title: thalidomide group, replicate 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating TPM using software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Fresh tumor and adjacent normal tissue samples were surgically removed from patients and immersed in a complete medium containing 90% Dulbecco’s modified eagle medium (DMEM; Cat# 11054001, GIBCO) and 10% fetal bovine serum (FBS; Cat# 16140071, GIBCO), and transported to the lab in a refrigerated container. Suitable small tissue blocks (no necrotic foci / no hemorrhagic foci /less fibrous connective tissue) were cut into pieces (diameter 1-3 mm). The pieces were transferred to the gentle MACS C Tubes (Cat# 130-096-334, Miltenyi Biotec), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Cat# 130-095-929, MiltenyiBiotec). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Cat# 130-093-235, MiltenyiBiotec) following these steps: milled; incubated at 37C for 30 min on a shaker; milled; incubated at 37C for 30 min; milled; filtered through a 70 mm filter, plus 2% FBS. Finally, the single-cell suspension was centrifugated at 400 g for 7 mins, resuspended in CELLSAVING (Cat# C40050, NCM biotech), cryopreserved in Cryotubes (Cat# 430488, Corning) and then stored at -80℃.
This process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not conThis process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not contain cells, and most of the remaining GEM contained one cell

value: hepatocellular carcinoma huh7 cell line under the condition of thalidomide


title: control group, replicate 3

status: Public on Apr 27 2025

type: SRA

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

country: China

institute: The Second Affiliated Hospital of Xinjiang Medical University

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: hepatocellular carcinoma cell

tag: treatment

value: control group


title: U2OS cells, starved_Ars: EBSS+VBL+Ars 3

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to the human reference genome sequences  (hg38) using STAR.
The aligned reads were quantitated by Htseq. The normalization and differentially expressed genes test were implemented by DESeq2.
Assembly: hg38
Supplementary files format and content: Excel file with all normalized counts for each sample

growth_protocol: U2OS cells  were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested with Zymo RNA extraction commercial kit
Illumina total RNA rRNA depletion library preparation kit (Illumina) was used from 1 ug of starting material. All RNA samples underwent Ribosomal depletion following the manufacturers' protocols. The libraries were amplified 10 PCR cycles in the PCR step.

treatment_protocol: Cells were treated with EBSS+VBL/Gln for 18 hours, Arsenite treatment for 50 minutes.

value: Osteosarcoma cancer cell line

tag: stress

value: EBSS+VBL+Arsenite


title: control group, replicate 2


title: U2OS cells, starved_Ars: EBSS+VBL+Ars 2


title: KO monosome RNA rep2

city: Suzhou

first: Zhou

last: Yu

address: 100 Chongwen Road

institute: Chinese Academy of Medical Sciences /Suzhou Institute of Systems Medicine

description: Library name: KO monosome RNA rep2

library_source: other

data_processing:
Sequence reads were trimmed for adaptor sequence/low-guality sequence using fastp(v 0.23.2).
Trimmed seguence reads were mapped to reference genome using Hisat2 (v 2.0.4).
Read count extraction andusing Stringtie(v 1.3.0).
Assembly: tab-delimited text fileincludes raw counts for each sample.
Supplementary files format and content: csv files include FPKM values for each Sample.

molecule: other

organism: Mus musculus

source_name: macrophage

growth_protocol: Bone marrow-derived macrophages were obtained by culturing thigh bone-derived bone marrow cells in complete RPMI-1640 medium containing 20ng/ml recombinant macrophage colony-stimulating factor for 6 days

extract_protocol:
the mRNA of whole cell lysate and the mRNA of polysome and monosome fraction after polysome profiling were harvested using Rneasy mini plus kit (Qlagen). mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: treat with LPS (100ng/ml) for 8h

value: macrophage

tag: genotype

value: Mkrn2 knockout

value: LPS (100ng/ml) for 8 hours


title: 14592.Yeo.17.sh [quant-norm]

type: RNA

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

hyb_protocol: Hybridization and washing was performed as described in the GeneChip WT PLUS Reagent Kit (Affymetrix).

scan_protocol: Scanning was performed on a 7G scanner and imaged with the AGCC portal.

data_processing: Cel files were analyzed using  Expression Console (build 1.4.1.46, Affymetrix) and data was processed with  Affymetrix  package (Affy Power Tools) apt-probeset-summarize.  Iter-plier algorithm was used to quantify probesets with RMA  normalization and DABG probe-level detection. Only probesets with detection  p-value ≤    0.05 in more than half of the microarray samples were considered for downstream  analysis. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by  SepScore (defined as the normalized change in exclusion minus the normalized  change in inclusion).

label: biotin

label_protocol: RNA of stably transduced Lenti-X™ HEK 293T cells was submitted to Affymetrix Human Transcriptome Arrays 2.0 to identify alternative splicing events. Microarray sample preparation was performed using Ambion WT Expression Kit (Thermo Fisher Scientific). Labeling was performed using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

growth_protocol: 293T cells were grown in standard media (DMEM + 10% FBS + 1X Penicillin Streptomycin).

extract_protocol: RNA was extracted by standard Trizol extraction.

treatment_protocol: Knockdowns were performed by transforming shRNA plasmid along with lentivirus packaging plasmids in 293T cells, filtering (.45 micron) supernatant, and infecting a new population of 293T cells. After 48 hours, infected cells were Puromycin selected (1 ug / mL) for 10 days, after which RNA and protein were harvested.


title: 14591.Yeo.16.sh [quant-norm]


title: 14806.Yeo.9.sh [quant-norm]

source_name: APOBEC4 Overexpression-6


title: U2OS cells, starved_Ars: EBSS+VBL+Ars 1


title: 14605.Yeo.30.sh [quant-norm]


title: KO monosome RNA rep1

description: Library name: KO monosome RNA rep1


title: WT monosome RNA rep3

description: Library name: WT monosome RNA rep3

value: wildtype


title: control group, replicate 1


title: disulfiram group, replicate 3

value: hepatocellular carcinoma huh7 cell line under the condition of disulfiram


title: U2OS cells, Arsenite 3

value: Arsenite


title: disulfiram group, replicate 2


title: U2OS cells, Arsenite 2


title: WT monosome RNA rep2

description: Library name: WT monosome RNA rep2


title: WT monosome RNA rep1

description: Library name: WT monosome RNA rep1


title: disulfiram group, replicate 1


title: KO polysome RNA rep3

description: Library name: KO polysome RNA rep3


title: combination group, replicate 3

value: hepatocellular carcinoma huh7 cell line under the condition of disulfiram and  thalidomide


title: KO polysome RNA rep2

description: Library name: KO polysome RNA rep2


title: combination group, replicate 2


title: KO polysome RNA rep1

description: Library name: KO polysome RNA rep1


title: combination group, replicate 1


title: WT polysome RNA rep2

description: Library name: WT polysome RNA rep2


title: WT polysome RNA rep3

description: Library name: WT polysome RNA rep3


title: WT polysome RNA rep1

description: Library name: WT polysome RNA rep1


title: KO total RNA rep3

description: Library name: KO total RNA rep3


title: KO total RNA rep2

description: Library name: KO total RNA rep2


title: KO total RNA rep1

description: Library name: KO total RNA rep1


title: WT total RNA rep3

description: Library name: WT total RNA rep3


title: U2OS cells, Arsenite 1


title: AC CM3

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

institute: The first affiliated hospital of nanjing medaical university

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Assembly: gencode v27
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: Macrophages

growth_protocol: To obtain primary bone marrow-derived macrophages, bone marrow cells first underwent lysis of red blood cells and were then resuspended in complete RPMI-1640 medium consisting of 25 ng/ml macrophage colony-stimulating factor (M-CSF) and cultured for 7 days.

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.

treatment_protocol: Macrophages were treated with culture medium from apoptotic chondrocytes and normal chondrocytes.

tag: strain

value: BMM derived macrophages

value: apoptotic chondrocytes culture medium


title: WT total RNA rep2

description: Library name: WT total RNA rep2


title: AC CM2


title: WT total RNA rep1

description: Library name: WT total RNA rep1


title: 832/13 cells, Kyono MPRA library, cDNA rep 3

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

data_processing:
We processed MPRA sequencing data using a custom pipeline that quantifies barcode counts while accounting for possible sequencing errors. We extracted DNA barcodes from the first 16 bases of the R1 fastq file for the input DNA sample and clustered these at an edit distance of 0. We repeated this process for the cDNA barcode counts and used an added step to remove PCR-duplicated barcodes using the UMI information. The UMI sequence was the reverse complement of the first 6 bp in the R2 file. Finally, we used starcode to cluster and count barcodes.
Assembly: hg19
Supplementary files format and content: "kyono_library_counts.txt" is a tab-delimited text file containing the barcode sequences, the RNA counts for the three replicates and DNA counts for the input sample. "kyono_library_barcode_pairing.txt" is a tab-delimited text file containing the oligo IDs and barcode pairing of each element tested in the MPRA library. "kyono_library_annotations.txt" is a tab-delimited text file containing the oligo IDs and hg19 coordinates of each element tested in the MPRA library.
Library strategy: MPRA amplicon library

organism: Rattus norvegicus

extract_protocol:
We electroporated 50 ug of plasmid into 25 million 832/13 rat insulinoma cells for each biological replicate and lysed cells with TRIzol 24 hours later. After phase separation, we used the Direct-zol RNA Miniprep Kit to isolate total RNA.
We enriched for mature mRNA transcripts with fragment(dT) beads then treated 2 ug of mRNA with DNase I to remove plasmid or genomic DNA contamination. We reverse transcribed 1 ug of mRNA using SuperScript III with a custom primer containing a 6-bp unique molecular identifier (UMI) targeting transcripts derived from the MPRA plasmids (Supplemental Table 3). We treated cDNA samples with DpnI to eliminate any residual plasmid DNA.

