title: female saline IM rep 2

description:
72 after single i.p, injection
FS2


title: RNF6 shRNA3

status: Public on Jan 01 2023

type: SRA

city: Shanghai

first: Yile

last: SUN

address: HuaiHai west road

country: China

institute: Shanghai chest hospital

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated.
All the downstream analyses were based on clean data with high quality.
Genome_build: GRch38
Supplementary_files_format_and_content: count, fpkm

molecule: total RNA

organism: Homo sapiens

source_name: H3255 cells

growth_protocol: H3255 lung adenocarcinoma cells cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FCS)

extract_protocol:
Total RNA was isolated using TRIzol reagent (Takara, Shiga, Japan) based on instructions provided by the manufacturer
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations

treatment_protocol: H3255 lung adenocarcinoma cells transfected with shRNF6 vs. scramble

tag: cell line

value: H3255 lung adenocarcinoma cells

tag: shRNA

value: RNF6 shRNA3


title: male cisplaint IM rep 6

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

country: USA

institute: University of Alabama at Birmingham

description:
72 after single i.p, injection
MC6

data_processing:
GeneWiz provided fastq files to the lab.
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star2.7.3a.  Counts were generated with the subread v2.0.1 and the featureCounts -p -t expm -g gene_id a -o
Count matrixes were then analyzed using DESeq2 v1.28.1 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Genome_build: mm10
Supplementary_files_format_and_content: excel files with Deseq2 log2FC and statistics, and normalize counts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
Inner medullae were quickly dissected and snap frozen in liquid nitrogen.  RNA was extracted using the Zymo Direct-Zol RNA miniprep kit.  RNA quality, quantity was assessed by GeneWiz, followed by cDNA library prepration and sequencing by Genewiz.
RNA libraries were prepared for sequencing using standard Illumina protocols, and poly A selection by GeneWiz

treatment_protocol: each mouse at 9-10 weeks of age was given a single, i.p. injection of saline or 15 mg/kg cisplatin (dissolved in saline) in 100 ul.  72 hours later mice were euthanized and samples collected

tag: strain

tag: tissue

value: inner medulla

tag: Sex

value: male

tag: treatment

value: cisplatin


title: RNF6 shRNA1

description: H3255 lung adenocarcinoma cells transfected with shRNF6

value: RNF6 shRNA1


title: Control shRNA3

description: H3255 lung adenocarcinoma cells transfected with srcambled control

value: Control shRNA3


title: male cisplaint IM rep 5

description:
72 after single i.p, injection
MC5


title: Pilot 1 2.0mm 78s

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

institute: Stanford University

description: UMI Matrix

library_source: transcriptomic single cell

data_processing:
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)

molecule: polyA RNA

organism: Zea mays

source_name: anther

growth_protocol: individuals were grown under greenhouse conditions in Stanford, CA, USA with 14-h day/10-h night lighting, approximating half of peak summer solar radiation including UV-A. Daily irrigation and fertilization maintained robust growth

extract_protocol:
Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.

value: anther

tag: cell type

value: anther single cell

tag: genotype


title: Control shRNA2

value: Control shRNA2


title: GL26140_CD31posP2_A04_R1

city: Boston

first: Elizabeth

last: Perez

state: MA

address: 30 Fruit Street

institute: MGH

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

source_name: brain

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

value: brain

value: Malignant

value: Los


title: male cisplaint IM rep 4

description:
72 after single i.p, injection
MC4


title: Pilot 1 2.0mm 89s

description: UMI Matrix


title: Pilot 2 2.0mm 36s

description: UMI Matrix


title: GL26140_CD31posP2_D12_R1


title: Control shRNA1

value: Control shRNA1


title: GL26140_CD31posP2_F12_R1


title: Pilot 2 2.0mm 60s

description: UMI Matrix


title: male cisplaint IM rep 3

description:
72 after single i.p, injection
MC3


title: Pilot 1 2.0mm 81s

description: UMI Matrix


title: siVCP-4

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

data_processing:
RTA v1.18.61 used for basecalling.
Trim adapters with cutadapt, Align to hg38 with STAR -2.7.5a
Generate count matrices with featureCounts and RSEM
Perform differential expression with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human cell line

extract_protocol:
Cells were lysed in Trizol Reagent (Ambion) and total RNA was purified with Direct-zol RNA Miniprep Plus Kit (Zymo Research) including DNase I treatment
Libarary was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: VCP siRNA


title: male cisplaint IM rep 2

description:
72 after single i.p, injection
MC2


title: female saline IM rep 1

description:
72 after single i.p, injection
FS1

value: female

value: saline control


title: Dynamic HUVECs -BMSC-CM 1

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 100 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
SMARTer + polyT adapters were removed using fqtrim (v0.9.7)
Pseudo counts were measured on the trimmed Fastq files using salmon (v1.3.0) using flags gcBias seqBias.
Database used for the analysis ensembl GRCh38.rel98
Data was analysed with DESeq2 package retrieved from bioconductor
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs, single donnor) were obtained from Lonza

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions. RNA concentration and size distribution profile were analyzed on an Agilent Bioanalyzer RNA 6000 Pico chip (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMSCs were seeded into T75 cm2 flasks at a density of 10 4 cells/cm 2 and grown until 70-80% confluence. After washes, cells were refreshed with α-MEM containing 0.1% BSA and incubated under 3% O2 for 48h as described. Supernatant (conditioned medium) was collected. HUVECs were treated with 300uM CoCl2 in the presence or abscence of BMSC-CM for 24h in static condition or dynamic condition

value: Umbillical cord

value: Human umbilical vein endothelial cells

value: 24h treated with 50%EBM+50%BMSC-CM and CoCl2


title: male cisplaint IM rep 1

description:
72 after single i.p, injection
MC1

value: inner medulla

value: male


title: male saline IM rep 6

description:
72 after single i.p, injection
MS6


title: Pilot 1 2.0mm 17s

description: UMI Matrix


title: GL26140_CD31posP2_B11_R1


title: siVCP-3


title: GL26140_CD31posP2_H12_R1


title: male saline IM rep 5

description:
72 after single i.p, injection
MS5


title: Pilot 2 2.0mm 42s

description: UMI Matrix


title: siTFE3-3

value: TFE3 siRNA


title: siTFE3-4


title: male saline IM rep 4

description:
72 after single i.p, injection
MS4


title: Pilot 2 2.0mm 33s

description: UMI Matrix


title: siSCR-4

value: scramble siRNA


title: GL26140_CD31posP2_E08_R1


title: male saline IM rep 3

description:
72 after single i.p, injection
MS3


title: siVCP-2


title: GL26140_CD31posP2_H10_R1


title: Pilot 2 2.0mm 20s

description: UMI Matrix

value: anther


title: GL26140_CD31posP2_D04_R1


title: siVCP-1


title: GL26140_CD31posP2_B04_R1


title: male saline IM rep 2

description:
72 after single i.p, injection
MS2


title: Pilot 2 2.0mm 58s

description: UMI Matrix

value: anther single cell


title: siTFE3-2


title: Pilot 1 2.0mm 64s

description: UMI Matrix


title: male saline IM rep 1

description:
72 after single i.p, injection
MS1


title: Pilot 1 2.0mm 4s

description: UMI Matrix


title: GL26140_CD31posP2_C09_R1


title: siTFE3-1


title: Pilot 2 2.0mm 2s

description: UMI Matrix


title: WT-9w-TRAP-rep4

city: Hamburg

first: Kent

middle: Edward

last: Duncan

address: Falkenried 94

department: Center for Molecular Neurobiology

country: Germany

institute: University Medical Center, Hamburg-Eppendorf

data_processing:
STAR aligment
Counting by featureCounts
DESeq2 analysis
Genome_build: mm10
Supplementary_files_format_and_content: Rows represent genes

source_name: Motor neurons from cervical spinal cord

extract_protocol:
Translating ribosome affinity purification (TRAP)
NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs)

value: Chat bacTRAP line DW167 DW167Htz/J

tag: disease state

value: Healthy control 1

value: Motor neurons


title: GL26140_CD31posP2_H08_R1

value: brain

value: Los


title: WT-9w-TRAP-rep3


title: Pilot 1 2.0mm 22s

description: UMI Matrix


title: siSCR-2


title: GL26140_CD31posP2_G10_R1

value: Malignant


title: GL26140_CD31posP2_D05_R1


title: WT-9w-TRAP-rep2


title: siSCR-3


title: Pilot 2 2.0mm 61s

description: UMI Matrix


title: Pilot 2 2.0mm 56s

description: UMI Matrix


title: Pilot 1 2.0mm 24s

description: UMI Matrix


title: GL26140_CD31posP2_A02_R1


title: GL26140_CD31posP2_F10_R1


title: WT-9w-SC-rep6

source_name: Cervical spinal cord

value: All spinal cord cells


title: Pilot 2 2.0mm 62s

description: UMI Matrix


title: WT-9w-SC-rep4


title: siSCR-1


title: GL26140_CD31posP2_B02_R1


title: GL26140_CD31posP2_B09_R1


title: WT-9w-TRAP-rep1


title: sh_0092339-rep2

city: Tianjin

first: Hanlin

state: Tianjin

address: 23, Pingjiang Rd, Hexi District

institute: Tianjin Medical University

data_processing:
we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Cutadapt software  was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software  to map reads to the genome ,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Genome_build: hg18
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LNCaP-AI cell line

