title: AoDa01_dsDNA_rep2

extract_protocol:
E. coli C2566 genomic DNA was purified using Monarch Genomic DNA Purification Kit (NEB Ipswich, MA), GM12878 genomic DNA was obtained from Coriell Cell Repositories (Camden, NJ).
Input DNA was sheared to 300 bp using the Covaris S2 instrument. Sheared material was transferred to a PCR strip tube to begin library construction. NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing, and adaptor ligation. The custom made Pyrollo-dC adaptor (NEB Organic Synthesis Division, Ipswich MA), where all dCs are replaced with Pyrollo-dC, was used. The ligated samples were purified using NEBNext Sample Purification Beads  according to the manufacturer’s instructions. For ssDNA libraries, prior to deamination the DNA was denatured by heating at 90oC for 10 minutes followed by cooling for 2 minutes on ice. The DNA was then deaminated using 1 µL of PURExpress (NEB, Ipswich, MA) synthesized deaminase protein following manufacturer's recommendations for 1 hour at 37oC. Then 1 µL of Thermolabile Proteinase K (NEB, Ipswich, MA) was added and incubated for 30 min at 37oC followed by 10 min at 60oC. Then the library was amplified using NEBNext Q5U Master Mix (NEB, Ipswich, MA, USA). Paired-end sequencing of 150 cycles (2 x 75 bp) was performed for all the sequencing runs.
DNA sequencing of deaminated double-stranded and single-stranded DNA

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: AoDa01_ssDNA_rep1

status: Public on Jan 31 2024

type: SRA

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

country: USA

institute: New England Biolabs

library_source: genomic

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text/bed files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq

molecule: genomic DNA

organism: Escherichia coli

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus

tag: cell type


title: vehicle, vehicle, 1wk of daily loading, rep1,lymph node,L [22]

city: Ithaca

first: Marjolein

last: van der Meulen

state: NY

address: Weill Hall

department: BME

institute: Cornell University

library_source: transcriptomic

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample

molecule: total RNA

organism: Mus musculus

source_name: lymph node

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols

tag: tissue

value: lymph node

tag: treatment

tag: limb

value: L

tag: age

value: 27 wks


title: vehicle, vehicle, 1wk of daily loading, rep4,lymph node,L [78]


title: T9_Transection, Triceps Brachii Muscle, Rep3

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Raw fastq was aligned to mouse reference genome GRCm38 with hisat2 v2.1.0.  Gene wise counts were generated with featureCounts from the subread package v1.5.1 for genes annotated by ensembl Mus_musculus.GRCm38.102, counting the primary alignment in the case of multimapped reads.  Raw counts were normalized by voom
Assembly: GRCm38
Supplementary files format and content: voom normalized counts

molecule: polyA RNA

source_name: Triceps Brachii Muscle

extract_protocol:
Mouse skeletal muscle tissue (~30 mg) was homogenized in Trizol reagent (Invitrogen) and extracted using RNeasy mini kit (Qiagen) according to manufacturer’s instructions. Total RNA concentration and integrity were determined by 260/280 and 260/230 nanodrop absorbance, as well as QUBIT and RNA6000 PicoAssay.
mRNA libraries were generated using NEBNext® Ultra™ II Directional (stranded) RNA library prep kit for Illumina (NEB #E7760L) and NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490). 200 ng total RNA was used for library input, fragmentation occurred for 10 minutes, and 12X PCR cycles were run. Library quality was assessed using High Sensitivity DNA Bioanalyzer and libraries were then sequenced by NovaSeq6000 SP Paired-End 150bp format at a sequencing depth of ~20 million reads per lane per sample.

value: Triceps Brachii Muscle

tag: Sex

value: Male

tag: disease

value: T9 Transection SCI

tag: timepoint

value: 3 days post surgery


title: AoDa01_dsDNA_rep1


title: BCBL1 ND RNAseq rep1

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
trim galore
align (STAR for RNAseq, bowtie2 for CUT&RUN, WALT for ATACme, HiCUP for HiChIP)
deeptools for making bigwig files
MICC for calling significant HiChIP loops
methPipe for call DNA methylation from ATACme data
Please note that processed data generated from both replicates is linked to the corresponding rep1  sample records.
Assembly: GRCh38, GQ994935.1
Supplementary files format and content: bigwig file for coverage, txt file for LANA HiChIP loops, txt raw counts for RNAseq

organism: Homo sapiens

source_name: BCBL1 ND, latent, RNAseq

growth_protocol: RPMI-1640, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: CUT&RUN/ATACme/HiChIP

tag: cell line

value: B cell


title: BCBL1 ND RNAseq rep2

source_name: BCBL1 ND, latent,  RNAseq


title: vehicle, vehicle, 1wk of daily loading, rep1,lymph node,Right [15]

value: Right


title: T9_Transection, Triceps Brachii Muscle, Rep2


title: vehicle, vehicle, 1wk of daily loading, rep1,cortical bone,L [10]

source_name: cortical bone

value: cortical bone


title: BCBL1 NTC RNAseq rep1

source_name: BCBL1 NTC, latent,  RNAseq


title: AoDa01_ssDNA_rep2


title: vehicle, vehicle, 1wk of daily loading, rep1,cancellous bone,L [9]

source_name: cancellous bone

value: cancellous bone


title: BCBL1 NTC RNAseq rep2


title: T9_Transection, Triceps Brachii Muscle, Rep1


title: XjaDa01_ssDNA_rep2


title: T3_Transection, Triceps Brachii Muscle, Rep6

value: T3 Transection SCI


title: XjaDa01_ssDNA_rep1


title: XjaDa01_dsDNA_rep2


title: T3_Transection, Triceps Brachii Muscle, Rep5


title: T3_Transection, Triceps Brachii Muscle, Rep4


title: vehicle, vehicle, 1wk of daily loading, rep1,cancellous bone,Right [2]


title: BCBL1_ND_LANA rep1

data_processing:
library strategy: CUT&RUN
trim galore
align (STAR for RNAseq, bowtie2 for CUT&RUN, WALT for ATACme, HiCUP for HiChIP)
deeptools for making bigwig files
MICC for calling significant HiChIP loops
methPipe for call DNA methylation from ATACme data
Please note that processed data generated from both replicates is linked to the corresponding rep1  sample records.
Assembly: GRCh38, GQ994935.1
Supplementary files format and content: bigwig file for coverage, txt file for LANA HiChIP loops, txt raw counts for RNAseq

source_name: BCBL1 ND, latent, CUT&RUN, LANA


title: BCBL1_ND_LANA rep2


title: XjaDa01_dsDNA_rep1


title: XinDa01_ssDNA_rep2


title: BCBL1_NTC_LANA rep2

source_name: BCBL1 NTC, latent, CUT&RUN, LANA


title: T3_Transection, Triceps Brachii Muscle, Rep3


title: BCBL1_NTC_LANA rep1


title: XinDa01_ssDNA_rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep8,cartilage,L [672]

source_name: cartilage

value: cartilage

value: 28 wks


title: PTH-pretreated, vehicle, 2wks of daily loading, rep8,cartilage,Right [665]


title: T3_Transection, Triceps Brachii Muscle, Rep2


title: BCBL1_ND_polII_S5p rep2

source_name: BCBL1 ND, latent, CUT&RUN, pol II phosph S6


title: XinDa01_dsDNA_rep2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep7,cartilage,L [658]


title: T3_Transection, Triceps Brachii Muscle, Rep1


title: XinDa01_dsDNA_rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep7,cartilage,Right [651]


title: Sham, Triceps Brachii Muscle, Rep6

value: Sham SCI


title: vehicle, vehicle, 1wk of daily loading, rep1,cortical bone,Right [3]


title: BCBL1_NTC_polII_S5p rep2

source_name: BCBL1 NTC, latent, CUT&RUN, Pol II phosph S5


title: Sham, Triceps Brachii Muscle, Rep5


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,cartilage,L [644]


title: BCBL1_NTC_polII_S5p rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,cartilage,Right [637]


title: SpDa01_ssDNA_rep2


title: SpDa01_ssDNA_rep1


title: Sham, Triceps Brachii Muscle, Rep4


title: SpDa01_dsDNA_rep2


title: BCBL1_ND_polII_S2p rep2

source_name: BCBL1 ND, latent, CUT&RUN, pol II phosph S2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,cartilage,L [630]


title: BCBL1_ND_polII_S2p rep1


title: SpDa01_dsDNA_rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,cartilage,Right [623]


title: Sham, Triceps Brachii Muscle, Rep2


title: BCBL1_NTC_polII_S2p rep2

source_name: BCBL1 NTC, latent, CUT&RUN, Pol II phosph S2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,cartilage,L [616]


title: Sham, Triceps Brachii Muscle, Rep1


title: BCBL1_NTC_polII_S2p rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,cartilage,Right [609]


title: T9_Transection, Gastrocnemius Muscle, Rep4

source_name: Gastrocnemius Muscle

value: Gastrocnemius Muscle


title: BCBL1_ND_polII_S5p rep1

source_name: BCBL1 ND, latent, CUT&RUN, pol II phosph S5


title: MsDa01_ssDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BCBL1_ND_polII_total rep2

source_name: BCBL1 ND, latent, CUT&RUN, pol II total


title: MsDa01_dsDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BCBL1_ND_polII_total rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,cartilage,L [602]


title: T9_Transection, Gastrocnemius Muscle, Rep3


title: MsDa01_dsDNA_rep1


title: T9_Transection, Gastrocnemius Muscle, Rep2


title: Sham, Triceps Brachii Muscle, Rep3

source_name: Triceps Brachii Muscle


title: BCBL1_NTC_polII_total rep2

source_name: BCBL1 NTC, latent, CUT&RUN, Pol II total


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,cartilage,Right [595]


title: T9_Transection, Gastrocnemius Muscle, Rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,cartilage,L [588]


title: LbDa02_ssDNA_rep2


title: BCBL1_NTC_polII_total rep1


title: MsDa01_ssDNA_rep2


title: T3_Transection, Gastrocnemius Muscle, Rep4


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,cartilage,Right [581]


title: T3_Transection, Gastrocnemius Muscle, Rep3


title: BCBL1_ND_IgG rep3

source_name: BCBL1 ND, latent, CUT&RUN, IgG


title: LbDa02_dsDNA_rep2


title: LbDa02_ssDNA_rep1


title: LbDa02_dsDNA_rep1


title: BCBL1_ND_IgG rep2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,cartilage,Right [567]


title: T3_Transection, Gastrocnemius Muscle, Rep2


title: vehicle, vehicle, 2wks of daily loading, rep8,cartilage,L [560]


title: BCBL1_NTC_IgG rep3

source_name: BCBL1 NTC, latent, CUT&RUN, IgG


title: vehicle, vehicle, 2wks of daily loading, rep8,cartilage,Right [553]


title: T3_Transection, Gastrocnemius Muscle, Rep1


title: BCBL1_ND_IgG_fixed

source_name: BCBL1 ND, latent, CUT&RUN, IgG 0.01% formaldehyde


title: vehicle, vehicle, 2wks of daily loading, rep7,cartilage,L [546]


title: Sham, Gastrocnemius Muscle, Rep4


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,cartilage,L [574]