value: Insulinoma


title: AC CM1


title: C CM3

value: normal chondrocytes culture medium


title: RA patient 06_CD4, ConA + LPS

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description:
6C
mapped to HG38

data_processing:
Aligned: STAR,  Ref.genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa (Ensembl),
quantification: featureCounts
Assembly: HG38
Supplementary files format and content: matrix with ENS number and samples in each one column

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells,

extract_protocol: Total RNA purification (Norgen, Ontario, Canada)

treatment_protocol: culture activated with anti-CD3, 48h total

tag: agent

value: ConA+LPS

tag: Sex

value: female

tag: disease

value: Rheumatoid arthritis


title: 832/13 cells, Kyono MPRA library, cDNA rep 2


title: RA patient 02_CD4, ConA + LPS

description:
2C
mapped to HG38


title: C CM2


title: 832/13 cells, Kyono MPRA library, cDNA rep 1


title: CD14+ PBMCs, blank control 1, stimulation - MCSF, Day 18

city: Berlin

first: Yi

last: Ren

state: Berlin

address: Charitéplatz 1 10117 Berlin

country: Germany

institute: Charité - Universitätsmedizin Berlin

description:
Library name: Sample1
biol rep 1

data_processing:
Samples were demultiplexed (bcl convert 3.8.4) to fastq data and quality controlled (FastQC, version 0.12.1). Trimmomatic (version 0.38) was used for adapter trimming and read filtering.
Assembly: The resulting reads were aligned to the reference genome (GRCh38.108) using Hisat2 (version 2.2.1).
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Blood

extract_protocol:
RNA extraction was performed with Rnasy mini kit (Qiagen).
Sequencing libraries were generated using the NEBNext Ultra II RNALibrary Prep Kit (New England Biolabs, USA)

tag: tissue

value: Blood

value: PBMC

value: Osteoclastic differentiation


title: RA patient 01_CD4, ConA + LPS

description:
1C
mapped to HG38


title: CD14+ PBMCs, stimulating PD-1 3, stimulation - MCSF + RANKL + sPD-L1, Day 18

description:
Library name: Sample9
biol rep 3


title: CD14+ PBMCs, control 1, stimulation - MCSF + RANKL, Day 18

description:
Library name: Sample4
biol rep 1


title: CD14+ PBMCs, inhibiting PD-1 2, stimulation - MCSF + RANKL + Nivolumab, Day 18

description:
Library name: Sample11
biol rep 2


title: CD14+ PBMCs, control 3, stimulation - MCSF + RANKL, Day 18

description:
Library name: Sample6
biol rep 3


title: CD14+ PBMCs, blank control 2, stimulation - MCSF, Day 18

description:
Library name: Sample2
biol rep 2


title: CD14+ PBMCs, stimulating PD-1 1, stimulation - MCSF + RANKL + sPD-L1, Day 18

description:
Library name: Sample7
biol rep 1


title: macrophage LPS, biological rep1

description: Gene expression data from mouse peritoneal macrophages treated with LPS for 6 hours.

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 controlled by Affymetrix GeneChip Command Console(AGCC).

data_processing: The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mouse macrophage treated with LPS for 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (The Ambion® WT Expression Kit protocol, 2009, Applied Biosystems).

growth_protocol: Peritoneal macrophages were harvested from mice 4 days after thioglycollate injection, and cultured in RPMI1640 supplemented with 10%FBS.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mouse peritoneal macrophages cells were plated into 6-cm dishes  and treated with LPS (100ng/ml) for 6 hours or untreated.

tag: age

value: 6 weeks

tag: gender


title: CD14+ PBMCs, blank control 3, stimulation - MCSF, Day 18

description:
Library name: Sample3
biol rep 3


title: CD14+ PBMCs, inhibiting PD-1 1, stimulation - MCSF + RANKL + Nivolumab, Day 18

description:
Library name: Sample10
biol rep 1


title: CD14+ PBMCs, stimulating PD-1 2, stimulation - MCSF + RANKL + sPD-L1, Day 18

description:
Library name: Sample8
biol rep 2


title: C CM1


title: CD14+ PBMCs, control 2, stimulation - MCSF + RANKL, Day 18

description:
Library name: Sample5
biol rep 2


title: thalidomide group, replicate 3

value: hepatocellular carcinoma cell

value: hepatocellular carcinoma huh7 cell line under the condition of thalidomide


title: CD14+ PBMCs, inhibiting PD-1 3, stimulation - MCSF + RANKL + Nivolumab, Day 18

description:
Library name: Sample12
biol rep 3


title: MM cells, LANA overexpression, bio rep 2

status: Public on Apr 26 2025

city: Pittsburgh

first: Shenyu

last: Sun

state: PA

address: 5117 Centre Ave, HCC G.1

institute: University of Pittsburgh

description: Library name: MM_LANA_2

data_processing:
RNA-seq data analysis was performed by first processing raw reads in fastq format to obtain clean reads, which were then aligned to the rat genome mRatBN7.2 using STAR. Transcripts were assembled, and raw gene counts were estimated using featureCounts and presented in TPM (transcripts per million). Differentially expressed genes (DEGs) were identified using DESeq2 with a significance threshold of P-adjusted value < 0.05 and fold change ≥ 2. ASEs were analyzed with SUPPA2 , and results were filtered based on significance (P-adjusted value < 0.05), percent spliced-in (PSI) changes (|ΔPSI| > 0.1), and SUM(TPMs of three replicates) ≥ 2.5. Gene ontology (GO) analysis for functional annotation of candidate alternative spliced transcripts was conducted using the online database for annotation, visualization, and integrated discovery.
Assembly: mRatBN7.2
Supplementary files format and content: csv filies include PSI vasues and TPM values for each sample

source_name: MM cell

growth_protocol: All cell lines were maintained in in DMEM supplemented with 10% fetal bovine serum (FBS) and antibotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using TRIZOL. 10 ug of total RNA was used for the consturction of sequencing libraries
RNA libraries for RNA-seq were prepared using mRNA-seq Library Prep Kit following manufacture's protocols, following by HMR rRNA depletion

treatment_protocol: FAM50A knockout was conducted by the CRIPSR-Cas9, KMM vFLIP, vCyclin, and miRNA deletion were conducted by the modification of BAC36 to generate the deletion mutant, MM LANA overexpression was conducted by plasmid and lentivirus transduction.

value: MM cell

value: mesenchymal stem cells

value: LANA overexpression

value: NO

tag: batch


title: MM cells, LANA overexpression, bio rep 3

description: Library name: MM_LANA_3


title: macrophage mock, biological rep1

description: Gene expression data from untreated mouse peritoneal macrophages.

source_name: Mouse macrophage untreated


title: MM cells, pIRES vector control, bio rep 3

description: Library name: MM_pIRES_3

value: pIRES vector control


title: MM cells, LANA overexpression, bio rep 1

description: Library name: MM_LANA_1


title: MM cells, pIRES vector control, bio rep 1

description: Library name: MM_pIRES_1


title: MM cells, pIRES vector control, bio rep 2

description: Library name: MM_pIRES_2


title: KMM cells, viral miRNA cluster Knockdout, bio rep 3

description: Library name: KMM_dmiR_3

source_name: KMM cell

value: KMM cell

value: viral miRNA cluster deletion


title: KMM cells, viral miRNA cluster Knockdout, bio rep 2

description: Library name: KMM_dmiR_2


title: KMM cells, viral miRNA cluster Knockdout, bio rep 1

description: Library name: KMM_dmiR_1


title: KMM cells, vCyclin Knockdout, bio rep 3

description: Library name: KMM_dvCyclin_3

value: vCyclin deletion


title: KMM cells, vCyclin Knockdout, bio rep 2

description: Library name: KMM_dvCyclin_2


title: KMM cells, sgFAM50A-3, bio rep 2

description: Library name: KMM_sg28ko_2

value: FAM50A knockout


title: KMM cells, vFLIP Knockout, bio rep 1

description: Library name: KMM_dvFLIP_1

value: vFLIP deletion


title: KMM cells, sgFAM50A-1, bio rep 3

description: Library name: KMM_sg15_3


title: KMM cells, WT, bio rep 2

description: Library name: KMM_2

value: WT


title: KMM cells, sgFAM50A-3, bio rep 1

description: Library name: KMM_sg28ko_1


title: MM cells, sgFAM50A-3, bio rep 1

description: Library name: MM_sg14_1


title: MM cells, sgFAM50A-2, bio rep 3

description: Library name: MM_sg12_3


title: KMM cells, vFLIP Knockout, bio rep 2

description: Library name: KMM_dvFLIP_2


title: control group, replicate3, input RNA

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome.
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m1A peaks with bed format.
HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: m1A-seq

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m1A-specific antibody in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: control group


title: KMM cells, vCyclin Knockdout, bio rep 1

description: Library name: KMM_dvCyclin_1


title: KMM cells, sgFAM50A-1, bio rep 2

description: Library name: KMM_sg15_2


title: KMM cells, sgFAM50A-2, bio rep 3

description: Library name: KMM_sg22_3


title: MM cells, sgFAM50A-3, bio rep 3

description: Library name: MM_sg14_3


title: KMM cells, sgFAM50A-2, bio rep 2

description: Library name: KMM_sg22_2


title: ATAC-seq of glioma sample MG5 (Glioblastoma, Grade IV, Primary, IDH1 WT)

city: Cincinnati

first: Matthew

last: Garrett

state: Ohio

address: 5061 myerdale drive

institute: Kettering Health

description: Library name: MG5

library_source: genomic

data_processing:
ATAC-seq reads in FASTQ format were subjected to quality control using FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1 to assess the need for trimming of adapter sequences or bad quality segments.
Trimmed reads were aligned to the reference human genome version GRCh38/hg38 with the program HISAT2 v2.0.5.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Peaks were called using the program MACS v2.1.2 using the broad peaks mode.
To obtain the consensus set of unique peaks, called peaks from all samples were merged at 50% overlap using BEDtools v2.27.0.
Assembly: GRCh38/hg38
Supplementary files format and content: Consensus peaks were converted to a Gene Transfer Format (GTF) to enable counting of reads under the peaks. Raw read counts were normalized with respect to library size and transformed to log2 scale using rlog() function in R package DESeq2. TPM matrices containing normalized read counts for the most variable peaks (5000 peaks), the 329 peaks selected by cox regression, and the 30 peaks used in the final prediction model.
Supplementary files format and content: Peak-gene correlation matrices listing peaks, their corresponding genes based on topologically associating domain (TAD) regions, and their correlation coefficients (r² > 0.6 and r² > 0.7). Quality control reports and quantification of peak counts above TPM threshold of 10.