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

value: castration-resistance cell line


title: sh_0092339-rep1


title: Pilot 1 2.0mm 67s

description: UMI Matrix


title: Pilot 1 2.0mm 7s

description: UMI Matrix


title: GL26140_CD31posP2_C12_R1


title: Negative control-rep3

value: Vector


title: sh_0092339-rep3


title: GL26140_CD31posP2_A05_R1


title: Pilot 1 2.0mm 12s

description: UMI Matrix


title: WT-9w-SC-rep5


title: WT-9w-SC-rep2


title: GL26140_CD31posP2_B06_R1


title: Pilot 2 2.0mm 14s

description: UMI Matrix


title: WT-9w-SC-rep1


title: Negative control-rep1


title: GL26140_CD31posP2_D02_R1


title: SF_control_rep3_scRNAseq

city: Schlieren

first: Caroline

last: Ospelt

address: Wagistrasse 14

department: Department of Rheumatology

country: Switzerland

institute: University Hospital Zurich

description:
metadata_HOTAIR.xlsx
382_gap_control_S3

data_processing:
Sequencing data reads were quality-checked with FastQC. Reads were trimmed with Trimmomatic and aligned to the reference genome and transcriptome (FASTA and GTF files, respectively, Ensembl GRCh37) with STAR. Gene expression was quantified using the R/Bioconductor package Rsubread version 1.22. Differentially expressed genes between conditions were identified using the R/Bioconductor package DESeq2.
Reads were aligned to the reference genome (hg19) using using BWA v. 0.7.5a. Samples were filtered for regions blacklisted by the ENCODE project. Subsequently samples were deduplicated using SAMtools version 1.3.1. Alignment coordinates were converted to BED format using BEDTools v.2.17. Peaks were annotated on gene and transcript level using the "ChIPpeakAnno", "ChIPQC", and "ChIPseeker" packages of R. "DiffBind" package was used for differential binding.
ScRNAseq data from cultured SF transfected with either control or HOTAIR targeting GapmeR (n = 3) were integrated with SF of publicly available datasets and two in-house datasets. R with Seurat package (version 4.0) was used. The standard Seurat protocol was followed and for the final integration we applied harmony within the Seurat workflow. First 30 PC’s were the defined dimensionality of the dataset and a resolution of 0.1 was set for the downstream clustering. Annotation of the different clusters were performed based on the expression or absence of known SF marker genes: CD55, THY1, CXCL12, POSTN, CD34 and MKI67.
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: xlsx file including normalized count and FPKM values for each sample
Supplementary_files_format_and_content: bed files including peak score
Supplementary_files_format_and_content: xlsx file with metadata

source_name: cultured synovial fibroblasts, transfected with CONTROL

extract_protocol:
Total RNA was isolated with the miRNeasy Mini kit (Qiagen) including on-column DNaseI digestion from SF silenced for HOTAIR and control (n = 3 each) 48h after. For measurements of H3K27me3 marks after HOTAIR silencing, SF pellets from OA knees transfected with GapmeR HOTAIR and GapmeR Control (n = 3 each) were prepared using the iDeal ChIP seq kit for Histones (Diagenode) with a shearing of 12 cycles (30′′ON 30′′OFF, Bioruptor Pico). 15’000 unsorted synovial cells (viability 60-88%) per patient were prepared for single cell analysis using the Chromium Single Cell 3’ Reagent kit (v3.1 chemistry; 10x Genomics).
Bulk RNAseq libraries were prepared using the Illumina TruSeq Stranded total RNA protocol; ChIPseq libraries were prepared using the MicroPLEX v2 protocol; scRNAseq libraries were prepared using the Chromium Single Cell 3’ Reagent kit (v3.1 chemistry; 10x Genomics)

treatment_protocol: Synovial fibroblasts were transfected with 50 nM antisense LNA HOTAIR GapmeR (Exiqon, Sequence: 5′-AGGCTTCTAAATCCGT-3′) using Lipofectamine 2000 (Invitrogen). Antisense LNA GapmeR Negative Control A (Cat No 300610) was used as transfection control.

value: cultured synovial fibroblast

value: transfected with Gapmer control

tag: localisation

value: Knee


title: Pilot 1 2.0mm 8s

description: UMI Matrix


title: WT-14w-TRAP-rep3


title: GL26140_CD31posP2_F11_R1


title: GL26140_CD31posP2_A06_R1


title: SF_control_rep2_scRNAseq

description:
metadata_HOTAIR.xlsx
357_gap_control_S6


title: WT-14w-TRAP-rep2


title: WT-9w-SC-rep3


title: WT-14w-TRAP-rep1


title: GL26140_CD31posP2_G03_R1


title: Pilot 1 2.0mm 34s

description: UMI Matrix


title: Negative control-rep2


title: GL26140_CD31posP2_A11_R1


title: SF_control_rep1_scRNAseq

description:
metadata_HOTAIR.xlsx
327_gap_control_S9


title: Pilot 1 2.0mm 77s

description: UMI Matrix


title: Pilot 2 2.0mm 75s

description: UMI Matrix


title: Pilot 2 2.0mm 68s

description: UMI Matrix


title: GL26140_CD31posP2_F07_R1


title: WT-14w-SC-rep4


title: SF_KD_HOTAIR_rep2_scRNAseq

description:
metadata_HOTAIR.xlsx
357_gap_HOTAIR_S5

source_name: cultured synovial fibroblasts, transfected with HOTAIR

value: transfected with Gapmer Hotair


title: WT-14w-TRAP-rep4


title: GL26140_CD31posP2_C02_R1


title: WT-14w-SC-rep5


title: ASPS1_input3

description:
18381X6
VCP.lambda_control.bw

library_source: genomic

data_processing:
paired-end 150bp sequencing on an IlluminaNovaSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a normalized pileup signal

molecule: genomic DNA

source_name: human ASPS1 cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and TARGET DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq library prep reagent set