title: BCBL1_ND_IRF4_fixed rep2

source_name: BCBL1 ND, latent, CUT&RUN, IRF4 0.01% formaldehyde


title: CaDa01_ssDNA_rep2


title: CaDa01_dsDNA_rep2


title: Sham, Gastrocnemius Muscle, Rep3


title: Sham, Gastrocnemius Muscle, Rep2


title: CaDa01_dsDNA_rep1


title: BCBL1_ND_IRF4_fixed rep1


title: BbDa01_ssDNA_rep2


title: BbDa01_ssDNA_rep1


title: BCBL1_NTC_IRF4_fixed rep2

source_name: BCBL1 NTC, latent, CUT&RUN, IRF4 0.01% formaldehyde


title: vehicle, vehicle, 2wks of daily loading, rep6,cartilage,Right [525]


title: vehicle, vehicle, 2wks of daily loading, rep6,cartilage,L [532]


title: BbDa01_dsDNA_rep2


title: CaDa01_ssDNA_rep1


title: Sham, Gastrocnemius Muscle, Rep1


title: BCBL1_NTC_IgG_fixed

source_name: BCBL1 NTC, latent, CUT&RUN, IgG 0.01% formaldehyde


title: BbDa01_dsDNA_rep1


title: vehicle, vehicle, 2wks of daily loading, rep5,cartilage,L [518]

source_name: cartilage


title: WT, batch2, scRNAseq

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced reads were processed with the cellranger pipeline (version 3.1.0) and aligned to the custom reference 10X genomics build mouse mm10 (version 3.0.0) with the GFP gene added using the mkref function.
Assembly: custom reference 10X genomics build mouse mm10 (version 3.0.0) with the GFP gene
Supplementary files format and content: h5

source_name: Bone Marrow

extract_protocol:
ESLAM HSCs were sorted as CD45+EPCR+CD150+CD48- and transduced with lentivirus containing STAT5B-YF, STAT5B-WT and EV in SCF and IL-11 cultures. Five days after infection, cells were sorted for viability (DAPI-, Thermo Fisher) and green fluorescent protein (GFP) expression.
The cells were processed with a Chromium Controller according to the Chromium NextGEM Single Cell 3’ GeneExpression v3.1 protocol. The libraries were pooled and sequenced on a Novaseq 6000

value: Bone Marrow

value: ESLAM HSCs

value: transduced with lentivirus containing STAT5B-WT, sorted for GFP+


title: YF, batch2, scRNAseq

description: 10x Genomics

value: transduced with lentivirus containing STAT5B-YF, sorted for GFP+


title: BCBL1_NTC_IgG rep2


title: vehicle, vehicle, 2wks of daily loading, rep5,cartilage,Right [511]


title: BCBL1_NTC_IRF4_fixed rep1


title: EV, batch2, scRNAseq

description: 10x Genomics

value: transduced with lentivirus containing EV, sorted for GFP+


title: vehicle, vehicle, 2wks of daily loading, rep4,cartilage,L [504]

value: L


title: BCBL1_ND_H3K4me1 rep2

source_name: BCBL1 ND, latent, CUT&RUN, H3K4me1


title: vehicle, vehicle, 2wks of daily loading, rep7,cartilage,Right [539]


title: EV, batch1, scRNAseq

description: 10x Genomics


title: AmDa03_ssDNA_rep2


title: BCBL1_ND_H3K4me1 rep1


title: vehicle, vehicle, 2wks of daily loading, rep4,cartilage,Right [497]


title: vehicle, vehicle, 2wks of daily loading, rep3,cartilage,L [490]


title: BCBL1_NTC_H3K4me1 rep2

source_name: BCBL1 NTC, latent, CUT&RUN, H3K4me1


title: AmDa03_dsDNA_rep2


title: WT, batch1, scRNAseq

description: 10x Genomics


title: AmDa03_ssDNA_rep1


title: vehicle, vehicle, 2wks of daily loading, rep3,cartilage,Right [483]


title: YF, batch1, scRNAseq

description: 10x Genomics


title: BCBL1_NTC_H3K4me1 rep1


title: AmDa03_dsDNA_rep1


title: KOPIC3

city: Seoul

first: Do-Wan

last: Shim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Microbiology

country: South Korea

institute: Yonsei university

description: Peritoneal myeloid cell from poly(I:C) injected myeloid Bmal1 KO mouse

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 Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Peritoneum

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

value: Peritoneum

value: Primary cells

value: Peritoneal myeloid cells

tag: genotype

value: Myeloid Bmal1 KO


title: vehicle, vehicle, 2wks of daily loading, rep2,cartilage,Right [469]

value: Right


title: vehicle, vehicle, 2wks of daily loading, rep2,cartilage,L [476]


title: BCBL1_ND_H3K27ac rep2

source_name: BCBL1 ND, latent, CUT&RUN, H3K27ac

value: B cell


title: VsDa01_ssDNA_rep1


title: VsDa01_ssDNA_rep2


title: KOPBS3

description: Peritoneal myeloid cell from PBS injected myeloid Bmal1 KO mouse

value: PBS


title: WTPIC3

description: Peritoneal myeloid cell from poly(I:C) injected WT mouse

value: WT


title: VsDa01_dsDNA_rep2


title: vehicle, vehicle, 2wks of daily loading, rep1,cartilage,L [462]

value: cartilage

value: 28 wks


title: WTPBS3

description: Peritoneal myeloid cell from PBS injected WT mouse


title: BCBL1_ND_H3K27ac rep1


title: VsDa01_dsDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BCBL1_NTC_IgG rep1


title: KOPIC2


title: vehicle, vehicle, 2wks of daily loading, rep1,cartilage,Right [455]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep7,cartilage,L [448]

value: 27 wks


title: KOPBS2


title: BCBL1_NTC_H3K27ac rep2

source_name: BCBL1 NTC, latent, CUT&RUN, H3K27ac


title: BCBL1_NTC_H3K27ac rep1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep7,cartilage,Right [441]


title: WTPIC2


title: RhDa01_extN10_ssDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BCBL1_ND_IgG rep1


title: RhDa01_extN10_dsDNA_rep2


title: LANA HIChIP rep3

data_processing:
library strategy: HiChIP
trim galore
align (STAR for RNAseq, bowtie2 for CUT&RUN, WALT for ATACme, HiCUP for HiChIP)
deeptools for making bigwig files
MICC for calling significant HiChIP loops
methPipe for call DNA methylation from ATACme data
Please note that processed data generated from both replicates is linked to the corresponding rep1  sample records.
Assembly: GRCh38, GQ994935.1
Supplementary files format and content: bigwig file for coverage, txt file for LANA HiChIP loops, txt raw counts for RNAseq

source_name: TREx-BCBL1-RTA, latent, HiChIP,  LANA


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep6,cartilage,L [434]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep6,cartilage,Right [427]


title: KOPIC1


title: RhDa01_extN10_dsDNA_rep1


title: LANA HIChIP rep1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,cartilage,L [420]


title: H3K4me3_rep2

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, H3K4me3


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,cartilage,Right [399]


title: RhDa01_extN10_ssDNA_rep2


title: WTPBS2


title: LANA HIChIP rep2


title: MGYPDa18_extN28_ssDNA_rep2


title: H3K4me3_rep1


title: WTPIC1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,cartilage,L [392]


title: WTPBS1


title: KOPBS1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,cartilage,Right [385]


title: MGYPDa18_extN28_dsDNA_rep1


title: MGYPDa18_extN28_dsDNA_rep2


title: MGYPDa18_extN28_ssDNA_rep1


title: BRD2_rep1

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, BRD2


title: BRD2_rep2


title: Eosinophils, L.m. 2 [C2]

city: Hangzhou

first: Jun

last: Zhou

address: 866 Yuhangtang Road

department: Institute of Immunology

institute: Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) were processed using Seqtk. Clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads.
Clean reads were mapped to reference sequences and/or reference gene set using Hisat2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample
The gene expression level is calculated by using FPKM method (Fragments Per Kilobase of exon model per Million mapped reads),
We use "q-value ≤0.05 and the absolute value of log2Ratio ≥1" as the threshold to judge the significance of gene expression difference.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized FPKM values for each Sample

source_name: Eosinophils

growth_protocol: Mature eosinophils were differentiated from mouse bone marrow progenitors

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Ribosomal RNA was removed from total RNA using Ribo-Zero rRNA removal beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

treatment_protocol:
We performed transcriptome sequencing on Listeria monocytogenes infected eosinophils and resting eosinophils to shed light on the transcriptional changes of cytokines and  chemokines.
3×106 Eosinophils were infected with Listeria monocytogenes for 8 hours.

value: Eosinophils

value: L.m. infected

tag: time

value: 8 hours


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,cartilage,L [378]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,cartilage,Right [371]


title: Eosinophils, Control 2 [C1]

value: no treatmemt


title: MGYPDa18_ssDNA_rep2


title: MGYPDa18_ssDNA_rep1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,cartilage,L [364]

value: L


title: EZH2_rep1

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, EZH2


title: Eosinophils, Control 1 [A1]


title: MGYPDa18_dsDNA_rep1


title: BRD4_rep2

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, BRD4


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,cartilage,Right [357]


title: BRD4_rep1


title: Peritoneal macrophages,Remodelin hydrobromide,IFN y 2

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus_musculus_Ensemble_106
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Peritoneal macrophages

growth_protocol: Peritoneal macrophages  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with Remodelin hydrobromide or not then treated with IFN y or not.

value: Peritoneal macrophages

value: Remodelin hydrobromide,IFN y


title: Peritoneal macrophages,Remodelin hydrobromide,IFN y 3


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,cartilage,L [350]


title: MGYPDa17_extN16_ssDNA_rep2


title: MGYPDa17_extN16_ssDNA_rep1


title: H3K27me3_rep2

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, H3K27me3


title: Peritoneal macrophages,Remodelin hydrobromide,IFN y 1


title: Eosinophils, L.m. 1 [A2]


title: H3K27me3_rep1

source_name: TREx-BCBL1-RTA, latent, CUT&RUN,  H3K27me3


title: PTH-pretreated, vehicle, 1wk of daily loading, rep8,cartilage,L [336]

source_name: cartilage


title: Peritoneal macrophages,Remodelin hydrobromide 3

value: Remodelin hydrobromide


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,cartilage,Right [343]


title: Peritoneal macrophages,Remodelin hydrobromide 2


title: EZH2_rep2


title: MGYPDa18_dsDNA_rep2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep7,cartilage,L [322]


title: H3K4me1_rep1

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, H3K4me1


title: MGYPDa17_extN16_dsDNA_rep1


title: PTH-pretreated, vehicle, 1wk of daily loading, rep7,cartilage,Right [315]


title: Peritoneal macrophages,Remodelin hydrobromide 1


title: MGYPDa17_ssDNA_rep1


title: MGYPDa17_dsDNA_rep2


title: Peritoneal macrophages,IFN y 3

value: IFN y


title: PTH-pretreated, vehicle, 1wk of daily loading, rep6,cartilage,L [308]


title: TB LANA CUT&RUN rep2

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, LANA


title: Peritoneal macrophages,IFN y 2


title: MGYPDa16_ssDNA_rep2


title: MGYPDa17_extN16_dsDNA_rep2


title: H3K27ac_rep1

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, H3K27ac


title: PTH-pretreated, vehicle, 1wk of daily loading, rep6,cartilage,Right [301]

value: Right


title: H3K4me1_rep2

value: B cell


title: TB LANA CUT&RUN rep1


title: Peritoneal macrophages,IFN y 1


title: Peritoneal macrophages 3

value: Control


title: TB IgG CUT&RUN rep2

source_name: TREx-BCBL1-RTA, latent, CUT&RUN, IgG


title: PTH-pretreated, vehicle, 1wk of daily loading, rep5,cartilage,L [294]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep8,cartilage,Right [329]


title: Peritoneal macrophages 2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep5,cartilage,Right [287]


title: MGYPDa16_dsDNA_rep1


title: MGYPDa16_ssDNA_rep1


title: H3K27ac_rep2


title: MGYPDa16_dsDNA_rep2


title: TB IgG CUT&RUN rep1


title: DaDa01_ssDNA_rep2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,cartilage,L [280]


title: BC3 LANA CUT&RUN rep2

source_name: BC3, latent, CUT&RUN, LANA


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,cartilage,Right [273]


title: MGYPDa17_dsDNA_rep1


title: Mel+LPS3_ip

city: Beijing

first: Shisu

last: Zhao

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

description: Mice were received intraperitoneal injections of melatonin  daily at 9:00 am on D1 to D4,  LPS was injected intraperitoneally 30 minutes after the melatonin injection on D3 and D4.