molecule: genomic DNA

source_name: Brain tissue

growth_protocol: Frozen patient tumor tissue (<0.5 cm) was collected from an IRB-approved biorepository.

extract_protocol:
Nuclei were isolated from patient tumor tissue as described by Habib et al., with slight modifications. Frozen tissue samples (<0.5 cm) were incubated on ice in 1 mL of Nuclei EZ Lysis Buffer (Sigma, #Nuc-101). The tissue was homogenized using a glass tissue grinder. Additional EZ Lysis Buffer was added, incubated on ice for 5 min, and filtered through a 70 μm cell strainer. Nuclei were collected by centrifugation and resuspended in ATAC-resuspension buffer.
ATAC-seq library preparation was performed as previously described by Buenrostro et al. Nuclei were filtered through 40 μm and 5 μm cell strainers and resuspended in ATAC-resuspension buffer (10 mM Tris–HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20).

treatment_protocol: All specimens denoted as "Grade II," "Grade III," or "Grade IV primary" were taken from the patient's initial surgery and had not been exposed to any chemotherapy or radiation treatment. Recurrent samples were from patients who underwent standard therapy including temozolomide and radiation after initial surgery.

value: Brain tissue

value: Glioblastoma

value: IDH1 WT


title: KMM cells, WT, bio rep 1

description: Library name: KMM_1


title: MM cells, sgFAM50A-1, bio rep 3

description: Library name: MM_sg11_3


title: MM cells, sgFAM50A-2, bio rep 2

description: Library name: MM_sg12_2


title: MM cells, sgFAM50A-2, bio rep 1

description: Library name: MM_sg12_1


title: MM cells, sgFAM50A-1, bio rep 2

description: Library name: MM_sg11_2


title: KMM cells, sgFAM50A-3, bio rep 3

description: Library name: KMM_sg28ko_3


title: KMM cells, vFLIP Knockout, bio rep 3

description: Library name: KMM_dvFLIP_3


title: MM cells, WT, bio rep 3

description: Library name: MM_3


title: MM cells, sgFAM50A-1, bio rep 1

description: Library name: MM_sg11_1


title: KMM cells, sgFAM50A-1, bio rep 1

description: Library name: KMM_sg15_1


title: T-cells, 48-hour activation, Levamisole 1mM,  Donor 3

city: Amsterdam

first: Gerarda

middle: Hendrika

last: Khan

address: Chico Mendesstraat 39

department: Pathology

country: Netherlands

institute: Amsterdam UMC - AMC

data_processing:
Performed in the Galaxy web platform (usegalaxy.org)
Quality assesment with FASTQC in Galaxy. All phred scores were >28 with a mean phred of 36, sequence reads were trimmed for adaptor sequence with Trim Galore! In Galaxy.
Trimmed sequence reads were mapped to GRCh38 with HISAT2 in Galaxy
Read count extraction was performed with Featurecounts in Galaxy and normalization was performed with DESeq2 (median of ratios) in Galaxy.
Assembly: GRCh38
Supplementary files format and content: tab-delimited csv file including DESeq2 median of ratios (counts) values for each Sample

source_name: Primary

growth_protocol: Purified T cells were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 2mM L-glutamin, 100 U/mL of penicillin, 100 μg/mL of streptomycin (Gibco, Thermo Fisher Scientific), and 10% fetal calf serum (FCS; HyClone, GE Healthcare Life Sciences). T cells were cultured at a density of 1x106 cells/mL at 37 °C/5% CO2. Purified T cells were activated for 1 to 2 days with Human T-Activator anti-CD3/CD28 dynabeads at a 1:2 bead-to-cell ratio (Gibco, Thermo Fisher Scientific). Prior to lysing the cells to obtain RNA, the T cells were detached from the dynabeads by manual dispersion and magnetic separation, as per the manufacturer’s instructions.

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 RNA-seq were prepared using Illumina TruSeq stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: At the start of activation, T cell samples were treated with 1mM levamisole (levamisole-hydrochloride, Sigma-Aldrich or 1:200 µL H2O (solvent control condition). T cell samples were debeaded, washed with cold PBS and lysed in TRI reagent (Thermo Fisher Scientific)

value: Primary

value: Isolated pan T-cells

value: Levamisole 1 mM

tag: activation

value: aCD3aCD28 dynabeads 1:2 bead-to-cell ratio

tag: time

value: 48 hour

tag: donor


title: MM cells, WT, bio rep 1

description: Library name: MM_1

value: MM cell

value: mesenchymal stem cells

value: NO


title: T-cells, 48-hour activation, Levamisole 1mM,  Donor 2


title: T-cells, 48-hour activation, Control, Donor 3

value: Solvent control


title: T-cells, 48-hour activation, Control, Donor 2


title: in vitro culture, M. marinum, biol rep 3

city: DURHAM

first: David

last: Tobin

state: NC

address: Duke University Medical Center

department: Molecular Genetics and Microbiology

institute: Duke University

description: Library name: Marinum_log_3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were pseudo-aligned to GRCz11/ASM1834v1 using Kallisto.
Read count extraction and normalization were performed using Kallisto.
Assembly: GRCz11, ASM1834v1
Supplementary files format and content: tsv files include TPM values for each transcript

organism: Mycobacterium marinum

source_name: log phase in vitro culture

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen). 500 ng of total RNA was used to construct sequencing libraries.
RNA samples were reverse transcribed into cDNA and then processed into sequencing libraries using the Illumina Total RNA-seq with Ribo-Zero Plus Microbiome kit with extra custom rRNA depletion probes for Zebrafish and Mycobacterium marinum (Illumina Code: 20072063). For bacterial RNA enrichmnet, Zebrafish mRNA was removed from total RNA using two oligo dT captures (Kapa mRNA HyperPrep Kit from Roche (KK8581)). Then, the remaining RNA in the supernatants were pooled, reverse transcribed into cDNA and processed into sequencing libraries as described above.

value: log phase in vitro culture

value: wild type bacteria


title: in vitro culture, M. marinum, biol rep 2

description: Library name: Marinum_log_2


title: T-cells, 48-hour activation, Levamisole 1mM,  Donor 1


title: in vitro culture, M. marinum, biol rep 1

description: Library name: Marinum_log_1


title: T-cells, 24-hour activation, Levamisole 1mM,  Donor 3

value: 24 hour


title: T-cells, 48-hour activation, Control, Donor 1

value: WT


title: hCO-D10-V190G-2

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description: gencode.genes.combined.txt

data_processing: EdgeR

molecule: cytoplasmic RNA

source_name: Neuroepithelium

growth_protocol: IPSC were maintained in mTESR-PLUS, EB/NE/BO are generated by human cerebral organoid protocol. Detailed protocol is available in the manuscript or upon request.

extract_protocol:
organoid pellet was lysed in lysis buffer(20mM Tris-Cl pH7.5, 5mM MgCl2, 150mM NaCl, 1mM DTT, 0.1% NP-40). Lysate was collected into 1.5mL tube and stay on ice for 15min. Lysate was then centrifuged at 21130g at 4°C for 10min to remove nuclei, mitochondria and debris. The supernatant was collected and the cytoplasmic RNA was extracted by Trizol-LS(ThermoFisher, 10296028) following the manufacturer’s protocol.
Ribo-minus TruSeq Stranded mRNA

value: Neuroepithelium


title: hCO-D10-V190G-1

description: gencode.genes.combined.txt


title: T-cells, 24-hour activation, Control, Donor 2


title: T-cells, 24-hour activation, Control, Donor 1


title: hCO-D10-WT-2

description: gencode.genes.combined.txt


title: T-cells, 24-hour activation, Levamisole 1mM,  Donor 1


title: hCO-D10-WT-1

description: gencode.genes.combined.txt


title: KO_1

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

institute: DKFZ

data_processing:
For all samples, low-quality bases were removed with the Fastq_quality_filter from the FASTX Toolkit 0.0.13 (FASTX-Toolkit) with 90% of the reads needing a quality phred score > 20. Homertools 4.7 (Heinz et al., 2010) were used for PolyA-tail trimming, and reads with a length < 17 were removed. Filtered reads were quantified with Kallisto (Bray et al., 2016) using RefSeq transcripts of the mouse mm10 reference (McGarvey et al., 2015) (kallisto parameters -b 10 -t 3 --plaintext --single -l 292 -s 50). Later, in the customized analysis, the gene identifiers were converted to Ensembl IDs with the org.Mm.eg.db R package, and the Gencode vM4 annotation, which included only protein-coding genes, was used for transcriptome annotation. TPM was used as the normalization method.
Assembly: mm10
Supplementary files format and content: txt file with counts and tpm values per sample.