tag: chip antibody

value: input


title: WT-14w-SC-rep3


title: SF_KD_HOTAIR_rep1_scRNAseq

description:
metadata_HOTAIR.xlsx
327_gap_HOTAIR_S8


title: Pilot 2 2.0mm 39s

description: UMI Matrix


title: ASPS1_input2

description:
18381X5
VCP.lambda_control.bw


title: WT-14w-SC-rep2


title: SF_KD_HOTAIR_rep3_scRNAseq

description:
metadata_HOTAIR.xlsx
382_gap_HOTAIR_S2


title: Pilot 1 2.0mm 30s

description: UMI Matrix


title: Pilot 1 2.0mm 33s

description: UMI Matrix


title: GL26140_CD31posP2_G05_R1


title: Pilot 1 2.0mm 38s

description: UMI Matrix


title: ASPS1_input1

description:
18381X4
VCP.lambda_control.bw


title: WT-14w-SC-rep1


title: GL26140_CD31posP2_H04_R1


title: GL26140_CD31posP2_F06_R1


title: TDP43WT-9w-TRAP-rep3

value: Chat bacTRAP line DW167 DW167Htz/J; TDP-43WT line 3cPtrc/J

value: Healthy control 2


title: ASPS1_VCP3

description:
18381X3
VCP.fragment.bw

value: VCP


title: GL26140_CD31posP2_B03_R1


title: ASPS1_VCP1

description:
18381X1
VCP.fragment.bw


title: Pilot 2 2.0mm 73s

description: UMI Matrix

value: anther

value: anther single cell


title: GL26140_CD31posP2_D01_R1


title: Pilot 2 2.0mm 66s

description: UMI Matrix


title: Pilot 2 2.0mm 93s

description: UMI Matrix


title: GL26140_CD31posP2_C06_R1


title: TDP43WT-9w-TRAP-rep2

value: Motor neurons


title: Pilot 2 2.0mm 40s

description: UMI Matrix


title: TDP43WT-9w-SC-rep6


title: Pilot 2 2.0mm 22s

description: UMI Matrix


title: TDP43WT-9w-TRAP-rep1


title: TDP43WT-9w-SC-rep5


title: Pilot 1 2.0mm 60s

description: UMI Matrix


title: TDP43WT-9w-SC-rep4


title: ASPS1-24h-C

tag: time


title: GL26140_CD31posP2_A01_R1

value: brain


title: ASPS1-2h-C


title: Pilot 2 2.0mm 67s

description: UMI Matrix


title: GL26140_CD31posP2_C08_R1

value: Los


title: GL26140_CD31posP2_G04_R1


title: ASPS1-48h-C

value: 48 hours


title: Pilot 2 2.0mm 5s

description: UMI Matrix


title: GL26140_CD31posP2_A03_R1

value: Malignant


title: TDP43WT-9w-SC-rep2

value: All spinal cord cells


title: ASPS1-0h-C

value: Control

value: 0 hours


title: ASPS1_VCP2

description:
18381X2
VCP.fragment.bw


title: ASPS1-48h-B


title: Pilot 1 2.0mm 66s

description: UMI Matrix


title: GL26140_CD31posP2_D03_R1


title: GL26140_CD31posP2_H06_R1


title: ASPS1-24h-B


title: Pilot 1 2.0mm 35s

description: UMI Matrix


title: TDP43WT-9w-SC-rep1


title: GL26140_CD31posP2_B08_R1


title: Pilot 1 2.0mm 65s

description: UMI Matrix


title: TDP43WT-14w-TRAP-rep5


title: ASPS1-2h-B


title: ASPS1-0h-B


title: Pilot 1 2.0mm 75s

description: UMI Matrix


title: ASPS1-48h-A


title: GL26140_CD31posP2_H07_R1


title: GL26140_CD31posP2_D11_R1


title: TDP43WT-14w-TRAP-rep4


title: Pilot 2 2.0mm 82s

description: UMI Matrix


title: TDP43WT-9w-SC-rep3


title: TDP43WT-14w-TRAP-rep3


title: ASPS1-2h-A


title: Pilot 1 2.0mm 96s

description: UMI Matrix


title: TDP43WT-14w-TRAP-rep2


title: TDP43WT-14w-SC-rep5


title: TDP43WT-14w-TRAP-rep1


title: GL26140_CD31posP2_C11_R1


title: GL26140_CD31posP2_H11_R1


title: Pilot 2 2.0mm 84s

description: UMI Matrix


title: ASPS1-0h-A


title: Pilot 2 2.0mm 13s

description: UMI Matrix


title: HEK-Cdelta-AT3-II-3

value: HEK

value: Cdelta

value: AT3 Type II overexpression


title: TDP43WT-14w-SC-rep4


title: Pilot 1 2.0mm 18s

description: UMI Matrix


title: HEK-Cdelta-AT3-I-3

value: AT3 Type I overexpression


title: GL26140_CD31posP2_E09_R1


title: GL26140_CD31posP2_A10_R1


title: ASPS1-24h-A


title: TDP43WT-14w-SC-rep2

value: Chat bacTRAP line DW167 DW167Htz/J; TDP-43WT line 3cPtrc/J


title: Pilot 1 2.0mm 15s

description: UMI Matrix


title: HEK-Cdelta-FL-TFE3-3

value: Full-Length TFE3 overexpression


title: GL26140_CD31posP2_C03_R1


title: Pilot 1 2.0mm 92s

description: UMI Matrix


title: GL26140_CD31posP2_E01_R1


title: TDP43WT-14w-SC-rep1

value: Healthy control 2


title: Pilot 1 2.0mm 58s

description: UMI Matrix

value: anther


title: HEK-AT3-I-3


title: TDP43MUT-9w-TRAP-rep5

value: Chat bacTRAP line DW167 DW167Htz/J; TDP-43A315T line 95Balo/J

value: Diseased


title: TDP43MUT-9w-TRAP-rep4

value: Motor neurons


title: Pilot 1 2.0mm 85s

description: UMI Matrix

value: anther single cell


title: TDP43MUT-9w-TRAP-rep3


title: GL26140_CD31posP2_E07_R1

value: brain

value: Los


title: HEK-FL-TFE3-3


title: HEK-GFP-3

value: GFP overexpression


title: Pilot 1 2.0mm 73s

description: UMI Matrix


title: TDP43WT-14w-SC-rep3

value: All spinal cord cells


title: Pilot 2 2.0mm 79s

description: UMI Matrix


title: GL26140_CD31posP2_C07_R1


title: TDP43MUT-9w-TRAP-rep2


title: TDP43MUT-9w-TRAP-rep1


title: HEK-Cdelta-AT3-II-2


title: HEK-Cdelta-AT3-I-2


title: GL26140_CD31posP2_H01_R1

value: Malignant


title: GL26140_CD31posP2_D06_R1


title: HEK-AT3-II-3

value: HEK

value: Control


title: Pilot 1 2.0mm 21s

description: UMI Matrix


title: TDP43MUT-9w-SC-rep5


title: HEK-Cdelta-FL-TFE3-2

value: Cdelta


title: GL26140_CD31posP2_F02_R1


title: GL26140_CD31posP2_G07_R1


title: Pilot 2 2.0mm 43s

description: UMI Matrix


title: TDP43MUT-9w-SC-rep4


title: HEK-AT3-II-2

value: AT3 Type II overexpression


title: GL26140_CD31posP2_D07_R1


title: GL26140_CD31posP2_E04_R1


title: Pilot 1 2.0mm 23s

description: UMI Matrix


title: Pilot 2 2.0mm 95s

description: UMI Matrix


title: HEK-AT3-I-2

value: AT3 Type I overexpression


title: TDP43MUT-9w-SC-rep3


title: TDP43MUT-9w-SC-rep2


title: Pilot 1 2.0mm 39s

description: UMI Matrix


title: HEK-FL-TFE3-2

value: Full-Length TFE3 overexpression


title: TDP43MUT-9w-SC-rep1


title: GL26140_CD31posP2_F03_R1


title: Pilot 1 2.0mm 10s

description: UMI Matrix


title: GL26140_CD31posP2_E11_R1


title: HEK-GFP-2


title: TDP43MUT-14w-TRAP-rep4


title: GL26130_CD31posP2_C03_R1

value: ctrl


title: Pilot 2 2.0mm 24s

description: UMI Matrix

value: anther


title: HEK-Cdelta-AT3-II-1


title: HEK-Cdelta-AT3-I-1


title: TDP43MUT-14w-TRAP-rep3

value: Chat bacTRAP line DW167 DW167Htz/J; TDP-43A315T line 95Balo/J


title: GL26130_CD31posP2_C01_R1


title: Pilot 1 2.0mm 70s

description: UMI Matrix


title: HEK-Cdelta-FL-TFE3-1


title: GL26130_CD31posP2_A12_R1


title: Pilot 1 2.0mm 37s

description: UMI Matrix


title: TDP43MUT-14w-TRAP-rep1

value: Diseased


title: Pilot 1 2.0mm 19s

description: UMI Matrix


title: GL26130_CD31posP2_C11_R1


title: HEK-AT3-II-1


title: TDP43MUT-14w-TRAP-rep2

value: Motor neurons


title: Pilot 1 2.0mm 26s

description: UMI Matrix

value: anther single cell


title: GL26140_CD31posP2_H02_R1

value: brain


title: GL26130_CD31posP2_F11_R1


title: Pilot 2 2.0mm 69s

description: UMI Matrix


title: TDP43MUT-14w-SC-rep3


title: TDP43MUT-14w-SC-rep4


title: HEK-AT3-I-1


title: GL26130_CD31posP2_H10_R1


title: GL26130_CD31posP2_C07_R1


title: Pilot 1 2.0mm 9s

description: UMI Matrix


title: GL26130_CD31posP2_D10_R1


title: Pilot 2 2.0mm 12s

description: UMI Matrix


title: TDP43MUT-14w-SC-rep1


title: HEK-GFP-1


title: HEK-FL-TFE3-1


title: Pilot 1 2.0mm 11s

description: UMI Matrix


title: FU-UR-1, dbl-65-30-3

value: Combined(VCP+TFE3) siRNA


title: Pilot 1 2.0mm 6s

description: UMI Matrix


title: GL26130_CD31posP2_H07_R1


title: FU-UR-1, dbl-67-31-3


title: GL26130_CD31posP2_A06_R1


title: FU-UR-1, TFE3-31-3

value: TFE3 siRNA


title: FU-UR-1, TFE3-30-3


title: GL26130_CD31posP2_H05_R1


title: FU-UR-1, VCP67-3

value: VCP siRNA


title: GL26130_CD31posP2_B12_R1

value: Malignant


title: TDP43MUT-14w-SC-rep2

value: All spinal cord cells


title: FU-UR-1, VCP65-3


title: GL26130_CD31posP2_F10_R1


title: GL26130_CD31posP2_E12_R1


title: FU-UR-1, dbl-67-31-2


title: GL26130_CD31posP2_A03_R1


title: GL26130_CD31posP2_E06_R1


title: Pilot 1 2.0mm 31s

description: UMI Matrix


title: FU-UR-1, TFE3-31-2


title: FU-UR-1, dbl-65-30-2


title: GL26130_CD31posP2_H08_R1


title: delta_Rv3193c-phenanthroline-rep1

city: College Station

first: Thomas

middle: R

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

data_processing:
base-calling done with with Casava
A custom C program was used to align reads to the reference genome.
A custom script was used to count reads mapping to each ORF and calculate RPKMs by the standard definition (excluding the rRNA locus from the read-counts totals).
Genome_build: NC_000962.2
Supplementary_files_format_and_content: comma-separated (.csv) file with read counts for each gene (unnormalized).
Supplementary_files_format_and_content: comma-separated (.csv) file with RPKMs for each gene (normalized).

organism: Mycobacterium tuberculosis

source_name: knockout of Rv3193c in H37Rv strain grown on 7H10+glycerol+phenanthroline

growth_protocol: Cultures were grown to OD 0.8.

extract_protocol:
RNA was extracted by bead-beating in Trizol, and then chloroform was added to get out of BSL3. Then the samples were re-extracted with chloroform and precipitated with isopropanol. The precipitate was washed with 70% ethanol once and that pellet was shipped on dry ice.
Samples were treated with RNAse and purified on Quiagen RNeasy columns.  Used Life Technologies's RiboMinus Bacteria for rRNA depletion.  Samples were then prepared by KAPA's Stranded RNA-Seq library preparation kit.

treatment_protocol: Low-chelated samples were treated with 1mM phenanthroline for 30 min before pelleting.

tag: medium

value: phenanthroline

tag: replicate


title: delta_Rv3193c-7H10-glycerol-rep1

source_name: knockout of Rv3193c in H37Rv strain grown on 7H10+glycerol


title: H37Rv-7H10-glycerol-rep2

source_name: wt H37Rv strain grown on 7H10+glycerol

value: wt


title: H37Rv-phenanthroline-rep2

source_name: wt H37Rv strain grown on 7H10+glycerol+phenanthroline


title: delta_Rv3193c-phenanthroline-rep2


title: H37Rv-phenanthroline-rep1


title: MCF7 KO16

type: RNA

city: MILAN

first: BIANCA

last: CIONI

state: MI

address: Via Amadeo 41

department: Molecular Oncology

country: Italy

institute: Istituto Nazionale Tumori

description: MCF7 JMJD6 KO16 replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol on GeneChip Scanner 3000 7G

data_processing:
Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software
MTA-1_0.r3.pgf
MTA-1_0.na35.mm10.transcript.csv

label: biotin

source_name: MCF7 KO16

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

growth_protocol: MCF7 cells were cultured in RPMI medium supplemented with 10% FBS

extract_protocol: Total RNA was extracted using Qiazol reagent and purified with the RNeasy kit on a QIAcube automated station (Qiagen) according to the manufacturers’ instructions

treatment_protocol: not applicable

value: breast cancer


title: FU-UR-1, TFE3-30-2


title: GL26130_CD31posP2_F07_R1


title: MCF7 KO8b

description: MCF7 JMJD6 KO8 replicate 2

source_name: MCF7 KO8b


title: delta_Rv3193c-7H10-glycerol-rep2


title: SCI, 3 days, non-SPF, replicate 3

city: Nanchang

first: Jian

last: Cao

state: Jiangxi

address: 1 Minde Road, East Laker District, Nanchang, Jiangxi, China

department: orthopaedics

institute: The Second Affiliated Hospital of Nanchang University

description: Gene expression after treated with a modified Allen’s weight-drop apparatus spinal cord tissue

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0   pmol Cy3/μg cRNA) was fragmented at 60°C for 30   minutes in a reaction volume of 22.5μl containing 1x   Agilent fragmentation buffer and 2x Agilent blocking   agent following the manufacturers' instructions. On   completion of the fragmentation reaction, 22.5μl of   2x Agilent hybridization buffer was added to the   fragmentation mixture and hybridized to Agilent   Human Gene Expression（8*60K）for 17 hours at 65°C   in a rotating Agilent hybridization oven. After   hybridization, microarrays were washed 1 minute at   room temperature with GE Wash Buffer 1 (Agilent)   and 1 minute with 37°C GE Wash buffer 2 (Agilent),   then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on   the Agilent DNA Microarray Scanner (G2505C) using   one color scan setting for 4x180k array slides (Scan   Area 61x21.6 mm, Scan resolution 3um, Dye channel   is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature   Extraction Software 10.7.1.1 (Agilent) using default   parameters to obtain background subtracted and   spatially detrended Processed Signal intensities as   the raw data. Raw data were normalized in quantile   algorithm with Genespring 13.0(Agilent). Probe that   at least 1 out of 2 samples flagged as Detected were   maintained.

organism: Rattus

source_name: Spinal cord tissue, treated with a modified Allen’s weight-drop apparatus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Studies were conducted using adult Sprague-Dawley rats (male, 200-250g) that had been housed under standard conditions (23-25°C, 12 h light/dark cycle) for at least one week before experimental use with free access to food and water.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1561 ) following the manufacturer's instructions.

treatment_protocol: Three rat SCI models was established by the modified Allen method. Rats were anesthetized by inhalation of isoflurane and were placed in the prone position on an operating table. The head and limbs were held in place and the fur along the back was removed for skin preparation. After strict disinfection, a median incision of approximately 3 cm in length was made at the T10 level. The skin, subcutaneous tissue, and myofascia were carefully separated and dissected, exposing and fenestrating the T10 lamina. The spinal cord was carefully exposed without damaging the dura mater. A heavy hammer weighing 10 g with a diameter of 2.5 mm was allowed to fall freely from a height of 8 cm, fully impacting the dural sac; the hammer was then retracted immediately after SCI. After the blow, the rats show a tail-wagging reflex with twitching and stretching of both hind limbs and the body; this is a stress reflex and indicates the success of the modeling. The sham operation group received the same procedure without injury to the spinal cord.