data_processing:
The antibody-RNA complex was isolated by incubation with protein A beads (Invitrogen, CA, USA). All libraries were sequenced on Illumina Hiseq X10 (Illumina, CA, USA).
Raw reads from Illumina sequencing were subjected to adaptor trimming and filtering of low-quality reads by Fastp (version 0.12.3). STAR (version 2.5.2a) was used to output a sorted genome-coordinate based Bam file.
The exomePeak2 (version 4.2) was used to perform peak calling analysis on the IP and Input file.
Difference peaks were analyzed using MACS2 (version 3.4). Peaks were annotated using CHIPseeker (version 1.22.1).
Motif analysis was performed using HOMER (version 4.10).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include peak annotation for each group

source_name: mouse uterus, Mel+LPS, rep3

extract_protocol:
100 μg total RNA was extracted from the uterus using TRIzon Reagent (CWBIO, Jiangsu, China).
mRNAs were fragmented into about 100-nt fragments and immunoprecipitated (IP) with 5 μg m6A antibody (Abcam, Cambridge, UK).

tag: group

value: IP

value: uterus

value: WT

value: Intraperitoneal injection of melatonin and LPS

value: Day 5 of pregnancy


title: BC3 LANA CUT&RUN rep1


title: Mel+LPS1_ip

source_name: mouse uterus, Mel+LPS, rep1


title: BC3 IgG CUT&RUN rep2

source_name: BC3, latent, CUT&RUN, IgG


title: ATACme rep2

source_name: TREx-BCBL1-RTA, latent, ATACme


title: LPS2_ip

description: Mice were received intraperitoneal injections of 0.9% sterile saline  daily at 9:00 am on D1 to D4,  LPS was injected intraperitoneally 30 minutes after the melatonin injection on D3 and D4.

source_name: mouse uterus, LPS, rep2

value: Intraperitoneal injection of LPS


title: Peritoneal macrophages 1


title: BC3 IgG CUT&RUN rep1


title: LPS3_ip

source_name: mouse uterus, LPS, rep3


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,cartilage,Right [245]

value: cartilage

value: 27 wks


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,cartilage,L [238]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,cartilage,Right [259]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,cartilage,L [266]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,cartilage,L [252]


title: ATACme rep1


title: Veh3_ip

description: Mice were received intraperitoneal injections of  0.9% sterile saline daily at 9:00 am on D1 to D4

source_name: mouse uterus, Vehicle, rep3

value: Intraperitoneal injection of saline


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,cartilage,Right [231]


title: vehicle, ALN-treated, 1wk of daily loading, rep8,cartilage,L [224]

value: L


title: Veh2_ip

source_name: mouse uterus, Vehicle, rep2


title: Mel+LPS2_ip

source_name: mouse uterus, Mel+LPS, rep2


title: TFEBKO treated with LLOMe washout 12h_rep2

city: Suita

first: Mengying

last: Cui

country: Japan

institute: Osaka University

data_processing:
Illumina package bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using TopHat (v2.1.1).
EdgeR output
Assembly: GRCh38

source_name: HeLa cells

growth_protocol: Cells were cultured in Dulbecco’s Modifed Eagle’s medium (D6046, Sigma) supplemented with 10% fetal bovine serum (10270106, Gibco) and penicillin-streptomycin (P4333, Sigma).

extract_protocol:
Isolation of total RNA was performed using RNeasy® Plus Mini Kit (74134, QIAGEN). TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were incubated with 10uM valinomycin (V0627, Sigma) for 6h or 7.5uM CCCP (C2759, Sigma) for 1.5h or 1uM LLOMe (L7393) for 1h followed by washout for 0h/6h/12h.

value: treated with LLOMe for 1h washout for 12h

value: HeLa cells

value: TFEBKO


title: TFEBKO treated with LLOMe washout 12h_rep4


title: CrDa01_dsDNA_rep2

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: DaDa01_ssDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: DaDa01_dsDNA_rep2


title: CrDa01_ssDNA_rep2


title: CrDa01_dsDNA_rep1


title: CrDa01_ssDNA_rep1


title: DaDa01_dsDNA_rep1


title: LPS1_ip

source_name: mouse uterus, LPS, rep1


title: Veh1_ip

source_name: mouse uterus, Vehicle, rep1


title: TFEBKO treated with LLOMe washout 12h_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep7,cartilage,L [210]

source_name: cartilage


title: Mel+LPS3_input

value: input


title: WT treated with LLOMe washout 12h_rep4


title: TFEBKO treated with LLOMe washout 12h_rep3


title: vehicle, ALN-treated, 1wk of daily loading, rep7,cartilage,Right [203]

value: Right


title: WT treated with LLOMe washout 12h_rep3


title: Mel+LPS2_input


title: vehicle, ALN-treated, 1wk of daily loading, rep6,cartilage,L [196]


title: WT treated with LLOMe washout 12h_rep2


title: BaDa02_ssDNA_rep2


title: vehicle, ALN-treated, 1wk of daily loading, rep6,cartilage,Right [189]


title: WT treated with LLOMe washout 12h_rep1


title: TFEBKO treated with LLOMe washout 6h_rep4

value: treated with LLOMe for 1h washout for 6h


title: vehicle, ALN-treated, 1wk of daily loading, rep8,cartilage,Right [217]


title: vehicle, ALN-treated, 1wk of daily loading, rep5,cartilage,L [182]


title: TFEBKO treated with LLOMe washout 6h_rep3


title: vehicle, ALN-treated, 1wk of daily loading, rep4,cartilage,L [168]


title: vehicle, ALN-treated, 1wk of daily loading, rep4,cartilage,Right [161]


title: vehicle, ALN-treated, 1wk of daily loading, rep3,cartilage,L [154]


title: LPS1_input


title: Veh3_input


title: Veh2_input


title: Veh1_input


title: LPS2_input


title: Mel+LPS1_input


title: vehicle, ALN-treated, 1wk of daily loading, rep5,cartilage,Right [175]


title: vehicle, ALN-treated, 1wk of daily loading, rep3,cartilage,Right [147]


title: WT treated with LLOMe washout 6h_rep4


title: TFEBKO treated with LLOMe washout 6h_rep2


title: TMRM_RNAseq_Low_2

city: Los Angeles

first: Wentao

last: Yang

state: California

address: 1441 Eastlake Ave

institute: university of southern california

description: Low mitochondrial membrane potential (Δ

data_processing:
The cutadapt (https://cutadapt.readthedocs.org/en/stable/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) tools wrapped in Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) were used to trim low quality bases (Q<20) and adapter for raw sequences.
RNA-seq data were mapped to the mm10 (GRCm38) genome of mouse and ERCC reference using Tophat2 (2.1.1)
Duplicated reads for pair-end data were then removed by SAMtools (v1.9)
Annotation of mRNA (GRCm38 v99) was downloaded from Ensembl database. LncRNA annotation was downloaded from NONCODE database and repeat annotation was downloaded from Homer (v4.10). All three annotations were merged into one for gene annotation. Fragment (or template) count for each feature was performed by using featureCounts with parameters “-g 'gene_id' -p  -M -O --fraction -C -F GTF -T 64 -s 0”
Fragment counts were transformed to fragments per kilobase of transcript per million (FPKM) by using edgeR
Assembly: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: embryonic stem cells

extract_protocol:
Total RNAs were extracted by the RNeasy mini kit (QIAGEN).
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L), NEBNext rRNA Depletion Dit (Human/Mouse/Rat) (NEB, #E6310X), NEBNext Multiplex Oligos for Illumina (NEB, #E6440L) and ERCC RNA Spike-In control Mix (Thermo Fisher Scientific, #4456740).

value: embryonic stem cells


title: MGYPDa687_dsDNA_rep2


title: BaDa02_ssDNA_rep1


title: MGYPDa687_ssDNA_rep2


title: MGYPDa687_dsDNA_rep1


title: MGYPDa917_ssDNA_rep2


title: MGYPDa917_ssDNA_rep1


title: BaDa02_dsDNA_rep1


title: MGYPDa917_dsDNA_rep2


title: MGYPDa687_ssDNA_rep1


title: MGYPDa917_dsDNA_rep1


title: WT treated with LLOMe washout 6h_rep3


title: vehicle, ALN-treated, 1wk of daily loading, rep2,cartilage,L [140]


title: MGYPDa624_ssDNA_rep2


title: TMRM_RNAseq_Low_1

description: Low mitochondrial membrane potential (Δ


title: TFEBKO treated with LLOMe washout 6h_rep1


title: WT treated with LLOMe washout 6h_rep2


title: MGYPDa624_ssDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep2,cartilage,Right [133]


title: WT treated with LLOMe washout 6h_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep1,cartilage,L [126]


title: vehicle, ALN-treated, 1wk of daily loading, rep1,cartilage,Right [119]


title: TFEBKO treated with LLOMe washout 0h_rep4

value: treated with LLOMe for 1h washout for 0h


title: TMRM_RNAseq_High_1

description: High mitochondrial membrane potential (Δ


title: MGYPDa624_dsDNA_rep2


title: vehicle, vehicle, 1wk of daily loading, rep7,cartilage,L [98]


title: MGYPDa624_dsDNA_rep1


title: vehicle, vehicle, 1wk of daily loading, rep6,cartilage,L [84]


title: TFEBKO treated with LLOMe washout 0h_rep1


title: TFEBKO treated with LLOMe washout 0h_rep2


title: MGYPDa408_ssDNA_rep2


title: TMRM_H3K4me3_High_2

data_processing:
For H3K4me3 and H3K27me3 CUT&RUN data, paired-end raw sequencing reads were trimmed with Trim Galore to remove adaptors and low-quality reads.
Processed read (>20 bp) were mapped back to the mouse mm10 reference genome using bowtie2 (v2.4.2) with the following parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 --threads 12’.
For H3K4me3, filtered BAM files for each sample were submitted to the callpeak function of MACS2 (v2.2.7.1) for peak regions calling with parameters “-p 1e-5 -g mm”.
For H3K27me3 domains, peak calling was performed using SICER (v1.1) with default parameters for calling broad peaks.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bed files (peaks called for H3K27me3 and H3K4me3)
Library strategy: CUT&RUN

growth_protocol: Naive ESCs were maintained in 2i/LIF culture condition, which contains N2B27 basal medium supplemented with PD0325901 (1 µM), CHIR99021 (3 µM) and LIF (1000 U/ml). N2B27 consists of a 1:1 mix of DMEM/F12 and Neurobasal, N2 (1:100), B27 (1:100), 2 mM Glutamine, Penicillin-Streptomycin (1:100) and 0.055 mM 2-mercaptoethanol.