source_name: lung

extract_protocol:
RNA from FACS-sorted EC was isolated with an Arcturus PicoPure RNA Isolation Kit. The frozen pellet was resuspended in 50 μl of Arcturus PicoPure extraction buffer, and RNA was isolated according to the manufacturer’s instructions. The RNA was eluted in 13 μl of RNase-free water, and the concentration was measured using a high-sensitivity RNA assay with a Qubit Fluorometer according to the manufacturer’s instructions.
A sequencing library was generated with 10 ng of total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) according to the manufacturer’s protocol. Sequencing reads (100 bp paired-end reads) were generated on the HiSeq platform (Illumina) with four samples per lane.

value: lung

value: endothelial cell

value: ko


title: 274-D30-BO-Mut

data_processing: Reads from scRNA-seq were aligned to the GRCh38 human reference genome and the cell-by-gene count matrices were produced using the Cell Ranger pipeline (10x Genomics). Data were analysed using the Seurat R package v.3.1.5using R v.4.2. Data from 10 individual runs were merged.

source_name: Brain organoid

extract_protocol:
Organoids were dissociated as described in  in the cited paper 38(Kanton, S., Boyle, M.J., He, Z. et al. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 574, 418–422 (2019).)
scRNA-seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 or v3.1 (10x Genomics, PN-1000075, PN-1000121).

value: Brain organoid


title: 274-D30-BO-WT


title: KO_3


title: thalidomide group, replicate 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating TPM using software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Fresh tumor and adjacent normal tissue samples were surgically removed from patients and immersed in a complete medium containing 90% Dulbecco’s modified eagle medium (DMEM; Cat# 11054001, GIBCO) and 10% fetal bovine serum (FBS; Cat# 16140071, GIBCO), and transported to the lab in a refrigerated container. Suitable small tissue blocks (no necrotic foci / no hemorrhagic foci /less fibrous connective tissue) were cut into pieces (diameter 1-3 mm). The pieces were transferred to the gentle MACS C Tubes (Cat# 130-096-334, Miltenyi Biotec), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Cat# 130-095-929, MiltenyiBiotec). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Cat# 130-093-235, MiltenyiBiotec) following these steps: milled; incubated at 37C for 30 min on a shaker; milled; incubated at 37C for 30 min; milled; filtered through a 70 mm filter, plus 2% FBS. Finally, the single-cell suspension was centrifugated at 400 g for 7 mins, resuspended in CELLSAVING (Cat# C40050, NCM biotech), cryopreserved in Cryotubes (Cat# 430488, Corning) and then stored at -80℃.
This process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not conThis process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not contain cells, and most of the remaining GEM contained one cell

value: hepatocellular carcinoma cell

value: hepatocellular carcinoma huh7 cell line under the condition of thalidomide


title: WT_3

value: wt


title: KO_2


title: T-cells, 24-hour activation, Levamisole 1mM,  Donor 2

value: Primary

value: Isolated pan T-cells

value: Levamisole 1 mM

value: aCD3aCD28 dynabeads 1:2 bead-to-cell ratio


title: 274-D15-NE-Mut


title: WT_2


title: 274-D10-NE-Mut


title: 274-D10-NE-WT


title: 274-D5-EB-Mut

source_name: Embryoid body

value: Embryoid body


title: 274-D15-NE-WT


title: 274-D5-EB-WT


title: WT_1


title: S1B

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: pre-cDCs DNGR-1 KO CD45.2 from spleen

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using RSEM v1.3.0  and STAR v2.5.2 with the “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Raw counts were processed using the bioconductor package DESeq2 v1.18.1 in R v3.4.3. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Assembly: GRCm38
Supplementary files format and content: tab delimited vst normalised expression data, where columns are samples and row are ensembl mouse IDs
Supplementary files format and content: tab delimited raw_counts output of STAR alignment and RSEM quantifications. Columns are samples and rows are ensembl mouse IDs

source_name: pre-cDCs DNGR-1 KO CD45.2 from spleen

extract_protocol:
RNeasy Micro kit [Qiagen]
Total RNA (KAPA Hyper prep with Riboerase)

treatment_protocol: No Treatment

value: pre-cDCs DNGR-1 KO CD45.2 from spleen

value: KO


title: T-cells, 24-hour activation, Control, Donor 3

value: Solvent control

value: 24 hour


title: S2B

description: pre-cDCs DNGR-1 KO CD45.2 from spleen


title: 274-D0-IPS-Mut

source_name: iPSC

extract_protocol:
Organoids were dissociated as described in  in the cited paper 38(Kanton, S., Boyle, M.J., He, Z. et al. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 574, 418–422 (2019).)
scRNA-seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 or v3.1 (10x Genomics, PN-1000075, PN-1000121)

value: iPSC


title: B3D

description: pre-cDCs DNGR-1 KO CD45.2 from bone marrow


title: Granulomas, Rac2D57N, enriched, biol rep 3

description: Library name: Rac2D57N_Enr_3

organism:
Mycobacterium marinum
Danio rerio

source_name: Granulomas

value: Granulomas

value: Neutrophil deficient mutant


title: B2D

source_name: pre-cDCs DNGR-1 KO CD45.2 from bone marrow


title: MM cells, WT, bio rep 2

description: Library name: MM_2

value: MM cell

value: mesenchymal stem cells

value: WT

value: NO


title: B1D

value: pre-cDCs DNGR-1 KO CD45.2 from bone marrow


title: 274-D0-IPS-WT


title: Granulomas, Rac2D57N, enriched, biol rep 2

description: Library name: Rac2D57N_Enr_2


title: B3C

description: pre-cDCs DNGR-1 WT CD45.2 from bone marrow

source_name: pre-cDCs DNGR-1 WT CD45.1 from bone marrow


title: Granulomas, Rac2D57N, enriched, biol rep 1

description: Library name: Rac2D57N_Enr_1


title: B2C

value: pre-cDCs DNGR-1 WT CD45.1 from bone marrow


title: Granulomas, wild-type, enriched, biol rep 4

description: Library name: WT_Enr_4

value: wild type


title: mAdu3

data_processing:
WGBS samples were processed by our in-house standard pipeline. The raw reads were aligned with BWA mem (version 0.7.8) on the mouse genome mm10 and additionally concatenated with the lambda genome to infer the bisulfite conversion rate. Methylation data were processed in a unified way for all experiments. The raw methylation values (i.e., the fraction of reads that were methylated at each CpG position) for the CpG dinucleotides were merged into a single value by weighting the CpG coverage. The methylation values were subsequently smoothed with the bsseq package (1.34.0). A window-based method was used for detecting DMRs. The genome was split into 1 kb windows, and the mean methylation level was calculated for each window. Windows with fewer than 5 CpG sites were filtered out.
Assembly: mm10
Supplementary files format and content: txt file containing the mean methylation per region and genotype.

extract_protocol:
Genomic DNA from sorted EC was isolated using the QIAamp DNA Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
T-WGBS was essentially performed as described previously (Wang et al., 2013) using 30 ng genomic mouse DNA as input. Three sequencing libraries were generated per sample and each was sequenced 100 bp, paired-end on one lane of a HiSeq2000 (Illumina, San Diego, California, US) machine.

value: lung

value: endothelial cell


title: mAdu2


title: Granulomas, wild-type, enriched, biol rep 3

description: Library name: WT_Enr_3


title: S2A

description: pre-cDCs DNGR-1 WT CD45.2 from spleen

source_name: pre-cDCs DNGR-1 WT CD45.1 from spleen

value: pre-cDCs DNGR-1 WT CD45.1 from spleen


title: mAdu1


title: Aged3


title: Aged1


title: Aged2


title: Granulomas, wild-type, enriched, biol rep 1

description: Library name: WT_Enr_1


title: wt-r3

data_processing:
WGBS samples were processed by our in-house standard pipeline. The raw reads were aligned with BWA mem (version 0.7.8) on the mouse genome mm10 and additionally concatenated with the lambda genome to infer the bisulfite conversion rate. Methylation data were processed in a unified way for all experiments. The raw methylation values (i.e., the fraction of reads that were methylated at each CpG position) for the CpG dinucleotides were merged into a single value by weighting the CpG coverage. The methylation values were subsequently smoothed with the bsseq package (1.34.0). A window-based method was used for detecting DMRs. The genome was split into 1 kb windows, and the mean methylation level was calculated for each window. Windows with fewer than 5 CpG sites were filtered out.
Assembly: mm10
Supplementary files format and content: txt file containing the mean methylation per region and per sample.

value: wt


title: wt-r2


title: wt-r1


title: Granulomas, Rac2D57N, biol rep 3

description: Library name: Rac2D57N_3


title: WT, replicate 2, scRNA-seq

city: Munich

first: Katalin

last: Todorov-Völgyi

address: Feodor-Lynen-Str 17

department: ISD

institute: LMU Munich

data_processing:
Raw fastq files were processed using cellranger count (v7.1.0; 10X Genomics) with default settings
Assembly: mm10-2020-A
Supplementary files format and content: cellranger output files (cell by gene matrices)

molecule: polyA RNA

source_name: brain

extract_protocol:
Brain endothelial cells (BECs) were isolated from whole mouse brain as previously described (see methods in manucript) and sorted using Fluorescence-activated cell sorting (FACS). Following CD31 enrichment, cell suspension was resuspended in Flow Cytometry buffer (Invitrogen, Cat# 00-4222-26) and stained with CD11b (Invitrogen, Cat# 53-0112-82), CD45 (Invitrogen, Cat# 53-0451-82) and Fixable Viability Dye eFluor™ 780 (Invitrogen, Cat# 65-0865-14). Doublets and microglia population (defined as CD11b and CD45+) were gated out prior to FACS. Viable ECs were sorted into RPMI media (Invitrogen, Cat# 11835030) supplemented with 10% FBS.
Fresh single cell suspensions were centrifuged and resuspended in PBS containing 0,04% ultra-pure BSA. Libraries for single-cell sequencing (scRNA-seq) were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics) following manufacturer’s instructions.