value: Sprague-Dawley

value: Spinal cord tissue

value: male

value: Spinal cord injury


title: H37Rv-7H10-glycerol-rep1


title: MCF7 KO16b

description: MCF7 JMJD6 KO16 replicate 1b

source_name: MCF7 KO16b


title: Sham, non-SPF, replicate 3

description: Gene expression after treated with laminectomy procedure spinal cord tissue

source_name: Spinal cord tissue, treated with laminectomy procedure

value: control


title: SCI, 3 days, non-SPF, replicate 2


title: Sham, non-SPF, replicate 2


title: FU-UR-1, SCR-3

source_name: human cell line

value: scramble siRNA


title: Sham, non-SPF, replicate 1


title: SCI, 3 days, non-SPF, replicate 1


title: GL26130_CD31posP2_H04_R1

source_name: brain

value: ctrl


title: delta_Rip1-phenanthroline-rep2

source_name: knockout of Rv2869c in Erdman strain grown on 7H10+glycerol+phenanthroline

value: Erdman


title: GL26130_CD31posP2_E02_R1

value: brain


title: FU-UR-1, VCP65-2


title: delta_Rip1-phenanthroline-rep1


title: MCF7 SCR 1b

description: MCF7 JMJD6 scramble 1 replicate 1b

source_name: MCF7 SCR 1b


title: MCF7 KO8

description: MCF7 JMJD6 KO8 replicate 1

source_name: MCF7 KO8


title: FU-UR-1, VCP67-2


title: delta_Rip1-7H10-glycerol-rep2

source_name: knockout of Rv2869c in Erdman strain grown on 7H10+glycerol


title: FU-UR-1, SCR-2


title: delta_Rip1-7H10-glycerol-rep1


title: GL26130_CD31posP2_E05_R1


title: FU-UR-1, dbl-65-30-1

value: Combined(VCP+TFE3) siRNA


title: FU-UR-1, dbl-67-31-1


title: GL26130_CD31posP2_E01_R1


title: FU-UR-1, TFE3-30-1

value: TFE3 siRNA


title: Erdman-phenanthroline-rep2

source_name: wt Erdman strain grown on 7H10+glycerol+phenanthroline


title: MCF7 SCR 2b

description: MCF7 JMJD6 scramble 2 replicate 1b

source_name: MCF7 SCR 2b


title: GL26130_CD31posP2_B09_R1


title: MCF7 SCR 1

description: MCF7 JMJD6 scramble 1 replicate 1

source_name: MCF7 SCR 1


title: GL26130_CD31posP2_B05_R1


title: Erdman-7H10-glycerol-rep2

source_name: wt Erdman strain grown on 7H10+glycerol


title: MCF7 WT4

description: MCF7 wild-type replicate 4

source_name: MCF7 WT4


title: GL26130_CD31posP2_A09_R1


title: FU-UR-1, VCP67-1

value: VCP siRNA


title: MCF7 SCR 2

description: MCF7 JMJD6 scramble 2 replicate 1

source_name: MCF7 SCR 2


title: GL26130_CD31posP2_E04_R1


title: Erdman-7H10-glycerol-rep1


title: MCF7 WT2

description: MCF7 wild-type replicate 2

source_name: MCF7 WT2


title: MCF7 WT3

description: MCF7 wild-type replicate 3

source_name: MCF7 WT3


title: GL26130_CD31posP2_G08_R1


title: FU-UR-1, SCR-1


title: GL26130_CD31posP2_F09_R1


title: Lps+ASIV3

city: Nanjing

first: Yun

last: Shan

address: No.138 Xianlin Avenue, Qixia District

institute: Nanjing University of Chinese Medicine

data_processing:
The raw tags were processed using the  following steps: remove low quality tags; remove tags with 5 primer contaminants;  remove tags without 3 primer; remove tags without insertion; remove tags with poly A;  remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the  reference genome and other sRNA database including miRbase, siRNA, piRNA and  snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam mapping.  The software miRDeep2 was used to predict novel miRNA by exploring the  secondary structure. RNAhybrid,  miRanda and TargetScan were used to predict target genes of miRNAs. The small  RNA expression level is calculated by counting absolute numbers of molecules using  unique molecular identifiers. Differential expression analysis was performed using  the DEGseq, Q value≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default  threshold to judge the significance of expression difference.
Genome_build: GCF_000001895.5_Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Rattus

growth_protocol: Primary peritoneal macrophages were obtained from untreated rat by peritoneal lavage. The total contents of the peritoneal lavage were centrifuged at 30ml for 5 min, then the cell pellet was resuspended in complete RPMI-1640 medium containing 10% FBS at 37 °C in 5% CO2.

extract_protocol:
Total RNA, including miRNA, was extracted using Total Exosome RNA & Protein Isolation Kit (Life Technologies; Gaithersburg, MD) from exosomal and passed the RNA quality control for sequencing.
The miRNA sequencing (BGISEQ-500 BGI; Shenzhen, China) following the manufacturer’s instructions

treatment_protocol: Control was treated with 1ul/ml DMSO for 24h. LPS was dissolved in dimethyl sulfoxide (DMSO) to create a 1000-fold stock, and added to the medium at 100ng/ml for 6h. AS-IV was dissolved in DMSO, and added to the medium at 150μM for 24h before LPS stimulation. DMSO was present in the control culture at a concentration 0.1% (v/v).

value: peritoneal macrophages

value: AS-IV was dissolved in DMSO, and added to the medium at 150uM concentrations for 24h before LPS stimulation.

tag: rna population

value: exosomal RNA


title: MCF7 WT1

description: MCF7 wild-type replicate 1

source_name: MCF7 WT1


title: FU-UR-1, TFE3-31-1


title: Lps+ASIV2


title: MDA-MB231 KO 7b

description: MDA-MB231 JMJD6 scramble 7 replicate 2

source_name: MDA-MB231 SCR 7b

growth_protocol: MDA-MB231 cells were cultured in RPMI medium supplemented with 10% FBS


title: Erdman-phenanthroline-rep1

value: wt

value: phenanthroline


title: ASPS1_input_3

data_processing:
Paired-end 50bp sequencing on an Illumina NovaSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a combined normalized pileup signal

source_name: human ASPS cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and TARGET DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set

value: INPUT


title: GL26130_CD31posP2_A08_R1

source_name: brain


title: Lps+ASIV1


title: ASPS1_input_2


title: GL26130_CD31posP2_H11_R1

value: Malignant


title: ASPS1_input_1


title: Lps3

value: LPS was dissolved in DMSO, and added to the medium at 100ng/ml for 6h.


title: GL26130_CD31posP2_E08_R1


title: ASPS1_Pol2_3

value: POLII


title: FU-UR-1, VCP65-1

source_name: human cell line


title: MDA-MB231 SCR 3b

description: MDA-MB231 JMJD6 scramble 3 replicate 2

source_name: MDA-MB231 SCR 3b

value: breast cancer


title: GL26130_CD31posP2_E03_R1


title: Lps1


title: MDA-MB231 SCR 3

description: MDA-MB231 JMJD6 scramble 3 replicate 1

source_name: MDA-MB231 SCR 3


title: ASPS1_Pol2_2


title: GL26130_CD31posP2_F03_R1


title: MDA-MB231 KO 6b

description: MDA-MB231 JMJD6 KO6 replicate 2

source_name: MDA-MB231 KO 6b


title: Con3

value: Control was treated with 1ul/ml DMSO for 24h.


title: ASPS1_ASPL_3


title: GL26130_CD31posP2_E09_R1

value: ctrl


title: MDA-MB231 SCR 7

description: MDA-MB231 JMJD6 scramble 7 replicate 1

source_name: MDA-MB231 SCR 7


title: Con1


title: ASPS1_ASPL_2


title: MDA-MB231 KO 6

description: MDA-MB231 JMJD6 KO6 replicate 1

source_name: MDA-MB231 KO 6


title: GL26130_CD31posP2_G07_R1


title: ASPS1_Pol2_1


title: GL26130_CD31posP2_D08_R1


title: Lps2


title: Con2


title: GL26130_CD31posP2_H01_R1


title: MDA-MB231 KO 5b

description: MDA-MB231 JMJD6 KO5 replicate 2

source_name: MDA-MB231 KO 5b


title: Fr_LL3_00_rep1

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
Illumina reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space. The minimal transcriptome was obtained as described in Gowik et al. (2011) and contains 22,079 protein coding genes.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of rpm of biological duplicate group (drought stage) were calculated.
Supplementary_files_format_and_content: Excel sheet (SDataset1.xlsx) file including Arabidopsis Gene Identifier (AGI) and TAIR10_short_description, raw counts, rpm for each sample and mean rpm for biological duplicates

organism: Flaveria robusta

source_name: Leaf

growth_protocol: Flaveria bidentis (C4) and Flaveria robusta (C3) plants were grown in the green house for 36 days and in a controlled growth chamber (10 hr light, 22 ˚C / 14 hr dark, 20 ˚C) for 6 days

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 100 bp read length) on an Illumina HiSeq 2000 platform.

treatment_protocol: After two days under entrained (10 hr light, 14 hr dark) conditions, plants were subjected to two days of free-running (constant light) conditions

tag: time of the day

tag: zeitgeber time

tag: light regime

value: Light

tag: day/night anticipation

value: Subjective day (free-running)


title: Fr_LL2_20_rep2

value: Subjective night (free-running)


title: GL26130_CD31posP2_C09_R1

value: brain


title: ASPS1_ASPL_1

tag: cell line


title: MDA-MB231 WT3

description: MDA-MB231 wild-type replicate 3

source_name: MDA-MB231 WT3


title: FUUR-ChIP-input-b

data_processing:
Paired-end 50bp sequencing on an Illumina HiSeq platform
ChIP-seq reads were aligned to the mm10 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a combined normalized pileup signal


title: MDA-MB231 WT4

description: MDA-MB231 wild-type replicate 4

source_name: MDA-MB231 WT4


title: FUUR-ChIP-input-a


title: Fr_LL2_20_rep1


title: GL26130_CD31posP2_H03_R1

tag: tissue


title: MDA-MB231 KO 5

description: MDA-MB231 JMJD6 KO5 replicate 1

source_name: MDA-MB231 KO 5


title: MDA-MB231 WT2

description: MDA-MB231 wild-type replicate 2

source_name: MDA-MB231 WT2


title: GL26130_CD31posP2_G04_R1


title: FUUR-ChIP-VCP740a

value: VCP (catalog# ab111740)


title: GL26130_CD31posP2_F04_R1


title: Fr_LL3_00_rep2


title: Fr_LL2_16_rep2


title: FUUR-ChIP-VCP740b


title: FUUR-ChIP-VCP146b

value: VCP (catalog# ab155146)


title: GL26130_CD31posP2_D06_R1


title: Fr_LL2_12_rep2


title: GL26130_CD31posP2_B03_R1


title: Fr_LL2_12_rep1


title: VCP67_input_3

extract_protocol:
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and histone DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set

tag: sirna


title: LG replicate 4

city: London

first: Timothy

middle: RH

last: Regnault

state: Ontario

address: Medical Sciences Building, Room 216

department: Physiology and Pharmacology

country: Canada

institute: Western University

description: Gene expression data from BeWo cytotrophoblasts treated with 7 mM glucose for 72 hours

hyb_protocol: 3.5 µg DNA was targeted to be hybridized on GeneChip®  Clariom™ S human (Thermo Fisher Scientific) and incubated at 45°C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (ThermoFisher) using GeneChip Hybridization Wash and Stain kit according to the manufacturer’s instructions (ThermoFisher)

