NDI1, 6


title: Liver, C57BL/6J Wild-Type, 9


title: Liver, C57BL/6J Wild-Type, 6


title: Liver, NDI1, 5


title: N87_NC1


title: Liver, NDI1, 8


title: Liver, C57BL/6J Wild-Type, 5


title: Liver, NDI1, 3


title: Liver, NDI1, 4


title: Liver, C57BL/6J Wild-Type, 4


title: Liver, C57BL/6J Wild-Type, 2


title: Liver, NDI1, 2


title: Liver, NDI1, 1


title: Liver, C57BL/6J Wild-Type, 3


title: Liver, C57BL/6J Wild-Type, 1


title: SM-J6UV8

city: Boston

first: Caroline

last: Wasen

state: MA

address: 60 Fenwood rd

institute: Harvard Medical School

data_processing:
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1.
Raw counts were normalized using DESeq2’s (v1.30.1) median of ratios method.
Genes were filtered out that had lower than 100 reads in more than 1/3 of the samples.
Differential expression was calculated with DESeq2, using the Wald significance tests and the Benjamini-Hochberg procedure for p-value adjustment.
Supplementary files format and content: Normalized counts and differential expression analysis.

source_name: Brain

extract_protocol:
1000 sorted cells were added to TCL lysis buffer prior to library preparation
Preparation of cDNA libraries was performed according to the Smart-seq2 protocol by the Broad Technology Labs. Illumina NextSeq500 and the High Output v2 kit was used to generate 2 x 25 bp reads.

value: Brain

value: Microglia

value: Metronidazole


title: SM-J6UV5


title: SM-J6UV7


title: SM-J6UV6


title: SM-J6UUX


title: SM-J6UV4


title: SM-J6UUV


title: SM-J6UUW


title: SM-J6UUU


title: SM-J6UUT


title: SM-J6UV2


title: SM-J6UV3


title: SM-J6UUZ


title: SM-J6UUY


title: ATAC LN 2  NOD

city: Salt Lake City

first: Maria

last: Bettini

state: Utah

address: University of Utah

department: Pathology

institute: University of Utah

data_processing:
scRNAseq data were analyzed with Seurat and Signac.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files

source_name: Non-draining Lymph node

extract_protocol:
non-draining lymph nodes and pancreatic islets were harvested from 10 week old female mice. Cells were sorted on TCR+ and were subjected to nuceli extraction and 10x scATAC and scRNA multiome sequencing using 10X Multiome kit.
Liberaries were created using 10X Genomic scATAC/scRNAseq multiome kit

value: Non-draining Lymph node

value: NOD

value: T cells

tag: library type

value: DNA and RNA


title: SM-J6UUP


title: SM-J6UUO


title: ATAC islet 2  NOD

source_name: Pancreatic islets

value: Pancreatic islets


title: SM-J6UUN

value: WT


title: ATAC LN 1  NOD


title: SM-J6UUM


title: ATAC islet 1  NOD


title: SM-J6UUK

value: Bacteroides fragilis


title: SM-J6UUL


title: GEX LN 1 NOD


title: SM-J6UUD

value: PBS


title: SM-J6UUI


title: GEX islet 2 NOD


title: ATAC pancreatic islet CD4 BDC2.5 T cells

library_source: genomic single cell

extract_protocol:
pancreatic islets, spleen+non-draining lymph nodes were harvested from BDC2.5 transferred cells into congenically labelled NOD mice. BDC2.5 CD4+Vb4 cells were sorted and subjected to nuceli extraction.
Liberaries were created using 10X Genomic scATAC/scRNAseq multiome kit
scATAC/scRNA multiome sequnce

treatment_protocol: BDC2.5 naïve cells transferred into congenic mice and harvested BDC2.5 after 5 weeks

value: ATAC


title: ATAC circulating CD4 BDC2.5 T cells

source_name: Non-draining Lymph node and spleen

value: Non-draining Lymph node and spleen


title: SM-J6UUC


title: SM-J6UUB


title: GEX pancreatic islet CD4 BDC2.5 T cells

value: GEX


title: SM-J6UUH

value: wildtype


title: GEX circulating CD4 BDC2.5 T cells


title: SM-J6UUG


title: SM-J6UV1


title: SM-J6UUQ


title: hkl_rep2

first: Xuemin

last: Xian

address: 253 Industrial Avenue

institute: Zhujiang Hospital, Southern Medical University

data_processing:
SOAPnuke (V1.5.6)
Assembly: Assembly: Homo_sapiens ensembl release-105
Supplementary files format and content: tab-delimited text file includes fpkm, tpm, read counts for each sample

source_name: human VSMCs

extract_protocol:
Total RNA of human smooth muscle cells was extracted using TRIzol regennts and RNA quality was determmined using Agilent 2100 Bioanalyser.
RNA libraries for RNAseq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for MGI.

value: human VSMCs


title: hkl_rep3


title: GEX LN 2 NOD


title: hkl_rep1


title: cal_rep2


title: SM-J6UUE


title: SM-J6UUF


title: cal_rep3


title: cal_rep1


title: SM-J6UUA


title: GEX islet 1 NOD


title: SM-J6UUJ


title: 3_ndln CD62L+

data_processing:
Differentially methylated regions (DMRs) were identified using BSmooth DMR finder56. Unbiased analysis of gene ontology of biological processes was performed for DMRs using the Genomic Regions Enrichment of Annotations Tool (GREAT version 4.0.4)
Assembly: mm10
Supplementary files format and content: Coverage files

source_name: NDLN

extract_protocol:
genomic DNA was isolated from ndLN and pancreatic islets of NOD mice
Library preparation quality was assessed by Agilent 2200 TapeStation and Invitrogen Qubit prior to sequencing on Illumina NovaSeq 6000 by the High-Throughput Genomics Shared Resource at the University of Utah
Whole Genome Enzymatic Methylation sequencing

value: NDLN

value: DNA


title: 4_ndln CD62L+


title: 4_islet CD62L+

source_name: Islet

value: Islet


title: 2_ndln CD62L+


title: 4_islet CD11a+


title: 1_ndln CD62L+


title: 3_islet CD62L+


title: SM-J6UU7

value: Brain

value: Microglia


title: 4_islet DN

value: NOD


title: IL21_treated_4 [R8]

city: Bern

first: Carsten

last: Riether

address: Murtenstrasse 35

department: DBMR

country: Switzerland

institute: University Bern

data_processing:
RNA-seq data was assessed using fastqc v.0.11.9
mapped to the reference genome using HiSat2 v.2.2.1
FeatureCounts v.2.0.1
DEG with DESeq2 v1.36.0
Assembly: GRCh38.104
Supplementary files format and content: excel (.xlsx)

source_name: CD34+ AML LSCs

extract_protocol:
Total RNA was extractedFACS-purified CD34+ AML LSCs treated with recombinant human IL21 and control LSCsusing the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Novogene

treatment_protocol: CD34+ AML LSCs cultured in presence and absence of recombinant human IL21 overnight.