extract_protocol:
Cells were sorted and resuspended in the wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM spermidine, 1X protease inhibitor cocktail). 10 µl of Concanavalin A-coated beads (Bangs Laboratories, Inc., #BP531) were added into the cell suspension with rotation for 10 min.
Bead-bound cells were then incubated overnight at 4oC with Rabbit anti-H3K4me3 (Millipore, #07-473) or Rabbit anti-H3K27me3 (Millipore, #07-449) antibody diluted in the antibody buffer (EDTA/Digitonin/wash buffer) (1 µg antibody in 500 µl antibody buffer). The beads were then washed three times with the wash buffer containing Digitonin (EMD Millipore, #300410), followed by an incubation with 200 µl pA-MNase (0.7 ng/µl) for 1 hour at 4oC. Next, the beads were washed three times with the wash buffer containing Digitonin before 2 mM of CaCl2 were added to active the pA-MNase for 30 min on ice. The reaction was quenched by 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 50 µg/ml RNase A (QIAGEN, #19101), 50 µg/ml glycogen (Roche, #10901393001) and 2 pg/ml Drosophila spike-in DNA) at 37oC for 10 min. The digested target chromatin was released and purified by phenol, chloroform, and ethanol. Libraries were prepared with the NEBNext UltraTM II DNA library Prep kit (NEB, #E7645L) and 10 cycles PCR.

tag: chip antibody

value: H3K4me3 (Millipore, #07-473


title: MGYPDa408_ssDNA_rep1


title: TFEBKO treated with LLOMe washout 0h_rep3


title: WT treated with LLOMe washout 0h_rep4

value: WT


title: TMRM_H3K27me3_Low_1

description: Low mitochondrial membrane potential (Δ

data_processing:
For H3K4me3 and H3K27me3 CUT&RUN data, paired-end raw sequencing reads were trimmed with Trim Galore to remove adaptors and low-quality reads.
Processed reads (>20 bp) were mapped back to the mouse mm10 reference genome using bowtie2 (v2.4.2) with the following parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 --threads 12’.
For H3K4me3, filtered BAM files for each sample were submitted to the callpeak function of MACS2 (v2.2.7.1) for peak regions calling with parameters “-p 1e-5 -g mm”.
For H3K27me3 domains, peak calling was performed using SICER (v1.1) with default parameters for calling broad peaks.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bed files (peaks called for H3K27me3 and H3K4me3)
Library strategy: CUT&RUN


title: TMRM_H3K4me3_Low_2

description: Low mitochondrial membrane potential (Δ


title: TMRM_H3K27me3_Low_2

description: Low mitochondrial membrane potential (Δ


title: TMRM_RNAseq_High_2


title: MGYPDa408_dsDNA_rep1


title: HmDa03_ssDNA_rep2


title: MGYPDa408_dsDNA_rep2


title: WT treated with LLOMe washout 0h_rep3


title: vehicle, vehicle, 1wk of daily loading, rep5,cartilage,L [70]


title: vehicle, vehicle, 1wk of daily loading, rep7,cartilage,Right [91]


title: TMRM_H3K4me3_Low_1

description: Low mitochondrial membrane potential (Δ


title: TMRM_H3K4me3_High_1


title: vehicle, vehicle, 1wk of daily loading, rep5,cartilage,Right [63]


title: vehicle, vehicle, 1wk of daily loading, rep6,cartilage,Right [77]


title: WT treated with LLOMe washout 0h_rep2


title: HmDa03_ssDNA_rep1


title: TMRM_H3K27me3_high_2


title: vehicle, vehicle, 1wk of daily loading, rep4,cartilage,L [56]


title: TMRM_low.ATAC.rep2

description: Low mitochondrial membrane potential (Δ

data_processing:
ATAC-seq paired-end raw sequencing reads were first trimmed with Trim Galore, then aligned to reference genome (mouse mm10) using Bowtie2 (v2.4.2) with parameters: “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 2000 --threads 12”.
The PCR duplicates from each dataset were removed using the rmdup function of samtools
Samples with well-correlated biological replicates were used for peak calling with MACS2 (v2.2.7.1) with following parameters:  “-B –nomodel –shif 100 –extsize 200”.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bed files

extract_protocol:
cells were washed in cold D-PBS and resuspended in 50 µl of cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630).
Samples were spun at 500 g for 10 min, 4oC. Each cell pellet was resuspended in 50 µl of transposition reaction mix containing 25 µl of 2X TD buffer (Illumina, #FC-121-1030), 2.5 µl Tn5 transposase (Illumina, #FC-121-1030) and 22.5 µl nuclear free H2O. Tagmentation by Tn5 was performed at 37oC, 30 min. Transposed DNA fragments were then purified with MinElute Kit (QIAGEN) and amplified by PCR with barcoded Nextera PCR primers. Amplified DNA products were then purified by MinElute Kit, and eluted in elution buffer (10 mM Tris Buffer, pH 8). Libraries were subject to quality control test on Bioanalyzer, and sequencing on the Illumina NovaSeq 6000 instrument with paired-end reads at the University of Michigan core facility.


title: TFEBKO ctrl_rep4

value: untreated


title: vehicle, vehicle, 1wk of daily loading, rep4,cartilage,Right [49]


title: vehicle, vehicle, 1wk of daily loading, rep3,cartilage,L [42]


title: TMRM_H3K27me3_high_1


title: TFEBKO ctrl_rep3


title: WT treated with LLOMe washout 0h_rep1


title: HmDa03_dsDNA_rep2


title: HmDa02_ssDNA_rep2


title: HmDa02_ssDNA_rep1


title: HmDa03_dsDNA_rep1


title: TMRM_high.ATAC.rep2


title: TFEBKO ctrl_rep2


title: TFEBKO ctrl_rep1


title: vehicle, vehicle, 1wk of daily loading, rep2,cartilage,L [28]


title: vehicle, vehicle, 1wk of daily loading, rep3,cartilage,Right [35]


title: WT ctrl_rep4


title: TMRM_high.ATAC.rep1


title: TMRM_low.ATAC.rep1

description: Low mitochondrial membrane potential (Δ


title: vehicle, vehicle, 1wk of daily loading, rep2,cartilage,Right [21]


title: HmDa02_dsDNA_rep2


title: HmDa02_dsDNA_rep1


title: WT ctrl_rep3


title: G93AL_Balb_C_rep3

city: Nagoya

first: Okiru

last: Komine

state: Aichi

address: Furo-cho, Chikusa-ku

department: Neuroscience and Pathobiology

institute: Research Institute of Environmental Medicine, Nagoya University

data_processing:
The reference genome assemblies and gene annotations, the mouse genome version UCSC mm10  were retrieved from iGenomes
The Illumina adapter sequences, as well as low quality bases (quality score < 20), were trimmed from 3’-ends of the sequencing reads with the Trim Galore v0.5.0
The reads were qualified with FastQC v0.11.8 before and after trimming.
The processed reads were mapped on the reference genome assembly with HISAT2 v2.1.0
Mapping reads prepared with the stranded kit was processed by employing strand specificity information. The alignments on rDNA regions were removed with BEDTools v2.25.0. From mapping data, expressions of the individual annotated genes were quantified with StringTie v1.3.5
Assembly: mm10
Supplementary files format and content: MS Excel file including TPM values of the individual genes for each sample.
Supplementary files format and content: MS Excel file including CPM values of the individual genes for each sample.

source_name: Spinal cord

extract_protocol:
Total RNAs from MACS-isolated microglia were purified using RNeasy Micro Kit (QIAGEN).
Libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina, USA) and sequenced with 151-nt paired-end reads using HiSeq X (Illumina, USA).

value: Spinal cord

value: isolated microglia


title: HmDa01_ssDNA_rep1

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text/bed files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq


title: vehicle, vehicle, 1wk of daily loading, rep1,cartilage,L [14]

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample

value: cartilage

value: 27 wks


title: WT ctrl_rep2


title: G93AL_Balb_C_rep4


title: vehicle, vehicle, 1wk of daily loading, rep1,cartilage,Right [7]


title: WT ctrl_rep1


title: WT_Balb_C_rep4

value: WT(Balb)


title: PTH-pretreated, non-loaded, replicate 15,cartilage,Right [847]

value: 26 wks


title: TFEB-FLAG-expressing treated with CCCP_rep3

value: treated with CCCP for 1.5h

value: HeLa cells

value: TFEB-FLAG-expressing


title: G93AL_Balb_C_rep1


title: HmDa01_dsDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: WT_Balb_C_rep3


title: TFEB-FLAG-expressing treated with CCCP_rep1


title: HmDa01_dsDNA_rep2


title: WT_Balb_C_rep2


title: PTH-pretreated, non-loaded, replicate 13,cartilage,Right [889]

value: Right


title: TFEB-FLAG-expressing treated with CCCP_rep2


title: CseDa01-200x_ssDNA_rep2


title: CseDa01-200x_dsDNA_rep2


title: PTH-pretreated, non-loaded, replicate 14,cartilage,Left [896]

value: Left


title: PTH-pretreated, non-loaded, replicate 12,cartilage,Left [882]


title: WT_Balb_C_rep1


title: FLAG-expressing treated with CCCP_rep2

value: FLAG-expressing


title: FLAG-expressing treated with CCCP_rep3


title: G93AL_Balb_C_rep2


title: FLAG-expressing treated with CCCP_rep1


title: CseDa01-200x_dsDNA_rep1


title: PTH-pretreated, non-loaded, replicate 16,cartilage,Left [854]


title: PTH-pretreated, non-loaded, replicate 11,cartilage,Right [875]


title: AmDa01_ssDNA_rep2


title: PTH-pretreated, non-loaded, replicate 10,cartilage,Left [868]


title: HmDa01_ssDNA_rep2


title: PTH-pretreated, non-loaded, replicate 9,cartilage,Right [861]


title: G93AL_B6_C_rep2


title: TFEB-FLAG-expressing_rep3


title: AmDa01_ssDNA_rep1


title: TFEB-FLAG-expressing_rep2


title: LPS3_input

value: input

value: uterus

value: Intraperitoneal injection of LPS

value: Day 5 of pregnancy


title: AmDa01_dsDNA_rep2


title: WT_B6_C_rep4

value: Spinal cord


title: PTH-pretreated, non-loaded, rep7,cartilage,Right [833]