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (ThermoFisher)

data_processing: Data were processed using Transcriptome Analysis Console (TAC v4.0) and were normalized using the Robust Multiple-Array Averaging (RMA) method. Samples from each independent collection were paired for analysis (e.g. HG replicate 1 paired with LG replicate 1)

source_name: BeWo Cytotrophoblast lysate_LG

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific)

growth_protocol: BeWo trophoblasts were plated at 3.5x10^5 in 60 mm plates and allowed to attach to plates overnight in basal F12K media. Treatment was initiated the next day at time: 0 hours and cells were collected after 72 hours of treatment

extract_protocol: Samples were lysed in 900 uL TRIzol Reagent and automated RNA extraction was completed via Qiacube connect as per manufacturer's specifications. RNA extraction and subsequent microarray processing was performed at The Genome Quebec Innovation Facility

treatment_protocol: Cells were treated for 72H with either low or high glucose F12K media for 72H with media replenised every 24H

tag: cell/sample type

value: BeWo Cytotrophoblast lysate

tag: treatment

value: low glucose for 72 Hours


title: Fr_LL2_08_rep2


title: VCP67_input_2


title: GL26130_CD31posP2_G02_R1

tag: cell type


title: LG replicate 3


title: Fr_LL2_08_rep1


title: LG replicate 5


title: Fr_LL2_16_rep1


title: VCP67_3


title: Fr_LL2_04_rep1


title: Fr_LL2_04_rep2


title: GL26130_CD31posP2_H12_R1


title: GL26130_CD31posP2_D04_R1


title: HG recplicate 3

description: Gene expression data from BeWo cytotrophoblasts treated with 25 mM glucose for 72 hours

source_name: BeWo Cytotrophoblast lysate_HG

value: high glucose for 72 Hours


title: LG replicate 1


title: Fr_LL2_00_rep2


title: FUUR-ChIP-VCP146a


title: VCP67_2


title: HG recplicate 4


title: LG replicate 2


title: HG recplicate 1


title: B3

city: Hohhot

first: Yuting

last: Fu

address: university west road

institute: Inner Mongolia University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
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 poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: Matrix table with clean gene counts for every gene and every sample

organism: Equus asinus x Equus caballus

source_name: miPSCs

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ear epithelial cells

value: mule iPSCs

tag: cross

value: female horse mated with male donkey


title: HG recplicate 2


title: GL26130_CD31posP2_C05_R1

value: Malignant


title: GL26130_CD31posP2_D07_R1


title: Fr_LL2_00_rep1


title: VCP65_input_3

source_name: human ASPS cell line


title: HG recplicate 5


title: GL26130_CD31posP2_F01_R1

source_name: brain


title: VCP67_input_1


title: B2


title: B1


title: VCP65_input_2


title: Fr_LL1_20_rep2


title: GL26130_CD31posP2_C08_R1


title: VCP67_1


title: GL26130_CD31posP2_D05_R1


title: A3

source_name: MAFs

value: mule adult fibroblasts


title: Fr_LL1_20_rep1


title: VCP65_input_1


title: GL26130_CD31posP2_D03_R1


title: A2


title: VCP65_3


title: GL26130_CD31posP2_F05_R1


title: Fr_LL1_16_rep2


title: A1


title: Fr_LL1_16_rep1


title: VCP65_1


title: Fr_LL1_12_rep1


title: Fr_LL1_12_rep2


title: GL26130_CD31posP2_B04_R1


title: TFE31_input_3


title: GL26130_CD31posP2_G06_R1


title: GL26130_CD31posP2_G01_R1


title: Fr_LL1_08_rep1

value: Day (free-running)


title: MDA-MB231 WT1

description: MDA-MB231 wild-type replicate 1

source_name: MDA-MB231 WT1

value: breast cancer


title: GL26130_CD31posP2_H02_R1

value: ctrl


title: TFE31_input_2


title: Fr_LL1_04_rep2

value: Light


title: TFE31_input_1


title: VCP65_2


title: TFE31_3


title: Fr_LL1_04_rep1


title: TFE31_2


title: GL26130_CD31posP2_D12_R1


title: GL26130_CD31posP2_A07_R1


title: Fr_LL1_00_rep2


title: TFE31_1


title: 137-T-MII-late

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Carassius auratus

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 12

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Two-year-old goldfish (Carassius auratus), 60 g mean weight, were obtained from outdoor ponds at INRAE U3E experimental facility (Rennes, France), and maintained in recycled water at 14°C for several weeks. Caudal fins were collected on euthanized fish following the French animal welfare guidelines and under the French registration authorization n° 78-25 (N. Chênais). Fin cells were isolated and cultured according to Chenais et al, 2019. Briefly, fins were minced and digested with 2 mg/mL collagenase. Released fin cells were plated in supplemented L15 culture medium. After 24 hours, adhering epithelial cells were discarded while the supernatant, enriched with slow adhering mesenchymal cells, was collected. These cells have previously been shown to be the most suitable for nuclear transfer. After filtration and washing, the mesenchymal cells were seeded at 0.2 x 106 cells per well in 24 well plates and cultured in L15 medium for 2 days (about 80 % confluence) until Xenopus egg treatment.

extract_protocol: Total DNA and RNA of the cultured cells were extracted simultaneously after cell lysis in RNAsin (1 µL) in Tri-Reagent, according the instructions for Miniprep DNA/RNA Direct-zol column extraction kit (Zymo Research, R2081)

treatment_protocol: Adherent mesenchymal cells were permeabilized with digitonin (30 ug/mL 2 min 4°C) before exposure to egg extract (1 h, 25 °C), according to 31. Cells were then incubated for 2 h in growth L15 medium supplemented with 2 mM CaCl2 (25 °C) to reseal the plasma membranes and then cultured at 25°C in ESM4 medium. Culture medium was changed every 3 days. After 8 days, cultured cells were collected after trypsinization and snap-frozen in liquid nitrogen. Non-permeabilized cells from the same batch as the treated ones were grown in L15 medium and used as controls. They followed the steps as the treated cells and were snap-frozen after 8 days.

value: Treated

tag: Stage

value: MII-late


title: 121-T-MII-late

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 9


title: 135-T-MII-late

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 11


title: 123-T-MII-late

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 10


title: 96-T-MII

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 8

value: MII


title: Fr_LL1_08_rep2

source_name: Leaf


title: GL26130_CD31posP2_A05_R1

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

value: brain


title: 82-T-MII

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 7


title: TFE30_input_3

tag: chip antibody


title: Fr_LL1_00_rep1


title: TFE30_input_2


title: GL26130_CD31posP2_B10_R1


title: GL26130_CD31posP2_G11_R1


title: Fr_LD2_20_rep2

value: Dark

value: Night (entrained)


title: GL26130_CD31posP2_F02_R1


title: Fr_LD2_20_rep1


title: TFE30_input_1


title: GL26130_CD31posP2_D11_R1


title: TFE30_3


title: GL26130_CD31posP2_D02_R1


title: Fr_LD2_16_rep1


title: Fr_LD2_16_rep2


title: TFE30_2


title: GL26130_CD31posP2_C10_R1


title: Fr_LD2_12_rep2


title: BY6_HindIII_EcoRI-norm_100_pct_cut_X

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: HindIII 100% cut

data_processing:
Library strategy: ORE-seq
bowtie2 (v. 2.4.4) alignment to joint S.cerevisiae/S.pombe genome Parameters  "-X 500 --no-discordant --no-mixed --no-unal"
filter multiply mapped reads using samtools view -hf 0x2
Coverage using bamCoverage (deepTools v. 3.5.1)
Genome_build: SacCer3 & EF2
Supplementary_files_format_and_content: BigWig file of genomic coverage

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: S. cerevisiae/S. pombe cells

growth_protocol: Grow 7 * 109 cells of S. cerevisiae or S. pombe wild type strain in YPD or YES medium, respectively, to a density of approx. 3 * 108 cells/ml.

extract_protocol:
Genomic DNA purified with Blood & Cell Culture DNA Midi Kit (QIAGEN) using 100/G QIAGEN Genomic-tip
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

treatment_protocol: no further treatment of cells prior to harvest; genomic DNA was digested or mock digested with restriction enzymes and sheared by sonication.

tag: restriction enzyme

value: EcoRI

tag: digestion degree[%]


title: 76-Control

source_name: Control fin cells cultured in L15 medium, batch 2

value: Control


title: TFE30_1


title: GL26130_CD31posP2_F12_R1


title: Fr_LD2_12_rep1


title: 83-Control

source_name: Control fin cells cultured in L15 medium, batch 3


title: 124-Control

source_name: Control fin cells cultured in L15 medium, batch 5


title: Fr_LD2_08_rep2

value: Day (entrained)


title: GL26130_CD31posP2_A02_R1


title: 80-T-MII

source_name: Xenopus egg extract treated cells cultured in ESM4 medium, batch 6


title: GL26130_CD31posP2_A10_R1


title: SCR_input_3

value: SCR


title: BY6_HindIII_EcoRI-norm_90_pct_cut_X

description: HindIII 90% cut


title: BY6_HindIII_EcoRI-norm_50_pct_cut_X

description: HindIII 50% cut


title: SCR_input_2


title: GL26130_CD31posP2_E10_R1


title: 67-Control

source_name: Control fin cells cultured in L15 medium, batch 1


title: BY6_HindIII_EcoRI-norm_30_pct_cut_X

description: HindIII 30% cut


title: SCR_input_1

source_name: human ASPS cell line


title: Fr_LD2_04_rep2


title: GL26130_CD31posP2_E07_R1

source_name: brain


title: SCR_input_4


title: BY6_HindIII_EcoRI-norm_10_pct_cut_X

description: HindIII 10% cut


title: Fr_LD2_08_rep1


title: SCR_4

description: SCR.fragment.bw


title: SCR_3

description: SCR.fragment.bw


title: BY6_HindIII_EcoRI-norm_0_pct_cut_X

description: HindIII 0% cut


title: GL26130_CD31posP2_G09_R1


title: GL26130_CD31posP2_A04_R1


title: Fr_LD2_00_rep1


title: BY6_HindIII_EcoRI-norm_70_pct_cut_X

description: HindIII 70% cut


title: SCR_2

description: SCR.fragment.bw


title: GL26130_CD31posP2_A01_R1


title: Fr_LD1_20_rep2


title: Fr_LD1_20_rep1


title: GL26130_CD31posP2_F06_R1


title: Ovaries, L1

city: Longyan

first: Yanfa

last: Sun

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

institute: Longyan University

data_processing:
Each library was indexed in order to multiplex four samples per sequencing run on the Illumina HiSeq 2500 platform.
A minimum of 6Gb 150bp sequencing reads were collected from each sample and data were analyzed using Genesifter software.
Raw data for each sample were aligned to the most recent Anas Platyrhynchos genome build in order to identify previously unknown regions that may encode for unique mRNAs.
Pairwise comparison of the alignment results was done using Genesifter for identification of mRNAs that are differentially expressed at a significant level, i.e. up- or down-regulated.
Genome_build: CAU_duck1.0 (GCA_002743455.1)
Supplementary_files_format_and_content: FPKMs.txt