value: CD34+ AML LSCs

value: recombinant human IL21


title: untreated_4 [R7]

value: untreated


title: 3_islet CD11a+

value: T cells


title: 3_islet DN


title: LH7725 3 Months KO

type: RNA

city: Toronto

first: Aaron

last: Wong

state: Ontario

address: 101 College Street

department: TGHRI

institute: University Health Network

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: R oligo package, annotations from brain array v17, RMA normalization

label: biotin

source_name: 3 Months KO

label_protocol: Standard Affymetrix protocol

growth_protocol: Mice were maintained in specific pathogen-free conditions on a 12-h light: 12-h dark cycle and fed an autoclaved laboratory chow and tap water ad libitum.

extract_protocol: Total RNA was purified using RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was tested using Nanodrop spectrophotometer (VWR) and Bioanalyzer (Agilent; Santa Clara, CA).

treatment_protocol: Generation of XB130 knockout mice can be found in our previous publication: https://doi.org/10.1371/journal.pone.0108952

tag: treatement

value: KO

value: mouse thyroid


title: LH7727 3 Months KO


title: 2_islet CD62L+


title: LH7726 3 Months WT

source_name: 3 Months WT

value: WT


title: SM-J6UU9

value: PBS


title: IL21_treated_3 [R6]


title: NAIN3-2, polyA+RNA

city: Stanford

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

institute: Stanford University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
Trimmed sequence reads were mapped to GRCh38 or human 18S and 28S rRNA sequence using bowtie2 (parameters: non-deterministic)
Read count extraction were performed using icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
R-scores were calculated using RBRP scripts (https://github.com/linglanfang/RBRP)
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly
Supplementary files format and content: txt files include mean R-scores of rRNAs
Supplementary files format and content: bigWig files include mean R-scores of polyA+RNAs and log-transformed p-value

source_name: embryonic kidney

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37˚C

extract_protocol:
To isolate total cellular RNA, cells were lysed with 6 mL of Trizol LS reagent according to the Supplementary Information. RNAs were then purified with a Zymo Quick-RNA Midiprep kit according to the manufacturer’s protocol. To enrich rRNAs, 1% agarose gel was used to purify 18S and 28S rRNA from total RNAs. To enrich poly(A)+ transcripts, a 250-µg aliquot of total cellular RNA was diluted to 600 µg/mL with RNA storage buffer and then purified with Poly(A)Purist MAG kit according to the manufacturer’s protocol. The captured RNAs were further purified with RNeasy Mini columns according to the manufacturer’s protocol, and stored as 500-ng aliquots at -80 ˚C.
RNA libraries for RNA-seq were prepared using a customized protocol developed in our lab ( Nat Chem, 2023, DOI: 10.1038/s41557-023-01309-8)

value: embryonic kidney

value: Human embryonic kidney

value: cells contain Adenovirus 5 DNA (PMID:11967234)

value: Cells were treated with 100mM NAIN3 for 10 min


title: SM-J6UU8

value: wildtype


title: 2_islet DN

value: Islet

value: DNA


title: NAIN3-1, polyA+RNA


title: untreated_3 [R5]


title: 2_islet CD11a+


title: LH7721 3 Months KO


title: DMSO-2, polyA+RNA

value: Cells were treated with 10% DMSO for 10 min


title: IL21_treated_2 [R4]


title: LH7724 3 Months WT


title: DMSO-1, polyA+RNA


title: 1_islet DN

value: NOD


title: LH7723 3 Months KO


title: LH7722 3 Months WT


title: LH7720 3 Months WT


title: AcIm-1, polyA+RNA

value: Cells were treated with 100mM AcIm for 10 min


title: LH7719 4 Weeks KO

source_name: 4 Weeks KO


title: IL21_treated_1 [R2]

value: CD34+ AML LSCs

value: recombinant human IL21


title: 1_islet CD11a+

value: T cells


title: untreated_2 [R3]

value: untreated


title: DMSO-2, rRNA


title: 1_islet CD62L+


title: LH7718 4 Weeks WT

source_name: 4 Weeks WT

value: mouse thyroid


title: DMSO-1, rRNA


title: untreated_1 [R1]


title: AcIm-2, polyA+RNA


title: LGMP8wt

data_processing:
RNA-seq data was assessed using fastqc v.0.11.9
mapped to the reference genome using HiSat2 v.2.2.1
FeatureCounts v.2.0.1
DEG with DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: excel (.xlsx)

source_name: bone marrow

extract_protocol:
Total RNA was extracted fromFACS- IL21R+/- or IL21-/- AML miceusing the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Novogene

treatment_protocol: FACS-purifiedIL21R+/- (WT) or IL21-/- (KO)LSKs were harvested and transduced twice with the MLL-AF9 onocogene. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 (IL21R+/- or IL21-/- AML mice). Upon AML development, L-GMPs fromIL21R+/- or IL21-/- AML micewere isolated

value: bone marrow


title: NAIN3-2, rRNA


title: patient_6_2hr

data_processing:
The cell ranger pipeline (v3.1.0, 10x Genomics) was used to demultiplex barcodes and map reads to the human reference genome (GRCh38-3.0.0).
Assembly: refdata-cellranger-GRCh38-3.0.0
Supplementary files format and content: barcodes.tsv.gz -single cell barcodes (filtered_feature_bc_matrix)
Supplementary files format and content: features.tsv.gz - gene names (filtered_feature_bc_matrix)
Supplementary files format and content: matrix.mtx.gz - raw counts (filtered_feature_bc_matrix)