title: G93AL_B6_C_rep1

value: isolated microglia


title: AmDa01_dsDNA_rep1


title: G93AL_B6_C_rep4


title: APOBEC3A_ssDNA_rep2


title: TFEB-FLAG-expressing_rep1

value: untreated


title: FLAG-expressing_rep3


title: PTH-pretreated, non-loaded, rep6,cartilage,Left [826]

value: cartilage


title: G93AL_B6_C_rep3


title: WT_B6_C_rep2


title: FLAG-expressing_rep2


title: WT_B6_C_rep3


title: PTH-pretreated, non-loaded, rep5,cartilage,Right [819]


title: WT_B6_C_rep1


title: FLAG-expressing_rep1


title: TFEBKO treated with val_rep3

value: treated with val for 6h

value: TFEBKO


title: APOBEC3A_dsDNA_rep2


title: APOBEC3A_ssDNA_rep1


title: PTH-pretreated, non-loaded, rep4,cartilage,Left [812]

value: 26 wks


title: APOBEC3A_dsDNA_rep1


title: PTH-pretreated, non-loaded, rep3,cartilage,Right [805]


title: CseDa01-200x_ssDNA_rep1


title: Tumor infiltrating lymphocytes，2W，TR2

data_processing:
Illumina Casava 1.8 software used for basecalling.
Single-cell RNA-seq data from each experiment were processed using a cell ranger count (10 × Genomics CellRanger [v3.1.0]), with reference to the mouse genome GRCm38 (mm10).
The digital gene expression matrices were analysed in R (v4.1.2) with the assistance of the Seurat (v4.0.0) package.
DoubletFinder software was used to identify and eliminate any potential doublets based on the proximity of each cell to artificial doublets. Cells exhibiting the expression of more than 10000 genes or fewer than 200 genes in UMI counts, along with those displaying over 10 % of mitochondrial gene expression, were excluded from the analysis. Subsequently, the filtered data underwent log normalisation and scaling to mitigate any cell-to-cell variations attributable to the UMI counts and percentage of mitochondrial reads.
Assembly: mouse genome GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Tumor infiltrating lymphocytes cell

growth_protocol: Tumor infiltrating lymphocytes were isolated from tumor of mice hepatocellular carcinoma orthotopic transplantation model.

extract_protocol:
single cell extracted from the mice bearing HCC were excised and mechanically dissociated into individual cells using a Tumour Dissociation Kit
These individual cells were then collected using the 10 × Genomics Chromium Single Cell 5′ Solution. RNA-seq libraries were prepared according to the manufacturer’s protocol (10 × Genomics).

treatment_protocol: TILs isolated from mice hepatocellular carcinoma orthotopic transplantation model for the three groups (P: control group, T: immunotherapy group, TR: immunotherapy plus REM group; n=2 per group) at two time points (1 w and 2 w)

value: Tumor infiltrating lymphocytes cell

value: T+A+Remodelin

value: 2 week


title: TFEBKO treated with val_rep2

value: HeLa cells


title: PTH-pretreated, non-loaded, rep2,cartilage,Left [798]

value: Left


title: WWTPDa05_ssDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: Tumor infiltrating lymphocytes cell，2W，TR1


title: WWTPDa05_ssDNA_rep1


title: PTH-pretreated, non-loaded, rep8,cartilage,Left [840]


title: PTH-pretreated, non-loaded, rep1,cartilage,Right [791]

value: Right


title: WT treated with val_rep3

value: WT


title: TFEBKO treated with val_rep1


title: vehicle, non-loaded, rep16,cartilage,Left [784]


title: Tumor infiltrating lymphocytes cell，2W，TA1

value: T+A


title: WWTPDa05_dsDNA_rep2


title: WT treated with val_rep2


title: vehicle, non-loaded, rep15,cartilage,Right [777]


title: vehicle, non-loaded, rep14,cartilage,Left [770]


title: Tumor infiltrating lymphocytes cell，2W，Con2

value: Control


title: WWTPDa04_ssDNA_rep2


title: TFEBKO_rep3


title: vehicle, non-loaded, rep13,cartilage,Right [763]


title: WWTPDa04_ssDNA_rep1


title: WWTPDa05_dsDNA_rep1


title: vehicle, non-loaded, rep12,cartilage,Left [756]


title: WWTPDa04_dsDNA_rep2


title: Tumor infiltrating lymphocytes cell，1W，TR1

value: 1 week


title: TFEBKO_rep1


title: Tumor infiltrating lymphocytes cell，1W，TR2


title: WWTPDa04_dsDNA_rep1


title: vehicle, non-loaded, rep11,cartilage,Right [749]


title: WT_rep3


title: Tumor infiltrating lymphocytes cell，2W，TA2


title: vehicle, non-loaded, rep10,cartilage,Left [742]


title: Tumor infiltrating lymphocytes，1W，TA2


title: TFEBKO_rep2


title: Tumor infiltrating lymphocytes cell，2W，Con1


title: VRDa06_ssDNA_rep2


title: Tumor infiltrating lymphocytes，1W，TA1


title: WT treated with valinomycin (val)_rep1


title: vehicle, non-loaded, rep9,cartilage,Right [735]


title: Tumor infiltrating lymphocytes，1W，Con2


title: VRDa06_ssDNA_rep1


title: WT_rep2


title: WT_rep1


title: vehicle, non-loaded, rep8,cartilage,Left [728]


title: Tumor infiltrating lymphocytes cell，1W，Con1


title: vehicle, non-loaded, rep7,cartilage,Right [721]


title: SzDa01_ssDNA_rep2


title: LesionB

city: Chengdu

first: Liang

last: Zhong

address: Renmin road

institute: Sichuan University

data_processing:
We use fastp to perform basic statistics on the quality of the raw reads. Generally, celltanger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.
Raw reads were demultiplexed and mapped to the reference genome by 10X  Genomics Cell Ranger pipeline (cellranger-5.0.1) using default parameters. All  downstream single-cell analyses were performed using Cell Ranger and Seurat  ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for  each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers  were counted to construct digital expression matrices. Secondary filtration by Seurat :  A gene with expression in more than 3 cells was considered as expressed, and each  cell was required to have at least 200 expressed genes. And filter out some of the  foreign cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: oral mucosa

extract_protocol:
The OLK tissues were washed by phosphate-buffered saline (Gibco, USA), cut into tiny cubes (2mm3), and transferred to the C tube (Miltenyi Biotec, Germany). The tissue dissociation was performed by skin dissociation kits (Miltenyi Biotec, Germany), following the manufacturer’s instructions. After dissociation, single-cells were spun down at 400g for 5 min and resuspended with 1X Red Blood Cell Lysis (Abcam, USA) for 5 minutes to remove the blood cells. Then, dead cells removing using Dead Cell Removal kits (STEMCELL Technologies, Canada). Single-cells were spun down at 400g for 5 minutes and adjusted to 1 x 106/ml. The total time from biopsy to loading on the 10X platform was within 3 hours.
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3, chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’  v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions (Illumina).

value: tongue

tag: diagnosis

value: Proliferative Verrucous Leukoplakia

tag: histopathological diagnosis

value: corrugated orthohyperkeratosis


title: LesionC

value: bulky hyperkeratotic epithelial proliferation


title: VRDa06_dsDNA_rep1


title: HepG2-NTCP, Control (3)

city: Oxford

first: James

last: Harris

state: Oxfordshire

address: Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina adapters were removed and data transformed to sequencing reads by CASAVA base recognition
Reads were mapped against the reference human genome (hg38) using STAR aligner.
Read counts were transformed to FPKM to account for sequencing depth and gene length (Mortazavi et al. 2008)
Genome_build: Human hg38
Supplementary_files_format_and_content: fpkm_samples.xls and reacount.xls contain all FPKM and readcount values for every gene in n=9 samples, respectively.

growth_protocol: HepG2-NTCP cells were seeded, and left overnight to adhere. Media was replaced and cells were transferred to culture conditions for 72 hours.

extract_protocol:
Following treatment as described above, cells were lysed in RLT buffer and RNA extracted using Qiagen RNAeasy kit. RNAs were treated with on-column DNAse (Qiagen), and 2uG of material was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hypoxic culture or drug treatment were applied for 72 hours.

value: Human hepatoma cell line

tag: culture condition

value: Untreated (Control)


title: vehicle, non-loaded, rep4,cartilage,Left [700]

value: cartilage

value: 26 wks


title: HepG2-NTCP, Control (2)


title: vehicle, non-loaded, rep2,cartilage,Left [686]


title: vehicle, non-loaded, rep5,cartilage,Right [707]


title: SzDa01_dsDNA_rep1

extract_protocol:
E. coli C2566 genomic DNA was purified using Monarch Genomic DNA Purification Kit (NEB Ipswich, MA), GM12878 genomic DNA was obtained from Coriell Cell Repositories (Camden, NJ).
Input DNA was sheared to 300 bp using the Covaris S2 instrument. Sheared material was transferred to a PCR strip tube to begin library construction. NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing, and adaptor ligation. The custom made Pyrollo-dC adaptor (NEB Organic Synthesis Division, Ipswich MA), where all dCs are replaced with Pyrollo-dC, was used. The ligated samples were purified using NEBNext Sample Purification Beads  according to the manufacturer’s instructions. For ssDNA libraries, prior to deamination the DNA was denatured by heating at 90oC for 10 minutes followed by cooling for 2 minutes on ice. The DNA was then deaminated using 1 µL of PURExpress (NEB, Ipswich, MA) synthesized deaminase protein following manufacturer's recommendations for 1 hour at 37oC. Then 1 µL of Thermolabile Proteinase K (NEB, Ipswich, MA) was added and incubated for 30 min at 37oC followed by 10 min at 60oC. Then the library was amplified using NEBNext Q5U Master Mix (NEB, Ipswich, MA, USA). Paired-end sequencing of 150 cycles (2 x 75 bp) was performed for all the sequencing runs.
DNA sequencing of deaminated double-stranded and single-stranded DNA


title: NsDa01_ssDNA_rep2


title: SzDa01_ssDNA_rep1


title: HepG2-NTCP, Control (1)


title: LesionA

value: keratosis of unknown significance


title: vehicle, non-loaded, rep1,cartilage,Right [679]

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols


title: vehicle, non-loaded, rep6,cartilage,Left [714]


title: HepG2-NTCP, QC6352 (3)


title: VRDa06_dsDNA_rep2


title: NsDa01_dsDNA_rep2


title: HepG2-NTCP, QC6352 (2)


title: SzDa01_dsDNA_rep2


title: Mouse, regular chow diet, liver, control 8

city: Jerusalem

first: Yonat

last: Tzur

address: Givat Ram Campus

country: Israel

institute: Hebrew University of Jerusalem

library_source: other

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control and reads were further trimmed and filtered using Flexbar (version 0.11.9). Sequences were aligned using miRExpress 2.1.4 to miRBase version 21 for microRNAs and  for tRFs MINTmap 1.0 has been used.
Assembly: miRBase version 21, MINTmap v. 1.0
Supplementary files format and content: raw counts from miRExpress and MINTmap

molecule: other

source_name: liver

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer's protocol, followed by RNA concentration determination (NanoDrop 2000, Thermo Scientific), standard gel electrophoresis for quality assesement, and RIN determination (Bioanalyzer 6000, Agilent). RIN was determined to be above 8.4 for all samples.
Libraries were constructed from 300 ng (liver) total RNA (NEBNext Multiplex Small RNA library prep set for Illumina, New England Biolabs, NEB-E7560S) and the small RNA fraction was sequenced on the NextSeq 500 System (Illumina) at the Center for Genomic Technologies Facility, the Hebrew University of Jerusalem
NEBNext Multiplex Small RNA library prep set for Illumina, New England Biolabs, NEB-E7560S

value: liver


title: NsDa01_dsDNA_rep1


title: vehicle, non-loaded, rep3,cartilage,Right [693]


title: SJSA1_200 nM THZ531_rep2

type: RNA

city: Guangzhou

first: Jiajun

last: Zhang

address: #58，Zhongshan 2nd Road

institute: the First Affiliated Hospital of Sun Yat-Sen University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