value: brain


title: Granulomas, Rac2D57N, biol rep 2

description: Library name: Rac2D57N_2


title: ko-r3

value: ko


title: Foxf2-ECKO, replicate 1, scRNA-seq

description: Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics)


title: HER2.eSPR macrophage treated

city: Duarte

first: Siqi

last: Chen

address: E 1500 Duarte Rd.

department: Department of Immuno-Oncology

institute: City of Hope Beckman Research Institute

description:
Library name: eSPR
Around 7,000 cells per sample were captured on a 10xGenomics Chromium controller using a 10X V3.1 Single Cell 3’ Solution kit (10xGenomics, Chromium Next GEM Single Cell 3’ Regent kits V3.1, Cat. PN-1000268). All protocols were performed following the manufacturer’s instructions. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) to determine the library size. The library concentration was determined with a Qubit High Sensitivity DNA assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired end setting of 28 cycles of read1, 101 cycles of R2, 10 cycles of index i7, and 10 cycles of index i5 read on Illumina NovaSeq 6000 platform with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at TGen.

data_processing:
The libraries were sequenced with the paired end setting of 28 cycles of read1, 101 cycles of R2, 10 cycles of index i7, and 10 cycles of index i5 read on Illumina NovaSeq 6000 platform with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at TGen.
Single-cell RNA-seq reads were quantified by Cell Ranger-7.1.0, aligned to transcriptome Mus musculus. GRCm39.105. Each sample resulted in over 190 million aligned reads, with over 95% of the reads aligning successfully. The raw data from UTD and HER2.eSPR macrophage-treated groups were combined and subjected to filtering to remove cells that expressed fewer than 500 genes, or more than 5,000 genes, or had more than 5% mitochondrial reads. The data was then normalized and log-transformed using the Normalize Data function from Seurat (v4.3.0).
The Seurat vst algorithm was employed to identify the top 2,000 highly variable genes. Subsequently, the data was scaled, and the jackstraw analysis was performed. The elbow plot of standard deviation in each principal component (PC) indicated that the first 20 PCs captured the majority of true signals. These PCs were used to generate the K-nearest neighbor (KNN) neighborhood graph, and clustering was performed using the Louvain algorithm with a 0.7 resolution.
Assembly: mm39
Supplementary files format and content: processed data files are formatted in tsv and mtx

source_name: tumor infiltrated leukocytes

extract_protocol:
Tumor tissues were extracted on experiment day 13 and processed, stained with anti-CD45 antibody and live CD45+ tumor-infiltrating leukocytes were sorted using BD Aria III sorter.
The samples were submitted to the Integrative Genomics Core at City of Hope for library preparation and subsequent RNA sequencing. Around 7,000 cells per sample were captured on a 10xGenomics Chromium controller using a 10X V3.1 Single Cell 3’ Solution kit (10xGenomics, Chromium Next GEM Single Cell 3’ Regent kits V3.1, Cat. PN-1000268). All protocols were performed following the manufacturer’s instructions. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) to determine the library size. The library concentration was determined with a Qubit High Sensitivity DNA assay Kit (Thermo, Cat. Q32854).

value: tumor infiltrated leukocytes

value: treated


title: Control vector treansfected keloid fibroblasts

city: Seoul

first: XIANGLAN

last: ZHANG

address: Yonsei roo

institute: Yonsei University

description: Gene expression data from keloid fibroblasts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software (AGCC). Signal intensities were normalized using RMA (Robust Multi-chip Average) algorithm via Affymetrix Expression Console 1.3.1.

source_name: Keloid fibroblast

label_protocol: 100ng total RNA labeling protocol was used.

growth_protocol: Keloid fibroblasts cultured in a mixture of Dulbecco’s modified Eagle’s medium (DMEM; Gibco BRL, Grand Island, NY) and Ham’s nutrient mixture F12 (Gibco BRL, Grand Island, NY) medium at a 3:1 ratio. The media were supplemented with 10% fetal bovine serum

treatment_protocol: Keloid fibroblasts were constructed using transfection with a CA9 human-tagged ORF clone (RG204839, Origene, MD, USA) or the related empty vector (E. vector) using the P2 primary cell 4D-nucleofector™ X Kit (Lonza Bioscience, Maryland, USA).

value: keloid


title: CA9 overexpression keloid fibroblasts


title: B1C


title: ko-r2


title: Granulomas, Rac2D57N, biol rep 1

description: Library name: Rac2D57N_1

value: Granulomas

value: Neutrophil deficient mutant


title: UTD macrophage treated

description:
Library name: UTD
Around 7,000 cells per sample were captured on a 10xGenomics Chromium controller using a 10X V3.1 Single Cell 3’ Solution kit (10xGenomics, Chromium Next GEM Single Cell 3’ Regent kits V3.1, Cat. PN-1000268). All protocols were performed following the manufacturer’s instructions. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) to determine the library size. The library concentration was determined with a Qubit High Sensitivity DNA assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired end setting of 28 cycles of read1, 101 cycles of R2, 10 cycles of index i7, and 10 cycles of index i5 read on Illumina NovaSeq 6000 platform with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at TGen.

value: control


title: Granulomas, wild-type, enriched, biol rep 2

description: Library name: WT_Enr_2


title: WT, replicate 1, scRNA-seq

value: WT


title: Foxf2-ECKO, replicate 3, scRNA-seq


title: TNFα + irisin treated group 2

city: Guangzhou

first: Taiqiu

state: Guangdong

address: 33, Yinfeng Road

institute: Sun yat-sen university

description: TNFα+iri 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Human nucleus pulposus cells

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: Human nucleus pulposus cells

value: regular culture with TNF-alpha and irisin treatment

value: Day 3


title: WT, replicate 3, scRNA-seq


title: Granulomas, wild-type, biol rep 4

description: Library name: WT_4

value: wild type


title: MUT_380

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut Street

department: Department of Orthopaedic Research

institute: Thomas Jefferson University

description: Opa1cKO 5

data_processing:
the sequence reads were aligned by STAR 2.7.11b, and counts data were retrieved by --quantMode option
Assembly: mm10
Supplementary files format and content: raw counts and TPM

source_name: Nucleus Pulposus

extract_protocol:
Caudal NP tissues from wild type and Opa1 conditional knockout mice (n=6 mice/genotype) were micro-dissected under a stereo microscope (Zeiss, Stemi 503) and immediately placed in RNAlater® Reagent (Invitrogen, Carlsbad, CA). Tissues were stored at -80°C until the time of RNA isolation, wherein they were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971), and RNA was extracted from the lysates using an RNeasy® Mini kit (Qiagen).
Libraries for whole transcriptome RNA sequencing were prepared using the Stranded Total RNAseq with Ribo-zero Plus kit (Illumina, San Diego, CA) as per manufacturer’s instructions starting with an input of 50 ng of RNA and 14 cycles of final PCR amplification.  Library size was assessed using the 4200 TapeStation and the DNA D5000 ScreenTape assay (Agilent, Santa Clara, CA).  Library concentration was determined using the Qubit Fluorometer 2.0 (ThermoFisher Scientific, Waltham, MA).

treatment_protocol: The Opa1 gene was selectively (Intervertebral disc compartment and cartilage) deleted in fully matured 3-month-old mice using AcanCre and aged for an additional 9 months. All genotypes received an intraperitoneal injection of 100 mg/kg tamoxifen (Sigma-Aldrich, St. Louis, MO, USA) dissolved in palm oil (Sigma-Aldrich) for 3 consecutive days to activate Cre recombinase. Mice were euthanized with CO2 asphyxiation.

value: Nucleus Pulposus

value: 12 months

value: Female


title: ko-r1

value: lung

value: endothelial cell


title: Granulomas, wild-type, biol rep 3

description: Library name: WT_3


title: d3a-wt-r2

data_processing:
ATAC-seq reads were processed using the ENCODE ATAC-seq pipeline kundajelab/atac_dnase_pipelines v1, unless otherwise specified (Lee et al., 2016). As a reference, the mm10 genome was used. Reads were trimmed using Cutadapt and the parameters -e 0.1 -m 5 and aligned using bowtie2 allowing 0 multimapping and -X2000 --mm –local parameters. Duplicated reads were marked using picard and mitochondrial reads were removed from the analysis.
Assembly: mm10
Supplementary files format and content: ATAC peak list per samples as txt file.

extract_protocol:
Murine pulmonary EC were subjected to FACS, pelleted for 7 min at 500 × g in a prechilled (4°C) fixed-angle centrifuge, and resuspended in 50 µl of cold lysis buffer (10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20, 0.01% Digitonin). The nuclei isolation reaction was incubated for 3 min at room temperature. After lysis, 1 ml of ATAC-RSB (10 mM Tris-HCL (pH 7.4), 10 mM NaCl, and 3 mM MgCl2) containing 0.1% Tween20 was added and mixed. Nuclei were pelleted for 10 min at 500 × g at 4°C and resuspended in 50 µl of transposition buffer (10 mM Tris-HCl (pH 7.6), 5 mM MgCl2, 10% Dimethyl Formamide, 2.5µl Transposase (100nM final concentration), 0.1% Tween20, 0.01% Digitonin,16.5µl PBS, 5µl H2O). Transposition reaction was incubated for 30 min at 37°C in a thermomixer shaking at 1000r.p.m. The reaction was stopped with 20 µl of 5 M guanidinium thiocyanate, the ATAC raw material was purified with a 2x volume of Ampure XP DNA purification beads, and the DNA was eluted in 25 µl of H2O.
The DNA eluate was PCR amplified using 1x NEBNext High Fidelity Mix in a total volume of 50 µl. The number of cycles used for library amplification depended on the observed amplification curve and varied between 10 and 15 cycles. ATAC libraries were purified with a 1.4x volume of Ampure XP DNA purification beads, and the DNA was eluted in 12 µl of elution buffer.