source_name: peripheral lung biopsy

extract_protocol:
Human peripheral lung biopsies were collected in the operating room and placed in chilled DPBS and transported to the lab on ice. All tools and reagents used for single cell dissociation were chilled on ice prior to use. A digestion solution comprising 10 mg/mL Substilin A (Sigma Aldrich P5380, St. Louis, MO), DNAse I 0.2 mg/mL (Sigma Aldrich D5025), Collagenase 1 mg/mL (Sigma Aldrich C2674), 45 µM actinomycin D (Sigma Aldrich A1410) and 5 mM CaCl2 (Sigma Aldrich 21115) in 1.2X EDTA free red blood cell (RBC) lysis buffer solution (diluted from a 10X stock: combine 4.15 g NH4Cl and 0.5 g KHCO3 in 50 mL of ddH20) was prepared and chilled on ice. From each peripheral lung biopsy, 0.2 g was sectioned and minced into pieces no larger than 2 mm x 2 mm x 2 mm. Minced biopsies were then placed in a 50 mL conical tube and rinsed with sterile chilled DPBS and then strained to remove as much red blood cells as possible. This was repeated until the DPBS ran clear. Minced lung tissue was then placed into a chilled C-tube (Miltenyi Biotec 130-096-334, Bergisch Gladbach, Germany) containing 2 mL of cold dissociation solution. A 10-minute timer was set, and the C-tube was allowed to sit in ice. Halfway through the incubation the C-tube was placed on the GentleMacs (Miltenyi Biotec) and the m_liver_02 program (42 seconds) was selected, and the tube was then returned to ice. At the end of the 10-minute incubation period, the contents of the C-tube were poured through a 40 µm cell strainer (Falcon C352340, Corning, NY) into a 50 mL conical tube. The C-tube was washed with an additional 6 mL of 5% fetal bovine serum (FBS) (Thermo Fisher A3160702, Waltham, MA) in DPBS which was also poured through the cell strainer. The plunger of a 3 mL syringe was then used to gently rub any remaining chunks on tissue against the cell strainer. The cell strainer was then washed with 3 mL of 5% FBS. The single cell suspension was then spun down in a centrifuge for 5 minutes at 400g. The supernatant was decanted, and the cells were resuspended in 10 mL of 0.04% bovine serum albumin (BSA) in PBS (buffer for 10X Chromium chip loading). Samples were submitted for single cell RNA sequencing on the 10X Genomics platform using 3’ v3.1 chemistry at the Princess Margaret Genomics Centre in Toronto, ON, Canada.
RNA libraries were prepared according to manufacturer instructions (single cell 3’ v3.1 protocol, 10x Genomics)

value: peripheral lung biopsy

tag: donor sex

value: M

tag: recipient sex


title: patient_6_cit

value: cit


title: NAIN3-1, rRNA

value: embryonic kidney

value: Human embryonic kidney

value: cells contain Adenovirus 5 DNA (PMID:11967234)


title: LH7717 4 Weeks KO

value: KO


title: LH7716 4 Weeks WT

value: WT


title: LH7713 4 Weeks KO


title: patient_5_2hr


title: AcIN3-2, rRNA

value: Cells were treated with 200mM AcIN3 for 10 min


title: LGMP7wt


title: LH7714 4 Weeks WT


title: LH7715 4 Weeks KO


title: AcIN3-1, rRNA


title: LGMP5wt


title: AcIm-2, rRNA


title: AcIm-1, rRNA


title: patient_4_2hr


title: patient_4_cit


title: LGMP3ko


title: patient_3_2hr


title: LH7711 2 Weeks KO

source_name: 2 Weeks KO


title: patient_5_cit


title: LGMP2ko


title: RAW_4h-N2 icSHAPE RNA-seq

first: Zongheng

last: Yang

address: Dongdansantiao 5th

institute: Peking Union Medical College, Chinese Academy of Medical Sciences

data_processing:
Primary sequencing data that produced by Illumina HiSeq 2500 , called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Reads preprocessing，mapping and icSHAPE reaction score analysis with raw data followed icSHAPE pipeline  pubulished in the article named Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE
mm10
tab-delimited text files include icSHAPE reaction scores for RAW264.7 cells with or without R837 stimulated

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
The isolated RNA by biotin magnetic beads was further processed into iCLIP-seq library and then standard illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were stimulated with R837 and treated with NAIN3 for click reaction.

value: RAW264.7 cells

value: murine macrophage  cell line

value: wild type

value: treated with R837 stimulation and NAIN3 for click reaction

tag: time


title: LH7709 2 Weeks KO


title: LH7710 2 Weeks WT

source_name: 2 Weeks WT


title: LGMP6wt


title: R5M_KO

extract_protocol:
Total RNA was extracted fromFACS-purified L-GMPs derived from bone marrow of BL/6 (WT) or IL21-/- (KO) AML miceusing the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Novogene

treatment_protocol: FACS-purified BL/6 LSKs were harvested and transduced twice with the MLL-AF9 onocogene. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 and IL21/-/- recipients (BL/6 and IL21-/- AML). Upon AML development, L-GMPs from BL/6 and IL21-/- AML mice were isolated.

value: IL21 KO


title: RAW_4h-N1 icSHAPE RNA-seq

value: treated with  R837 stimulation and NAIN3 for click reaction


title: LH7708 2 Weeks WT

value: mouse thyroid


title: LH7712 4 Weeks WT


title: R6M_KO

value: bone marrow


title: LH7707 2 Weeks KO


title: LGMP4ko


title: RAW_4h-D1 icSHAPE RNA-seq

value: treated with  NAIN3 for click reaction


title: RAW_4h-D2 icSHAPE RNA-seq


title: R4M_KO


title: patient_2_cit

value: peripheral lung biopsy

value: M

value: F


title: SKOV3-Carbo+COM33-treated-3

city: Wenzhou

first: Jie-Xue

last: Pan

state: Zhejiang

address: Nanbaixiang Street, Ouhai District

department: Reproductive Medicine Center

institute: The First Affiliated Hospital of Wenzhou Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0). P < 0.05 and absolute log2 (fold change) > 1.0 were set as the threshold for significantly differential expression.
Genome_build: Tab-delimited text files include FPKM values for each sample

source_name: SKOV3 cell line

growth_protocol: The cells were cultured in RPMI 1640 supplemented with 10% (v/v) fetal bovine serum (FBS) (Gibco, USA) and 1% (v/v) penicillin-streptomycin (Gibco). Cells were maintained in a humidified cell incubator at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted by using TRIzol (Invitrogen) according to the manufacturer's instructions.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.

treatment_protocol: Cells were treated by control/Carbo/Carbo+COM33

tag: treat


title: R3M_WT

tag: tissue


title: LH7705 2 Weeks KO


title: RAW_0h-N2 icSHAPE RNA-seq

value: Treated with R838 stimulation and DMSO


title: SKOV3-Carbo+COM33-treated-2


title: R2M_WT


title: LH7704 2 Weeks WT


title: RAW_0h-D2 icSHAPE RNA-seq

value: Treated with DMSO


title: RAW_0h-N1 icSHAPE RNA-seq

value: Treated with R837 stimulation and DMSO


title: SKOV3-Carbo+COM33-treated-1


title: patient_1_cit

value: cit


title: R1M_WT

value: WT


title: SKOV3-Carbo-treated-3

value: Carbo


title: Endosome RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5
Assemble of RNA-Seq alignments into mm10 transcripts. FPKM calculation and Differential expression analysis of Endosome RNA-seq and TLR7-activated-HA-iCLIP-seq was performed by cufflinks, cuffdiff and cuffmege.
mm10
tab-delimited text files include FPKM values for Endosome RNA-seq and TLR7-activated-HA-iCLIP-seq

growth_protocol: RAW264.7 cells stably expressing HA-mTLR7 were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Invent Endosome isolate Kit was applied to isolate endosome. RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for lncRNA-seq were prepared using NEBNext® UltraTM Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: RAW264.7 cells stably expressing HA-mTLR7 were collected after UV cross-linking.