organism: Anas platyrhynchos

source_name: ovarian tissue

extract_protocol:
ovarian tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TRIzol RNA Isolation Reagents was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovarian tissue

tag: age

value: week 71

tag: phenotype

value: low egg number


title: Ovaries, L3


title: SCR_1

description: SCR.fragment.bw


title: Ovaries, L2


title: SLC_input

data_processing:
paired-end 50bp sequencing on an Illumina HiSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a normalized pileup signal

source_name: human ASPS tumor

extract_protocol:
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and TARGET DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set

value: human ASPS tumor

tag: patient id (city where they are from)

value: SLC


title: GL26130_CD31posP2_G10_R1

value: Malignant

value: ctrl


title: Fr_LD1_16_rep1

tag: time of the day

tag: zeitgeber time


title: Ovaries, H3

value: high egg number


title: Input Control 3

city: Mainz

first: Simon

last: Rumpel

state: Rheinland-Pfalz

address: Hanns-Dieter-Hüsch Weg 19

department: Institute of Physiology

institute: Universitätsmedizin Mainz

description: AAV8-packaged mouse BAC DNA library

data_processing:
Library strategy: STARR-seq
Illumina bcl2fastq version 2.19 was used for base calling and demultiplexing.
Sequencing reads were  mapped to the mouse mm10 genome assembly using bowtie2 (v2.3.4), using very sensitive matching but requiring full end-to-end matches, with a maximum genomic match length of 1 kbp (bowtie2 options: --very-sensitive --phred33 --fr --end-to-end --maxins 1000 --minins 0). Mapped reads were filtered to remove those that could not be uniquely mapped to a single location, using samtools (v1.9) to exclude read pairs with a mapping quality (MAPQ) lower than 3 (samtools options: samtools view -f 2 -q 3).
Bigwig tracks were generated using a combination of the UCSC Kent utilities (v385) genomeCoverageBed (options: -bg -pc -split -scale $SCALE) and bedGraphToBigWig. The $SCALE scaling factor was calculated as 1000000/total_mapped_reads, to normalize the coverage scores across samples with different sequencing depths.
Peaks were called using the STARRPeaker program (Lee et al., 2020) (v1.0, obtained from “https://github.com/gersteinlab/starrpeaker” on 22 March 2021 and modified to run with Python 3). A sliding window of 500 bp with step size 100 bp was used, and RNA secondary structure potential and GC-content as covariates. RNA secondary structure potential of the BAC-covered genomic regions was performed using LinearFold (Huang et al., 2019) (obtained from “https://github.com/LinearFold/LinearFold” on 22 March 2021). GC content for the mouse mm10 genome assembly was downloaded from the UCSC Genome Browser website. Sample 6 was excluded from peak calling due to having a much lower sequencing depth than the others.
The final peak set was determined as follows. For each RNA sample, peaks were called separately for each of the three AAV-packaged input DNA technical replicate input controls. The resulting peaks were merged across input control replicates, and only those detected in more than one replicate were retained. Peaks common to all five processed RNA samples were used as the final peak set.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated as described above.
Supplementary_files_format_and_content: Peak files per sample, generated as described above.
Supplementary_files_format_and_content: Final peak file, with peaks common to all five processed samples.

source_name: AAV8-packaged mouse DNA fragments

extract_protocol:
The STARR-seq protocol was performed according to the recommendations of Muerdter et al. 2018. After sacrificing the mice, cortical tissue surrounding the injection sites was quickly removed and frozen using liquid nitrogen. Total mRNA was isolated from individual brain tissue samples using the AllPrep DNA/RNA Mini Kit (Qiagen; Cat. No. 80204) according to the manufacturer’s protocol (version 2005). Oligo-dT selection of mRNA was performed with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB; Cat. No. E7490S/L) with a starting amount of 5µg (except for sample 1 with a starting amount of 2.7µg). Reverse Transcription was performed with SuperScriptIII (Invitrogen; Cat. No. 18080093) using a Gene specific primer (CTCATCAATGTATCTTATCATGTCTG). RT was followed by RNAse Treatment and junction PCR with 15 cycles. Libraries were amplified in 8 Cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Neocortices of wild type mice were stereotactically injected with a STARR-seq screening DNA library packaged into AAV8 capsids (1.52e+12 vg/ml, 200 nl per site for twelve sites, 0.5-2.5 mm lateral, 1-2 mm posterior, relative to bregma, and 0.6 mm ventral relative to the brain surface), and incubated for 7 days.

tag: sample type

value: input


title: Fr_LD2_04_rep1

tag: light regime

value: Light

tag: day/night anticipation


title: Fr_LD1_16_rep2


title: SLC_VCP

value: VCP

tag: tissue


title: Fr_LD1_12_rep2

value: Dark


title: Ovaries, H2


title: Ovaries, H1


title: Fr_LD2_00_rep2


title: Input Control 2

description: AAV8-packaged mouse BAC DNA library


title: SLC_ASPL


title: Input Control 1

description: AAV8-packaged mouse BAC DNA library


title: SLC_Pol2

value: POLII


title: Fr_LD1_12_rep1

value: Night (entrained)


title: SFO_input

value: SFO


title: Mouse 6

source_name: Neocortex

tag: strain

value: Neocortex

value: 6-10 weeks


title: B16F10 cells, shSQLE [S5]

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: No.55, West of ZhongShan Avenue, Tianhe District

institute: Department of Brain Science and Rehabilitation Medicine

data_processing:
WriteFQ and FastQC and STAR and RSEM
Sequencing reads were constructed using WriteFQ
Sequence reads were cleaned for adaptor sequence/low-quality sequence using FastQC
Trimmed sequence reads were mapped to GRCm39 using STAR
Read count extraction and normalization were performed using RSEM
Differential gene analysis was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: Count values for each Sample

source_name: Subcutaneous tumors

growth_protocol: B16F10 cells 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 GenJET RNA Purification Kit(thermo scientific). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by MGI DNBSEQ-T7 PE150

value: Subcutaneous tumors

tag: cell line

value: Melanoma cells

tag: genotype

value: SQLE knockdown

tag: treatment

value: no


title: Fr_LD1_08_rep2

value: Day (entrained)


title: Fr_LD1_08_rep1


title: 92-Control

source_name: Control fin cells cultured in L15 medium, batch 4

value: Control

tag: Stage


title: B16F10 cells, shSQLE [S1]

tag: cell type


title: B16F10 cells, shControl [W5]

value: WT


title: Mouse 4


title: Mouse 5


title: VCP65_2 (HiChIP)

city: Beijing

first: Jinxiu

address: Yuanmingyuan west road 2#

institute: China Agricutural University

data_processing:
Library strategy: HiChIP
Paired-end 150bp sequencing on an Illumina HiSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using novoalign-4.00.01
The HiChIP sequencing reads were aligned to the hg38 reference genome using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were identified by the Hichipper pipeline (Lareau and Aryee, 2018).
Genome_build: hg38
Supplementary_files_format_and_content: bedpe, including loops with at least four pairs of valid reads (PETs) and an FDR value < 0.01

source_name: human ASPS cell lines

extract_protocol:
Lysates were clarified from sonicated nuclei and Histone DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set
HiChIP of H3K27ac

value: siRNA against VCP

tag: chip antibody


title: SFO_ASPL

value: human ASPS tumor


title: Mouse 3


title: FUUR1_2 (HiChIP)

value: baseline


title: Fr_LD1_04_rep1

source_name: Leaf

value: Light


title: B16F10 cells, shControl [W1]


title: FUUR1_1 (HiChIP)


title: Mouse 2


title: Mouse 1


title: AireKO_mTEClo_3

status: Public on Dec 31 2022

city: Tokyo

first: Ryunosuke

last: Muro

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Immunology,

country: Japan

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

data_processing:
CLC Genomics Workbench (CLC)
Assembly: mm10
Supplementary files format and content: 200515_Prmt5_RNA-seq_all.xlsx

source_name: Thymus

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Thymus

value: mTEClo

value: Aire-KO


title: AireKO_mTEChi_3

value: mTEChi


title: AireKO_mTEClo_1


title: AireKO_mTEChi_1


title: Prmt5cKO_cTEC_3

value: cTEC

value: Prmt-cKO


title: B16F10 cells, shSQLE [S2]

value: Subcutaneous tumors


title: Fr_LD1_04_rep2


title: VCP67_1 (HiChIP)

last: Li


title: Prmt5cKO_mTEClo_1


title: Prmt5cKO_mTEClo_3


title: Prmt5cKO_mTEChi_2


title: Prmt5cKO_mTEChi_3


title: Prmt5cKO_mTEChi_1


title: B16F10 cells, shControl [W4]

value: Melanoma cells


title: control_cTEC_3


title: control_cTEC_2


title: control_cTEC_1


title: control_mTEClo_1


title: AireKO_mTEClo_2


title: control_mTEChi _2


title: control_mTEClo_3


title: control mTEClo_2


title: control_mTEChi_1


title: vGAT_INTACT_Rep2

city: Waltham

first: Albert

middle: Dayuan

last: Yu

address: 415 South St.