value: wt


title: Granulomas, wild-type, biol rep 2

description: Library name: WT_2


title: Foxf2-ECKO, replicate 2, scRNA-seq

value: brain


title: MUT_376

description: Opa1cKO 4

value: Male


title: Granulomas, wild-type, biol rep 1

description: Library name: WT_1


title: MUT_373

description: Opa1cKO 3


title: TNFα treated group 2

description: TNFα 2

value: regular culture with TNF-alpha treatment


title: d3a-wt-r1


title: TNFα treated group 1

description: TNFα 1


title: KMM cells, sgFAM50A-2, bio rep 1

description: Library name: KMM_sg22_1

data_processing:
RNA-seq data analysis was performed by first processing raw reads in fastq format to obtain clean reads, which were then aligned to the rat genome mRatBN7.2 using STAR. Transcripts were assembled, and raw gene counts were estimated using featureCounts and presented in TPM (transcripts per million). Differentially expressed genes (DEGs) were identified using DESeq2 with a significance threshold of P-adjusted value < 0.05 and fold change ≥ 2. ASEs were analyzed with SUPPA2 , and results were filtered based on significance (P-adjusted value < 0.05), percent spliced-in (PSI) changes (|ΔPSI| > 0.1), and SUM(TPMs of three replicates) ≥ 2.5. Gene ontology (GO) analysis for functional annotation of candidate alternative spliced transcripts was conducted using the online database for annotation, visualization, and integrated discovery.
Assembly: mRatBN7.2
Supplementary files format and content: csv filies include PSI vasues and TPM values for each sample

source_name: KMM cell

extract_protocol:
Total RNA was harvested using TRIZOL. 10 ug of total RNA was used for the consturction of sequencing libraries
RNA libraries for RNA-seq were prepared using mRNA-seq Library Prep Kit following manufacture's protocols, following by HMR rRNA depletion

value: KMM cell

value: mesenchymal stem cells

value: FAM50A knockout

value: NO


title: MUT_372

description: Opa1cKO 2


title: KMM cells, WT, bio rep 3

description: Library name: KMM_3

value: WT


title: MUT_381

description: Opa1cKO 6


title: d3a-ko-r1

value: ko


title: H3K4me3-wt3

data_processing:
Trim Galore v. 0.4.4 (Krueger F, 2017) was applied in conjunction with Cutadapt v. 1.14 (Martin, 2011) using the nondefault options “--nextera”, “--paired”, “--length_1 35”, and “--length_2 35” to carry out quality and adapter trimming. Mapping of trimmed reads was performed against the Genome Reference Consortium Mouse Build version 38 by means of Bowtie2 v. 2.2.6 (Langmead and Salzberg, 2012) using the “--very-sensitive” flag and an insertion length maximum of 2,500 bp. Mapped reads that belonged to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (Li et al., 2009). Discordant alignments with a Phred score less than 20 were removed using SAMtools view. Since Adey et al. (Adey et al., 2010) had shown that fragments obtained from tagmentation cannot be smaller than 38 bp, all alignments that corresponded to fragments sizes below that threshold were removed. To represent the center of the transposition event, reads were shifted as previously described by Buenrostro et al. (Buenrostro et al., 2013). Furthermore, trimmed reads were aligned against the Saccharomyces cerevisiae R64 reference genome, followed by postalignment filtering. To obtain a library-specific scaling factor, we derived the multiplicative inverse of the number of filtered reads mapped against the yeast genome. Coverage tracks were made by means of the bamCoverage functionality of Deeptools v. 3.1.1 (Ramírez et al., 2016) using the nondefault parameters “--ignoreForNormalization chrM chrY chrX” and “--effectiveGenomeSize 2652783500” as well as the “--scaleRatio” option to specify the spike-in-based scaling factor. The analysis procedure was implemented as fully containerized workflows using the common workflow language v. 1.0 (Amstutz et al., 2016), which is publicly accessible (Breuer K et al., 2020). For the downstream analysis, peak calling was performed with Macs2 (version 2.1.2.1), and overlapping histone-specific marks per genotype were merged.
Assembly: mm10
Supplementary files format and content: Merged histone-specific peaks per genotype as txt file.
Library strategy: ACT-seq

extract_protocol:
Murine lung EC were subjected to FACS, pelleted for 5 min at 300 × g at 4°C and resuspended in 50 µl of cold complex formation buffer (1xCB) (50 mM Tris-HCL, pH 7.5; 150 mM NaCl; 0.05% Triton X-100; 12.5% glycerol). The cells were permeabilized for 10 min on ice. For each antibody, 0.16 µg of transposase was incubated with 3.3 µM adapter sequence in 1x CB buffer for 10 min. After adapter loading, 1 µg of antibody (H3K27ac, ab4729; H3K4me1, ab8895; H3K4me3, ab8580; H3K27me3, Cell Signaling, C36B11; H3K9me3, abab8898) was added, and the mixture was incubated for 30 min at room temperature. The transposon-adapter-antibody complex was added to the permeabilized cell suspension and incubated for 1 h at room temperature. In parallel, 7.5 x 102 permeabilized yeast nuclei were incubated with H2B (Hölzel Diagnostika, BOS-M30930) targeting the transposase complex. After 1 h of incubation, the yeast-transposase-H2B antibody mixture was added to the murine cell suspension, which was subsequently washed 3 times with washing buffer (50 mM Tris-HCL (pH 7.5), 150 mM NaCl, and 0.05% Triton X-100). The cell pellet was resuspended in 50 µl of washing buffer, and 1 µl of 1 M MgCl2 was added to initiate the transposition reaction. The solution was incubated for 1 h at 37°C. The transposase reaction was stopped by adding 4 µl of 0.5 M EDTA (pH 8), 2 µl of 10% SDS, and 1 µl of proteinase K (20 mg/ml; Qiagen), and the mixture was incubated for 1 h at 55°C following DNA purification with a MinElute PCR Purification Kit (Qiagen).
The DNA was eluted 2x with 12 µl of elution buffer. The DNA eluate was PCR amplified using 1x NEBNext High Fidelity Mix in a total volume of 50 µl. ACT libraries were purified with a 1.4x volume of Ampure XP DNA purification beads, and the DNA was eluted in 12 µl of elution buffer.

tag: act antibody


title: MUT_370

description: Opa1cKO 1


title: TNFα + irisin treated group 1

description: TNFα+iri 1

value: Human nucleus pulposus cells

value: regular culture with TNF-alpha and irisin treatment

value: Day 3


title: WT_384

description: WT 6

value: Nucleus Pulposus

value: 12 months


title: H3K4me3-wt2

value: lung


title: H3K4me3-wt1

value: endothelial cell


title: P120_TIL_tumor_CoCulture_CD137_neg, TCR

city: Milwaukee

first: Joseph

last: Zenga

state: WI

address: 9200 W WISCONSIN AVE

institute: MEDICAL COLLEGE OF WISCONSIN

description: Library name: P120_TIL_tumor_CoCulture_CD137_neg_TCR

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem. Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated PBMCs.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json
Library strategy: TCR-Seq

source_name: Patient-derived tumor-infiltrating lymphocyes, CD137 negative

extract_protocol:
Bulk RNAseq: Total RNA was extracted from tumor tissue, PBMCs, or cell lines using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol. RNA concentration and quality were assessed using NanoDrop.  Whole exome sequencing: Genomic DNA was extracted from tumor tissue, PBMCs, or cell lines using the Qiagen DNeasy Blood & Tissue Kit following the manufacturer’s instructions. DNA concentration and purity were assessed with NanoDrop. Extracted DNA was used for exome library preparation. Single-cell sequecing: Single-cell suspensions were prepared from tumor or PBMCs, and viable cells were loaded into the 10x Genomics Chromium platform for partitioning. RNA from individual cells was reverse-transcribed, and libraries were prepared according to the 10x Genomics protocol. Spatial: Slides were processed through the 10x Genomics Gene Expression workflow with pre-sequencing H&E imaging completed on the Keyence Microscope per 10x Genomics workflows. Next, transcripts were de-crosslinked, hybridized to a probe panel, ligation completed, and probes released for capture on the gridded, barcoded surface of the Visium slide (CytAssist, 10x Genomics, RRID:SCR_024570). After barcoding, the samples underwent library preparation, amplification, and clean-up with quality assessment ensuring that fragments were ~240bp.
Bulk RNAseq: RNA was extracted and used for mRNA library preparation with poly(A) enrichment, following Novogene's standard protocol. Library construction and sequencing were performed on the NovaSeq X Plus Series platform with paired-end 150 bp (PE150) reads. Whole exome sequencing: Genomic DNA was extracted and used for library preparation with the Agilent V6 kit, according to Novogene's standard workflow. Library quality was assessed, and sequencing was conducted on the NovaSeq X Plus Series platform with paired-end 150 bp (PE150) reads. Single-cell sequencing: Library preparation was completed at the MCW Mellowes Center (RRID:SCR_022926) with 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits (10X Genomics, sample dual indexes with cellular and molecular barcodes with VDJ amplification). Target capture of 10,000 cells per sample was used. Prior to sequencing, libraries were quantified and pooled by qPCR (Kapa Library Quantification Kit, Kapa Biosystems). Spatial: Libraries were sequenced at the Mellowes Center Facility on the Illumina NovaSeq6000 with paired end reads per the 10x Genomics protocol and generating 25 million read pairs per spot covered by tissue. The quality control of raw reads was processed by FastQC.