value: RAW264.7 cells

value: murine macrophage  cell line

value: HA-mTLR7 stable overexpression

value: isolate endosome with invent kit


title: Cas-Input_mRNA

city: Hangzhou

first: Jianzhao

last: Liu

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

institute: Zhejiang University

data_processing:
Raw reads were first subject to fastqc (https://www.bioinformatics.babraham.ac.uk/projects /fastqc/) for quality control, and adapters were trimmed using fastp (https://github.com/OpenGene/fastp). The minimum quality threshold was set to 20, and the minimum length after adapter trimming was 25 nt. The remaining reads were then used for downstream analysis.
Both the input and IP reads data were mapped to GRCh38 using hisat2. The sam files were sorted and reordered into bam files with samtools (https://github.com/samtools/samtools). The m6A peaks were called according to the work of Lijia et al., 2017 (PMC5340966). To call peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp steps. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between IP and input samples by using the edgeR package, combining information from all replicates in the two groups. The window was called as positive with a false discovery rate of FC>=2 to FC>=1.5 . Overlapping positive windows were merged. The m6A motif (consensus sequence) was extracted from its peak distribution files using Homer2 (http://homer.ucsd.edu/homer/index.html).

source_name: HEK293T cells

growth_protocol: 293T cells were grown in DMEM containing 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin until 80% confluency.

extract_protocol:
Cells were harvested after another 24 h. About 1/6 cells were used for western blotting validation, and the rest cells were treated with Trizol for total RNA extraction. Polyadenylated RNA was further enriched from total RNA by using GenElute mRNA Miniprep kit (Sigma, MRN10).
The MeRIP-seq was carried out as previously described[6], with several modifications. Briefly, 10 ug isolated polyadenylated RNA was fragmented to a mean size of 100–300 nucleotides by incubation in fragment buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0) for 7 min at 70 °C. A portion of fragmented RNA was saved as input. The remaining RNA samples were incubated with anti-m6A antibody (SYSY, 202 003) in IP buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% CA-630 and 4 U / µL Recombinant RNase Inhibitor) for 2 h at 4 °C. 40 µL recombinant protein A bead was washed twice in IP buffer and blocked in 0.5 mg/mL BSA for 2 h at 4 °C. After washed twice, recombinant protein A bead was incubated with reaction mix for 2 h at 4 °C. To remove unbound RNA, samples were washed three times with IP buffer. RNA was eluted with elution buffer (6.7 mM m6AMP in IP buffer). RNA libraries for the RNA input and IP were constructed using Illumina TruSeq-stranded mRNA library construction kit following the manufacturer’s protocol. The library sizes were validated using an Agilent 2100 Bioanalyzer and sequenced on an Illumina NovaS4 system with paired-end 2×150bp read length.

treatment_protocol: Cells were co-transfected with dCas13b-M14 and gRNA using Polyethylenimine HCl MAX (Polyscience, 24765) according to the manufacturer’s guide.

tag: antibody


title: RAW_0h-D1 icSHAPE RNA-seq

value: wild type

tag: treatment


title: Cas-IP_mRNA


title: LH7706 2 Weeks WT

value: mouse thyroid


title: RAW264.7 cells,Lnc-Atg16l1 kd,4h-3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5
Assemble of RNA-Seq alignments into mm10 transcripts. FPKM calculation and Differential expression analysis was performed by cufflinks, cuffdiff and cuffmege.
mm10
tab-delimited text files include FPKM values for each Sample
tab-delimited text files include different expresion significance for each group

growth_protocol: RAW264.7 cells of Lnc-Atg16l1 knocked out and wild type  were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for lncRNA-seq were prepared using NEBNext® UltraTM Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: RAW264.7 cells of Lnc-Atg16l1 knocked out and wild type  were stimulated with R837 and collected after UV cross-linking.

value: Lnc-Atg16l1 knock out

value: R837 stimulated


title: SKOV3-Carbo-treated-2


title: RAW264.7 cells,Lnc-Atg16l1 kd,4h-2


title: Ctrl-Input_mRNA


title: Yaa-N1 icSHAPE RNA-seq

data_processing:
Primary sequencing data that produced by Illumina HiSeq 2500 , called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Reads preprocessing，mapping and icSHAPE reaction score analysis with raw data followed icSHAPE pipeline  pubulished in the article named Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE
mm10
tab-delimited text files include icSHAPE reaction scores for BXSB.B6 and BXSB.Yaa mouse spleens.

source_name: spleen cells

growth_protocol: BXSB.B6 and BXSB,Yaa mice grow in SPF  envirenment

treatment_protocol: The spleens cells were grinded and blood cells were ruptured. The rest spleen cells were treated with NAIN3 for click reaction.

value: spleen cells

value: treated with  NAIN3 for click reaction

value: 18 weeks


title: Ctrl-IP_mRNA


title: SKOV3-Carbo-treated-1


title: SKOV3-control-3

value: control


title: patient_1_2hr

value: peripheral lung biopsy

value: M

value: F


title: RAW264.7 cells,Lnc-Atg16l1 kd,4h-1


title: patient_2_2hr


title: Yaa-D2 icSHAPE RNA-seq

value: treated with DMSO as ctrl


title: RAW264.7 cells,Lnc-Atg16l1 kd,0h-3


title: Yaa-D1 icSHAPE RNA-seq


title: SKOV3-control-2


title: SKOV3-control-1


title: Kyp, H3K9me2, Rep2

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

description: Bio rep 2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam  -c Input.bam -g 829069930 -p 0.05 --extsize 150 --bw 500 -B -n --outdir
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptools

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.