department: Molecular and Cell Biology

institute: Brandeis University

data_processing:
Fastp
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default settings and overlap analysis
UMItools
UMIs were extracted and appended to reads with UMItools, and later deduplicated with UMItools after STAR alignment
STAR
Reads were mapped to dm6 using STAR and the following settings: --outFilterMismatchNoverLmax 0.06 --outFilterMatchNmin 15 --outFilterMultimapNmax 1 --outSJfilterReads Unique --alignMatesGapMax 25000
FeatureCounts
A count table was produced using FeatureCounts
DESeq2
Differential expression was conducted using DESeq2
Assembly: dm6
Supplementary files format and content: tab-delimited text file consists of a non-normalized count table, with one column per experiment

organism: Drosophila melanogaster

source_name: VAChT:VGAT split-Gal4/UAS-UNC84 nuclei

growth_protocol: Crosses were reared and standard yeast/cornmeal-agar food to an age of 10 days

extract_protocol:
Flies were snap frozen and ~0.2ml of fly heads were collected by sieving. Fly heads were homogenized according to the mini-INTACT protocol, and RNA was extracted using Trizol. Poly(A) RNA was isolated using the Poly(A)-purist kit.
RNA libraries for RNA-seq were prepared using NEXTFLEX Rapid Directional qRNA-Seq kit according to manufacturer's protocol

value: VAChT:VGAT split-Gal4/UAS-UNC84 nuclei

value: Neuronal Nuclei

tag: time

value: 10 Day Old


title: control_mTEChi_3

value: Control


title: vGAT_INTACT_Rep1


title: Prmt5cKO_mTEClo_2


title: Prmt5cKO_cTEC_2


title: Fr_LD1_00_rep2

value: Day (entrained)


title: Fr_LD1_00_rep1


title: vGlut_INTACT_Rep1

source_name: VAChT:VGlut split-Gal4/UAS-UNC84

value: VAChT:VGlut split-Gal4/UAS-UNC84


title: AireKO_mTEChi_2


title: vGlut_INTACT_Rep2


title: Prmt5cKO_cTEC_1


title: stage III, Rep#3, Exp #2, cell lineage

status: Public on Dec 27 2022

city: Shanghai

first: Zhiwen

last: You

address: 320 Yueyang Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

description: Cell lineage barcode, Biological replicate #3

library_source: other

data_processing:
scRNA-seq data were aligned with the human reference genome, GRCh38-3.0.0, and demultiplexed using the default parameters of Cellranger software (10x Genomics, v3.0.2 or v4.0.0). Obtained filtered count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: DNA-seq

molecule: other

extract_protocol:
For scRNA-seq, the neuro-spheres were digested by TrypLE Enzyme at 37℃ for 10 minutes and dissociated into single cells. After 35-µm cell sieve filtering, the digested cells were sorted by FACS to collected EGFP-positive cells, which were then concentrated by centrifuge at 400 g for 5 minutes. All the sorted EGFP-positive cells were used to construct single cell library using Chromium Single Cell 3' Reagent Kits (v2 and v3) following the manufacturer’s guidelines (10X Genomics).
scRNA-seq library was performed according to the manufacter’s instructions (single cell 3’ v2 and v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. For barcoded viral library, we designed primer pairs with illumina adaptors to amplify the random barcode sequences from the retroviral barcode library plasmid pool (Forward, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTATTCGGAGGACGACCCTATTTG; Reverse, CAAGCAGAAGACGGCATACGAGATAGGATTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGATCACTCTCGGCATGGACG) with the following PCR program: 1, 98 °C, 3 min; 2, 98 °C, 10 s; 3, 60 °C, 10 s; 4, 72 °C, 25 s; 5, repeat steps 2–4 15 times; 6, 72 °C, 3 min; 7, 4 °C, hold. The PCR products were purified by 0.85× left-sided size selection using Ampure XP bead (Beckman Coulter, catalogue number A63880) and then sequenced on Illumina HiSeq PE150. For cell lineage barcode recovered from single cell transcriptome, following the reverse transcription of mRNA and first strand cDNA amplification, 50 ng of the unfragmented cDNA libraries were used as templates to specifically amplify cell barcodes and virus barcodes with primers pairs: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC and CAAGCAGAAGACGGCATACGAGATAGGATTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGCATGGACGAGCTGTACAAATAA, using the following program: 1, 98 °C, 3 min; 2, 98 °C, 10 s; 3, 60 °C, 15 s; 4, 72 °C, 1 min; 5, repeat steps 2–4 20 times; 6, 72 °C, 3 min; 7, 4 °C, hold. The PCR products were then purified by 0.8-0.6× dual-sided size selection using Ampure XP bead and sequenced using Illumina HiSeq PE150.

value: H9-derive neural progenitors

value: WT

tag: age

value: stage III (day 30)


title: stage III, Rep#3, Exp #3, cell lineage


title: stage IV, Rep#3, Exp #3, cell lineage

value: stage IV (day 45)


title: stage IV, Rep#2, Exp #3, cell lineage

description: Cell lineage barcode, Biological replicate #2


title: stage II, Rep#2, Exp #2, cell lineage

value: stage II (day 21)


title: stage II, Rep#3, Exp #1, cell lineage


title: stage III, Rep#2, Exp #2, cell lineage


title: stage I, Rep#3, Exp #1, cell lineage

value: stage I (day 13)


title: stage II, Rep#2, Exp #1, cell lineage


title: stage II, Rep#3, Exp #2, cell lineage


title: stage I, Rep#2, Exp #1, cell lineage


title: stage IV, Rep#3, Exp #3, scRNAseq

description: 10x Genomics, Biological replicate #3

data_processing:
scRNA-seq data were aligned with the human reference genome, GRCh38-3.0.0, and demultiplexed using the default parameters of Cellranger software (10x Genomics, v3.0.2 or v4.0.0). Obtained filtered count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files


title: stage III, Rep#3, Exp #3, scRNAseq

description: 10x Genomics, Biological replicate #3


title: stage I, Rep#3, Exp #1, scRNAseq

description: 10x Genomics, Biological replicate #3


title: stage IV, Rep#2, Exp #3, scRNAseq

description: 10x Genomics, Biological replicate #2


title: stage II, Rep#3, Exp #1, scRNAseq

description: 10x Genomics, Biological replicate #3


title: stage II, Rep#3, Exp #2, scRNAseq

description: 10x Genomics, Biological replicate #3


title: stage III, Rep#3, Exp #2, scRNAseq

description: 10x Genomics, Biological replicate #3


title: stage III, Rep#2, Exp #3, scRNAseq

description: 10x Genomics, Biological replicate #2


title: stage II, Rep#2, Exp #2, scRNAseq

description: 10x Genomics, Biological replicate #2


title: stage I, Rep#2, Exp #1, scRNAseq

description: 10x Genomics, Biological replicate #2


title: MI-Treated_HADF_D5

city: Pittsburgh

first: Chandan

middle: K

last: Sen

state: Pennsylvania

address: 450 Technology Drive

department: Surgery

institute: University of Pittsburgh

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Quality control, clustering and differential gene expression analysis were performed using Seurat v.3.1.1
Trajectory inference and pseudotime calculations were performed using Monocle v.1.10.1
Genome_build: hg:38
Supplementary_files_format_and_content: barcode files
Supplementary_files_format_and_content: gene names file
Supplementary_files_format_and_content: count matrix file

source_name: Primary human adult dermal fibroblasts

growth_protocol: Primary human adult dermal fibroblasts (ATCC, Manassas, VA, cat. no. PCS-201-012) were expanded in fibroblast basal medium (ATCC cat. no. PCS-201-030) supplemented with fibroblast growth kit-serum-free (ATCC, cat. no. PCS-201-040) containing Penicillin-Streptomycin (10,000 U/mL) solution (GibcoTM/Life Technologies, Waltham, MA, cat. no. 15140122) at 37°C in humidified chamber consisting of 95% air and 5% CO2.

extract_protocol:
Single cells were isolated from cultured cells (untreated HADF MI treated HADF cells at d1, d3, d5 and d7) and kept in 1XHBSS with 0.04%BSA until single cell cDNA synthesis. Single cells were encapsulated for NEXT GEMs preparation using barcoded beads and cDNA synthesis using the Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics).
library construction was done according to the manufacturer’s recommendations  (10X Genomics)

treatment_protocol: In vitro nanoelectroporation was conducted via 3D Nanochannel Electroporation (NEP) as described previously (Gallego-Perez et al., 2016). Briefly, the cells were first grown to full confluency overnight on the 3D NEP device. Subsequently, a pulsed electric field was used to deliver control or miR-200b inhibitor (50nM) into the cells. The cells were then harvested 24 h after miRNA delivery, placed in EBM-2 basal medium (Lonza, cat. no. CC-3156) supplemented with EGM-2 MV SingleQuot kit components (Lonza, cat. no. CC-4147) and processed further for single cell RNA sequencing at diffrent time-points.

value: human adult dermal fibroblasts (HADF)

value: miRIDIAN microRNA hsa-miR-200b-3p hairpin inhibitor (MI) transfection

tag: timepoint


title: MI-Treated_HADF_D7


title: stage III, Rep#2, Exp #3, cell lineage


title: MI-Treated_HADF_D1


title: KMS rep5

status: Public on Dec 26 2022

first: Rao

last: hanyu

address: Huashan Road NO.1954

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <50 bp) and low quality reads using Cutadapt (v1.9.1)(Anthony M et al., Bioinformatics 2014) and Trimmomatic (v0.35) (Martin M et al., EMBnet.J 2011).
Then FastQC (Andrews S et. al., FastQC 2010) is used to ensure high reads quality.
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 (Kim, D et al., Nat. Methods 2015) software.
Peak detection was performed using the MACS (v2.1.1) (Zhang et al., Genome Biol 2008) peak finding algorithm with 0.01 set as the p-value cutoff.
Assembly: mm10
Supplementary files format and content: Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie. Ballgown, a R package, were used to measure differential gene expression.The false discovery rate (FDR) control method was used to calculate the adjusted P-values in multiple testing in order to evaluate the significance of the differences. Here, only gene with an adjusted P-value <0.05 were used for subsequent analysis.

source_name: Renal primary tubular epithelial cells

growth_protocol: renal primary tubular epithelial cells were isolated from mice kidney cortex segment

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies Corp.), and further treated with DNase to remove genomic DNA contamination.
Isolation of mRNA was performed using the NEBNext PolyA mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

value: Kidney

value: Ksp1.3/cre; MYCfl/fl;Setd2fl/fl


title: KMS rep4


title: KMS rep3


title: MI-Treated_HADF_D3


title: KMS rep2


title: KMS rep1


title: KM rep5

value: Ksp1.3/cre; MYCfl/fl


title: KM rep4


title: KM rep2


title: TRAMPTIM3.2

status: Public on Dec 22 2022

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

description: P14 TCR transgenic CD8 T cells specific for GP33 epitope of LCMV. Activated P14s sorted from LCMV Armstrong infection, TDLN and tumor of TRAMPC1-GP bearing mice, or naïve spleen.

data_processing:
Aligned with HISAT2
Reads counted with subread/featurecounts
normalization and differential expression with DESEQ2
Assembly: mm10
Supplementary files format and content:CSV file with raw counts for all genes and samples

source_name: Tumor

extract_protocol: Cell sorting was performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. Qiagen micro RNA/DNA all prep columns were used for RNA extraction.