title: WT_377

description: WT 5


title: P120_TIL_tumor_CoCulture_CD137_neg, GEX

description: Library name: P120_TIL_tumor_CoCulture_CD137_neg_GEX

value: Patient-derived tumor-infiltrating lymphocyes, CD137 negative


title: P120_TIL_tumor_CoCulture_CD137_pos, TCR

description: Library name: P120_TIL_tumor_CoCulture_CD137_pos_TCR

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem. Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated PBMCs.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json

source_name: Patient-derived tumor-infiltrating lymphocyes, CD137 positive


title: FOEC6 ZOL

city: kagoshima city

first: Tatsuo

last: OKUI

state: Kagoshima

address: 8-35-1, Sakuragaoka

department: oral surgery

country: Japan

institute: kagoshima university

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: FOEC6　cells were cultured in DMEM F12 medium

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: FOEC6 cells were treated with zoledronic acid (10μM)  for 24h

tag: cell line

value: ZOL


title: FOEC6 control

value: control


title: d3a-ko-r2

source_name: lung

tag: cell type


title: WT_369

description: WT 4

value: Female


title: WT_366

description: WT 2


title: H3K4me1-wt1

value: wt


title: H3K4me1-wt2


title: H3K27me3-wt3


title: WT_365

description: WT 1


title: H3K27me3-wt2


title: EpiLC replicate 3

first: Man

last: Zhang

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

data_processing:
The clean reads were mapped to the mouse genome (GRCm38) using STAR (V2.7.9a). Raw counts for each gene were estimated using RSEM (V1.3.1) from the aligned BAM files.
Assembly: mm10
Supplementary files format and content: tab-demilited text file includes raw counts for each sample

source_name: embryo

extract_protocol:
Total RNA was extracted from cells. Nanodrop2000 (Thermo Scientific, USA) was used to detect the concentration and purity of the extracted RNA. Agarose gel electrophoresis was used to detect RNA integrity, and Agilent5300 (Agilent Technologies, Santa Clara, CA, USA) was used to determine RQN value.
The libraries were constructed by Majorbio BioTech Co. (Shanghai, China)

value: embryo

value: EpiLCs

tag: treatment


title: IR_017_1

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

description: Library name: IR_017_1

data_processing:
Novogene Standard RNA-Seq pipeline
Assembly: Homo_sapiens_hg38
Supplementary files format and content: standard BAM files

source_name: Glioblastoma

growth_protocol: HK-374 cells were grown in DMEM containing 10% FBS, 1% pen/strep media at 37°C in a 5% CO2 incubator. Cells were grown as monolayers and plated into 6-well plates at 40,000 cells per well.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
The RNA sequencing library was generated using NEBNext® Ultra RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies), and then diluted to 1 ng/uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: HK-374 monolayers were trypsinized and seeded into 10-cm Petri dishes. The following day, cells were treated with MXC-017 (10 μM) or vehicle control, then exposed to 4 Gy irradiation or sham-irradiated one hour later. RNA was isolated 48 hours post-irradiation.

value: Glioblastoma


title: IR_017_3

description: Library name: IR_017_3


title: H3K4me1-wt3


title: FAS_AIA_4

city: Zagreb

first: Nina

last: Lukač

address: Šalata 11

department: Department of Anatomy

country: Croatia

institute: University of Zagreb School of Medicine

hyb_protocol: Hybridization mix was prepared using GeneChip® Hybridization, Wash, and Stain Kit (Applied Biosystems™, Thermo Fisher Scientific) and biotinylated cDNA was hybridized to chips in hybridization oven (GeneChipTM Hybridzation Oven 645) according to the manufacturer's instructions.

scan_protocol: Chips were scanned using GeneChipTM Scanner 3000 System (Applied Biosystems™, Thermo Fisher Scientific).

data_processing: Signal intensity values were normalized, probe sets summarized, and background signal was corrected with RMA (robust multi-array average) algorithm (Irizarry, Biostatistics, 2003).

source_name: synovial myeloid cells from Fas-/- mice with arthritis

label_protocol: Biotinylated cDNA was prepared using GeneChipTM WT Pico Reagent Kit (Affymetrix™, Thermo Fisher Scientific) according to the manufacturer's instructions, using 20 μg of cRNA for ss-cDNA synthesis.

growth_protocol: Antigen-induced arthritis (AIA) was induced by immunization of mice with methylated bovine serum albumin (mBSA) in complete Freund’s adjuvant (CFA) and subsequent intra-articular injection of mBSA. Immunized control (CTRL) mice were intra-articulary injected with phosphate buffered saline (PBS). Ten days after intra-articular injection knee joints were harvested.

treatment_protocol: Synovial cells were released from joints by collagenase type IV and labeled with anti-mouse CD45-FITC, CD11b-PE, Gr1-PECy7, B220/CD3/NK1.1/CD31/TER119-APC, and CD51-APCeF780. CD11b+Gr-1+ population was sorted using BD FACSAria. Approximately 500,000 cells per sample were placed in Trizol for RNA isolation.

value: sorted synovial myeloid cells

value: Fas -/-

value: 16 weeks

value: antigen-induced arthritis


title: FAS_AIA_3


title: M374_IR_3

description: Library name: M374_IR_3


title: EpiLC replicate 2


title: H3K27me3-wt1


title: M374_IR_2

description: Library name: M374_IR_2


title: P120_TIL_tumor_CoCulture_CD137_pos, GEX

description: Library name: P120_TIL_tumor_CoCulture_CD137_pos_GEX

value: Patient-derived tumor-infiltrating lymphocyes, CD137 positive


title: WT_367

description: WT 3

value: Nucleus Pulposus

value: WT


title: FAS_AIA_2


title: H3K27ac-wt3

value: lung


title: FAS_CTRL_4

source_name: synovial myeloid cells from control Fas-/- mice


title: FAS_CTRL_3


title: IR_017_2

description: Library name: IR_017_2


title: EpiLC replicate 1


title: FAS_AIA_1


title: H3K27ac-wt2

value: endothelial cell


title: H3K27ac-wt1


title: M374_017_3

description: Library name: M374_017_3


title: pEpiLC replicate 2

value: 24 hours in the presence of the Wnt/ß-catenin signalling agonist CHIR99021 and Activin


title: FAS_CTRL_1


title: pEpiLC replicate 1


title: B6_AIA_4

source_name: synovial myeloid cells from wild type mice with arthritis

value: wild type


title: M374_017_1

description: Library name: M374_017_1


title: H3K4me3-ko2

value: ko


title: M374_017_2

description: Library name: M374_017_2


title: aEpiLC replicate 3

value: 24-hour culture of EpiLCs in N2B27 basal media


title: M374_CON_2

description: Library name: M374_CON_2


title: H3K4me3-ko3


title: MM cells, sgFAM50A-3, bio rep 2

first: Shenyu

address: 5117 Centre Ave, HCC G.1

institute: University of Pittsburgh

description: Library name: MM_sg14_2

source_name: MM cell

value: MM cell

value: mesenchymal stem cells

value: FAM50A knockout

value: NO


title: H3K4me3-ko1


title: FAS_CTRL_2

value: sorted synovial myeloid cells

value: control


title: aEpiLC replicate 2

value: embryo

value: EpiLCs


title: aEpiLC replicate 1


title: M374_IR_1

description: Library name: M374_IR_1

value: Glioblastoma


title: B6_AIA_3

value: 16 weeks

value: antigen-induced arthritis


title: pEpiLC replicate 3


title: M374_CON_1

description: Library name: M374_CON_1


title: H3K4me1-ko2

value: lung


title: Ribo-Mut_Rep2

data_processing:
Data processing was carried out using Riboflow (Ozadam, H. et al, 2020, Bioinformatics).  UMI (Unique Molecular Identifier) sequences were extracted using the following parameters: “umi_tools extract -p “^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$”–extract-method=regex”.  Reads were then clipped with the parameters “-a AAAAAAAAAACAAAAAAAAAA–overlap=4–trimmed-only”.  Trimmed reads were filtered by utilizing unaligned reads after aligning to rRNA and tRNA using bowtie2.  Alignments with a mapping quality greater than 2 were preserved, and deduplication was performed using UMI-tools when applicable.
Library strategy: Ribo-seq

source_name: Brain organoid

extract_protocol:
Cells were lysed in 5 µl of lysis buffer containing 20 mM BisTris (titrated, pH 7.2), 1.0% Triton-X100, 5 mM MgCl2, 5 mM CaCl2, 100 mM NaCl, 100 µg/mL cycloheximide, and 1 mM DTT using a pipette. Digestion was initiated by adding 1 µl of RNase I (NEB) at a dilution of 1:300, followed by incubation at 37°C in a thermal cycler with a heated lid for 15 minutes. The reaction was terminated by adding 1 µl of 1% SDS. Subsequently, samples were promptly placed on ice and kept there until processing through Ribo-ITP.
Ribo-ITP and library preparation were conducted following the method described in the cited paper (Ozadam, H. et al, 2023, Nature). Libraries were generated using the D-Plex Small RNA-seq kit (C05030001, Diagenode) with minor modifications as outlined in the paper. Each sample was processed using a unique dual index module, and the complementary DNA was amplified for 12 cycles.

value: Brain organoid


title: B6_CTRL_3

source_name: synovial myeloid cells from control wild type mice


title: B6_CTRL_4


title: G20-3

city: Hohhot

first: Kai

last: Cao

address: Inner Mongolia Agricultural University

department: agricultural college

institute: Inner Mongolia Agricultural University

description:
Library name: sample6
G20-3_FPKM

data_processing:
After sequencing data, the bioinformatics analysis process provided by BMKCloud ( www.biocloud.net ) was used for data analysis. Clean Data was obtained by filtering the offline data, and sequence alignment was performed with the designated reference genome. After obtaining Mapped Data, library quality assessment, structural level analysis, differential expression analysis, gene function annotation and functional enrichment were performed. In addition, in-depth data mining analysis can also be carried out through the B & M cloud platform BMKCloud ( www.biocloud.net ) to achieve a series of personalized interactive operations of transcriptome, such as gene retrieval mapping, unique and common gene analysis, construction of protein interaction network, gene set enrichment analysis ( GSEA ), differential gene co-expression analysis and gene co-expression network construction ( WGCNA ).
Assembly: GCF_002127325.2
Supplementary files format and content: tab-delimited txt files include FPKM values for each Sample

organism: Helianthus annuus

source_name: Leaf compact inbred lines

extract_protocol:
( 1 ) NanoDrop 2000 spectrophotometer : detection of RNA purity and concentration ;( 2 ) Agient2100 / LabChip GX detection : Accurate detection of RNA integrity.
( 1 ) Eukaryotic mRNA was enriched by magnetic beads with Oligo ( dT ) ;  ( 2 ) Fragmentation Buffer was added to randomly interrupt mRNA ;  ( 3 ) The first and second cDNA strands were synthesized using mRNA as template, and cDNA was purified.  ( 4 ) The purified double-stranded cDNA was subjected to terminal repair, A tail and ligation of the sequencing adapter, and then the fragment size was selected with AMPure XP beads ;  ( 5 ) Finally, the cDNA library was obtained by PCR enrichment.