extract_protocol:
ChIP-seq assays were performed on 4-week-old tomato fourth branch of leaves according to Bio-protocol of Ramirez-Prado, J.S. et al (2021) by using anti-H3K9ac (Millipore. 07-352), anti-H3K9me2 (Abcam. ab1220) antibodies.
ChIP-seq libraries were prepared from 10ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions. One biological replicate was generated for each condition. DNA libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

value: Leaf

value: Kyp


title: B6-N1 icSHAPE RNA-seq


title: Kyp, H3K9ac, Rep2

description: Bio rep 2


title: B6-N2 icSHAPE RNA-seq


title: Yaa-N2 icSHAPE RNA-seq


title: B6-D2 icSHAPE RNA-seq


title: RAW264.7 cells,WT,4h-3

value: RAW264.7 cells

value: murine macrophage  cell line

value: WT


title: B6-D1 icSHAPE RNA-seq


title: RAW264.7 cells,WT,4h-2


title: RAW264.7 cells,WT,4h-1


title: Kyp, H3K9me2, Rep1

description: Bio rep 1


title: M82, H3K9ac, Rep2

description: Bio rep 2


title: Myd88-iCLIP-seq

data_processing:
Primary sequencing data that produced by Illumina HiSeq 2500 , called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Reads preprocessing，mapping and CITS analysis with raw data followed CLIP Tool Kit pubulished in the article named CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
mm10
bed files for iclip truncation sites

growth_protocol: RAW264.7 cells stably expressing HA-mTLR7 or wild-type were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
iCLIP was performed usign anti-HA,TLR7 and Myd88 antibody, and the isolated RNA was further processed into iCLIP-seq library and then standard illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells stably expressing HA-mTLR7 or wild-type were collected after UV cross-linking.

value: wild type

value: UV-crosslinking and Myd88-antibody purified


title: RAW264.7 cells,WT,0h-3


title: RAW264.7 cells,Lnc-Atg16l1 kd,0h-2

value: Lnc-Atg16l1 knock out


title: Kyp, H3K9ac, Rep1

description: Bio rep 1


title: mTLR7-iCLIP-seq

value: UV-crosslinking and mTLR7-antibody purified


title: RAW264.7 cells,Lnc-Atg16l1 kd,0h-1


title: RAW264.7 cells,WT,0h-2


title: patient_3_cit

value: cit


title: CET4

city: Shanghai

first: Mingsu

last: Shi

state: Shanghai

address: Dongan Road

institute: Eye & ENT Hospital of Fudan University

description: LncRNA and gene expression

hyb_protocol: Following labeling, the samples were hybridized to the Agilent SureHyb microarray (Agilent Technologies, USA) to allow for specific binding of labeled RNA to complementary DNA probes on the array.

scan_protocol: After hybridization, the microarrays were washed to remove any non-specifically bound RNA. The arrays were then scanned using the Agilent DNA Microarray Scanner (Agilent Technologies, USA) to capture the fluorescent signals. Signal intensities were extracted using the Agilent Feature Extraction software (version 11.0.1.1).

data_processing: To ensure comparability of data across different samples, the raw signal intensities were normalized using the Agilent GeneSpring GX software (version 12.1).

source_name: Extraocular muscle

label_protocol: RNA samples were labeled using the Arraystar RNA Flash Labeling Kit (Arraystar, USA) according to the manufacturer's protocol.

extract_protocol: In brief, total RNA was isolated from EOM samples using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The quantity and quality of total RNA samples were measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Samples with an OD260/280 ratio between 1.8 and 2.1 were considered acceptable. RNA integrity was evaluated using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), with samples having an RNA integrity number (RIN) > 7 selected for subsequent treatments.

value: Extraocular muscle

tag: gender

value: Male


title: M82, H3K9me2, Rep2

description: Bio rep 2


title: CET5

description: LncRNA and gene expression


title: M82, H3K9me2, Rep1

description: Bio rep 1


title: RAW264.7 cells,WT,0h-1

tag: cell type


title: TLR7-activated-HA-iCLIP-seq

tag: genotype

value: HA-mTLR7 stable overexpression

value: UV-crosslinking and HA-antibody purified


title: CET3

description: LncRNA and gene expression

value: Female


title: TLR7-activated-Myd88-iCLIP-seq

tag: cell line

value: Stimulated by R837 for 4 hours, UV-crosslinking and Myd88-antibody purified


title: M82, H3K9ac, Rep1

description: Bio rep 1


title: CET2

description: LncRNA and gene expression


title: CET1

description: LncRNA and gene expression


title: Trained2, DG

status: Public on Oct 11 2024

city: Brooklyn

first: Oleg

middle: V

last: Evgrafov

state: New York

address: 450 Clarkson Ave

institute: SUNY Downstate Health Sciences University

data_processing:
Raw sequencing data was processed using the bcl2fastq v2.20 tool (Illumina) to convert BCL files into FASTQ format.
The FASTQ files were further subjected to quality control using FastQC
The FASTQ files were subjected to quality control using FastQC and adaptor trimming using Trim Galore
The trimmed reads were aligned to the mouse reference genome (GRCm38) using STAR aligner.
Normalized Gene counts were generated using DESeq2.
Assembly: GRCm38

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA, United States) according to the manufacturer’s protocol.
Samples with a RIN greater than 7 were processed for library preparation with NEBnext rRNA depletion kit and ULTRAII FS RNA-seq Library Preparation Kit for Illumina (New England Biolabs, Ipswich, MA, United States).

value: hippocampus


title: Trained1, DG


title: Trained2, CA3


title: Untrained1, D.Hipp, Spatial

data_processing:
Raw sequencing reads (FASTQ files) were processed using Space Ranger (v2.0.0), aligning the reads to the mm10 reference genome.
Quality control was performed automatically by Space Ranger, filtering out low-quality reads and assigning high-quality reads to spatial barcodes.
Gene expression was quantified for each spatial spot using Space Ranger's count pipeline.
Spatial feature detection was also performed, mapping reads to specific regions of the tissue based on spatial barcodes.
Assembly: mm10
Supplementary files format and content: Processed data includes a sparse gene expression matrix (matrix.mtx) in Sparse matrix format, gene identifiers (genes.tsv), and barcodes (barcodes.tsv) in tab-separated formats. Filtered feature-barcode matrices are provided in HDF5 format (filtered_feature_bc_matrix.h5). Spatial positions of each barcode are stored in a CSV file (tissue_positions.csv). Tissue images are provided in high- and low-resolution PNG formats (tissue_hires_image.png, tissue_lowres_image.png). Fiducial markers and detected tissue areas are included as JPEG images (aligned_fiducials.jpg, detected_tissue_image.jpg). Spatial enrichment data are provided in CSV format (spatial_enrichment.csv), and alignment scalefactors in JSON format (scalefactors_json.json).
Library strategy: Spatial Transcriptomics

source_name: Coronal Mouse Brain with Bilateral Dorsal Hippocampus

extract_protocol:
mRNA was extracted and libraries were prepared following the Visium Spatial Gene Expression User Guide (Genomics, 2023).
Libraries were indexed using the Dual Index Kit TT Set A (PN-1000215). Indexed libraries were loaded at 300 pM and sequenced on a NovaSeq 6000 System (Illumina) using a NovaSeq S4 Reagent Kit (200 cycles, catalog no. 20027466, Illumina), targeting a sequencing depth of approximately 2.0 × 108 read-pairs per sample.