value: Tumor

value: Endo CD8 T cell

tag: sequencing batch


title: TDLNUndiv.2

source_name: TDLN

value: TDLN

value: P14 CD8 T cell


title: Naive4

source_name: Spleen

value: Spleen


title: TDLNDiv1.3


title: TRAMPTIM3.3


title: TRAMP127.2


title: stage III, Rep#2, Exp #2, scRNAseq

description: 10x Genomics, Biological replicate #2


title: TDLND7.2


title: TDLNDiv2.2


title: TRAMP127.3


title: TDLND7.1


title: stage II, Rep#2, Exp #1, scRNAseq

description: 10x Genomics, Biological replicate #2


title: TRAMPTIM3.1


title: TRAMP127.1


title: untreated_HADF

value: untreated


title: TDLNDiv1.1


title: TDLNUndiv.1


title: Naive3


title: LCMVUndiv.2


title: Naive2


title: LCMVDiv2.2


title: LCMVDiv1.1


title: KM rep3


title: KM rep1


title: LCMVDiv2.1


title: LCMVDiv1.2


title: LCMVUndiv.1


title: Naïve1


title: TDLNDiv2.1


title: TDLNDiv1.2


title: Human_scRNA-seq_K297_APC

data_processing:
Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1. Data were further analyzed using Seurat v.3.074. Briefly, cells with a percentage of mitochondrial genes below 0.05% were included. Cells with more than 4,000 or less than 1,000 detected genes were considered as outliers and excluded from the downstream analyses. Raw unique molecular identifier counts were normalized to unique molecular identifier count per million total counts and log-transformed. Variable genes were selected based on average expression and dispersion. PCA was performed using variable genes. Clusters were identified using the shared nearest neighbor algorithmin Seurat and t-SNE plots were generated based on selected principal component analysis dimensions. Marker genes were identified by the Seurat function FindAllMarkers. Log normalized data are shown in the form of feature plots with the scale in a range of0 (grey) to 2.5~5 (purple). Gene set scoring was performed using the VISION R package v.1.1.0. Briefly, expression of signature genes is weighted based on predicted dropout probability calculated from nearest neighbors, and the normalized expression summed for all genes in the gene set.
Assembly: HG38
Supplementary files format and content: Gene name and raw counts for sequenced cells for each sample

extract_protocol:
Cell sorting was performed byFACS Aria II (BD Biosciences). For scRNA-seq (10x) of mouse samples live, CD3-CD19-Ly6G+ I-A/I-E+ cells were sorted from naïve LN, tumor-draining LN, and TRAMPC1-GP tumors. For human scRNA-seq (10x) fresh kidney tumors were used, antigen-presenting cells were sorted as live, CD45+, CD3-, HLADR+
Single cell RNAseq libraries were generated using the Chromium Single Cell 5’1007Library & Gel Bead Kit (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were sorted and captured into the Gel Beads-in-emulsion (GEMs). After reverse transcription, the GEMs were disrupted and the barcoded cDNA was isolated, pooled, and amplified by PCR (13cycles). The amplified cDNA was fragmented, and subjected to end repair and A-tailing followed by a sample index PCR (16 cycles). The purified libraries were sequenced to a depth of 50,000 reads/cell on a 1013HiSeq3000 (Illumina) with 26 cycles for read 1, 8 cycles for index 1 (i7), and 91 cycles for read 2.

value: Antigen presenting cells

tag: disease state

value: ccRCC


title: TDLND7.1_mouse_methylation

data_processing:
Sequenced data was aligned to the mouse genome using Hisat2 and analyzed using custom R and Python scripts. Fisher’s exact test was used to define regions of statistically (p value less that 1x10-4) differentially methylated CpG motifs. Continuous regions of differentially methylated CpGs were identified by finding regions where at least 6 out of 10 CpGs in a continuous stretch were differentially methylated. These regions were then collapsed and analyzed as single ‘differentially methylated regions’ (DMRs).
Assembly: mm10
Supplementary files format and content: CSV file with raw counts for all genes and samples

extract_protocol:
Cell sorting was performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. Qiagen micro RNA/DNA all prep columns were used for RNA extraction.
DNA was isolated using the AllPrep DNA/RNA Micro kit (Qiagen) and sonicated to generate random 300 to 500-bp fragments. DNA was end-repaired and A-tailed using the Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol. Sequencing adapters that contained fully methylated cytosine residues (Integrated DNA Technologies) were ligated using the Hyper Prep Kit (KAPA Biosystems). Adapter-ligated DNA was bisulfite converted using the EpiTect Bisulfite Kit (Qiagen), with a denaturation time of 10 min. Final libraries were PCR amplified 8–11 times using Tru-seq (Illunima)-compatible custom index primers, as previously described in (Barwick et al., 2016), and HiFi Uracil (KAPA Biosystems). The resulting WGBS libraries were quality checked by Bioanalyzer, pooled at equimolar ratios and sequenced on a NovaSeq S4


title: K348_T_39_human_methylation

description: CD8 T cell populations were sorted from human PBMCs, lymph nodes, and tumor.

data_processing:
Sequenced data was aligned to the human genome using Hisat2 and analyzed using custom R and Python scripts. Fisher’s exact test was used to define regions of statistically (p value less that 1x10-4) differentially methylated CpG motifs. Continuous regions of differentially methylated CpGs were identified by finding regions where at least 6 out of 10 CpGs in a continuous stretch were differentially methylated. These regions were then collapsed and analyzed as single ‘differentially methylated regions’ (DMRs).
Assembly: HG38
Supplementary files format and content: CSV file with raw counts for all genes and samples

extract_protocol:
Cell sorting was performed by FACS Aria II (BD Biosciences). DNA was extracted using Qiagen RNA/DNA micro allprep columns
DNA was isolated using the AllPrep DNA/RNA Micro kit (Qiagen) and sonicated to generate random 300 to 500-bp fragments. DNA was end-repaired and A-tailed using the Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol. Sequencing adapters that contained fully methylated cytosine residues (Integrated DNA Technologies) were ligated using the Hyper Prep Kit (KAPA Biosystems). Adapter-ligated DNA was bisulfite converted using the EpiTect Bisulfite Kit (Qiagen), with a denaturation time of 10 min. Final libraries were PCR amplified 8–11 times using Tru-seq (Illunima)-compatible custom index primers, as previously described in (Barwick et al., 2016), and HiFi Uracil (KAPA Biosystems). The resulting WGBS libraries were quality checked by Bioanalyzer, pooled at equimolar ratios and sequenced on a NovaSeq S4

value: CD8 T cell


title: Human_scRNA-seq_K416_APC

description: Cell sorting was performed byFACS Aria II (BD Biosciences). For scRNA-seq (10x) of mouse samples live, CD3-CD19-Ly6G+ I-A/I-E+ cells were sorted from naïve LN, tumor-draining LN, and TRAMPC1-GP tumors. For human scRNA-seq (10x) fresh kidney tumors were used, antigen-presenting cells were sorted as live, CD45+, CD3-, HLADR+


title: Mouse_scRNA-seq_TDLN_APC

data_processing:
Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1. Data were further analyzed using Seurat v.3.074. Briefly, cells with a percentage of mitochondrial genes below 0.05% were included. Cells with more than 4,000 or less than 1,000 detected genes were considered as outliers and excluded from the downstream analyses. Raw unique molecular identifier counts were normalized to unique molecular identifier count per million total counts and log-transformed. Variable genes were selected based on average expression and dispersion. PCA was performed using variable genes. Clusters were identified using the shared nearest neighbor algorithmin Seurat and t-SNE plots were generated based on selected principal component analysis dimensions. Marker genes were identified by the Seurat function FindAllMarkers. Log normalized data are shown in the form of feature plots with the scale in a range of0 (grey) to 2.5~5 (purple). Gene set scoring was performed using the VISION R package v.1.1.0. Briefly, expression of signature genes is weighted based on predicted dropout probability calculated from nearest neighbors, and the normalized expression summed for all genes in the gene set.
Assembly: mm10
Supplementary files format and content: Gene name and raw counts for sequenced cells for each sample

source_name: LN

value: LN

value: TRAMPC1-GP tumor bearing


title: Mouse_scRNA-seq_NaïveLN_APC

value: Naive


title: TRAMP127_mouse_methylation


title: K300_T_39_human_methylation


title: Naïve3_mouse_methylation


title: TDLNDiv2_mouse_methylation


title: Naïve2_mouse_methylation


title: K300_T_28_human_methylation


title: K28_T_39_human_methylation


title: K28_T_28_human_methylation


title: TDLNUndiv_mouse_methylation


title: TDLNDiv1_mouse_methylation


title: K300_LN_human_methylation


title: LCMVDiv1_mouse_methylation


title: K80_LN_human_methylation


title: K241_LN_human_methylation


title: LCMVDiv2_mouse_methylation


title: LCMVUndiv_mouse_methylation


title: Naïve1_mouse_methylation


title: Naive1_human_methylation

source_name: PBMC

value: PBMC


title: Naive2_human_methylation


title: TRAMPTIM3_mouse_methylation


title: TDLND7.2_mouse_methylation


title: Mouse_scRNA-seq_Tumor_APC


title: S12_Tumor04

status: Public on Dec 08 2022

city: Boston

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.2.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 700.
Assembly: GRCh37/hg19
Supplementary files format and content: count matrix in csv

source_name: prostate

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Single cells from the tumor and the normal adjacent kidney samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

value: prostate

tag: condition

tag: grade


title: S10_Tumor02


title: S8_Benign04


title: S9_Tumor01


title: S6_Benign02


title: S7_Benign03


title: K348_T_28_human_methylation


title: S5_Benign01


title: S2_HP2

value: Healthy


title: S3_HP3


title: S4_HP4


title: S1_HP1


title: SCG-PCA24-N-CplusD

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 3.0.1). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: count matrix in csv

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Single cells from the tumor and the normal adjacent prostate samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

tag: gleason

value: Normal


title: SCG-PCA22-T-HG


title: SCG-PCA24-N-Rocky


title: SCG-PCA19-T-HG


title: SCG-PCA18-T-LG


title: SCG-PCA19-N-HG


title: SCG-PCA22-N-HG


title: SCG-PCA18-N-LG


title: SCG-PCA20-N-LG


title: SCG-PCA17-T-LG


title: SCG-PCA17-N-LG


title: SCG-PCA15-T-HG


title: SCG-PCA16-T-HG


title: S11_Tumor03


title: SCG-PCA11-T-LG


title: SCG-PCA12-N-LG


title: SCG-PCA9-T-LG


title: SCG-PCA11-N-LG


title: SCG-PCA12-T-LG


title: SCG-PCA10-T-LG

value: 3+3=6, tertiary 4


title: SCG-PCA15-N-HG


title: SCG-PCA8-T-HG

value: Tumor


title: SCG-PCA7-T-HG


title: SCG-PCA6-N-HG


title: SCG-PCA20-T-LG


title: SCG-PCA5-T-LG


title: SCG-PCA6-T-HG


title: SCG-PCA21-N-LG


title: HP4

description: Gemcitabine/cisplatin x4 preoperatively


title: HP3

description: Prior intravesical BCG 1/2019 and intravesical gemcitabine


title: WA_PIZZ1ZZ (10X)

status: Public on Dec 06 2022

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
The sample was processed using the standard cellranger pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the STARsolo count pipeline:

extract_protocol:
10X Chromium system
NextSeq 500

value: hepatic


title: SCG-PCA21-T-LG


title: SCG-PCA3-N-LG


title: SCG-PCA4-T-HG


title: HP0

description: Afatinib (Partial Response for 8 years) Osimertinib (Stable Disease)


title: WA_PIZZ6 (10X)


title: HP2

description: Prior intravesical BCG 6/2019


title: SCG-PCA9-N-LG


title: HP1

description: Gemcitabine/cisplatin x4 preoperatively


title: SCG-PCA4-N-HG


title: SCG-PCA5-N-LG


title: SCG-PCA3-T-LG