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

label: biotin

source_name: SJSA-1 treated with 200 nM THZ531 for 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: U2-OS and SJSA-1 were maintained in Dulbecco’s modified Eagle medium. All media were supplemented with 10% fetal bovine serum, penicillin (100 U/mL) and streptomycin (100 mg/mL). Cells were incubated at 37℃ with 5% CO2.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Plate the target cells in a 10-cm dish in 10 ml of DMEM supplemented with 10% fetal bovine serum, penicillin (100 U/mL) and streptomycin (100 mg/mL) 24 hours prior to treatment. Replace medium with fresh complete medium containing the various concentration of THZ531 or DMSO in the next day. Make sure the cells reach same confluent at the time of treatment. Continue incubation in the CO2 incubator at 37℃. Total RNA was extracted from U2-OS or SJSA-1 cells treated with DMSO (control) and different doses of THZ531, respectively, using TRIzol reagent according to manufacturer’s instructions.

value: bone

value: osteosarcoma

value: 200 nM THZ531 for 6 hours


title: NsDa01_ssDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: SJSA1_800 nM THZ531_rep3

source_name: SJSA-1 treated with 800 nM THZ531 for 6 hours

value: 800 nM THZ531 for 6 hours


title: SJSA1_200 nM THZ531_rep3


title: SJSA1_200 nM THZ531_rep1


title: SJSA1_800 nM THZ531_rep1


title: SJSA1_50 nM THZ531_rep3

source_name: SJSA-1 treated with 50 nM THZ531 for 6 hours

value: 50 nM THZ531 for 6 hours


title: HepG2-NTCP, 1% Oxygen (2)

value: 1% Oxygen


title: Mouse, regular chow diet, liver, control 6


title: KsDa01_ssDNA_rep1


title: Mouse, regular chow diet, liver, control 5


title: SJSA1_50 nM THZ531_rep2


title: Mouse, regular chow diet, liver, control 4


title: HepG2-NTCP, 1% Oxygen (1)


title: HepG2-NTCP, QC6352 (1)


title: Mouse, regular chow diet, liver, control 3


title: KsDa01_dsDNA_rep1


title: Cd4_PeDa01_ssDNA_rep2


title: KsDa01_dsDNA_rep2


title: pooled liver tissue, fed high frass diet, rep3 [B1]

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description:
Counts_Table_liver.txt
frasshigh_liver_rep3

data_processing:
Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Raw FASTQ files were trimmed of adapters and poor quality reads using Trimmomatic v0.38.
Reads passing quality control were aligned to the channel catfish genome using STAR v2.7.8a with the two-pass mapping option.
Resultant BAM alignment files were assessed for quality using RSeQC v4.0.0.
Counts information from BAM alignment files were generated using HTSeq v0.9.0. Analysis parameters include gene-level quantification using feature "exon" and group by "parent," with overlap mode "union".
Pairwise differential gene expression analyses were performed using DESeq2 v1.40.1.
P-values were adjusted with fdrtool v1.2.17.
Assembly: GCA_001660625.3
Supplementary files format and content: tab-delimited text file of raw counts for each sample

organism: Ictalurus punctatus

extract_protocol:
Tissue samples were pooled in groups of 3 and total RNA was extracted with the Qiagen RNeasy Plus Mini Kit per the included protocol.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (New England Biolabs, Ipswich, MA, USA)

tag: time-point

value: 10 weeks

tag: diet

value: 300g frass per kg diet


title: Mouse, regular chow diet, liver, control 7

tag: tissue


title: HepG2-NTCP, 1% Oxygen (3)

tag: cell type


title: SJSA1_800 nM THZ531_rep2

tag: treatment


title: KsDa01_ssDNA_rep2

city: Ipswich

last: Sun

institute: New England Biolabs


title: Mouse, regular chow diet, liver, control 2


title: Cd4_PeDa01_ssDNA_rep1


title: SJSA1_50 nM THZ531_rep1


title: SJSA1_DMSO_rep3

source_name: SJSA-1 treated with DMSO(control) for 6 hours

value: DMSO(control) for 6 hours


title: pooled liver tissue, fed high frass diet, rep2 [A8]

description:
Counts_Table_liver.txt
frasshigh_liver_rep2


title: Mouse, regular chow diet, liver, control 1


title: SJSA1_DMSO_rep2


title: pooled liver tissue, fed high frass diet, rep4 [B6]

description:
Counts_Table_liver.txt
frasshigh_liver_rep4


title: SJSA1_DMSO_rep1


title: Mouse, AM608-treated, liver, control 8


title: pooled liver tissue, fed high frass diet, rep1 [A2]

description:
Counts_Table_liver.txt
frasshigh_liver_rep1


title: pooled liver tissue, fed low frass diet, rep3 [B2]

description:
Counts_Table_liver.txt
frasslow_liver_rep3

value: 50g frass per kg diet


title: pooled liver tissue, fed low frass diet, rep4 [B7]

description:
Counts_Table_liver.txt
frasslow_liver_rep4


title: Cd4_PeDa01_dsDNA_rep2


title: Cd4_PeDa01_dsDNA_rep1


title: AdDa01_ssDNA_rep2


title: pooled liver tissue, fed low frass diet, rep2 [A7]

description:
Counts_Table_liver.txt
frasslow_liver_rep2


title: U2-OS_800 nM THZ531_rep2

source_name: U2-OS treated with 800 nM THZ531 for 6 hours


title: AdDa01_ssDNA_rep1


title: Mouse, AM608-treated, liver, control 6


title: Mouse, AM608-treated, liver, control 5


title: pooled liver tissue, fed low frass diet, rep1 [A1]

description:
Counts_Table_liver.txt
frasslow_liver_rep1


title: AdDa01_dsDNA_rep2


title: Mouse, AM608-treated, liver, control 4


title: AdDa01_dsDNA_rep1


title: Mouse, AM608-treated, liver, control 7


title: pooled liver tissue, fed control diet, rep3 [B4]

description:
Counts_Table_liver.txt
frasscont_liver_rep3

value: no frass


title: U2-OS_800 nM THZ531_rep3


title: XcDa01_ssDNA_rep2


title: U2-OS_800 nM THZ531_rep1


title: U2-OS_200 nM THZ531_rep3

source_name: U2-OS treated with 200 nM THZ531 for 6 hours


title: Mouse, AM608-treated, liver, control 2


title: U2-OS_200 nM THZ531_rep2


title: Mouse, AM608-treated, liver, control 1


title: pooled liver tissue, fed control diet, rep2 [A6]

description:
Counts_Table_liver.txt
frasscont_liver_rep2


title: pooled liver tissue, fed control diet, rep1 [A3]

description:
Counts_Table_liver.txt
frasscont_liver_rep1


title: XcDa01_ssDNA_rep1


title: Mouse, AM132-treated, liver, sample 8


title: XcDa01_dsDNA_rep2


title: Mouse, AM132-treated, liver, sample 7


title: U2-OS_50 nM THZ531_rep3

source_name: U2-OS treated with 50 nM THZ531 for 6 hours


title: pooled intestine tissue, fed high frass diet, rep4 [B6]

description:
Counts_Table_intestine.txt
frasshigh_int_rep4

source_name: intestine

value: intestine


title: Mouse, AM608-treated, liver, control 3


title: pooled liver tissue, fed control diet, rep4 [B10]

description:
Counts_Table_liver.txt
frasscont_liver_rep4


title: pooled intestine tissue, fed high frass diet, rep3 [B1]

description:
Counts_Table_intestine.txt
frasshigh_int_rep3


title: WcDa01_ssDNA_rep2

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: U2-OS_50 nM THZ531_rep2


title: pooled intestine tissue, fed high frass diet, rep2 [A8]

description:
Counts_Table_intestine.txt
frasshigh_int_rep2


title: WcDa01_ssDNA_rep1


title: Mouse, AM132-treated, liver, sample 5


title: Mouse, AM132-treated, liver, sample 6


title: pooled intestine tissue, fed high frass diet, rep1 [A2]

description:
Counts_Table_intestine.txt
frasshigh_int_rep1


title: WcDa01_dsDNA_rep2


title: XcDa01_dsDNA_rep1


title: pooled intestine tissue, fed control diet, rep4 [B10]

description:
Counts_Table_intestine.txt
frasscont_int_rep4


title: U2-OS_DMSO rep2

source_name: U2-OS treated with DMSO(control) for 6 hours


title: Mouse, AM132-treated, liver, sample 3


title: Mouse, AM132-treated, liver, sample 2


title: SjDa01_ssDNA_rep1


title: pooled intestine tissue, fed control diet, rep2 [A6]

description:
Counts_Table_intestine.txt
frasscont_int_rep2


title: SjDa01_dsDNA_rep2


title: U2-OS_DMSO rep3


title: pooled intestine tissue, fed control diet, rep3 [B4]

description:
Counts_Table_intestine.txt
frasscont_int_rep3


title: SjDa01_ssDNA_rep2


title: WcDa01_dsDNA_rep1


title: pooled Intestine tissue, fed low frass, rep4 [B7]

description:
Counts_Table_intestine.txt
frasslow_int_rep4


title: Mouse, AM132-treated, liver, sample 1


title: SjDa01_dsDNA_rep1


title: Mouse, AM132-treated, sample 16

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control and reads were further trimmed and filtered using Flexbar (version 0.11.9). Sequences were aligned using miRDeep2 to miRBase version 21 for microRNAs and  for tRFs MINTmap 1.0 has been used.
Assembly: miRBase version 21, MINTmap v. 1.0
Supplementary files format and content: raw counts from miRDeep2 and MINTmap

source_name: hypothalamus

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer's protocol, followed by RNA concentration determination (NanoDrop 2000, Thermo Scientific), standard gel electrophoresis for quality assesement, and RIN determination (Bioanalyzer 6000, Agilent). RIN was determined to be above 8.4 for all samples.
Libraries were constructed from 200ng total RNA (NEBNext Multiplex Small RNA library prep set for Illumina, New England Biolabs, NEB-E7560S) and the small RNA fraction was sequenced on the NextSeq 500 System (Illumina) at the Center for Genomic Technologies Facility, the Hebrew University of Jerusalem
NEBNext Multiplex Small RNA library prep set for Illumina, New England Biolabs, NEB-E7560S

value: hypothalamus

tag: batch


title: CseDa01-50x_ssDNA_rep2


title: pooled intestine tissue, fed control diet, rep1 [A3]

description:
Counts_Table_intestine.txt
frasscont_int_rep1


title: Mouse, AM608-treated, control 16


title: Mouse, AM132-treated, liver, sample 4


title: U2-OS_DMSO rep1


title: pooled Intestine tissue, fed low frass, rep2 [A7]

description:
Counts_Table_intestine.txt
frasslow_int_rep2


title: pooled Intestine tissue, fed low frass, rep3 [B2]

description:
Counts_Table_intestine.txt
frasslow_int_rep3


title: Tumor_Fresh frozen [OSCC_IL6low_4]

city: Toon

first: Tomoko

last: Adachi

state: Ehime

address: Shitsukawa

department: Department of Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

hyb_protocol: Hyb protocol was performed according to the manufacturer's instructions.