title: Trained1, D.Hipp, Spatial

value: Coronal Mouse Brain with Bilateral Dorsal Hippocampus


title: Trained1, CA3


title: Untrained3, DG


title: GO4

description: LncRNA and gene expression


title: Untrained2, CA3


title: Trained3, CA1


title: GO2

description: LncRNA and gene expression


title: Trained3, CA3


title: Trained2, CA1


title: GO3

description: LncRNA and gene expression


title: GO5

description: LncRNA and gene expression


title: Untrained3, CA1


title: Untrained1, CA1


title: Untrained2, CA1


title: GO1

description: LncRNA and gene expression


title: Trained3, DG


title: 14wk TNF-Tg mice, lung_scRNA

city: Rochester

first: Benjamin

last: Korman

state: NY

address: 601 Elmwood Avenue, Box 695

institute: AIR

description: 10x Genomics

data_processing:
Demultiplexing and Counting were made using 10X provided cellranger-5.0.0. Samples were aligned to 10X provided reference refdata-gex-mm10-2020-A
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
100,000-300,000 7-AAD-/CD45-/CD326- flow sorted cells were collected and submitted for single cell capture.  Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead–in–Emulsions. Single-cell RNA-seq libraries were prepared using Chromium Single-Cell 3′ Library & Gel Bead Kit (version 1.1; 10x Genomics). Libraries were sequenced using Illumina’s NovaSeq6000 instrument.  5000-6000 cells were captured per condition at a read depth of 50,000 reads per cells.  The sequencing reads were examined by quality metrics, transcripts mapped to reference mouse genome and assigned to individual cells according to cell barcodes, using Cell Ranger (10× Genomics).
Single-cell RNA-seq libraries were prepared using Chromium Single-Cell 3′ Library & Gel Bead Kit (version 1.1; 10x Genomics).

value: non-immune primary cells

value: lung

value: 14 weeks


title: Untrained1, CA3


title: 20wk Littermate WT control mice, lung_scRNA

description: 10x Genomics

value: 20 weeks


title: 14wk Littermate WT control mice, lung_scRNA

description: 10x Genomics


title: 8wk TNF-Tg mice, lung_scRNA

description: 10x Genomics

value: 8 weeks


title: 8wk Littermate WT control mice, lung_scRNA

description: 10x Genomics


title: Untrained1, DG


title: 20wk TNF-Tg mice, lung_scRNA

description: 10x Genomics


title: CD4 positive T cells, MBP only, Tet+

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
See methods for more details
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices, matrices with gene symbols, and barcodes for each sample, as well as vdj filtered contig outputs

source_name: Tetramer positive population harvested from inguinal lymph nodes immunized with MBP peptides.

extract_protocol:
10X Genomics Chromium Single Cell preparation
NGS Illumina NextSeq
5' RNAseq with TCR

value: iLN

value: T cells

value: MBP peptide


title: CD4 positive T cells, MBP+MOG, Tet-

source_name: Tetramer negative population harvested from inguinal lymph nodes immunized with MOG and MBP peptides together.

value: MBP+MOG peptide


title: CD4 positive T cells, MBP only, Tet-

source_name: Tetramer negative population harvested from inguinal lymph nodes immunized with MBP peptides.


title: Trained1, CA1


title: CD4 positive T cells, MBP+MOG, Tet+

source_name: Tetramer positive population harvested from inguinal lymph nodes immunized with MOG and MBP peptides together.


title: LLC_cachexia_muscle_RNAseq_N3

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

data_processing:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/mm10 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
ATAC-seq raw files (fastq, paired-end) were aligned to the GRCm38/mm10 version of the mouse reference genome using Bowtie2 with default parameters. Peaks were called using MACS2. HOMER was then used to construct tag directories from the SAM files, remove duplicate reads, call peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.

source_name: Muscle

growth_protocol: C57BL/6 mice were maintained under standard housing conditions and received a regular diet.

extract_protocol:
Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of LC Bio Technology CO., Ltd.

treatment_protocol: A cancer cachexia model was created by subcutaneously injecting a specific number of Lewis lung cancer (LLC) cells into mice. Cachexia symptoms appeared within 3 weeks. The mice were divided into two groups: control (NC) and cachexia (LLC). Cachexia was induced by injection of LLC cells into C57BL/6J mice. Body weight and food consumption were monitored daily. After 22 days, mice were euthanized for tissue collection.

value: Muscle

value: cachexia

value: PBS injection


title: LLC_cachexia_muscle_RNAseq_N1


title: LLC_cachexia_muscle_RNAseq_CC3

value: 500000 LLC cells injection


title: LLC_cachexia_muscle_RNAseq_CC2


title: C2C12_myotubes_ATACseq_C26_CC2

description: anno_C2C12_C26_ATAC_seq_norm_107_counts.txt

growth_protocol: C2C12 myotubes cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
C2C12 cells were seeded in triplicate in 12-well plates 7 days before the experiments. After reaching confluence, myoblasts were induced by culturing in DMEM containing 2% horse serum for 4-7 days. Differentiated C2C12 myotubes were induced by incubation with C26 conditioned medium for 24 hours to establish the muscle cell degradation model. The cells were washed with PBS, resuspended in lysis buffer, and the nuclei were spun down. The nuclei were then transferred to the transposition reaction buffer and incubated at 37°C for 30 minutes with 105 cells. Genomic DNA was extracted using the Qiagen MinElute PCR Purification Kit. The ATAC-seq library was prepared according to a previously reported protocol (Buenrostro et al., 2015). The purified ATAC-seq DNA library mix was sequenced on an Illumina NovaSeq 6000 (PE150 reads).
The ATAC-seq Library preparation was performed through the manufacturer's introduction.

treatment_protocol: With Colon-26 (C26) cell conditional medium treatment for 24 hours.