value: Leaf compact inbred lines

value: petiole


title: G20-2

description:
Library name: sample5
G20-2_FPKM


title: H3K4me1-ko1

value: endothelial cell

value: ko


title: B6_AIA_2

value: wild type


title: B6_AIA_1


title: B6_CTRL_2


title: B6_CTRL_1


title: M374_CON_3

description: Library name: M374_CON_3


title: H3K4me1-ko3


title: G20-1

description:
Library name: sample4
G20-1_FPKM


title: Ribo-Mut_Rep1


title: Ribo-WT_Rep3

value: WT


title: Ribo-WT_Rep1


title: H3K27me3-ko1


title: LPS_rep2

first: Ju Ri

last: Ye

address: Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: KyungHee university

description: Library name: LPS_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Dental pulp cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Dental pulp cell


title: H3K27me3-ko2


title: UT_rep3

description: Library name: UT


title: Exo_OD_rep3

description: Library name: Exo_OD_3


title: G19-1

description:
Library name: sample1
G19-1_FPKM

source_name: Leaf flat type

value: Leaf flat type


title: LPS_rep1

description: Library name: LPS_1


title: TIGR4 MUC5AC glycans 5 h 4

city: Cambridge

first: Katharina

last: Ribbeck

state: MA

address: 32 Vassar St

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Sequencing reads were mapped to the TIGR4 genome with the Burrows-Wheeler aligner
Read counts were quantified via the featureCounts package
Differential gene expression was quantified via the DESeq2 package in the R Bioconductor package
P-values were adjusted for multiple hypothesis testing using the Benjamini-Hochberg method
Assembly: NC_003028.3
Supplementary files format and content: Comma-separated value file includes raw counts for each gene in each sample

organism: Streptococcus pneumoniae TIGR4

extract_protocol:
RNA was extracted using the MasterPure complete DNA and RNA purification kit (Biosearch Technologies) and DNA was removed using the Turbo DNA-free kit (Invitrogen).
80 ng of RNA was used as input and the NEBNext Ultra II RNA library prep kit for Illumina with rRNA depletion was used for RNA library construction for RNA-seq.

value: 0.1% MUC5AC glycans


title: H3K27ac-ko3


title: Ribo-WT_Rep2

first: Michael

address: 5323 Harry Hines Boulevard

institute: University of Texas Southwestern Medical Center


title: H3K27ac-ko2

first: Stephanie

address: Im Neuenheimer Feld

institute: DKFZ


title: Exo_OD_rep2

description: Library name: Exo_OD_2


title: TIGR4 MUC5AC glycans 5 h 3


title: rep2_WT_UV_60min

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Replicate 2

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences. A sequencing read count was assigned to both positions in the dipyrimidine sequence
Library strategy: CPD-seq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a 30 degree shaking incubator.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O.
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACGGAT; A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. After UV irradiation, 1/3 of cells were pelleted and taken as the '0min' timepoint. The remaining 2/3 of cells were resuspended in 2% glucose and placed in a petri dish under UVA light for 30 and 60 minutes. After UVA incubation, cells were spun down and kept at -80˚C until genomic DNA isolation.

value: Yeast cells

value: UV irradiated 125 J/m2

tag: repair time_with_uva_light

value: 60 min


title: Exo_OD_rep1

description: Library name: Exo_OD_1


title: H3K27me3-ko3

tag: genotype


title: H3K27ac-ko1


title: rep2_WT_UV_30min

description: Replicate 2

value: 30 min


title: G19-3

description:
Library name: sample3
G19-3_FPKM


title: LPS_rep3

description: Library name: LPS_3


title: Posterior area opaca without exogenous OTX2

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: 1-1 Murasaki-cho

institute: Biohistory Research Hall

description: Library name: AC

data_processing:
The gene transcripts were assembled with StringTie, and the gene expression profile was represented by FPKM and TPM for a sample.
Assembly: GCF_016700215.2 bGalGal1.pat.whiteleghornlayer.GRCg7w as the reference with annotation by NCBI Gallus gallus Annotation Release 106.
Supplementary files format and content: Expression_Profile.GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w_with_MusOtx2_EGFP_genomic.gene.txt
Supplementary files format and content: Expression_Profile.GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w_with_MusOtx2_EGFP_genomic.transcript.txt

organism: Gallus gallus

source_name: Posterior area opaca

growth_protocol: Fertile chicken eggs were incubated at 38 °C to st. 4/5. Embryos on the vitelline membrane with a filter ring support were excised, electroporated, and cultured to st. 10/11.

extract_protocol:
Total RNAs isolated from tissues of four pooled embryos at st. 10-st.11 using Trizol reagents constituted a sample
Libraries for mRNA sequence reads were prepared using TruSeq Etrant mRNA LT Sample Prep Kit.

treatment_protocol: The DNAs of Otx2 expression vector pCAGGS-mOtx2 carrying mouse Otx2 cDNA sequence (Iwafuchi-Doi et al., 2012) at 0.25 µg and pCAGGS-EGFP at 0.2 µg in 1 µl of 10 mM Tris/HCl 1 mM EDTA at pH 7.5 were injected in the space between the epiblasts and the vitelline membrane and electroporated by the standard procedure.

value: Posterior area opaca

tag: developmental stage

value: pCAGGS-EGFP electroporation


title: TIGR4 MUC5AC glycans 5 h 2


title: rep2_WT_UV_0min

description: Replicate 2

value: 0 min


title: TIGR4 MUC5AC glycans 5 h 1


title: Exo_rep3

description: Library name: Exo_3


title: Sinus rhomboidalis portion without exogenous OTX2

description: Library name: CT2

source_name: Sinus rhomboidalis

value: Sinus rhomboidalis

value: No electroporation


title: Exo_rep2

description: Library name: Exo_2


title: Sinus rhomboidalis portion without electroporation

description: Library name: NewCT1


title: rep1_WT_UV_60min

description: Replicate 1


title: TIGR4 MUC5AC 5 h 3

value: 0.5% MUC5AC


title: TIGR4 MUC5AC 5 h 4


title: Exo_rep1

description: Library name: Exo_1


title: Midbrain-hindbrain portion without exogenous OTX2_2

description: Library name: CH2

source_name: Midbrain-hindbrain

value: Midbrain-hindbrain


title: organoid_5x2Gy_2wk

description:
Library name: organoid_5x2Gy_2wk
10x Genomics

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) and processed using the PIPseeker software, version 3.3.3 (Fluent Biosciences). Raw matrices were in processed in Seurat version 5 20. Cells with less than 500 genes were filtered out and cells with high mitochondrial gene count (>5%) were removed.
Assembly: human genome (hg38)
Supplementary files format and content: FASTQ and matrix files

source_name: patient-derived cell line

growth_protocol: hips23-derived mature brain organoids (day 120) were culcured in SASAI M4 media, which includes DMEM/F- 12 with Glutamax, 1X N-2 supplement, 1X B27 Supplement (w/Vit.A/Insulin), 1X Lipid Concentrate, 1X Penicillin/streptomycin, 10% Fetal Bovine Serum (GIBCO), 5 μg/mL Heparin (Sigma H3149), and 1% Growth factor reduced Matrigel.

extract_protocol:
At 72 hours and 2 weeks following the final radiation dose, organoids were collected and dissociated into single-cell suspensions using the Papain Dissociation Kit (#LK003150, VWR) according to the manufacturer’s instructions. Cell counts were determined using a cell counter, and the resulting suspensions were processed for sequencing using the PIPseq T2 kit.
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp.

treatment_protocol: Organoids were irradiated at room temperature using an experimental X-ray irradiator (Gulmay Medical Inc. Atlanta, GA) at a dose rate of 5.519 Gy/min. Control samples were sham-irradiated. The X-ray beam was operated at 300 kV and hardened using a 4 mm Be, a 3 mm Al, and a 1.5 mm Cu filter and calibrated using NIST-traceable dosimetry. Corresponding controls were sham irradiated. In this experiment, the organoids were exposed to fractionated irradiation, receiving 2 Gy per day for five consecutive days (total of 5 fractions)

value: IPSC

value: ipsc23 derived brain organoid

value: 5 x 2 Gy_2 weeks


title: rep1_WT_UV_30min

description: Replicate 1

value: WT


title: Midbrain-hindbrain portion without exogenous OTX2_1

description: Library name: CH1


title: rep1_WT_UV_0min

description: Replicate 1


title: rep2_rad14_60min_UV

description: Replicate 2


title: TIGR4 MUC5AC 5 h 2


title: organoid_5x2Gy_72h

description:
Library name: organoid_5x2Gy_72h
10x Genomics

value: 5 x 2 Gy_72 hours


title: TIGR4 MUC5AC 5 h 1


title: Posterior area opaca with exogenous OTX2

description: Library name: AO


title: TIGR4 THY 5 h 4

value: No treatment