scan_protocol: The signal was developed and scanning was undertaken using a GeneAtlas Imaging Station(Affymetrix).

data_processing:
Obtained CEL files were log2 transformed by Expression Console without normalization and then quantile normalized by  GeneSpring GX 14.9.1 software.
The samples of each clinical condition were independently divided into retrospective study. With this study, an unpaired Student’s t tests for continuous variables were used to compare the characteristics between the 2 clinical groups. We set differences with P values of less than 0.05 were considered statistically significant.

source_name: gingiva_ope sample

label_protocol: 500 ng of total RNA was labeled using according to the manufacturer's instructions.

extract_protocol: Total RNA was harvested from the fresh-frozen OSCC samples, which were collected at the time of surgery. When collected the samples in surgery, put in ISOGEN and stored at -80 degrees. Total RNA used in this study was extracted by tissues after homogenization with TissueLyser (Qiagen) and ISOGEN (Nippon Gene) according to the manufacturer's protocol. The collected total RNA was quantified to 10 ng/μl by Qubit Fluorometer (Thermo Fisher Scientific) and stored at -80 degrees.

tag: Sex

value: male

tag: age

tag: clinical tumour size

tag: clinical stage

value: ⅣA

tag: pathological stage

tag: pathological diagnosis

value: SCC

tag: pathological grade


title: Mouse, AM608-treated, control 15


title: Tumor_Fresh frozen [OSCC_IL6low_5]

value: ⅣB


title: U2-OS_200 nM THZ531_rep1

value: bone

tag: disease

value: osteosarcoma

tag: cell line


title: Mouse, AM608-treated, control 14


title: Tumor_Fresh frozen [OSCC_IL6low_9]

source_name: tongue_ope sample

value: female

value: Ⅱ


title: Tumor_Fresh frozen [OSCC_IL6low_7]


title: Tumor_Fresh frozen [OSCC_IL6low_8]


title: CseDa01-50x_dsDNA_rep2

first: Zhiyi

address: 240 County Road

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BadTF3_ssDNA_rep2


title: CseDa01-50x_dsDNA_rep1


title: CseDa01-50x_ssDNA_rep1


title: BadTF3_ssDNA_rep1


title: Tumor_Fresh frozen [OSCC_IL6low_6]

source_name: buccalmucosa_ope sample


title: Tumor_Fresh frozen [OSCC_IL6low_3]

source_name: mandible_ope sample


title: Mouse, AM132-treated, sample 15


title: D3

city: Tongliao

first: Yujie

last: Chen

address: No.996 Xilamulun Street, Tongliao city, Inner Mongolia, China

institute: Inner Mongolia Minzu University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomics workbench (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to Genome assembly JCVI_RCG_1.1 (parameters-mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Genome assemblyJCVI_RCG_1.1
Supplementary files format and content: The Excel file includes the FPKM value for each Sample

organism: Ricinus communis

source_name: internode

growth_protocol: 6 castor internode tissues were collected and maintained from a fast growth period (8-10 leaves) in the field.

extract_protocol:
Approximately 6 plants were dissected to obtain the internode tissue
Qualified RNA were processed for library construction. The procedures are described as follow:(1) mRNA was isolated by Oligo(dT)-attached magnetic beads.(2) mRNA was then randomly fragmented in fragmentation buffer.(3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.(4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.(5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

value: internode

tag: phenotype

value: short-stalk

tag: genotype


title: BadTF3_dsDNA_rep2


title: D2


title: pooled Intestine tissue, fed low frass, rep1 [A1]

description:
Counts_Table_intestine.txt
frasslow_int_rep1

tag: time-point

value: 10 weeks


title: BaDa01_ssDNA_rep4


title: Mouse, AM608-treated, control 12


title: L3

value: high-stalk

value: Zhansihao


title: L2


title: Mouse, AM608-treated, control 13


title: Tumor_Fresh frozen [OSCC_IL6low_1]

value: Ⅲ


title: L1


title: Tumor_Fresh frozen [OSCC_IL6high_9]


title: BadTF3_dsDNA_rep1


title: Tumor_Fresh frozen [OSCC_IL6low_2]


title: Mouse, AM132-treated, sample 13


title: Mouse, AM132-treated, sample 14


title: mouse10, F, striatum

city: Birmingham

first: Brittany

last: Lasseigne

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

data_processing:
We merged each sample's six fastq_pass files (quality minimum of 9) with cat to create one fastq per sample (this is called final_merged_sampleNN.fastq.gz).
We next used the nf-core nanoseq pipeline with the following options: version 2.0.1, protocol cDNA, flow cell FLO-MIN106, kit SQK-PCB109, skip_basecalling, skip_demultiplexing, skip_differential_analysis, profile cheaha, and a custom configuration file specifying nanoplot version 1.32.1. to generate the counts_gene.txt and counts_transcript.txt for downstream analyses.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes Bambu counts per gene for each sample
Supplementary files format and content: tab-delimited text file includes Bambu counts per transcript for each sample
Supplementary files format and content: general transfer format (gtf) containing annotation information for annotated and novel transcripts identified by Bambu

source_name: striatum

extract_protocol:
For each sample, we transferred ~30 mg of each brain region (or the entire brain region, if less than 30 mg) into an MP Biomedical Lysis D Matrix, 2ml tube (#6913500) containing 500μl of TRIzol reagent (Invitrogen #15596018) and lysed cells from each tissue on the FastPrep-24 5G bead beating grinder and lysis system (MP Biomedical #116005500). After lysis, we added 100μl of chloroform to the tube and centrifuged at 12,000×g for 15 minutes, and then transferred the clear top layer of the supernatant into a fresh tube. We next added an equivolume amount of isopropanol to the clear liquid and centrifuged at 12,000×g for 10 minutes. We decanted the supernatant, washed the pellet twice with 75% ethanol, and resuspended the air-dried pellet in RNAse-free water. We incubated the final RNA product with TURBO DNase (Invitrogen #AM1907) for 30 minutes and assessed for RNA quality using a Qubit fluorometer and Agilent Fragment Analyzer. All RNA extractions had an RNA quality number (RQN) score >7.
We processed RNA samples for nanopore sequencing using the PCR-cDNA Barcoding Kit (SQK-PCB111.24) in two batches (20 samples each, batches A and B) according to manufacturer instructions and prepared libraries in equimolar amounts based on fragment length and concentration to make 15 fmol of cDNA library per flow cell, or 105 fmol of pooled cDNA library in a total volume of 77 μl for six flow cells (11μl per flow cell + 1 extra).

value: striatum

tag: strain

tag: mouse id

value: F

value: 20 weeks


title: Mouse, regular chow diet, control 12

tag: tissue

value: hypothalamus


title: mouse10, F, hippocampus

source_name: hippocampus

value: hippocampus


title: Tumor_Fresh frozen [OSCC_IL6high_6]

value: male

value: ⅣA

value: SCC


title: Genomic DNA from ependymoma 1450

type: genomic

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

label: Cy5 and Cy3

source_name: ependymoma 1450

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: localization

value: spinal

tag: patho diagnosis

value: Ependymoma II

tag: classification result v12

tag: classification score


title: Tumor_Fresh frozen [OSCC_IL6high_8]

tag: Sex

tag: age

tag: clinical tumour size


title: D1


title: Tumor_Fresh frozen [OSCC_IL6high_7]

value: female

tag: clinical stage

value: Ⅰ

tag: pathological stage

value: Ⅱ

tag: pathological diagnosis


title: BaDa01_ssDNA_rep3

tag: cell type

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: Genomic DNA from ependymoma 1449

source_name: ependymoma 1449


title: Mouse, regular chow diet, control 10

tag: batch


title: Genomic DNA from ependymoma 1447

source_name: ependymoma 1447


title: mouse05, M, striatum

value: M


title: Mouse, AM608-treated, control 11


title: Mouse, AM132-treated, sample 12


title: DddA_ssDNA_rep2


title: Tumor_Fresh frozen [OSCC_IL6high_5]

tag: pathological grade


title: Tumor_Fresh frozen [OSCC_IL6high_4]


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 54

first: Swenja

last: Gödicke

address: Martinistrasse 52

institute: Research Institute Children‘s Cancer Center Hamburg

description:
9379082092_R02C02
54_overall

hyb_protocol: 100-500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

source_name: Posterior fossa

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions.

value: Posterior fossa ependymoma


title: Mouse, AM132-treated, sample 10


title: Genomic DNA from ependymoma 1446

source_name: ependymoma 1446


title: Tumor_Fresh frozen [OSCC_IL6high_3]

value: Ⅲ


title: U2-OS_50 nM THZ531_rep1

source_name: U2-OS treated with 50 nM THZ531 for 6 hours

value: bone

tag: disease

value: osteosarcoma

tag: cell line

tag: treatment

value: 50 nM THZ531 for 6 hours


title: BaDa01_dsDNA_rep3


title: Tumor_Fresh frozen [OSCC_IL6high_2]


title: mouse10, F, cerebellum

source_name: cerebellum

tag: tissue

value: cerebellum

tag: strain

tag: mouse id

value: F

value: 20 weeks


title: Mouse, AM608-treated, control 10

value: hypothalamus


title: BaDa01_dsDNA_rep4

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: Mouse, AM132-treated, sample 11


title: Genomic DNA from ependymoma 1448

source_name: ependymoma 1448

tag: localization

tag: patho diagnosis

tag: classification result v12


title: mouse10, F, cortex

source_name: cortex

value: cortex

tag: Sex

tag: age


title: DddA_ssDNA_rep1


title: DddA_dsDNA_rep1


title: PwDa01_ssDNA_rep2


title: DddA_dsDNA_rep2


title: Mouse, regular chow diet, control 9

source_name: hypothalamus


title: Genomic DNA from ependymoma 1444

source_name: ependymoma 1444

value: spinal

tag: classification score


title: mouse05, M, hippocampus

value: hippocampus


title: mouse05, M, cerebellum


title: mouse11, F, striatum

value: striatum


title: Genomic DNA from ependymoma 1443

source_name: ependymoma 1443

value: Ependymoma II


title: Genomic DNA from ependymoma 1445

source_name: ependymoma 1445


title: mouse05, M, cortex


title: Tumor_Fresh frozen [OSCC_IL6high_1]