value: Myoblast

value: C26 Conditional medium treatment


title: LLC_cachexia_muscle_RNAseq_N2


title: C2C12_myotubes_ATACseq_C26_CC3


title: C2C12_myotubes_ATACseq_Ctrl_N1

value: Control


title: C2C12_myotubes_ATACseq_Ctrl_N2


title: C2C12_myotubes_ATACseq_C26_CC1


title: CUTTag_CHD4_INTS15-KO_Eu-Myc_Rep2

first: runyuan

last: mao

address: 131 Dongan Road, Xuhui District, Shanghai

institute: Fudan University

data_processing:
The raw CUT&Tag reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to mouse mm10 assemblies using Bowtie v2.3.5.1 with  the parameters “-N 1 -L 25 -X 700 --no-mixed --no-discordant”.
Low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 and Picard v2.23.3 (https:// broadinstitute.github.io/picard/).
The reads were shifted to compensate for the offset in tagmentation site relative to the Tn5 binding site using the alignmentSieve function of deepTools v.3.5.1 with the ‘--ATACshift’ option.
The ENCODE blacklist regions were removed using bedtools v2.29.2.
Peak calling was performed by macs2 v2.2.6 with a q-value threshold of 0.05.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: Mouse Eμ-Myc p19Arf-/- cells were cultured in B cell medium (45% Dulbecco’s modified Eagle’s medium and 45% Iscove’s modified Dulbecco’s media, supplemented with 10% fetal bovine serum, L-glutamate, and 50 μM β-mercaptoethanol) with 1× Penicillin-Streptomycin (Gibico) at 37°C, 5% CO2.

extract_protocol:
Protein-DNA complexes were isolated with antibody from CoA beads binding cells.
Briefly, DNA was PCR amplified with Illumina primers for 13 cycles and library fragments were purified with DNA cleanup beads. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were untreated or treated with DMSO or JQ1 for 48h.

value: Eu-Myc cells

tag: chip antibody

value: CHD4 (Bethyl Labs, Cat.#A301-081A)


title: CUTTag_CHD4_Ctr_Eu-Myc_Rep1

source_name: wild type

value: wild type


title: CUTTag_CHD4_Ctr_Eu-Myc_Rep2


title: CUTTag_CHD4_INTS15-KO_Eu-Myc_Rep1


title: CUTTag_MBD3_INTS15-KO_Eu-Myc_Rep1

value: MBD3 (Proteintech, Cat.#14258-1-AP)


title: CUTTag_MBD3_INTS15-KO_Eu-Myc_Rep2


title: CUTTag_MBD3_Ctr_Eu-Myc_Rep1


title: CUTTag_MBD3_Ctr_Eu-Myc_Rep2


title: CUTTag_KDM5C_INTS15-KO_Eu-Myc_Rep2

value: KDM5C (Abclonal, Cat.#A15740)


title: CUTTag_KDM5C_INTS15-KO_Eu-Myc_Rep1


title: CUTTag_KDM5C_Ctr_Eu-Myc_Rep1


title: CUTTag_KDM5C_Ctr_Eu-Myc_Rep2


title: CUTTag_RACK7_INTS15-KO_Eu-Myc_Rep1

value: RACK7 (Bethyl Labs, Cat.#A302-090A)


title: CUTTag_INTS10_INTS15-KO_Eu-Myc_Rep2

value: INTS10 (Proteintech, Cat.#15271-1-AP)


title: LLC_cachexia_muscle_RNAseq_CC1


title: CUTTag_RACK7_INTS15-KO_Eu-Myc_Rep2


title: CUTTag_RACK7_Ctr_Eu-Myc_Rep1


title: CUTTag_INTS10_INTS15-KO_Eu-Myc_Rep1


title: CUTTag_RACK7_Ctr_Eu-Myc_Rep2


title: CUTTag_INTS10_Ctr_Eu-Myc_Rep1


title: CUTTag_H3K4me3_JQ1-48h_INTS10-KO_Eu-Myc_Rep2

value: H3K4me3 (Abclonal, Cat.#A2357)


title: C2C12_myotubes_ATACseq_Ctrl_N3


title: CUTTag_H3K4me3_DMSO-48h_INTS10-KO_Eu-Myc_Rep2


title: CUTTag_H3K4me3_DMSO-48h_INTS10-KO_Eu-Myc_Rep1


title: CUTTag_INTS10_Ctr_Eu-Myc_Rep2


title: CUTTag_H3K4me3_JQ1-48h_INTS15-KO_Eu-Myc_Rep2


title: CUTTag_H3K4me3_JQ1-48h_INTS15-KO_Eu-Myc_Rep1


title: CUTTag_H3K4me3_DMSO-48h_INTS15-KO_Eu-Myc_Rep2


title: CUTTag_H3K4me3_DMSO-48h_INTS15-KO_Eu-Myc_Rep1


title: CUTTag_INTS15_INTS15-KO_Eu-Myc_Rep2

value: INTS15 (This paper)


title: CUTTag_INTS15_INTS15-KO_Eu-Myc_Rep1


title: CUTTag_INTS15_Ctr_Eu-Myc_Rep1


title: CUTTag_INTS15_Ctr_Eu-Myc_Rep2


title: CUTTag_H3K4me3_DMSO-48h_Ctr_Eu-Myc_Rep2


title: CUTTag_H3K4me3_JQ1-48h_Ctr_Eu-Myc_Rep2


title: CUTTag_H3K4me3_DMSO-48h_Ctr_Eu-Myc_Rep1


title: RNA-seq_JQ1-48h_Ctr_Eμ-Myc_E2_Rep2

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6, followed by mapping to the mm10 genome using STAR v2.7.5c with parameter ‘‘--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 3’’
Low mapping quality reads and PCR duplicates were removed using SAMtools v1.9 and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific normalized bigwigs were generated by deeptools v3.5.0.
We collected the counts per gene by the featureCounts tool from Rsubread R package v2.0.1, differential expression analysis was then performed using DESeq2 R package v1.26.0.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Eu-Myc cells

extract_protocol:
RNA was isolated with TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO, JQ1 or MS67 combined with JQ1 for 48h.

value: lymphoma cells

value: treated with JQ1 for 48 hours


title: RNA-seq_JQ1-48h_INTS15-KO_Eμ-Myc_E2_Rep2


title: RNA-seq_MS67-JQ1-48h_INTS15-KO_Eμ-Myc_E2_Rep2

value: treated with MS67 and JQ1 for 48 hours


title: CUTTag_H3K4me3_JQ1-48h_INTS10-KO_Eu-Myc_Rep1


title: RNA-seq_JQ1-48h_Ctr_Eμ-Myc_E2_Rep1


title: RNA-seq_DMSO-48h_Ctr_Eμ-Myc_E2_Rep2

value: treated with DMSO for 48 hours


title: CUTTag_H3K4me3_JQ1-48h_Ctr_Eu-Myc_Rep1


title: RNA-seq_DMSO-48h_INTS15-KO_Eμ-Myc_Rep2


title: RNA-seq_MS67-JQ1-48h_INTS15-KO_Eμ-Myc_E2_Rep1


title: RNA-seq_DMSO-48h_INTS15-KO_Eμ-Myc_Rep1


title: RNA-seq_JQ1-48h_INTS10-KO_Eμ-Myc_Rep1


title: RNA-seq_JQ1-48h_INTS10-KO_Eμ-Myc_Rep2


title: RNA-seq_JQ1-48h_Ctr_Eμ-Myc_Rep2


title: RNA-seq_JQ1-48h_INTS15-KO_Eμ-Myc_Rep2


title: RNA-seq_JQ1-48h_INTS15-KO_Eμ-Myc_E2_Rep1


title: RNA-seq_DMSO-48h_INTS10-KO_Eμ-Myc_Rep2


title: RNA-seq_DMSO-48h_INTS10-KO_Eμ-Myc_Rep1


title: RNA-seq_JQ1-48h_Ctr_Eμ-Myc_Rep1


title: RNA-seq_DMSO-48h_Ctr_Eμ-Myc_Rep2


title: RNA-seq_DMSO-48h_Ctr_Eμ-Myc_E2_Rep1


title: RNA-seq_DMSO-48h_Ctr_Eμ-Myc_Rep1


title: Dura Tcells, Control peptide

source_name: Dura

extract_protocol:
10X Genomics Chromium Single Cell preparation
NGS Illumina NextSeq - 5' RNAseq with TCR

treatment_protocol: Dura were harvested from mice who received an i.c.m injection of vesicles with control peptides and then sorted for CD45+TCRb+

value: Dura

value: T cells


title: Dura Tcells, MBP peptide

treatment_protocol: Dura were harvested from mice who received an i.c.m injection of vesicles with MBP peptides and then sorted for CD45+TCRb+


title: Dura Tcells, Empty vesicle

treatment_protocol: Dura were harvested from mice who received an i.c.m injection of empty vesicles and then sorted for CD45+TCRb+

value: Empty extracellular vesicles


title: dCLN Tcells, MBP peptide

source_name: dCLN

treatment_protocol: Deep cervical lymph nodes were harvested from mice who received an i.c.m injection of vesicles with MBP peptides and then sorted for CD45+TCRb+

value: dCLN


title: dCLN Tcells, Empty vesicle

treatment_protocol: Deep cervical lymph nodes were harvested from mice who received an i.c.m injection of empty vesicles and then sorted for CD45+TCRb+


title: dCLN Tcells, Control peptide

treatment_protocol: Deep cervical lymph nodes were harvested from mice who received an i.c.m injection of vesicles with control peptides and then sorted for CD45+TCRb+


title: Dura immune cells, empty vesicles

description: Dura were harvested from mice who received an i.c.m injection of empty vesicles and then sorted for CD45+TCRb+

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
See methods for more details
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices, matrices with gene symbols, and barcodes for each sample
Library strategy: 5' RNAseq with TCR

extract_protocol:
10X Genomics Chromium Single Cell preparation
NGS Illumina NextSeq

value: Immune cells


title: RNA-seq_JQ1-48h_INTS15-KO_Eμ-Myc_Rep1

value: Eu-Myc cells


title: Dura immune cells, MBP peptides

description: Dura were harvested from mice who received an i.c.m injection of vesicles with MBP peptides and then sorted for CD45+TCRb+


title: Dura immune cells, control peptide

description: Dura were harvested from mice who received an i.c.m injection of vesicles with control peptides and then sorted for CD45+TCRb+


title: SMAD7fl/fl -2

city: Chongqing

first: Jianguo

last: Hu

state: Chongqing

address: Linjiang Road, No. 76

department: Department of Obstetrics and Gynecology

institute: Chongqing Medical University Second Affiliated Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: FileincludeCountandFPKMvaluesforeachsample

source_name: uterus; endometrium

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The gRNA of the mouse Smad7 gene, the donor vector containing loxP sites, and Cas9 mRNA were co-injected into fertilized mouse eggs.

value: uterus; endometrium

value: blank


title: SMAD7 Cre+/- -2

value: CKO


title: SMAD7 Cre+/- -1


title: 4T1_Radioresistant2

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

data_processing:
The analysis were performed on the OneStopRNASeq platform.
Specifically, paired-end RNASeq reads were aligned to mouse genome mm10 with STAR
Gene expression were quantified with featureCounts
Genome annotation file used was gencode.vM25.primary_assembly
Differential analysis processed with DESeq2
Assembly: mm10
Supplementary files format and content: excel: count and TPM

source_name: TNBC Cells

extract_protocol:
RNA was harvested using the Macherey-Nagel RNA Nucleospin Kit.
400ng of total RNA was used for library preparation
RNA-seq using NovaSeq PE-150 at 30 million raw reads pairs per sample

value: TNBC Cells


title: 4T1_Radioresistant1


title: 4T1_Radioresistant3


title: SMAD7fl/fl -1


title: 4T1_Parental2


title: 4T1_Parental1


title: 4T1_Parental3


title: Trabectedin-treated K7M2 flank tumor

city: Columbus

first: Emily

middle: M.

last: Ringwalt

state: OH

address: 575 Children's Xrd

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description: Trabectedin-treated K7M2 flank tumor

data_processing:
BCL files were converted to fastq files using cellranger mkfastq
Fastq files were processed using cellranger count
Further processing and analyses performed are outlined on GitHub (https://github.com/kidcancerlab/oHSV-trabectedin)
Assembly: The reference genome was built from mm10, hg19, and HSV-1 strain 17 (concatenated into one reference genome).
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

source_name: flank tumor (subQ)

extract_protocol:
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10XGenomics, PN-1000120) according to the manufacturer's instructions.
Libraries were constructed per 10x protocols

treatment_protocol: The Ewing sarcoma human xenografts were treated with either oHSV (1e7 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Osteosarcoma mouse models were treated with either oHSV (1e8 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Tumors were harvested on Day 3.

value: flank tumor (subQ)

value: Osteosarcoma

value: Trabectedin


title: oHSV-treated K7M2 flank tumor

description: oHSV-treated K7M2 flank tumor

value: oHSV


title: BBN-NUMB_KO rep3

city: Milan

first: Salvatore

last: Pece

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology IRCCS,

data_processing:
Sequenced raw reads were processed with NF-CORE RNASeq pipeline, using the human GRCh38 and mouse GRCm39 as reference genomes. Transcript abundances were quantified using the Salmon pseudo-aligner.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text file containing Salmongene-level quantification for each sample, including feature length, effective length, TPM, and number of reads.

source_name: urothelial bladder cancer

extract_protocol:
Total RNA was extracted with QIAzol™ Reagentand then purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Goldkit according to the manufacturer’s protocol

value: urothelial bladder cancer


title: BBN-NUMB_KO Vehicle rep1

value: vehicle