source_name: gingiva_ope sample

value: female

tag: clinical tumour size

tag: clinical stage

value: ⅣA

tag: pathological stage

value: SCC


title: Mouse, regular chow diet, control 11

tag: batch


title: Mouse, AM132-treated, sample 9


title: PwDa01_dsDNA_rep2

tag: cell type

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: PwDa01_ssDNA_rep1


title: Mouse, AM608-treated, control 9


title: Genomic DNA from ependymoma 1441

source_name: ependymoma 1441


title: mouse11, F, hippocampus

source_name: hippocampus


title: Mouse, regular chow diet, control 8


title: Genomic DNA from ependymoma 1440

source_name: ependymoma 1440


title: Genomic DNA from ependymoma 1442

source_name: ependymoma 1442


title: mouse11, F, cerebellum


title: Mouse, AM608-treated, control 8


title: PwDa01_dsDNA_rep1


title: MGYPDa829_ssDNA_rep2


title: Mouse, regular chow diet, control 7


title: Mouse, AM132-treated, sample 8


title: mouse11, F, cortex


title: Genomic DNA from ependymoma 1439

source_name: ependymoma 1439


title: Genomic DNA from ependymoma 1437

source_name: ependymoma 1437


title: mouse04, M, hippocampus

value: M


title: Mouse, AM608-treated, control 7


title: Genomic DNA from ependymoma 1438

source_name: ependymoma 1438


title: Mouse, AM132-treated, sample 7


title: MGYPDa829_ssDNA_rep1


title: Genomic DNA from ependymoma 1436

source_name: ependymoma 1436


title: mouse04, M, cerebellum

source_name: cerebellum


title: MGYPDa829_dsDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: MGYPDa829_dsDNA_rep2


title: EcDa01_ssDNA_rep2


title: mouse04, M, cortex


title: Genomic DNA from ependymoma 1435

source_name: ependymoma 1435


title: mouse12, F, striatum

source_name: striatum


title: EcDa01_ssDNA_rep1


title: Mouse, AM608-treated, control 6

source_name: hypothalamus


title: EcDa01_dsDNA_rep2


title: mouse12, F, hippocampus


title: mouse04, M, striatum


title: Genomic DNA from ependymoma 1434

source_name: ependymoma 1434


title: Mouse, regular chow diet, control 5


title: EcDa01_dsDNA_rep1


title: CbDa01_ssDNA_rep4


title: Genomic DNA from ependymoma 1433

source_name: ependymoma 1433


title: Mouse, AM608-treated, control 5


title: Genomic DNA from ependymoma 1432

source_name: ependymoma 1432


title: CbDa01_ssDNA_rep3


title: Mouse, regular chow diet, control 6


title: mouse03, M, striatum


title: Mouse, AM132-treated, sample 5


title: mouse12, F, cortex

source_name: cortex


title: Mouse, regular chow diet, control 4


title: Genomic DNA from ependymoma 1429

source_name: ependymoma 1429


title: Mouse, AM608-treated, control 4


title: mouse03, M, cerebellum


title: mouse03, M, cortex


title: Mouse, AM132-treated, sample 6


title: Genomic DNA from ependymoma 1431

source_name: ependymoma 1431


title: Mouse, AM132-treated, sample 4


title: Genomic DNA from ependymoma 1428

source_name: ependymoma 1428


title: Mouse, regular chow diet, control 3


title: mouse12, F, cerebellum


title: MGYPDa13_ssDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: MGYPDa13_ssDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: CbDa01_dsDNA_rep3


title: Genomic DNA from ependymoma 1426

source_name: ependymoma 1426


title: mouse13, F, cerebellum


title: mouse13, F, striatum


title: mouse03, M, hippocampus

source_name: hippocampus


title: Genomic DNA from ependymoma 1430

source_name: ependymoma 1430


title: Mouse, AM132-treated, sample 3


title: Mouse, AM608-treated, control 3


title: Genomic DNA from ependymoma 1427

source_name: ependymoma 1427


title: Mouse, regular chow diet, control 2


title: mouse13, F, hippocampus


title: mouse13, F, cortex


title: MGYPDa09_ssDNA_rep2


title: MGYPDa10_ssDNA_rep1


title: Genomic DNA from ependymoma 1425

source_name: ependymoma 1425


title: CbDa01_dsDNA_rep4

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: Genomic DNA from ependymoma 1424

source_name: ependymoma 1424


title: MGYPDa09_ssDNA_rep1


title: Genomic DNA from ependymoma 1423

source_name: ependymoma 1423


title: mouse02, M, striatum

source_name: striatum


title: MGYPDa10_ssDNA_rep2


title: Mouse, AM132-treated, sample 2

source_name: hypothalamus


title: MGYPDa13_dsDNA_rep2


title: mouse02, M, hippocampus


title: MGYPDa13_dsDNA_rep1


title: Genomic DNA from ependymoma 1422

source_name: ependymoma 1422


title: Mouse, AM608-treated, control 1


title: Genomic DNA from ependymoma 1421

source_name: ependymoma 1421


title: mouse02, M, cerebellum

source_name: cerebellum


title: MGYPDa10_dsDNA_rep1


title: MGYPDa10_dsDNA_rep2


title: Genomic DNA from ependymoma 1419

source_name: ependymoma 1419


title: mouse14, F, striatum


title: Genomic DNA from ependymoma 1420

source_name: ependymoma 1420


title: Mouse, AM132-treated, sample 1


title: Mouse, AM608-treated, control 2


title: mouse02, M, cortex

source_name: cortex


title: Genomic DNA from ependymoma 1417

source_name: ependymoma 1417


title: Negative_n3

city: Montreal

first: Moutih

last: Rafei

address: Montreal

country: Canada

institute: Universite de Montreal

description: STAR aligner 2.7 and FeatureCounts 2.0

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were aligned and mapped with STAR 2.7 to the reference genome Gencode version 35
Expression values were also computed using FeatureCounts version 2.0 based on the same assembly (GTF GRCm38)
Assembly: Mus_musculus.GRCm38 (ENSEMBL 102 mouse Mouse(Mus musculus)
Supplementary files format and content: Raw Readcounts: Tab-delimited file where 1st column is the Ensembl gene identifier, counts for forward stranded RNA,

source_name: Bone marrow

growth_protocol: Mesenchymal stromal cells were maintained in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing; ssRNA-seq

treatment_protocol: Treatment was added post confluency of 80%. A1 condition consisted of 50uM of A1 diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin. A1+OVA condition consisted of 50uM of A1, plus 1 mg/mL of Albumin from chicken egg white, diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin/ml insulin (Sigma). Cell were treated and incubated for 6h in humidified atmosphere with 5% CO2 at 37C.

value: Bone marrow

value: Primary cell

value: Mesenchymal stromal cell

tag: genotype

value: WT

value: untreated


title: MGYPDa09_dsDNA_rep2

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: Genomic DNA from ependymoma 1418

source_name: ependymoma 1418


title: MGYPDa09_dsDNA_rep1


title: mouse14, F, cerebellum

value: cerebellum

value: F

value: 20 weeks


title: Negative_n2

description: STAR aligner 2.7 and FeatureCounts 2.0

tag: cell line


title: mouse14, F, cortex

value: cortex


title: mouse14, F, hippocampus

source_name: hippocampus

value: hippocampus


title: CseDa01_ssDNA_rep3

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-


title: Negative_n1

description: STAR aligner 2.7 and FeatureCounts 2.0

tag: treatment


title: Mouse, regular chow diet, control 1

tag: tissue

value: hypothalamus


title: Genomic DNA from ependymoma 698

source_name: ependymoma 698

value: Ependymoma III

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]


title: CseDa01_dsDNA_rep4

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-


title: Genomic DNA from ependymoma 684

source_name: ependymoma 684

tag: classification result v12


title: mouse01, M, hippocampus

tag: strain

tag: mouse id

tag: Sex


title: Genomic DNA from ependymoma 683

source_name: ependymoma 683

tag: classification score


title: Negative_n4

description: STAR aligner 2.7 and FeatureCounts 2.0


title: Genomic DNA from ependymoma 682

source_name: ependymoma 682

tag: age

tag: localization

value: posterior fossa

tag: resection

value: GTR

tag: patho diagnosis


title: mouse01, M, cerebellum

value: M


title: A1-OVA_n3

description: STAR aligner 2.7 and FeatureCounts 2.0

tag: cell type

tag: genotype

value: 50 uM of A1 + 1 mg/mL of ovalbumin


title: CseDa01_dsDNA_rep3


title: PeDa01_extN21_ssDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: A1-OVA_n2

description: STAR aligner 2.7 and FeatureCounts 2.0

value: Bone marrow

tag: cell line

value: Primary cell

tag: treatment


title: CseDa01_ssDNA_rep4


title: Genomic DNA from ependymoma 681

source_name: ependymoma 681

value: supratentorial

tag: OS status


title: mouse01, M, cortex

tag: tissue


title: PeDa01_extN21_ssDNA_rep1


title: Genomic DNA from ependymoma 680

source_name: ependymoma 680

tag: os [months]

tag: pfs status

value: unclear, in evaluation


title: A1_n4

description: STAR aligner 2.7 and FeatureCounts 2.0

value: Mesenchymal stromal cell

value: WT

value: 50 uM of A1


title: PeDa01_extN21_dsDNA_rep2


title: A1-OVA_n1

description: STAR aligner 2.7 and FeatureCounts 2.0


title: DM178 NL 101719 BF

type: protein

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridization and RT-PCR was performed per Olink Proteomics manufacturer's protocol

scan_protocol: Plates were read fee-for-service at Olink Proteomics in Watertown, MA

data_processing: Data were analyzed with Olink NPX manager software 2.1.0.224

label: antibody-linked oligonucleotide tag

molecule: protein

source_name: blister biopsy

label_protocol: Sample labeling was performed per Olink Proteomics manufacturer's protocol

extract_protocol: Blister biopsies and/or EDTA anticoagulated blood samples were centrifuged at 330xg for 10 minutes. Interstitial skin fluid and/or plasma was frozen in 1mL aliquots and stored at -70C until analysis.

tag: disease status

value: DM

tag: location

value: nonlesional


title: Genomic DNA from ependymoma 679

source_name: ependymoma 679

value: F

tag: pfs [months]

tag: classification result v12


title: VB067 L BF

value: CLE

value: lesional


title: DM193 NL 081720 BF


title: A1_n3

description: STAR aligner 2.7 and FeatureCounts 2.0

tag: strain


title: PeDa01_extN21_dsDNA_rep1


title: mouse01, M, striatum

source_name: striatum

value: striatum

tag: mouse id

tag: Sex

tag: age

value: 20 weeks


title: Genomic DNA from ependymoma 678

source_name: ependymoma 678

tag: localization

value: posterior fossa

tag: resection

value: GTR

tag: patho diagnosis

value: Ependymoma III

tag: classification score


title: A1_n2

description: STAR aligner 2.7 and FeatureCounts 2.0

value: Bone marrow

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: A1_n1

description: STAR aligner 2.7 and FeatureCounts 2.0

tag: tissue

value: Primary cell


title: PeDa01_ssDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: Genomic DNA from ependymoma 676

source_name: ependymoma 676

value: M

tag: OS status

tag: os [months]

tag: pfs status


title: PeDa01_ssDNA_rep1